diff --git a/communities/all/resources/tools.html b/communities/all/resources/tools.html
index 1d53d59e..706fb01a 100644
--- a/communities/all/resources/tools.html
+++ b/communities/all/resources/tools.html
@@ -95,7 +95,6 @@
       <th>Tools available on CoralSNP</th>
       <th>Tools available on CropGalaxy</th>
       <th>Tools available on Dintor</th>
-      <th>Tools available on FreeBioinfo</th>
       <th>Tools available on GASLINI</th>
       <th>Tools available on Galaxy@AuBi</th>
       <th>Tools available on Galaxy@Pasteur</th>
@@ -112,12 +111,27 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
+      <th>Tools available on PhagePromotor</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
       <th>Tools available on Viral Variant Visualizer (VVV)</th>
-      <th>No. of tool users (2022-2023) (usegalaxy.eu)</th>
-      <th>Total tool usage (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.eu)</th>
+      <th>No. of tool users (all time) (usegalaxy.eu)</th>
+      <th>Tool usage (5 years) (usegalaxy.eu)</th>
+      <th>Tool usage (all time) (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org)</th>
+      <th>No. of tool users (all time) (usegalaxy.org)</th>
+      <th>Tool usage (5 years) (usegalaxy.org)</th>
+      <th>Tool usage (all time) (usegalaxy.org)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org.au)</th>
+      <th>No. of tool users (all time) (usegalaxy.org.au)</th>
+      <th>Tool usage (5 years) (usegalaxy.org.au)</th>
+      <th>Tool usage (all time) (usegalaxy.org.au)</th>
+      <th>No. of tool users (5 years) - all main servers</th>
+      <th>No. of tool users (all time) - all main servers</th>
+      <th>Tool usage (5 years) - all main servers</th>
+      <th>Tool usage (all time) - all main servers</th>
     </tr>
   </thead>
   <tbody>
@@ -148,9 +162,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -178,12 +191,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>39</td>
-      <td>6541</td>
+      <td>1434</td>
+      <td>6746</td>
+      <td>120</td>
+      <td>122</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>305</td>
+      <td>305</td>
+      <td>11</td>
+      <td>11</td>
+      <td>1739</td>
+      <td>7051</td>
+      <td>131</td>
+      <td>133</td>
     </tr>
     <tr>
       <td></td>
@@ -246,8 +274,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>19</td>
-      <td>13760</td>
+      <td>1156</td>
+      <td>13842</td>
+      <td>40</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1277</td>
+      <td>13963</td>
+      <td>44</td>
+      <td>46</td>
     </tr>
     <tr>
       <td></td>
@@ -310,8 +352,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>18</td>
-      <td>6834</td>
+      <td>591</td>
+      <td>6863</td>
+      <td>38</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>119</td>
+      <td>3</td>
+      <td>3</td>
+      <td>710</td>
+      <td>6982</td>
+      <td>41</td>
+      <td>43</td>
     </tr>
     <tr>
       <td></td>
@@ -340,11 +396,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
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       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -374,8 +430,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>39</td>
-      <td>656</td>
+      <td>762</td>
+      <td>782</td>
+      <td>100</td>
+      <td>101</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>230</td>
+      <td>230</td>
+      <td>14</td>
+      <td>14</td>
+      <td>992</td>
+      <td>1012</td>
+      <td>114</td>
+      <td>115</td>
     </tr>
     <tr>
       <td></td>
@@ -404,9 +474,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -434,76 +503,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>35</td>
-      <td>6156</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>3d_tensor_feature_dimension_reduction</td>
-      <td>ip_3d_tensor_feature_dimension_reduction</td>
-      <td>Dimensionality reduction for features (channels) of 3D tensor data using UMAP</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis</td>
-      <td>Imaging</td>
-      <td>3d_tensor_feature_dimension_reduction</td>
-      <td>imgteam</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction</td>
-      <td>0.0.1</td>
-      <td>numpy</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
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-      <td>0</td>
-      <td>0</td>
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-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>948</td>
+      <td>6261</td>
+      <td>98</td>
+      <td>100</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>153</td>
+      <td>153</td>
+      <td>13</td>
+      <td>13</td>
+      <td>1101</td>
+      <td>6414</td>
+      <td>111</td>
+      <td>113</td>
     </tr>
     <tr>
       <td></td>
@@ -566,8 +586,22 @@
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>47</td>
-      <td>2889</td>
+      <td>474</td>
+      <td>2914</td>
+      <td>132</td>
+      <td>163</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>474</td>
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+      <td>132</td>
+      <td>163</td>
     </tr>
     <tr>
       <td></td>
@@ -630,8 +664,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>40</td>
+      <td>47</td>
+      <td>6</td>
+      <td>6</td>
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       <td>0</td>
-      <td>45</td>
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+      <td>6</td>
+      <td>6</td>
     </tr>
     <tr>
       <td></td>
@@ -676,7 +724,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -691,11 +738,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>23</td>
-      <td>984</td>
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+      <td>48</td>
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+      <td>1003</td>
+      <td>1022</td>
+      <td>48</td>
+      <td>52</td>
     </tr>
     <tr>
       <td></td>
@@ -724,11 +786,10 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -760,6 +821,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -822,8 +898,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>36</td>
+      <td>41</td>
+      <td>2</td>
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       <td>0</td>
-      <td>40</td>
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+      <td>0</td>
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+      <td>36</td>
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+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -886,8 +976,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>4</td>
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       <td>1</td>
-      <td>3</td>
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     </tr>
     <tr>
       <td></td>
@@ -950,8 +1054,22 @@
       <td>9</td>
       <td>9</td>
       <td>0</td>
-      <td>301</td>
-      <td>1896</td>
+      <td>3600</td>
+      <td>3760</td>
+      <td>883</td>
+      <td>911</td>
+      <td>6</td>
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+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>3606</td>
+      <td>3766</td>
+      <td>887</td>
+      <td>915</td>
     </tr>
     <tr>
       <td></td>
@@ -1016,6 +1134,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -1080,6 +1212,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -1124,7 +1270,6 @@
       <td>0</td>
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@@ -1144,6 +1289,21 @@
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -1206,8 +1366,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -1272,6 +1446,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td></td>
@@ -1316,7 +1504,6 @@
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1336,6 +1523,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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@@ -1364,11 +1566,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>0</td>
       <td>0</td>
@@ -1464,6 +1680,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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+      <td>0</td>
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+      <td>123</td>
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+      <td>0</td>
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+      <td>0</td>
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+      <td>123</td>
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     </tr>
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       <td></td>
@@ -1492,9 +1722,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
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       <td>0</td>
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       <td>0</td>
@@ -1522,12 +1751,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
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-      <td>1523</td>
+      <td>1635</td>
+      <td>1671</td>
+      <td>123</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>334</td>
+      <td>334</td>
+      <td>21</td>
+      <td>21</td>
+      <td>1969</td>
+      <td>2005</td>
+      <td>144</td>
+      <td>145</td>
     </tr>
     <tr>
       <td></td>
@@ -1590,8 +1834,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>34</td>
-      <td>1273</td>
+      <td>401</td>
+      <td>1385</td>
+      <td>87</td>
+      <td>88</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>188</td>
+      <td>188</td>
+      <td>9</td>
+      <td>9</td>
+      <td>589</td>
+      <td>1573</td>
+      <td>96</td>
+      <td>97</td>
     </tr>
     <tr>
       <td></td>
@@ -1654,8 +1912,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>24</td>
+      <td>29</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
       <td>29</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -1684,10 +1956,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1719,7 +1990,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
+      <td>61</td>
+      <td>61</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>61</td>
+      <td>61</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -1784,6 +2070,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -1848,6 +2148,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -1910,72 +2224,100 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>27</td>
-      <td>296</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>braker</td>
-      <td>braker</td>
-      <td>BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/Gaius-Augustus/BRAKER</td>
-      <td>Genome annotation</td>
-      <td>braker</td>
-      <td>genouest</td>
-      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/braker</td>
-      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/braker</td>
-      <td>2.1.6</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>417</td>
+      <td>438</td>
+      <td>99</td>
+      <td>104</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>417</td>
+      <td>438</td>
+      <td>99</td>
+      <td>104</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>braker</td>
+      <td>braker</td>
+      <td>BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/Gaius-Augustus/BRAKER</td>
+      <td>Genome annotation</td>
+      <td>braker</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/braker</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/braker</td>
+      <td>2.1.6</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
       <td>0</td>
+      <td>165</td>
+      <td>165</td>
+      <td>48</td>
+      <td>48</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>17</td>
-      <td>109</td>
+      <td>165</td>
+      <td>165</td>
+      <td>48</td>
+      <td>48</td>
     </tr>
     <tr>
       <td></td>
@@ -2004,11 +2346,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2038,8 +2380,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>10</td>
-      <td>567</td>
+      <td>1938</td>
+      <td>1938</td>
+      <td>294</td>
+      <td>294</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>412</td>
+      <td>412</td>
+      <td>71</td>
+      <td>71</td>
+      <td>2350</td>
+      <td>2350</td>
+      <td>365</td>
+      <td>365</td>
     </tr>
     <tr>
       <td></td>
@@ -2068,9 +2424,7 @@
       <td>0</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>0</td>
@@ -2085,6 +2439,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2104,6 +2459,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1518</td>
+      <td>1526</td>
+      <td>73</td>
+      <td>76</td>
+      <td>1520</td>
+      <td>1528</td>
+      <td>74</td>
+      <td>77</td>
     </tr>
     <tr>
       <td></td>
@@ -2132,11 +2502,11 @@
       <td>1</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>1</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2166,8 +2536,22 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
+      <td>677</td>
+      <td>787</td>
+      <td>114</td>
+      <td>120</td>
+      <td>60</td>
+      <td>60</td>
       <td>30</td>
-      <td>623</td>
+      <td>30</td>
+      <td>734</td>
+      <td>746</td>
+      <td>26</td>
+      <td>26</td>
+      <td>1471</td>
+      <td>1593</td>
+      <td>170</td>
+      <td>176</td>
     </tr>
     <tr>
       <td></td>
@@ -2232,6 +2616,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2296,6 +2694,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2324,8 +2736,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2354,16 +2765,31 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1583</td>
-      <td>33934</td>
+      <td>39518</td>
+      <td>40471</td>
+      <td>3555</td>
+      <td>3629</td>
+      <td>22007</td>
+      <td>24841</td>
+      <td>3536</td>
+      <td>4045</td>
+      <td>3969</td>
+      <td>4101</td>
+      <td>814</td>
+      <td>835</td>
+      <td>65494</td>
+      <td>69413</td>
+      <td>7905</td>
+      <td>8509</td>
     </tr>
     <tr>
       <td></td>
-      <td>color-deconvolution</td>
+      <td>color_deconvolution</td>
       <td>ip_color_deconvolution</td>
       <td>Color-deconvolution methods</td>
       <td>galaxy_image_analysis</td>
@@ -2379,7 +2805,7 @@
       <td>color_deconvolution</td>
       <td>imgteam</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution</td>
       <td>0.8-2</td>
       <td>scikit-image</td>
       <td></td>
@@ -2422,8 +2848,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>15</td>
       <td>16</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>16</td>
+      <td>2</td>
+      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -2486,8 +2926,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -2552,6 +3006,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2616,6 +3084,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2680,6 +3162,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2742,8 +3238,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3</td>
-      <td>78</td>
+      <td>76</td>
+      <td>82</td>
+      <td>11</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>76</td>
+      <td>82</td>
+      <td>11</td>
+      <td>12</td>
     </tr>
     <tr>
       <td></td>
@@ -2808,6 +3318,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -2870,8 +3394,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>8</td>
-      <td>16546</td>
+      <td>16077</td>
+      <td>16547</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16077</td>
+      <td>16547</td>
+      <td>11</td>
+      <td>11</td>
     </tr>
     <tr>
       <td></td>
@@ -2900,11 +3438,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2964,9 +3516,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -2994,12 +3545,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>25</td>
-      <td>272</td>
+      <td>314</td>
+      <td>326</td>
+      <td>73</td>
+      <td>75</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>129</td>
+      <td>129</td>
+      <td>6</td>
+      <td>6</td>
+      <td>443</td>
+      <td>455</td>
+      <td>79</td>
+      <td>81</td>
     </tr>
     <tr>
       <td></td>
@@ -3062,8 +3628,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>16</td>
-      <td>8518</td>
+      <td>9942</td>
+      <td>9942</td>
+      <td>26</td>
+      <td>26</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9942</td>
+      <td>9942</td>
+      <td>26</td>
+      <td>26</td>
     </tr>
     <tr>
       <td></td>
@@ -3092,11 +3672,10 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3128,41 +3707,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>curl_post</td>
-      <td>curl_post</td>
-      <td>Send file via cURL POST</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/bmcv</td>
-      <td>Data Export, Web Services</td>
-      <td>curl_post</td>
-      <td>imgteam</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post</td>
-      <td>0.0.2</td>
-      <td>curl</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3178,20 +3722,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>27</td>
-      <td>440</td>
     </tr>
     <tr>
       <td></td>
@@ -3254,8 +3784,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -3318,8 +3862,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
-      <td>46</td>
+      <td>43</td>
+      <td>48</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>48</td>
+      <td>8</td>
+      <td>8</td>
     </tr>
     <tr>
       <td></td>
@@ -3364,7 +3922,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3379,11 +3936,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>53</td>
-      <td>9907</td>
+      <td>12996</td>
+      <td>12996</td>
+      <td>137</td>
+      <td>137</td>
+      <td>10</td>
+      <td>10</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13006</td>
+      <td>13006</td>
+      <td>138</td>
+      <td>138</td>
     </tr>
     <tr>
       <td></td>
@@ -3412,10 +3984,9 @@
       <td>0</td>
       <td>0</td>
       <td>7</td>
-      <td>7</td>
       <td>0</td>
       <td>0</td>
-      <td>7</td>
+      <td>0</td>
       <td>7</td>
       <td>0</td>
       <td>0</td>
@@ -3443,11 +4014,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>7</td>
       <td>7</td>
       <td>0</td>
-      <td>45</td>
-      <td>899</td>
+      <td>820</td>
+      <td>966</td>
+      <td>89</td>
+      <td>106</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>820</td>
+      <td>966</td>
+      <td>89</td>
+      <td>106</td>
     </tr>
     <tr>
       <td></td>
@@ -3512,6 +4098,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -3576,6 +4176,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -3627,7 +4241,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3640,6 +4253,21 @@
       <td>0</td>
       <td>0</td>
       <td>10</td>
+      <td>10</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1286</td>
+      <td>1827</td>
+      <td>144</td>
+      <td>181</td>
+      <td>1296</td>
+      <td>1837</td>
+      <td>145</td>
+      <td>182</td>
     </tr>
     <tr>
       <td></td>
@@ -3704,6 +4332,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -3768,6 +4410,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -3832,37 +4488,50 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>filter_spades_repeats</td>
-      <td>filter_spades_repeat</td>
-      <td>Remove short and repeat contigs/scaffolds</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/phac-nml/galaxy_tools/</td>
-      <td>Assembly</td>
-      <td>filter_spades_repeats</td>
-      <td>nml</td>
-      <td>https://github.com/phac-nml/galaxy_tools/</td>
-      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats</td>
-      <td>1.0.1</td>
-      <td>perl-bioperl</td>
-      <td>1.7.8</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_spades_repeats</td>
+      <td>filter_spades_repeat</td>
+      <td>Remove short and repeat contigs/scaffolds</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools/</td>
+      <td>Assembly</td>
+      <td>filter_spades_repeats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools/</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats</td>
+      <td>1.0.1</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3896,6 +4565,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -3924,9 +4608,7 @@
       <td>0</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>0</td>
@@ -3940,6 +4622,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3954,12 +4637,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>466</td>
+      <td>466</td>
+      <td>62</td>
+      <td>62</td>
+      <td>466</td>
+      <td>466</td>
+      <td>62</td>
+      <td>62</td>
     </tr>
     <tr>
       <td></td>
@@ -4024,6 +4722,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4088,6 +4800,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4116,11 +4842,10 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4151,7 +4876,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -4214,8 +4954,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>68</td>
+      <td>68</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>68</td>
+      <td>68</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -4280,6 +5034,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4324,7 +5092,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4344,6 +5111,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4408,6 +5190,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4470,8 +5266,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>4</td>
-      <td>397</td>
+      <td>377</td>
+      <td>400</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>377</td>
+      <td>400</td>
+      <td>17</td>
+      <td>17</td>
     </tr>
     <tr>
       <td></td>
@@ -4534,8 +5344,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>13</td>
-      <td>238</td>
+      <td>243</td>
+      <td>263</td>
+      <td>54</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>243</td>
+      <td>263</td>
+      <td>54</td>
+      <td>57</td>
     </tr>
     <tr>
       <td></td>
@@ -4598,8 +5422,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>7</td>
-      <td>290</td>
+      <td>266</td>
+      <td>293</td>
+      <td>22</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>266</td>
+      <td>293</td>
+      <td>22</td>
+      <td>25</td>
     </tr>
     <tr>
       <td></td>
@@ -4628,11 +5466,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4662,8 +5500,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>93</td>
+      <td>267</td>
+      <td>267</td>
+      <td>39</td>
+      <td>39</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>80</td>
+      <td>80</td>
+      <td>7</td>
+      <td>7</td>
+      <td>347</td>
+      <td>347</td>
+      <td>46</td>
+      <td>46</td>
     </tr>
     <tr>
       <td></td>
@@ -4711,7 +5563,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4728,6 +5579,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -4756,9 +5622,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4786,12 +5651,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>41</td>
-      <td>621</td>
+      <td>273</td>
+      <td>659</td>
+      <td>101</td>
+      <td>102</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>153</td>
+      <td>153</td>
+      <td>15</td>
+      <td>15</td>
+      <td>426</td>
+      <td>812</td>
+      <td>116</td>
+      <td>117</td>
     </tr>
     <tr>
       <td></td>
@@ -4854,8 +5734,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -4918,8 +5812,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>12</td>
+      <td>16</td>
+      <td>16</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -4982,8 +5890,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>7</td>
-      <td>21825</td>
+      <td>21409</td>
+      <td>21849</td>
+      <td>10</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21409</td>
+      <td>21849</td>
+      <td>10</td>
+      <td>12</td>
     </tr>
     <tr>
       <td></td>
@@ -5012,11 +5934,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5076,11 +6012,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5176,6 +6126,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5204,11 +6168,11 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5238,8 +6202,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>2</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3</td>
+      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -5304,6 +6282,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5368,6 +6360,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5432,6 +6438,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5496,6 +6516,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5560,6 +6594,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -5624,6 +6672,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5688,47 +6750,61 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>labelimage2points</td>
-      <td>ip_labelimage_to_points</td>
-      <td>Label Image to Points</td>
-      <td>galaxy_image_analysis</td>
-      <td>galaxy_image_analysis</td>
-      <td></td>
-      <td>Galaxy Image Analysis</td>
-      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
-      <td>Image analysis</td>
-      <td>Imaging, Bioinformatics</td>
-      <td>To update</td>
-      <td>https://github.com/bmcv</td>
-      <td>Imaging</td>
-      <td>labelimage2points</td>
-      <td>imgteam</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points</td>
-      <td>0.2-2</td>
-      <td>scikit-image</td>
-      <td></td>
-      <td>Image analysis</td>
-      <td>Imaging, Bioinformatics</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>labelimage2points</td>
+      <td>ip_labelimage_to_points</td>
+      <td>Label Image to Points</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>labelimage2points</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points</td>
+      <td>0.2-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5750,8 +6826,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>34</td>
+      <td>38</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
       <td>0</td>
-      <td>36</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>38</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -5814,8 +6904,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>9</td>
-      <td>857</td>
+      <td>887</td>
+      <td>927</td>
+      <td>13</td>
+      <td>15</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>891</td>
+      <td>931</td>
+      <td>16</td>
+      <td>18</td>
     </tr>
     <tr>
       <td></td>
@@ -5880,6 +6984,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -5942,12 +7060,26 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>114</td>
-      <td>936</td>
+      <td>1219</td>
+      <td>1219</td>
+      <td>182</td>
+      <td>182</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>37</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1256</td>
+      <td>1256</td>
+      <td>186</td>
+      <td>186</td>
     </tr>
     <tr>
       <td></td>
-      <td>mahotas-features</td>
+      <td>mahotas_features</td>
       <td>ip_mahotas_features</td>
       <td>Compute image features using mahotas.</td>
       <td></td>
@@ -5963,7 +7095,7 @@
       <td>mahotas_features</td>
       <td>imgteam</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features</td>
       <td>0.7-2</td>
       <td>mahotas</td>
       <td></td>
@@ -6006,8 +7138,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>39</td>
+      <td>44</td>
+      <td>6</td>
+      <td>6</td>
       <td>0</td>
-      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>44</td>
+      <td>6</td>
+      <td>6</td>
     </tr>
     <tr>
       <td></td>
@@ -6072,6 +7218,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -6136,6 +7296,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -6198,8 +7372,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>18</td>
+      <td>25</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
       <td>25</td>
+      <td>2</td>
+      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -6228,10 +7416,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6259,11 +7446,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>6</td>
-      <td>153</td>
+      <td>192</td>
+      <td>192</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>192</td>
+      <td>192</td>
+      <td>20</td>
+      <td>20</td>
     </tr>
     <tr>
       <td></td>
@@ -6326,8 +7528,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>6</td>
-      <td>12</td>
+      <td>50</td>
+      <td>50</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>50</td>
+      <td>50</td>
+      <td>14</td>
+      <td>14</td>
     </tr>
     <tr>
       <td></td>
@@ -6356,10 +7572,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6390,8 +7605,23 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>41</td>
-      <td>6076</td>
+      <td>0</td>
+      <td>6408</td>
+      <td>6514</td>
+      <td>94</td>
+      <td>99</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6408</td>
+      <td>6514</td>
+      <td>94</td>
+      <td>99</td>
     </tr>
     <tr>
       <td></td>
@@ -6456,6 +7686,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -6483,7 +7727,6 @@
       <td></td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6520,6 +7763,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -6548,9 +7806,8 @@
       <td>0</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -6579,11 +7836,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>322</td>
-      <td>89021</td>
+      <td>119024</td>
+      <td>119024</td>
+      <td>628</td>
+      <td>628</td>
+      <td>42</td>
+      <td>42</td>
+      <td>2</td>
+      <td>2</td>
+      <td>36310</td>
+      <td>36310</td>
+      <td>191</td>
+      <td>191</td>
+      <td>155376</td>
+      <td>155376</td>
+      <td>821</td>
+      <td>821</td>
     </tr>
     <tr>
       <td></td>
@@ -6648,6 +7920,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -6691,7 +7977,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6706,12 +7991,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -6740,11 +8040,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6804,11 +8118,11 @@
       <td>0</td>
       <td>0</td>
       <td>10</td>
-      <td>11</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>10</td>
-      <td>11</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6838,8 +8152,22 @@
       <td>10</td>
       <td>10</td>
       <td>0</td>
-      <td>40</td>
-      <td>709</td>
+      <td>848</td>
+      <td>848</td>
+      <td>91</td>
+      <td>91</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>848</td>
+      <td>848</td>
+      <td>91</td>
+      <td>91</td>
     </tr>
     <tr>
       <td></td>
@@ -6904,56 +8232,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>mykrobe_parser</td>
-      <td>mykrobe_parseR</td>
-      <td>RScript to parse the results of mykrobe predictor.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/phac-nml/mykrobe-parser</td>
-      <td>Sequence Analysis</td>
-      <td>mykrobe_parser</td>
-      <td>nml</td>
-      <td>https://github.com/phac-nml/mykrobe-parser</td>
-      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser</td>
-      <td>0.1.4.1</td>
-      <td>r-base</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6971,9 +8249,9 @@
     </tr>
     <tr>
       <td></td>
-      <td>ncbi_egapx</td>
-      <td>ncbi_egapx</td>
-      <td>Eukaryotic Genome Annotation Pipeline - External (EGAPx)</td>
+      <td>mykrobe_parser</td>
+      <td>mykrobe_parseR</td>
+      <td>RScript to parse the results of mykrobe predictor.</td>
       <td></td>
       <td></td>
       <td></td>
@@ -6982,33 +8260,17 @@
       <td></td>
       <td></td>
       <td>To update</td>
-      <td>https://github.com/ncbi/egapx</td>
-      <td>Genome annotation</td>
-      <td>ncbi_egapx</td>
-      <td>richard-burhans</td>
-      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx</td>
-      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx</td>
-      <td>0.2-alpha</td>
-      <td></td>
+      <td>https://github.com/phac-nml/mykrobe-parser</td>
+      <td>Sequence Analysis</td>
+      <td>mykrobe_parser</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/mykrobe-parser</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser</td>
+      <td>0.1.4.1</td>
+      <td>r-base</td>
       <td></td>
       <td></td>
       <td></td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7032,37 +8294,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>ncbi_fcs_adaptor</td>
-      <td>ncbi_fcs_adaptor</td>
-      <td>FCS-adaptor detects adaptor and vector contamination in genome sequences.</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/ncbi/fcs</td>
-      <td>Sequence Analysis</td>
-      <td>ncbi_fcs_adaptor</td>
-      <td>richard-burhans</td>
-      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor</td>
-      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor</td>
-      <td>0.5.0</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7077,9 +8308,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7099,9 +8327,9 @@
     </tr>
     <tr>
       <td></td>
-      <td>nmr_annotation</td>
-      <td>NmrAnnotation</td>
-      <td>[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation</td>
+      <td>mzxmlshaper</td>
+      <td>mzxmlshaper</td>
+      <td>Convert mzML, mzXML or netCDF files to mzML or mzXML</td>
       <td></td>
       <td></td>
       <td></td>
@@ -7110,34 +8338,17 @@
       <td></td>
       <td></td>
       <td>To update</td>
-      <td>http://workflow4metabolomics.org</td>
+      <td>https://rdrr.io/bioc/mzR/</td>
       <td>Metabolomics</td>
-      <td>nmr_annotation</td>
-      <td>marie-tremblay-metatoul</td>
-      <td>https://github.com/workflow4metabolomics/nmr_annotation</td>
-      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation</td>
-      <td>3.0.0</td>
-      <td>r-batch</td>
-      <td>1.1_4</td>
+      <td>mzxmlshaper</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper</td>
+      <td>1.0.0+galaxy0</td>
+      <td>r-base</td>
+      <td></td>
       <td></td>
       <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7155,44 +8366,323 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>3</td>
-      <td>47</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>nmr_annotation2d</td>
-      <td>2DNmrAnnotation</td>
-      <td>[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>http://workflow4metabolomics.org</td>
-      <td>Metabolomics</td>
-      <td>2dnmrannotation</td>
-      <td>marie-tremblay-metatoul</td>
-      <td>https://github.com/workflow4metabolomics/tools-metabolomics</td>
-      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d</td>
-      <td>2.0.0</td>
-      <td>r-batch</td>
-      <td>1.1_4</td>
-      <td></td>
-      <td></td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_egapx</td>
+      <td>ncbi_egapx</td>
+      <td>Eukaryotic Genome Annotation Pipeline - External (EGAPx)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ncbi/egapx</td>
+      <td>Genome annotation</td>
+      <td>ncbi_egapx</td>
+      <td>richard-burhans</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx</td>
+      <td>0.2-alpha</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>6</td>
+      <td>6</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_fcs_adaptor</td>
+      <td>ncbi_fcs_adaptor</td>
+      <td>FCS-adaptor detects adaptor and vector contamination in genome sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ncbi/fcs</td>
+      <td>Sequence Analysis</td>
+      <td>ncbi_fcs_adaptor</td>
+      <td>richard-burhans</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor</td>
+      <td>0.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>842</td>
+      <td>842</td>
+      <td>93</td>
+      <td>93</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>842</td>
+      <td>842</td>
+      <td>93</td>
+      <td>93</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nmr_annotation</td>
+      <td>NmrAnnotation</td>
+      <td>[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>nmr_annotation</td>
+      <td>marie-tremblay-metatoul</td>
+      <td>https://github.com/workflow4metabolomics/nmr_annotation</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation</td>
+      <td>3.0.0</td>
+      <td>r-batch</td>
+      <td>1.1_4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>49</td>
+      <td>49</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>49</td>
+      <td>49</td>
+      <td>5</td>
+      <td>5</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nmr_annotation2d</td>
+      <td>2DNmrAnnotation</td>
+      <td>[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>2dnmrannotation</td>
+      <td>marie-tremblay-metatoul</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d</td>
+      <td>2.0.0</td>
+      <td>r-batch</td>
+      <td>1.1_4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7252,11 +8742,11 @@
       <td>0</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7286,8 +8776,22 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>4</td>
-      <td>140</td>
+      <td>142</td>
+      <td>142</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>335</td>
+      <td>341</td>
+      <td>9</td>
+      <td>9</td>
+      <td>477</td>
+      <td>483</td>
+      <td>17</td>
+      <td>17</td>
     </tr>
     <tr>
       <td></td>
@@ -7316,11 +8820,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7350,8 +8854,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>13</td>
-      <td>133</td>
+      <td>152</td>
+      <td>162</td>
+      <td>39</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>233</td>
+      <td>236</td>
+      <td>12</td>
+      <td>12</td>
+      <td>385</td>
+      <td>398</td>
+      <td>51</td>
+      <td>52</td>
     </tr>
     <tr>
       <td></td>
@@ -7416,6 +8934,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -7480,6 +9012,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -7508,9 +9054,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7539,11 +9084,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>21</td>
-      <td>60</td>
+      <td>149</td>
+      <td>149</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td>167</td>
+      <td>167</td>
+      <td>32</td>
+      <td>32</td>
     </tr>
     <tr>
       <td></td>
@@ -7572,8 +9132,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -7602,12 +9161,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>7457</td>
+      <td>7457</td>
+      <td>508</td>
+      <td>508</td>
+      <td>8518</td>
+      <td>8518</td>
+      <td>377</td>
+      <td>377</td>
+      <td>2760</td>
+      <td>2760</td>
       <td>259</td>
-      <td>7276</td>
+      <td>259</td>
+      <td>18735</td>
+      <td>18735</td>
+      <td>1144</td>
+      <td>1144</td>
     </tr>
     <tr>
       <td></td>
@@ -7672,6 +9246,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -7700,11 +9288,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7798,8 +9400,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>36</td>
+      <td>42</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>36</td>
       <td>42</td>
+      <td>1</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -7828,11 +9444,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7892,11 +9522,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7992,6 +9636,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8036,7 +9694,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8056,6 +9713,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8120,6 +9792,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8163,7 +9849,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8184,6 +9869,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8235,7 +9935,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8248,6 +9947,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8312,52 +10026,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>points2binaryimage</td>
-      <td>ip_points_to_binaryimage</td>
-      <td>Points to Binary Image</td>
-      <td>galaxy_image_analysis</td>
-      <td>galaxy_image_analysis</td>
-      <td></td>
-      <td>Galaxy Image Analysis</td>
-      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
-      <td>Image analysis</td>
-      <td>Imaging, Bioinformatics</td>
-      <td>To update</td>
-      <td>https://github.com/bmcv</td>
-      <td>Imaging</td>
-      <td>points2binaryimage</td>
-      <td>imgteam</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage</td>
-      <td>0.3</td>
-      <td>scikit-image</td>
-      <td></td>
-      <td>Image analysis</td>
-      <td>Imaging, Bioinformatics</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8371,11 +10039,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>2</td>
-      <td>41</td>
     </tr>
     <tr>
       <td></td>
@@ -8438,8 +10102,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
       <td>0</td>
-      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -8502,8 +10180,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
       <td>29</td>
+      <td>29</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -8566,8 +10258,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>85</td>
+      <td>40</td>
+      <td>86</td>
+      <td>4</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>86</td>
+      <td>4</td>
+      <td>6</td>
     </tr>
     <tr>
       <td></td>
@@ -8627,45 +10333,73 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>9</td>
-      <td>21343</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>promer</td>
-      <td>promer4_substitutions</td>
-      <td>Aligns two sets of contigs and reports amino acid substitutions between them</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/phac-nml/promer</td>
-      <td>Assembly</td>
-      <td>promer</td>
-      <td>nml</td>
-      <td>https://github.com/phac-nml/promer</td>
-      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer</td>
-      <td>1.2</td>
-      <td>python</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20858</td>
+      <td>21444</td>
+      <td>14</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20858</td>
+      <td>21444</td>
+      <td>14</td>
+      <td>18</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>promer</td>
+      <td>promer4_substitutions</td>
+      <td>Aligns two sets of contigs and reports amino acid substitutions between them</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/promer</td>
+      <td>Assembly</td>
+      <td>promer</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/promer</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer</td>
+      <td>1.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8760,6 +10494,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8788,9 +10536,7 @@
       <td>0</td>
       <td>12</td>
       <td>0</td>
-      <td>12</td>
       <td>0</td>
-      <td>12</td>
       <td>0</td>
       <td>12</td>
       <td>0</td>
@@ -8805,6 +10551,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>12</td>
       <td>0</td>
       <td>0</td>
@@ -8824,6 +10571,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13483</td>
+      <td>13483</td>
+      <td>434</td>
+      <td>434</td>
+      <td>13483</td>
+      <td>13483</td>
+      <td>434</td>
+      <td>434</td>
     </tr>
     <tr>
       <td></td>
@@ -8888,6 +10650,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -8916,10 +10692,9 @@
       <td>2</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -8951,7 +10726,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>428</td>
+      <td>428</td>
+      <td>35</td>
+      <td>35</td>
+      <td>141</td>
+      <td>141</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>569</td>
+      <td>569</td>
+      <td>77</td>
+      <td>77</td>
     </tr>
     <tr>
       <td></td>
@@ -9014,8 +10804,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -9078,8 +10882,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>95</td>
+      <td>95</td>
+      <td>38</td>
+      <td>38</td>
       <td>0</td>
-      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>95</td>
+      <td>95</td>
+      <td>38</td>
+      <td>38</td>
     </tr>
     <tr>
       <td></td>
@@ -9142,8 +10960,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>20</td>
-      <td>537</td>
+      <td>514</td>
+      <td>573</td>
+      <td>69</td>
+      <td>83</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>514</td>
+      <td>573</td>
+      <td>69</td>
+      <td>83</td>
     </tr>
     <tr>
       <td></td>
@@ -9206,7 +11038,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>7</td>
       <td>7</td>
     </tr>
     <tr>
@@ -9272,6 +11118,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -9334,8 +11194,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>9</td>
-      <td>512</td>
+      <td>477</td>
+      <td>520</td>
+      <td>13</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>477</td>
+      <td>520</td>
+      <td>13</td>
+      <td>16</td>
     </tr>
     <tr>
       <td></td>
@@ -9400,6 +11274,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>252</td>
+      <td>252</td>
+      <td>47</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>252</td>
+      <td>252</td>
+      <td>47</td>
+      <td>47</td>
     </tr>
     <tr>
       <td></td>
@@ -9462,8 +11350,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>2</td>
       <td>2</td>
-      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -9528,6 +11430,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -9572,7 +11488,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9587,11 +11502,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>133</td>
-      <td>2489</td>
+      <td>3457</td>
+      <td>3457</td>
+      <td>301</td>
+      <td>301</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>556</td>
+      <td>556</td>
+      <td>65</td>
+      <td>65</td>
+      <td>4013</td>
+      <td>4013</td>
+      <td>366</td>
+      <td>366</td>
     </tr>
     <tr>
       <td></td>
@@ -9620,11 +11550,25 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -9718,8 +11662,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>96</td>
+      <td>103</td>
+      <td>4</td>
+      <td>5</td>
+      <td>0</td>
       <td>0</td>
-      <td>102</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>100</td>
+      <td>107</td>
+      <td>5</td>
+      <td>6</td>
     </tr>
     <tr>
       <td></td>
@@ -9764,7 +11722,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9784,6 +11741,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -9848,6 +11820,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -9910,8 +11896,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>9</td>
-      <td>493</td>
+      <td>499</td>
+      <td>499</td>
+      <td>16</td>
+      <td>16</td>
+      <td>44</td>
+      <td>44</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>543</td>
+      <td>543</td>
+      <td>26</td>
+      <td>26</td>
     </tr>
     <tr>
       <td></td>
@@ -9976,6 +11976,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -10040,6 +12054,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -10102,8 +12130,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>44</td>
+      <td>51</td>
+      <td>2</td>
+      <td>3</td>
       <td>0</td>
-      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>44</td>
+      <td>51</td>
+      <td>2</td>
+      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -10168,6 +12210,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -10230,8 +12286,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
       <td>16</td>
+      <td>16</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -10276,7 +12346,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10291,11 +12360,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>22</td>
-      <td>205</td>
+      <td>297</td>
+      <td>297</td>
+      <td>40</td>
+      <td>40</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>368</td>
+      <td>368</td>
+      <td>41</td>
+      <td>41</td>
     </tr>
     <tr>
       <td></td>
@@ -10324,8 +12408,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -10354,12 +12437,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>889</td>
-      <td>12673</td>
+      <td>20778</td>
+      <td>20891</td>
+      <td>2030</td>
+      <td>2045</td>
+      <td>9520</td>
+      <td>9520</td>
+      <td>1424</td>
+      <td>1424</td>
+      <td>6753</td>
+      <td>6753</td>
+      <td>864</td>
+      <td>864</td>
+      <td>37051</td>
+      <td>37164</td>
+      <td>4318</td>
+      <td>4333</td>
     </tr>
     <tr>
       <td></td>
@@ -10404,7 +12502,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10424,6 +12521,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -10452,8 +12564,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -10483,11 +12594,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>6</td>
-      <td>13</td>
+      <td>249</td>
+      <td>249</td>
+      <td>32</td>
+      <td>32</td>
+      <td>16</td>
+      <td>16</td>
+      <td>10</td>
+      <td>10</td>
+      <td>102</td>
+      <td>102</td>
+      <td>16</td>
+      <td>16</td>
+      <td>367</td>
+      <td>367</td>
+      <td>58</td>
+      <td>58</td>
     </tr>
     <tr>
       <td></td>
@@ -10516,11 +12642,11 @@
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>2</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -10550,8 +12676,22 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>5</td>
+      <td>117</td>
+      <td>117</td>
+      <td>41</td>
+      <td>41</td>
+      <td>84</td>
+      <td>84</td>
+      <td>24</td>
+      <td>24</td>
+      <td>161</td>
+      <td>161</td>
+      <td>13</td>
+      <td>13</td>
+      <td>362</td>
+      <td>362</td>
+      <td>78</td>
+      <td>78</td>
     </tr>
     <tr>
       <td></td>
@@ -10580,11 +12720,11 @@
       <td>4</td>
       <td>4</td>
       <td>4</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -10614,8 +12754,22 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
-      <td>67</td>
+      <td>217</td>
+      <td>217</td>
+      <td>47</td>
+      <td>47</td>
+      <td>42</td>
+      <td>42</td>
+      <td>20</td>
+      <td>20</td>
+      <td>96</td>
+      <td>96</td>
+      <td>12</td>
+      <td>12</td>
+      <td>355</td>
+      <td>355</td>
+      <td>79</td>
+      <td>79</td>
     </tr>
     <tr>
       <td></td>
@@ -10644,11 +12798,11 @@
       <td>4</td>
       <td>4</td>
       <td>4</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -10678,8 +12832,22 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>31</td>
-      <td>202</td>
+      <td>721</td>
+      <td>721</td>
+      <td>160</td>
+      <td>160</td>
+      <td>350</td>
+      <td>350</td>
+      <td>91</td>
+      <td>91</td>
+      <td>214</td>
+      <td>214</td>
+      <td>35</td>
+      <td>35</td>
+      <td>1285</td>
+      <td>1285</td>
+      <td>286</td>
+      <td>286</td>
     </tr>
     <tr>
       <td></td>
@@ -10708,11 +12876,11 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -10742,8 +12910,22 @@
       <td>3</td>
       <td>0</td>
       <td>0</td>
+      <td>125</td>
+      <td>125</td>
+      <td>30</td>
+      <td>30</td>
+      <td>13</td>
+      <td>13</td>
       <td>9</td>
-      <td>73</td>
+      <td>9</td>
+      <td>83</td>
+      <td>83</td>
+      <td>8</td>
+      <td>8</td>
+      <td>221</td>
+      <td>221</td>
+      <td>47</td>
+      <td>47</td>
     </tr>
     <tr>
       <td></td>
@@ -10772,8 +12954,7 @@
       <td>6</td>
       <td>6</td>
       <td>6</td>
-      <td>6</td>
-      <td>6</td>
+      <td>0</td>
       <td>6</td>
       <td>6</td>
       <td>6</td>
@@ -10803,11 +12984,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
-      <td>26</td>
-      <td>114</td>
+      <td>396</td>
+      <td>396</td>
+      <td>134</td>
+      <td>134</td>
+      <td>121</td>
+      <td>121</td>
+      <td>57</td>
+      <td>57</td>
+      <td>144</td>
+      <td>144</td>
+      <td>39</td>
+      <td>39</td>
+      <td>661</td>
+      <td>661</td>
+      <td>230</td>
+      <td>230</td>
     </tr>
     <tr>
       <td></td>
@@ -10836,11 +13032,11 @@
       <td>21</td>
       <td>21</td>
       <td>22</td>
-      <td>21</td>
+      <td>0</td>
       <td>21</td>
       <td>21</td>
       <td>22</td>
-      <td>21</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -10870,8 +13066,22 @@
       <td>21</td>
       <td>0</td>
       <td>0</td>
-      <td>43</td>
-      <td>168</td>
+      <td>964</td>
+      <td>964</td>
+      <td>318</td>
+      <td>318</td>
+      <td>249</td>
+      <td>249</td>
+      <td>118</td>
+      <td>118</td>
+      <td>475</td>
+      <td>475</td>
+      <td>108</td>
+      <td>108</td>
+      <td>1688</td>
+      <td>1688</td>
+      <td>544</td>
+      <td>544</td>
     </tr>
     <tr>
       <td></td>
@@ -10900,8 +13110,7 @@
       <td>12</td>
       <td>12</td>
       <td>12</td>
-      <td>12</td>
-      <td>12</td>
+      <td>0</td>
       <td>12</td>
       <td>12</td>
       <td>12</td>
@@ -10931,11 +13140,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>12</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
-      <td>4</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>13</td>
+      <td>13</td>
+      <td>11</td>
+      <td>11</td>
+      <td>1302</td>
+      <td>1302</td>
+      <td>19</td>
+      <td>19</td>
+      <td>1323</td>
+      <td>1323</td>
+      <td>38</td>
+      <td>38</td>
     </tr>
     <tr>
       <td></td>
@@ -10964,8 +13188,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -10995,11 +13218,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>6</td>
+      <td>58</td>
+      <td>58</td>
+      <td>23</td>
+      <td>23</td>
+      <td>24</td>
+      <td>24</td>
+      <td>11</td>
+      <td>11</td>
+      <td>92</td>
+      <td>92</td>
+      <td>11</td>
+      <td>11</td>
+      <td>174</td>
+      <td>174</td>
+      <td>45</td>
+      <td>45</td>
     </tr>
     <tr>
       <td></td>
@@ -11028,8 +13266,7 @@
       <td>10</td>
       <td>10</td>
       <td>10</td>
-      <td>10</td>
-      <td>10</td>
+      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>10</td>
@@ -11059,11 +13296,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>10</td>
       <td>0</td>
       <td>0</td>
-      <td>48</td>
-      <td>263</td>
+      <td>863</td>
+      <td>863</td>
+      <td>220</td>
+      <td>220</td>
+      <td>237</td>
+      <td>237</td>
+      <td>98</td>
+      <td>98</td>
+      <td>181</td>
+      <td>181</td>
+      <td>41</td>
+      <td>41</td>
+      <td>1281</td>
+      <td>1281</td>
+      <td>359</td>
+      <td>359</td>
     </tr>
     <tr>
       <td></td>
@@ -11092,8 +13344,7 @@
       <td>17</td>
       <td>17</td>
       <td>17</td>
-      <td>17</td>
-      <td>17</td>
+      <td>0</td>
       <td>17</td>
       <td>17</td>
       <td>17</td>
@@ -11123,11 +13374,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>17</td>
       <td>0</td>
       <td>0</td>
-      <td>59</td>
-      <td>213</td>
+      <td>983</td>
+      <td>983</td>
+      <td>287</td>
+      <td>287</td>
+      <td>375</td>
+      <td>375</td>
+      <td>144</td>
+      <td>144</td>
+      <td>907</td>
+      <td>907</td>
+      <td>106</td>
+      <td>106</td>
+      <td>2265</td>
+      <td>2265</td>
+      <td>537</td>
+      <td>537</td>
     </tr>
     <tr>
       <td></td>
@@ -11156,8 +13422,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -11187,11 +13452,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>6</td>
-      <td>20</td>
+      <td>46</td>
+      <td>46</td>
+      <td>13</td>
+      <td>13</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>55</td>
+      <td>18</td>
+      <td>18</td>
     </tr>
     <tr>
       <td></td>
@@ -11220,11 +13500,11 @@
       <td>11</td>
       <td>11</td>
       <td>11</td>
+      <td>0</td>
       <td>11</td>
       <td>11</td>
       <td>11</td>
-      <td>11</td>
-      <td>11</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11254,8 +13534,22 @@
       <td>11</td>
       <td>0</td>
       <td>0</td>
-      <td>6</td>
+      <td>37</td>
+      <td>37</td>
+      <td>16</td>
+      <td>16</td>
+      <td>22</td>
+      <td>22</td>
+      <td>7</td>
+      <td>7</td>
+      <td>89</td>
+      <td>89</td>
+      <td>14</td>
       <td>14</td>
+      <td>148</td>
+      <td>148</td>
+      <td>37</td>
+      <td>37</td>
     </tr>
     <tr>
       <td></td>
@@ -11284,11 +13578,11 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11318,8 +13612,22 @@
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>40</td>
-      <td>232</td>
+      <td>615</td>
+      <td>615</td>
+      <td>143</td>
+      <td>143</td>
+      <td>246</td>
+      <td>246</td>
+      <td>75</td>
+      <td>75</td>
+      <td>115</td>
+      <td>115</td>
+      <td>27</td>
+      <td>27</td>
+      <td>976</td>
+      <td>976</td>
+      <td>245</td>
+      <td>245</td>
     </tr>
     <tr>
       <td></td>
@@ -11348,11 +13656,11 @@
       <td>12</td>
       <td>12</td>
       <td>12</td>
+      <td>0</td>
       <td>12</td>
       <td>12</td>
       <td>12</td>
-      <td>12</td>
-      <td>12</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11382,8 +13690,22 @@
       <td>12</td>
       <td>0</td>
       <td>0</td>
-      <td>12</td>
-      <td>37</td>
+      <td>330</td>
+      <td>330</td>
+      <td>83</td>
+      <td>83</td>
+      <td>64</td>
+      <td>64</td>
+      <td>40</td>
+      <td>40</td>
+      <td>195</td>
+      <td>195</td>
+      <td>49</td>
+      <td>49</td>
+      <td>589</td>
+      <td>589</td>
+      <td>172</td>
+      <td>172</td>
     </tr>
     <tr>
       <td></td>
@@ -11412,12 +13734,10 @@
       <td>6</td>
       <td>6</td>
       <td>6</td>
+      <td>0</td>
       <td>6</td>
       <td>6</td>
       <td>6</td>
-      <td>6</td>
-      <td>6</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11443,11 +13763,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>6</td>
       <td>0</td>
       <td>0</td>
+      <td>6</td>
       <td>0</td>
       <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
     </tr>
     <tr>
       <td></td>
@@ -11476,11 +13812,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11510,8 +13846,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>14</td>
+      <td>14</td>
+      <td>16</td>
+      <td>16</td>
+      <td>6</td>
+      <td>6</td>
+      <td>37</td>
+      <td>37</td>
       <td>2</td>
-      <td>13</td>
+      <td>2</td>
+      <td>82</td>
+      <td>82</td>
+      <td>22</td>
+      <td>22</td>
     </tr>
     <tr>
       <td></td>
@@ -11576,6 +13926,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -11604,11 +13968,11 @@
       <td>15</td>
       <td>15</td>
       <td>15</td>
+      <td>0</td>
       <td>15</td>
       <td>15</td>
       <td>15</td>
-      <td>15</td>
-      <td>15</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11638,8 +14002,22 @@
       <td>15</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
+      <td>10</td>
+      <td>10</td>
+      <td>3</td>
+      <td>3</td>
+      <td>14</td>
+      <td>14</td>
+      <td>10</td>
+      <td>10</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>29</td>
+      <td>29</td>
+      <td>18</td>
+      <td>18</td>
     </tr>
     <tr>
       <td></td>
@@ -11668,8 +14046,7 @@
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
@@ -11699,11 +14076,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>22</td>
-      <td>172</td>
+      <td>664</td>
+      <td>664</td>
+      <td>145</td>
+      <td>145</td>
+      <td>113</td>
+      <td>113</td>
+      <td>43</td>
+      <td>43</td>
+      <td>255</td>
+      <td>255</td>
+      <td>50</td>
+      <td>50</td>
+      <td>1032</td>
+      <td>1032</td>
+      <td>238</td>
+      <td>238</td>
     </tr>
     <tr>
       <td></td>
@@ -11732,11 +14124,11 @@
       <td>8</td>
       <td>8</td>
       <td>8</td>
-      <td>7</td>
+      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>8</td>
-      <td>7</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11766,8 +14158,22 @@
       <td>8</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
+      <td>84</td>
+      <td>84</td>
+      <td>52</td>
+      <td>52</td>
+      <td>25</td>
+      <td>25</td>
       <td>16</td>
+      <td>16</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>118</td>
+      <td>118</td>
+      <td>73</td>
+      <td>73</td>
     </tr>
     <tr>
       <td></td>
@@ -11832,6 +14238,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -11860,8 +14280,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -11891,11 +14310,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>124</td>
-      <td>7087</td>
+      <td>14941</td>
+      <td>14941</td>
+      <td>383</td>
+      <td>383</td>
+      <td>25941</td>
+      <td>25941</td>
+      <td>255</td>
+      <td>255</td>
+      <td>2856</td>
+      <td>2856</td>
+      <td>112</td>
+      <td>112</td>
+      <td>43738</td>
+      <td>43738</td>
+      <td>750</td>
+      <td>750</td>
     </tr>
     <tr>
       <td></td>
@@ -11958,8 +14392,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>16</td>
+      <td>26</td>
+      <td>26</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -12022,8 +14470,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>70</td>
-      <td>8690</td>
+      <td>3783</td>
+      <td>9125</td>
+      <td>211</td>
+      <td>229</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3784</td>
+      <td>9126</td>
+      <td>212</td>
+      <td>230</td>
     </tr>
     <tr>
       <td></td>
@@ -12068,7 +14530,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12088,6 +14549,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -12152,6 +14628,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -12180,9 +14670,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -12210,16 +14699,31 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>508</td>
-      <td>5370</td>
+      <td>6942</td>
+      <td>7024</td>
+      <td>1345</td>
+      <td>1356</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2461</td>
+      <td>2461</td>
+      <td>266</td>
+      <td>266</td>
+      <td>9404</td>
+      <td>9486</td>
+      <td>1612</td>
+      <td>1623</td>
     </tr>
     <tr>
       <td></td>
-      <td>visceral-evaluatesegmentation</td>
+      <td>visceral_evaluatesegmentation</td>
       <td>ip_visceral_evaluatesegmentation</td>
       <td>Visceral Project - Evaluate Segmentation Tool</td>
       <td></td>
@@ -12235,7 +14739,7 @@
       <td>visceral_evaluatesegmentation</td>
       <td>imgteam</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation</td>
       <td>0.5-2</td>
       <td>visceral-evaluatesegmentation</td>
       <td>2015.07.03</td>
@@ -12278,8 +14782,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>20</td>
+      <td>25</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
       <td>25</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -12342,8 +14860,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>3</td>
+      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -12406,8 +14938,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3</td>
-      <td>2834</td>
+      <td>2370</td>
+      <td>2836</td>
+      <td>9</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1482</td>
+      <td>1509</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3852</td>
+      <td>4345</td>
+      <td>13</td>
+      <td>14</td>
     </tr>
     <tr>
       <td></td>
@@ -12436,11 +14982,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -12534,8 +15094,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5</td>
-      <td>368</td>
+      <td>238</td>
+      <td>375</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>2</td>
+      <td>2</td>
+      <td>248</td>
+      <td>385</td>
+      <td>12</td>
+      <td>12</td>
     </tr>
     <tr>
       <td></td>
@@ -12598,8 +15172,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
+      <td>150</td>
       <td>171</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>2</td>
+      <td>2</td>
+      <td>157</td>
+      <td>178</td>
+      <td>9</td>
+      <td>9</td>
     </tr>
     <tr>
       <td></td>
@@ -12664,6 +15252,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -12726,8 +15328,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>32</td>
+      <td>38</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>32</td>
       <td>38</td>
+      <td>2</td>
+      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -12756,11 +15372,11 @@
       <td>9</td>
       <td>11</td>
       <td>12</td>
-      <td>12</td>
+      <td>0</td>
       <td>9</td>
       <td>11</td>
       <td>12</td>
-      <td>12</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -12790,8 +15406,22 @@
       <td>10</td>
       <td>9</td>
       <td>0</td>
-      <td>356</td>
-      <td>29809</td>
+      <td>31909</td>
+      <td>35790</td>
+      <td>1357</td>
+      <td>1384</td>
+      <td>7099</td>
+      <td>7099</td>
+      <td>413</td>
+      <td>413</td>
+      <td>5333</td>
+      <td>5357</td>
+      <td>330</td>
+      <td>330</td>
+      <td>44341</td>
+      <td>48246</td>
+      <td>2100</td>
+      <td>2127</td>
     </tr>
     <tr>
       <td></td>
@@ -12854,8 +15484,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>46</td>
-      <td>228</td>
+      <td>307</td>
+      <td>307</td>
+      <td>80</td>
+      <td>80</td>
+      <td>8</td>
+      <td>8</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1</td>
+      <td>1</td>
+      <td>318</td>
+      <td>318</td>
+      <td>84</td>
+      <td>84</td>
     </tr>
     <tr>
       <td></td>
@@ -12918,8 +15562,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>6</td>
-      <td>116</td>
+      <td>45</td>
+      <td>119</td>
+      <td>14</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45</td>
+      <td>119</td>
+      <td>14</td>
+      <td>17</td>
     </tr>
     <tr>
       <td></td>
@@ -12982,8 +15640,22 @@
       <td>0</td>
       <td>1</td>
       <td>0</td>
-      <td>10</td>
-      <td>3060</td>
+      <td>189</td>
+      <td>3094</td>
+      <td>23</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>189</td>
+      <td>3094</td>
+      <td>23</td>
+      <td>25</td>
     </tr>
     <tr>
       <td></td>
@@ -13046,8 +15718,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>14</td>
-      <td>45191</td>
+      <td>25532</td>
+      <td>50045</td>
+      <td>45</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25532</td>
+      <td>50045</td>
+      <td>45</td>
+      <td>57</td>
     </tr>
     <tr>
       <td></td>
@@ -13110,8 +15796,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>14</td>
-      <td>1961</td>
+      <td>1119</td>
+      <td>2115</td>
+      <td>50</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1119</td>
+      <td>2115</td>
+      <td>50</td>
+      <td>62</td>
     </tr>
     <tr>
       <td></td>
@@ -13174,8 +15874,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>37</td>
+      <td>108</td>
+      <td>1</td>
+      <td>3</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
       <td>108</td>
+      <td>1</td>
+      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -13238,8 +15952,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>4</td>
-      <td>133</td>
+      <td>80</td>
+      <td>150</td>
+      <td>18</td>
+      <td>23</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>80</td>
+      <td>150</td>
+      <td>18</td>
+      <td>23</td>
     </tr>
     <tr>
       <td></td>
@@ -13302,8 +16030,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>13</td>
-      <td>45325</td>
+      <td>25572</td>
+      <td>50177</td>
+      <td>45</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25572</td>
+      <td>50177</td>
+      <td>45</td>
+      <td>57</td>
     </tr>
     <tr>
       <td></td>
@@ -13366,8 +16108,22 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>28</td>
-      <td>62388</td>
+      <td>3210</td>
+      <td>62854</td>
+      <td>96</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3210</td>
+      <td>62854</td>
+      <td>96</td>
+      <td>124</td>
     </tr>
     <tr>
       <td></td>
@@ -13430,8 +16186,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3</td>
-      <td>68</td>
+      <td>45</td>
+      <td>71</td>
+      <td>9</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45</td>
+      <td>71</td>
+      <td>9</td>
+      <td>10</td>
     </tr>
     <tr>
       <td></td>
@@ -13494,8 +16264,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>15</td>
-      <td>1932</td>
+      <td>1202</td>
+      <td>2121</td>
+      <td>48</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1202</td>
+      <td>2121</td>
+      <td>48</td>
+      <td>62</td>
     </tr>
     <tr>
       <td></td>
@@ -13558,8 +16342,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>18</td>
-      <td>1758</td>
+      <td>1116</td>
+      <td>1897</td>
+      <td>57</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1116</td>
+      <td>1897</td>
+      <td>57</td>
+      <td>71</td>
     </tr>
     <tr>
       <td></td>
@@ -13622,8 +16420,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>16</td>
-      <td>2925</td>
+      <td>991</td>
+      <td>3060</td>
+      <td>50</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>991</td>
+      <td>3060</td>
+      <td>50</td>
+      <td>62</td>
     </tr>
     <tr>
       <td></td>
@@ -13686,8 +16498,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>193</td>
-      <td>14480</td>
+      <td>15933</td>
+      <td>15933</td>
+      <td>378</td>
+      <td>378</td>
+      <td>1736</td>
+      <td>1736</td>
+      <td>214</td>
+      <td>214</td>
+      <td>380</td>
+      <td>380</td>
+      <td>28</td>
+      <td>28</td>
+      <td>18049</td>
+      <td>18049</td>
+      <td>620</td>
+      <td>620</td>
     </tr>
     <tr>
       <td></td>
@@ -13716,11 +16542,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -13729,7 +16555,6 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -13746,12 +16571,27 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>591</td>
-      <td>367167</td>
+      <td>37860</td>
+      <td>374587</td>
+      <td>1293</td>
+      <td>1610</td>
+      <td>17588</td>
+      <td>293713</td>
+      <td>1243</td>
+      <td>6197</td>
+      <td>3873</td>
+      <td>4397</td>
+      <td>202</td>
+      <td>229</td>
+      <td>59321</td>
+      <td>672697</td>
+      <td>2738</td>
+      <td>8036</td>
     </tr>
     <tr>
       <td></td>
@@ -13780,9 +16620,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -13811,11 +16650,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>42</td>
-      <td>481</td>
+      <td>1436</td>
+      <td>1436</td>
+      <td>244</td>
+      <td>244</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>119</td>
+      <td>10</td>
+      <td>10</td>
+      <td>1555</td>
+      <td>1555</td>
+      <td>254</td>
+      <td>254</td>
     </tr>
     <tr>
       <td></td>
@@ -13878,8 +16732,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>11</td>
-      <td>329</td>
+      <td>511</td>
+      <td>541</td>
+      <td>32</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>511</td>
+      <td>541</td>
+      <td>32</td>
+      <td>35</td>
     </tr>
     <tr>
       <td></td>
@@ -13942,8 +16810,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
-      <td>52</td>
+      <td>292</td>
+      <td>306</td>
+      <td>5</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>292</td>
+      <td>306</td>
+      <td>5</td>
+      <td>7</td>
     </tr>
     <tr>
       <td></td>
@@ -13985,7 +16867,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -14003,11 +16884,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>279</td>
-      <td>14596</td>
+      <td>15949</td>
+      <td>16490</td>
+      <td>726</td>
+      <td>811</td>
+      <td>5113</td>
+      <td>5113</td>
+      <td>649</td>
+      <td>649</td>
+      <td>6043</td>
+      <td>6043</td>
+      <td>169</td>
+      <td>169</td>
+      <td>27105</td>
+      <td>27646</td>
+      <td>1544</td>
+      <td>1629</td>
     </tr>
     <tr>
       <td></td>
@@ -14070,8 +16966,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>4</td>
-      <td>65</td>
+      <td>59</td>
+      <td>74</td>
+      <td>10</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>59</td>
+      <td>74</td>
+      <td>10</td>
+      <td>12</td>
     </tr>
     <tr>
       <td></td>
@@ -14134,8 +17044,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>26</td>
-      <td>257</td>
+      <td>232</td>
+      <td>279</td>
+      <td>62</td>
+      <td>72</td>
+      <td>0</td>
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+      <td>279</td>
+      <td>62</td>
+      <td>72</td>
     </tr>
     <tr>
       <td></td>
@@ -14164,8 +17088,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -14194,12 +17117,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>516</td>
-      <td>8864</td>
+      <td>10109</td>
+      <td>11052</td>
+      <td>1378</td>
+      <td>1509</td>
+      <td>12573</td>
+      <td>12573</td>
+      <td>2206</td>
+      <td>2206</td>
+      <td>5274</td>
+      <td>5274</td>
+      <td>369</td>
+      <td>369</td>
+      <td>27956</td>
+      <td>28899</td>
+      <td>3953</td>
+      <td>4084</td>
     </tr>
     <tr>
       <td></td>
@@ -14262,8 +17200,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>15</td>
-      <td>169</td>
+      <td>158</td>
+      <td>181</td>
+      <td>40</td>
+      <td>44</td>
+      <td>0</td>
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+      <td>158</td>
+      <td>181</td>
+      <td>40</td>
+      <td>44</td>
     </tr>
     <tr>
       <td></td>
@@ -14328,6 +17280,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -14356,8 +17322,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -14386,12 +17351,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
+      <td>226</td>
       <td>308</td>
+      <td>27</td>
+      <td>35</td>
+      <td>2615</td>
+      <td>45557</td>
+      <td>302</td>
+      <td>2284</td>
+      <td>482</td>
+      <td>522</td>
+      <td>32</td>
+      <td>36</td>
+      <td>3323</td>
+      <td>46387</td>
+      <td>361</td>
+      <td>2355</td>
     </tr>
     <tr>
       <td></td>
@@ -14420,10 +17400,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -14450,12 +17429,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
+      <td>4</td>
+      <td>3</td>
+      <td>4</td>
+      <td>14</td>
+      <td>253</td>
+      <td>7</td>
+      <td>72</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>257</td>
+      <td>10</td>
+      <td>76</td>
     </tr>
     <tr>
       <td></td>
@@ -14518,7 +17512,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
       <td>2</td>
     </tr>
     <tr>
@@ -14563,7 +17571,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -14579,11 +17586,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>200</td>
-      <td>5749</td>
+      <td>5769</td>
+      <td>6802</td>
+      <td>567</td>
+      <td>650</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1</td>
+      <td>5769</td>
+      <td>6805</td>
+      <td>567</td>
+      <td>651</td>
     </tr>
     <tr>
       <td></td>
@@ -14646,8 +17668,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
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+      <td>0</td>
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       <td>0</td>
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+      <td>0</td>
+      <td>2</td>
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+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -14710,8 +17746,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>25</td>
+      <td>25</td>
+      <td>11</td>
+      <td>11</td>
       <td>0</td>
-      <td>13</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>25</td>
+      <td>25</td>
+      <td>11</td>
+      <td>11</td>
     </tr>
     <tr>
       <td></td>
@@ -14774,8 +17824,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>112</td>
-      <td>531</td>
+      <td>547</td>
+      <td>547</td>
+      <td>151</td>
+      <td>151</td>
+      <td>143</td>
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+      <td>43</td>
+      <td>596</td>
+      <td>596</td>
+      <td>22</td>
+      <td>22</td>
+      <td>1286</td>
+      <td>1286</td>
+      <td>216</td>
+      <td>216</td>
     </tr>
     <tr>
       <td></td>
@@ -14804,9 +17868,8 @@
       <td>0</td>
       <td>4</td>
       <td>4</td>
-      <td>4</td>
       <td>0</td>
-      <td>4</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
@@ -14834,12 +17897,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>4</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
-      <td>332</td>
-      <td>12876</td>
+      <td>13715</td>
+      <td>14997</td>
+      <td>992</td>
+      <td>1099</td>
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+      <td>0</td>
+      <td>197</td>
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+      <td>22</td>
+      <td>22</td>
+      <td>13912</td>
+      <td>15194</td>
+      <td>1014</td>
+      <td>1121</td>
     </tr>
     <tr>
       <td></td>
@@ -14904,6 +17982,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -14968,6 +18060,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -15030,8 +18136,22 @@
       <td>1</td>
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       <td>0</td>
-      <td>21</td>
-      <td>685</td>
+      <td>1527</td>
+      <td>1527</td>
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+      <td>6</td>
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+      <td>1</td>
+      <td>1</td>
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+      <td>26</td>
+      <td>26</td>
+      <td>1850</td>
+      <td>1850</td>
+      <td>106</td>
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     </tr>
     <tr>
       <td></td>
@@ -15083,19 +18203,33 @@
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+      <td>0</td>
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-      <td>34</td>
-      <td>3009</td>
+      <td>768</td>
+      <td>3043</td>
+      <td>97</td>
+      <td>119</td>
+      <td>14</td>
+      <td>14</td>
+      <td>11</td>
+      <td>11</td>
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+      <td>276</td>
+      <td>9</td>
+      <td>9</td>
+      <td>1058</td>
+      <td>3333</td>
+      <td>117</td>
+      <td>139</td>
     </tr>
     <tr>
       <td></td>
@@ -15147,19 +18281,33 @@
       <td>0</td>
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       <td>1</td>
       <td>0</td>
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       <td>1</td>
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+      <td>811</td>
+      <td>1501</td>
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+      <td>561</td>
+      <td>15</td>
       <td>15</td>
-      <td>1478</td>
+      <td>1436</td>
+      <td>2126</td>
+      <td>98</td>
+      <td>123</td>
     </tr>
     <tr>
       <td></td>
@@ -15203,7 +18351,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -15218,12 +18365,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
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-      <td>506</td>
-      <td>22988</td>
+      <td>24164</td>
+      <td>25149</td>
+      <td>1320</td>
+      <td>1480</td>
+      <td>17537</td>
+      <td>203397</td>
+      <td>1330</td>
+      <td>17491</td>
+      <td>15654</td>
+      <td>15992</td>
+      <td>291</td>
+      <td>351</td>
+      <td>57355</td>
+      <td>244538</td>
+      <td>2941</td>
+      <td>19322</td>
     </tr>
     <tr>
       <td></td>
@@ -15252,11 +18414,11 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
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+      <td>0</td>
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@@ -15286,8 +18448,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>10</td>
-      <td>74</td>
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+      <td>580</td>
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     </tr>
     <tr>
       <td></td>
@@ -15316,9 +18492,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -15347,11 +18522,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>0</td>
-      <td>533</td>
-      <td>13021</td>
+      <td>13360</td>
+      <td>14618</td>
+      <td>1383</td>
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+      <td>385</td>
+      <td>16902</td>
+      <td>18160</td>
+      <td>1768</td>
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     </tr>
     <tr>
       <td></td>
@@ -15414,8 +18604,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>40</td>
+      <td>37</td>
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+      <td>16</td>
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     </tr>
     <tr>
       <td></td>
@@ -15478,8 +18682,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>15</td>
-      <td>173</td>
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+      <td>175</td>
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     </tr>
     <tr>
       <td></td>
@@ -15524,7 +18742,6 @@
       <td>0</td>
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-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -15544,6 +18761,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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+      <td>5946</td>
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+      <td>7379</td>
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     </tr>
     <tr>
       <td></td>
@@ -15606,8 +18838,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>14</td>
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     </tr>
     <tr>
       <td></td>
@@ -15636,11 +18882,11 @@
       <td>0</td>
       <td>23</td>
       <td>23</td>
-      <td>19</td>
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@@ -15670,8 +18916,22 @@
       <td>23</td>
       <td>19</td>
       <td>0</td>
-      <td>178</td>
-      <td>4614</td>
+      <td>4773</td>
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+      <td>10461</td>
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+      <td>843</td>
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     </tr>
     <tr>
       <td></td>
@@ -15700,10 +18960,9 @@
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       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
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@@ -15731,11 +18990,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -15764,11 +19038,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
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       <td>1</td>
       <td>1</td>
-      <td>1</td>
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@@ -15777,7 +19051,6 @@
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       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -15794,12 +19067,27 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>931</td>
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+      <td>10606</td>
+      <td>12531</td>
+      <td>2204</td>
+      <td>2547</td>
+      <td>9044</td>
+      <td>17167</td>
+      <td>1748</td>
+      <td>2394</td>
+      <td>923</td>
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+      <td>240</td>
+      <td>245</td>
+      <td>20573</td>
+      <td>30636</td>
+      <td>4192</td>
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     </tr>
     <tr>
       <td></td>
@@ -15862,8 +19150,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>62</td>
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     </tr>
     <tr>
       <td></td>
@@ -15915,7 +19217,6 @@
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@@ -15923,11 +19224,26 @@
       <td>0</td>
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-      <td>418</td>
-      <td>15690</td>
+      <td>16468</td>
+      <td>18344</td>
+      <td>956</td>
+      <td>991</td>
+      <td>33692</td>
+      <td>34453</td>
+      <td>2559</td>
+      <td>2625</td>
+      <td>2948</td>
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+      <td>104</td>
+      <td>104</td>
+      <td>53108</td>
+      <td>55745</td>
+      <td>3619</td>
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     </tr>
     <tr>
       <td></td>
@@ -15992,6 +19308,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -16054,8 +19384,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>8</td>
-      <td>251</td>
+      <td>211</td>
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+      <td>420</td>
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+      <td>38</td>
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     </tr>
     <tr>
       <td></td>
@@ -16120,6 +19464,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -16184,6 +19542,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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+      <td>548</td>
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     </tr>
     <tr>
       <td></td>
@@ -16212,8 +19584,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
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       <td>1</td>
@@ -16242,12 +19613,27 @@
       <td>0</td>
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-      <td>1</td>
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+      <td>513</td>
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+      <td>18</td>
+      <td>35</td>
+      <td>2406</td>
+      <td>30579</td>
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+      <td>1547</td>
+      <td>1353</td>
+      <td>1393</td>
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+      <td>20</td>
+      <td>4272</td>
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     </tr>
     <tr>
       <td></td>
@@ -16310,8 +19696,22 @@
       <td>1</td>
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       <td>0</td>
-      <td>1</td>
-      <td>102</td>
+      <td>2609</td>
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     </tr>
     <tr>
       <td></td>
@@ -16374,8 +19774,22 @@
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       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -16438,8 +19852,22 @@
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-      <td>8</td>
-      <td>342</td>
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     </tr>
     <tr>
       <td></td>
@@ -16468,8 +19896,7 @@
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       <td>1</td>
-      <td>1</td>
-      <td>1</td>
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@@ -16498,12 +19925,27 @@
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     </tr>
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@@ -16566,8 +20008,22 @@
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     </tr>
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       <td></td>
@@ -16630,8 +20086,22 @@
       <td>1</td>
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@@ -16694,8 +20164,22 @@
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+      <td>332</td>
+      <td>28</td>
+      <td>32</td>
     </tr>
     <tr>
       <td></td>
@@ -16724,8 +20208,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -16754,12 +20237,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>187</td>
       <td>233</td>
+      <td>15</td>
+      <td>20</td>
+      <td>495</td>
+      <td>4810</td>
+      <td>165</td>
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+      <td>405</td>
+      <td>451</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1087</td>
+      <td>5494</td>
+      <td>187</td>
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     </tr>
     <tr>
       <td></td>
@@ -16822,8 +20320,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
-      <td>94</td>
+      <td>85</td>
+      <td>96</td>
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+      <td>17</td>
+      <td>18</td>
     </tr>
     <tr>
       <td></td>
@@ -16886,8 +20398,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
+      <td>55</td>
       <td>65</td>
+      <td>2</td>
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+      <td>7</td>
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     </tr>
     <tr>
       <td></td>
@@ -16952,6 +20478,20 @@
       <td>0</td>
       <td>0</td>
       <td>35</td>
+      <td>0</td>
+      <td>3</td>
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+      <td>0</td>
+      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -16980,8 +20520,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -17010,12 +20549,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>309</td>
-      <td>564900</td>
+      <td>575128</td>
+      <td>575441</td>
+      <td>694</td>
+      <td>783</td>
+      <td>43420</td>
+      <td>85345</td>
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+      <td>19330</td>
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+      <td>104</td>
+      <td>117</td>
+      <td>637878</td>
+      <td>680204</td>
+      <td>1427</td>
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     </tr>
     <tr>
       <td></td>
@@ -17060,7 +20614,6 @@
       <td>0</td>
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       <td>0</td>
-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -17080,6 +20633,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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+      <td>47</td>
+      <td>2173</td>
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+      <td>368</td>
+      <td>195</td>
+      <td>205</td>
+      <td>8</td>
+      <td>8</td>
+      <td>242</td>
+      <td>2378</td>
+      <td>36</td>
+      <td>376</td>
     </tr>
     <tr>
       <td></td>
@@ -17108,11 +20676,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -17121,7 +20689,6 @@
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       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -17138,12 +20705,27 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>475</td>
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+      <td>23589</td>
+      <td>28986</td>
+      <td>1061</td>
+      <td>1200</td>
+      <td>23507</td>
+      <td>160693</td>
+      <td>2302</td>
+      <td>8699</td>
+      <td>5413</td>
+      <td>6446</td>
+      <td>251</td>
+      <td>329</td>
+      <td>52509</td>
+      <td>196125</td>
+      <td>3614</td>
+      <td>10228</td>
     </tr>
     <tr>
       <td></td>
@@ -17208,6 +20790,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -17272,6 +20868,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -17300,9 +20910,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
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@@ -17330,12 +20939,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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-      <td>47</td>
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+      <td>398</td>
+      <td>876</td>
+      <td>106</td>
+      <td>134</td>
+      <td>412</td>
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+      <td>27</td>
+      <td>1002</td>
+      <td>6683</td>
+      <td>232</td>
+      <td>916</td>
     </tr>
     <tr>
       <td></td>
@@ -17364,11 +20988,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
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@@ -17398,8 +21022,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>49</td>
-      <td>271</td>
+      <td>280</td>
+      <td>307</td>
+      <td>110</td>
+      <td>124</td>
+      <td>712</td>
+      <td>1277</td>
+      <td>332</td>
+      <td>628</td>
+      <td>476</td>
+      <td>541</td>
+      <td>55</td>
+      <td>79</td>
+      <td>1468</td>
+      <td>2125</td>
+      <td>497</td>
+      <td>831</td>
     </tr>
     <tr>
       <td></td>
@@ -17444,7 +21082,6 @@
       <td>0</td>
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-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -17464,6 +21101,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -17492,8 +21144,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
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       <td>1</td>
@@ -17522,12 +21173,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
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-      <td>17</td>
-      <td>1502</td>
+      <td>1560</td>
+      <td>1725</td>
+      <td>43</td>
+      <td>58</td>
+      <td>4328</td>
+      <td>44209</td>
+      <td>193</td>
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+      <td>283</td>
+      <td>316</td>
+      <td>16</td>
+      <td>18</td>
+      <td>6171</td>
+      <td>46250</td>
+      <td>252</td>
+      <td>2189</td>
     </tr>
     <tr>
       <td></td>
@@ -17572,7 +21238,6 @@
       <td>0</td>
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       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -17592,6 +21257,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -17620,11 +21300,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
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       <td>0</td>
@@ -17654,8 +21334,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>21</td>
-      <td>134</td>
+      <td>204</td>
+      <td>204</td>
+      <td>47</td>
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+      <td>165</td>
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+      <td>40</td>
+      <td>40</td>
+      <td>125</td>
+      <td>125</td>
+      <td>7</td>
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+      <td>494</td>
+      <td>494</td>
+      <td>94</td>
+      <td>94</td>
     </tr>
     <tr>
       <td></td>
@@ -17700,7 +21394,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -17715,11 +21408,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>74</td>
-      <td>3389</td>
+      <td>4066</td>
+      <td>4139</td>
+      <td>166</td>
+      <td>180</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>4066</td>
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+      <td>166</td>
+      <td>180</td>
     </tr>
     <tr>
       <td></td>
@@ -17782,8 +21490,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>13</td>
-      <td>203</td>
+      <td>196</td>
+      <td>211</td>
+      <td>41</td>
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+      <td>1</td>
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+      <td>197</td>
+      <td>658</td>
+      <td>42</td>
+      <td>209</td>
     </tr>
     <tr>
       <td></td>
@@ -17846,8 +21568,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>31</td>
-      <td>1782</td>
+      <td>1251</td>
+      <td>1803</td>
+      <td>98</td>
+      <td>166</td>
+      <td>3461</td>
+      <td>15159</td>
+      <td>486</td>
+      <td>2044</td>
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+      <td>159</td>
+      <td>7137</td>
+      <td>20300</td>
+      <td>641</td>
+      <td>2369</td>
     </tr>
     <tr>
       <td></td>
@@ -17910,8 +21646,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>13</td>
-      <td>1204</td>
+      <td>888</td>
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+      <td>97</td>
+      <td>1334</td>
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+      <td>2222</td>
+      <td>3891</td>
+      <td>144</td>
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     </tr>
     <tr>
       <td></td>
@@ -17940,11 +21690,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
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@@ -17953,7 +21703,6 @@
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-      <td>0</td>
       <td>1</td>
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       <td>1</td>
@@ -17970,12 +21719,27 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>5064</td>
-      <td>1957541</td>
+      <td>1973168</td>
+      <td>2034965</td>
+      <td>11939</td>
+      <td>12833</td>
+      <td>352364</td>
+      <td>803522</td>
+      <td>12967</td>
+      <td>30199</td>
+      <td>128777</td>
+      <td>133584</td>
+      <td>2341</td>
+      <td>2572</td>
+      <td>2454309</td>
+      <td>2972071</td>
+      <td>27247</td>
+      <td>45604</td>
     </tr>
     <tr>
       <td></td>
@@ -18038,8 +21802,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
-      <td>39</td>
+      <td>33</td>
+      <td>40</td>
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+      <td>6</td>
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     </tr>
     <tr>
       <td></td>
@@ -18102,8 +21880,22 @@
       <td>1</td>
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       <td>0</td>
-      <td>11</td>
-      <td>72</td>
+      <td>89</td>
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     </tr>
     <tr>
       <td></td>
@@ -18166,8 +21958,22 @@
       <td>1</td>
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-      <td>7</td>
-      <td>65</td>
+      <td>59</td>
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     </tr>
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       <td></td>
@@ -18230,8 +22036,22 @@
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-      <td>30</td>
-      <td>235</td>
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     </tr>
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@@ -18296,50 +22116,6 @@
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-    </tr>
-    <tr>
-      <td></td>
-      <td>divide_pg_snp</td>
-      <td>dividePgSnp</td>
-      <td>Separate pgSnp alleles into columns</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Sequence Analysis</td>
-      <td>divide_pg_snp</td>
-      <td>devteam</td>
-      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp</td>
-      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp</td>
-      <td>1.0.0</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -18354,18 +22130,168 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>divide_pg_snp</td>
+      <td>dividePgSnp</td>
+      <td>Separate pgSnp alleles into columns</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>divide_pg_snp</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>26</td>
+      <td>32</td>
+      <td>8</td>
+      <td>9</td>
+      <td>86</td>
+      <td>172</td>
+      <td>20</td>
+      <td>53</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>112</td>
+      <td>204</td>
+      <td>28</td>
+      <td>62</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dorina</td>
+      <td>dorina_search</td>
+      <td>data source for RNA interactions in post-transcriptional regulation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA, Data Source</td>
+      <td>dorina</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>921</td>
+      <td>1626</td>
+      <td>4</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>32</td>
+      <td>921</td>
+      <td>1626</td>
+      <td>4</td>
+      <td>31</td>
     </tr>
     <tr>
       <td></td>
-      <td>dorina</td>
-      <td>dorina_search</td>
-      <td>data source for RNA interactions in post-transcriptional regulation</td>
+      <td>dot2ct</td>
+      <td>rnastructure_dot2ct</td>
+      <td>Dot-Bracket to Connect Table (CT)</td>
       <td></td>
       <td></td>
       <td></td>
@@ -18375,28 +22301,18 @@
       <td></td>
       <td>To update</td>
       <td></td>
-      <td>RNA, Data Source</td>
-      <td>dorina</td>
+      <td>Sequence Analysis, RNA</td>
+      <td>dot2ct</td>
       <td>rnateam</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina</td>
-      <td>1.0</td>
-      <td></td>
-      <td></td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct</td>
+      <td>5.7.a</td>
+      <td>rnastructure</td>
+      <td>6.4</td>
       <td></td>
       <td></td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -18419,46 +22335,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1576</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>dot2ct</td>
-      <td>rnastructure_dot2ct</td>
-      <td>Dot-Bracket to Connect Table (CT)</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Sequence Analysis, RNA</td>
-      <td>dot2ct</td>
-      <td>rnateam</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct</td>
-      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct</td>
-      <td>5.7.a</td>
-      <td>rnastructure</td>
-      <td>6.4</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -18550,8 +22426,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>83</td>
+      <td>74</td>
+      <td>88</td>
+      <td>12</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>74</td>
+      <td>88</td>
+      <td>12</td>
+      <td>15</td>
     </tr>
     <tr>
       <td></td>
@@ -18580,9 +22470,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18610,12 +22499,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>12</td>
-      <td>173</td>
+      <td>189</td>
+      <td>216</td>
+      <td>47</td>
+      <td>52</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>183</td>
+      <td>213</td>
+      <td>22</td>
+      <td>31</td>
+      <td>372</td>
+      <td>429</td>
+      <td>69</td>
+      <td>83</td>
     </tr>
     <tr>
       <td></td>
@@ -18680,6 +22584,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>136</td>
+      <td>141</td>
+      <td>8</td>
+      <td>11</td>
+      <td>136</td>
+      <td>141</td>
+      <td>8</td>
+      <td>11</td>
     </tr>
     <tr>
       <td></td>
@@ -18744,6 +22662,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>124</td>
+      <td>124</td>
+      <td>7</td>
+      <td>7</td>
+      <td>124</td>
+      <td>124</td>
+      <td>7</td>
+      <td>7</td>
     </tr>
     <tr>
       <td></td>
@@ -18808,6 +22740,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>123</td>
+      <td>5</td>
+      <td>7</td>
+      <td>121</td>
+      <td>123</td>
+      <td>5</td>
+      <td>7</td>
     </tr>
     <tr>
       <td></td>
@@ -18872,59 +22818,73 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>dwt_var_perfeature</td>
-      <td>dwt_var1</td>
-      <td>Wavelet variance using Discrete Wavelet Transfoms</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>Statistics</td>
-      <td>dwt_var_perfeature</td>
-      <td>devteam</td>
-      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature</td>
-      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature</td>
-      <td>1.0.2</td>
-      <td>r-bitops</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>131</td>
+      <td>132</td>
+      <td>7</td>
+      <td>8</td>
+      <td>131</td>
+      <td>132</td>
+      <td>7</td>
+      <td>8</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dwt_var_perfeature</td>
+      <td>dwt_var1</td>
+      <td>Wavelet variance using Discrete Wavelet Transfoms</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>dwt_var_perfeature</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature</td>
+      <td>1.0.2</td>
+      <td>r-bitops</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -18934,8 +22894,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>0</td>
+      <td>30</td>
       <td>36</td>
+      <td>2</td>
+      <td>4</td>
+      <td>11</td>
+      <td>11</td>
+      <td>4</td>
+      <td>4</td>
+      <td>206</td>
+      <td>220</td>
+      <td>6</td>
+      <td>7</td>
+      <td>247</td>
+      <td>267</td>
+      <td>12</td>
+      <td>15</td>
     </tr>
     <tr>
       <td></td>
@@ -18998,8 +22972,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>28</td>
+      <td>28</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>28</td>
+      <td>28</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -19062,8 +23050,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>58</td>
-      <td>484</td>
+      <td>4495</td>
+      <td>4495</td>
+      <td>111</td>
+      <td>111</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4495</td>
+      <td>4495</td>
+      <td>111</td>
+      <td>111</td>
     </tr>
     <tr>
       <td></td>
@@ -19128,6 +23130,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -19190,8 +23206,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5</td>
-      <td>245</td>
+      <td>160</td>
+      <td>252</td>
+      <td>17</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>160</td>
+      <td>252</td>
+      <td>17</td>
+      <td>21</td>
     </tr>
     <tr>
       <td></td>
@@ -19256,6 +23286,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -19299,7 +23343,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -19314,12 +23357,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>12</td>
-      <td>325</td>
+      <td>278</td>
+      <td>337</td>
+      <td>34</td>
+      <td>45</td>
+      <td>0</td>
+      <td>1184</td>
+      <td>0</td>
+      <td>117</td>
+      <td>2402</td>
+      <td>2844</td>
+      <td>23</td>
+      <td>60</td>
+      <td>2680</td>
+      <td>4365</td>
+      <td>57</td>
+      <td>222</td>
     </tr>
     <tr>
       <td></td>
@@ -19334,13 +23392,13 @@
       <td></td>
       <td></td>
       <td>To update</td>
-      <td></td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length</td>
       <td>Fasta Manipulation</td>
       <td>fasta_compute_length</td>
       <td>devteam</td>
       <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length</td>
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length</td>
-      <td>1.0.3</td>
+      <td>1.0.4</td>
       <td>python</td>
       <td></td>
       <td></td>
@@ -19348,8 +23406,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -19378,12 +23435,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>380</td>
-      <td>7758</td>
+      <td>8547</td>
+      <td>9136</td>
+      <td>978</td>
+      <td>1129</td>
+      <td>17748</td>
+      <td>51150</td>
+      <td>1404</td>
+      <td>5670</td>
+      <td>4239</td>
+      <td>4404</td>
+      <td>162</td>
+      <td>190</td>
+      <td>30534</td>
+      <td>64690</td>
+      <td>2544</td>
+      <td>6989</td>
     </tr>
     <tr>
       <td></td>
@@ -19412,8 +23484,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -19442,12 +23513,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>88</td>
-      <td>35793</td>
+      <td>39695</td>
+      <td>39742</td>
+      <td>242</td>
+      <td>255</td>
+      <td>13660</td>
+      <td>19007</td>
+      <td>600</td>
+      <td>1398</td>
+      <td>1521</td>
+      <td>1603</td>
+      <td>92</td>
+      <td>112</td>
+      <td>54876</td>
+      <td>60352</td>
+      <td>934</td>
+      <td>1765</td>
     </tr>
     <tr>
       <td></td>
@@ -19470,7 +23556,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id</td>
       <td>0.0.7</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -19512,6 +23598,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -19540,8 +23640,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -19570,12 +23669,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>350</td>
-      <td>48649</td>
+      <td>47494</td>
+      <td>51924</td>
+      <td>889</td>
+      <td>997</td>
+      <td>50663</td>
+      <td>101663</td>
+      <td>1488</td>
+      <td>3742</td>
+      <td>3919</td>
+      <td>5601</td>
+      <td>241</td>
+      <td>276</td>
+      <td>102076</td>
+      <td>159188</td>
+      <td>2618</td>
+      <td>5015</td>
     </tr>
     <tr>
       <td></td>
@@ -19604,8 +23718,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -19634,12 +23747,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>622</td>
-      <td>105935</td>
+      <td>108876</td>
+      <td>113638</td>
+      <td>1572</td>
+      <td>1793</td>
+      <td>82527</td>
+      <td>192112</td>
+      <td>2209</td>
+      <td>8565</td>
+      <td>5711</td>
+      <td>7649</td>
+      <td>275</td>
+      <td>334</td>
+      <td>197114</td>
+      <td>313399</td>
+      <td>4056</td>
+      <td>10692</td>
     </tr>
     <tr>
       <td></td>
@@ -19662,7 +23790,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id</td>
       <td>0.0.7</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -19704,6 +23832,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -19748,7 +23890,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -19763,11 +23904,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>679</td>
-      <td>5765</td>
+      <td>7560</td>
+      <td>7560</td>
+      <td>1266</td>
+      <td>1266</td>
+      <td>6539</td>
+      <td>6539</td>
+      <td>1581</td>
+      <td>1581</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14099</td>
+      <td>14099</td>
+      <td>2847</td>
+      <td>2847</td>
     </tr>
     <tr>
       <td></td>
@@ -19790,7 +23946,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names</td>
       <td>0.0.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -19832,6 +23988,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -19854,7 +24024,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired</td>
       <td>0.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -19896,6 +24066,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -19909,7 +24093,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td></td>
       <td>Fastq Manipulation</td>
       <td>fastq_trimmer_by_quality</td>
@@ -19918,14 +24102,13 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -19954,12 +24137,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>459</td>
-      <td>5676</td>
+      <td>4881</td>
+      <td>6165</td>
+      <td>859</td>
+      <td>967</td>
+      <td>29458</td>
+      <td>99179</td>
+      <td>3455</td>
+      <td>11369</td>
+      <td>2171</td>
+      <td>2678</td>
+      <td>259</td>
+      <td>338</td>
+      <td>36510</td>
+      <td>108022</td>
+      <td>4573</td>
+      <td>12674</td>
     </tr>
     <tr>
       <td></td>
@@ -20024,6 +24222,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -20068,7 +24280,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -20082,12 +24293,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>6</td>
-      <td>22385</td>
+      <td>22308</td>
+      <td>22388</td>
+      <td>16</td>
+      <td>19</td>
+      <td>350</td>
+      <td>13711</td>
+      <td>54</td>
+      <td>349</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22658</td>
+      <td>36099</td>
+      <td>70</td>
+      <td>368</td>
     </tr>
     <tr>
       <td></td>
@@ -20116,10 +24342,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -20146,12 +24371,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>176</td>
-      <td>8496</td>
+      <td>6690</td>
+      <td>8818</td>
+      <td>554</td>
+      <td>612</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6690</td>
+      <td>8818</td>
+      <td>554</td>
+      <td>612</td>
     </tr>
     <tr>
       <td></td>
@@ -20180,11 +24420,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -20214,8 +24454,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>20</td>
+      <td>23</td>
+      <td>24</td>
+      <td>9</td>
+      <td>10</td>
+      <td>62</td>
+      <td>635</td>
+      <td>26</td>
+      <td>241</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>87</td>
+      <td>661</td>
+      <td>37</td>
+      <td>253</td>
     </tr>
     <tr>
       <td></td>
@@ -20260,7 +24514,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -20274,12 +24527,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5</td>
-      <td>69</td>
+      <td>62</td>
+      <td>70</td>
+      <td>10</td>
+      <td>12</td>
+      <td>3</td>
+      <td>1787</td>
+      <td>1</td>
+      <td>204</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>1857</td>
+      <td>11</td>
+      <td>216</td>
     </tr>
     <tr>
       <td></td>
@@ -20342,8 +24610,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>31</td>
-      <td>763</td>
+      <td>554</td>
+      <td>784</td>
+      <td>69</td>
+      <td>79</td>
+      <td>2820</td>
+      <td>3047</td>
+      <td>323</td>
+      <td>361</td>
+      <td>20</td>
+      <td>20</td>
+      <td>1</td>
+      <td>1</td>
+      <td>3394</td>
+      <td>3851</td>
+      <td>393</td>
+      <td>441</td>
     </tr>
     <tr>
       <td></td>
@@ -20372,8 +24654,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -20402,12 +24683,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>20</td>
-      <td>671</td>
+      <td>589</td>
+      <td>731</td>
+      <td>51</td>
+      <td>63</td>
+      <td>2445</td>
+      <td>32847</td>
+      <td>304</td>
+      <td>2549</td>
+      <td>1214</td>
+      <td>1294</td>
+      <td>15</td>
+      <td>22</td>
+      <td>4248</td>
+      <td>34872</td>
+      <td>370</td>
+      <td>2634</td>
     </tr>
     <tr>
       <td></td>
@@ -20470,8 +24766,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -20500,8 +24810,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -20530,12 +24839,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1499</td>
-      <td>20904</td>
+      <td>32514</td>
+      <td>32675</td>
+      <td>3379</td>
+      <td>3422</td>
+      <td>19434</td>
+      <td>19434</td>
+      <td>2537</td>
+      <td>2537</td>
+      <td>9843</td>
+      <td>9843</td>
+      <td>1624</td>
+      <td>1624</td>
+      <td>61791</td>
+      <td>61952</td>
+      <td>7540</td>
+      <td>7583</td>
     </tr>
     <tr>
       <td></td>
@@ -20598,8 +24922,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>57</td>
+      <td>57</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -20662,8 +25000,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>20</td>
-      <td>166</td>
+      <td>189</td>
+      <td>203</td>
+      <td>57</td>
+      <td>60</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>189</td>
+      <td>203</td>
+      <td>57</td>
+      <td>60</td>
     </tr>
     <tr>
       <td></td>
@@ -20708,7 +25060,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -20722,12 +25073,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>166</td>
-      <td>5588</td>
+      <td>5940</td>
+      <td>6474</td>
+      <td>558</td>
+      <td>608</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5940</td>
+      <td>6474</td>
+      <td>558</td>
+      <td>608</td>
     </tr>
     <tr>
       <td></td>
@@ -20756,11 +25122,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -20790,8 +25156,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>12</td>
-      <td>119</td>
+      <td>115</td>
+      <td>124</td>
+      <td>29</td>
+      <td>30</td>
+      <td>518</td>
+      <td>1029</td>
+      <td>102</td>
+      <td>261</td>
+      <td>184</td>
+      <td>198</td>
+      <td>14</td>
+      <td>17</td>
+      <td>817</td>
+      <td>1351</td>
+      <td>145</td>
+      <td>308</td>
     </tr>
     <tr>
       <td></td>
@@ -20820,8 +25200,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -20850,12 +25229,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>555</td>
-      <td>324598</td>
+      <td>3768</td>
+      <td>325011</td>
+      <td>1462</td>
+      <td>2044</td>
+      <td>9350</td>
+      <td>242043</td>
+      <td>2201</td>
+      <td>6583</td>
+      <td>787</td>
+      <td>1070</td>
+      <td>119</td>
+      <td>146</td>
+      <td>13905</td>
+      <td>568124</td>
+      <td>3782</td>
+      <td>8773</td>
     </tr>
     <tr>
       <td></td>
@@ -20884,9 +25278,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -20914,12 +25307,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>15</td>
-      <td>186</td>
+      <td>746</td>
+      <td>746</td>
+      <td>136</td>
+      <td>136</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1504</td>
+      <td>1504</td>
+      <td>244</td>
+      <td>244</td>
+      <td>2250</td>
+      <td>2250</td>
+      <td>380</td>
+      <td>380</td>
     </tr>
     <tr>
       <td></td>
@@ -20984,6 +25392,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>290</td>
+      <td>20</td>
+      <td>86</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>290</td>
+      <td>20</td>
+      <td>86</td>
     </tr>
     <tr>
       <td></td>
@@ -21048,6 +25470,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>74</td>
+      <td>237</td>
+      <td>24</td>
+      <td>61</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>74</td>
+      <td>237</td>
+      <td>24</td>
+      <td>61</td>
     </tr>
     <tr>
       <td></td>
@@ -21092,7 +25528,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -21107,11 +25542,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>418</td>
-      <td>8159</td>
+      <td>11748</td>
+      <td>11748</td>
+      <td>767</td>
+      <td>767</td>
+      <td>6560</td>
+      <td>6560</td>
+      <td>397</td>
+      <td>397</td>
+      <td>2556</td>
+      <td>2556</td>
+      <td>106</td>
+      <td>106</td>
+      <td>20864</td>
+      <td>20864</td>
+      <td>1270</td>
+      <td>1270</td>
     </tr>
     <tr>
       <td></td>
@@ -21155,7 +25605,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -21170,12 +25619,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>27</td>
-      <td>660</td>
+      <td>490</td>
+      <td>682</td>
+      <td>74</td>
+      <td>109</td>
+      <td>127</td>
+      <td>14058</td>
+      <td>20</td>
+      <td>1798</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>617</td>
+      <td>14740</td>
+      <td>94</td>
+      <td>1907</td>
     </tr>
     <tr>
       <td></td>
@@ -21240,6 +25704,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -21268,8 +25746,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -21298,12 +25775,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>4</td>
       <td>11</td>
+      <td>11</td>
+      <td>6</td>
+      <td>6</td>
+      <td>85</td>
+      <td>984</td>
+      <td>29</td>
+      <td>230</td>
+      <td>10</td>
+      <td>11</td>
+      <td>7</td>
+      <td>8</td>
+      <td>106</td>
+      <td>1006</td>
+      <td>42</td>
+      <td>244</td>
     </tr>
     <tr>
       <td></td>
@@ -21366,8 +25858,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>71</td>
+      <td>34</td>
+      <td>72</td>
+      <td>5</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>72</td>
+      <td>5</td>
+      <td>7</td>
     </tr>
     <tr>
       <td></td>
@@ -21432,6 +25938,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -21496,6 +26016,20 @@
       <td>0</td>
       <td>0</td>
       <td>6</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -21558,8 +26092,22 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>43</td>
-      <td>2605</td>
+      <td>1725</td>
+      <td>2708</td>
+      <td>97</td>
+      <td>99</td>
+      <td>2</td>
+      <td>2</td>
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+      <td>2</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>1727</td>
+      <td>2710</td>
+      <td>99</td>
+      <td>101</td>
     </tr>
     <tr>
       <td></td>
@@ -21604,7 +26152,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -21618,12 +26165,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>136</td>
-      <td>6651</td>
+      <td>7012</td>
+      <td>7344</td>
+      <td>323</td>
+      <td>338</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>7012</td>
+      <td>7344</td>
+      <td>323</td>
+      <td>338</td>
     </tr>
     <tr>
       <td></td>
@@ -21686,8 +26248,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>6</td>
-      <td>474</td>
+      <td>463</td>
+      <td>484</td>
+      <td>18</td>
+      <td>19</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>463</td>
+      <td>484</td>
+      <td>18</td>
+      <td>19</td>
     </tr>
     <tr>
       <td></td>
@@ -21752,6 +26328,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -21816,6 +26406,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>145</td>
+      <td>1794</td>
+      <td>33</td>
+      <td>397</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>145</td>
+      <td>1794</td>
+      <td>33</td>
+      <td>397</td>
     </tr>
     <tr>
       <td></td>
@@ -21880,6 +26484,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>265</td>
+      <td>16</td>
+      <td>60</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>265</td>
+      <td>16</td>
+      <td>60</td>
     </tr>
     <tr>
       <td></td>
@@ -21942,8 +26560,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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       <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>9</td>
+      <td>9</td>
     </tr>
     <tr>
       <td></td>
@@ -22006,8 +26638,22 @@
       <td>7</td>
       <td>6</td>
       <td>0</td>
-      <td>76</td>
-      <td>921</td>
+      <td>901</td>
+      <td>1020</td>
+      <td>160</td>
+      <td>184</td>
+      <td>440</td>
+      <td>440</td>
+      <td>111</td>
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+      <td>0</td>
+      <td>1341</td>
+      <td>1460</td>
+      <td>271</td>
+      <td>295</td>
     </tr>
     <tr>
       <td></td>
@@ -22052,7 +26698,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -22071,7 +26716,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>228</td>
+      <td>0</td>
+      <td>12</td>
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+      <td>0</td>
+      <td>12</td>
     </tr>
     <tr>
       <td></td>
@@ -22100,8 +26760,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -22130,12 +26789,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>242</td>
-      <td>4350</td>
+      <td>3748</td>
+      <td>4661</td>
+      <td>866</td>
+      <td>1002</td>
+      <td>5993</td>
+      <td>48272</td>
+      <td>1507</td>
+      <td>7101</td>
+      <td>549</td>
+      <td>746</td>
+      <td>152</td>
+      <td>253</td>
+      <td>10290</td>
+      <td>53679</td>
+      <td>2525</td>
+      <td>8356</td>
     </tr>
     <tr>
       <td></td>
@@ -22200,6 +26874,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -22262,8 +26950,22 @@
       <td>1</td>
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       <td>0</td>
-      <td>15</td>
-      <td>77</td>
+      <td>98</td>
+      <td>98</td>
+      <td>19</td>
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     </tr>
     <tr>
       <td></td>
@@ -22328,6 +27030,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -22390,8 +27106,22 @@
       <td>27</td>
       <td>27</td>
       <td>0</td>
-      <td>26</td>
-      <td>1537</td>
+      <td>1731</td>
+      <td>1731</td>
+      <td>109</td>
+      <td>109</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1731</td>
+      <td>1731</td>
+      <td>109</td>
+      <td>109</td>
     </tr>
     <tr>
       <td></td>
@@ -22456,6 +27186,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -22518,7 +27262,21 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>18</td>
+      <td>22</td>
+      <td>1</td>
+      <td>1</td>
+      <td>44</td>
+      <td>292</td>
+      <td>3</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>62</td>
+      <td>314</td>
+      <td>4</td>
       <td>22</td>
     </tr>
     <tr>
@@ -22582,8 +27340,22 @@
       <td>6</td>
       <td>6</td>
       <td>0</td>
-      <td>67</td>
-      <td>100294</td>
+      <td>59700</td>
+      <td>112582</td>
+      <td>223</td>
+      <td>282</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1157</td>
+      <td>1221</td>
+      <td>34</td>
+      <td>35</td>
+      <td>60857</td>
+      <td>113803</td>
+      <td>257</td>
+      <td>317</td>
     </tr>
     <tr>
       <td></td>
@@ -22648,6 +27420,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -22710,8 +27496,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>157</td>
+      <td>157</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
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+      <td>157</td>
+      <td>157</td>
+      <td>14</td>
       <td>14</td>
-      <td>139</td>
     </tr>
     <tr>
       <td></td>
@@ -22774,8 +27574,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>23</td>
-      <td>7569</td>
+      <td>3071</td>
+      <td>7652</td>
+      <td>41</td>
+      <td>47</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3071</td>
+      <td>7652</td>
+      <td>41</td>
+      <td>47</td>
     </tr>
     <tr>
       <td></td>
@@ -22804,8 +27618,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -22834,12 +27647,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1003</td>
-      <td>348449</td>
+      <td>20472</td>
+      <td>349984</td>
+      <td>2351</td>
+      <td>3007</td>
+      <td>45587</td>
+      <td>778988</td>
+      <td>4359</td>
+      <td>14116</td>
+      <td>6087</td>
+      <td>7417</td>
+      <td>484</td>
+      <td>561</td>
+      <td>72146</td>
+      <td>1136389</td>
+      <td>7194</td>
+      <td>17684</td>
     </tr>
     <tr>
       <td></td>
@@ -22904,6 +27732,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -22966,8 +27808,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>38</td>
-      <td>868</td>
+      <td>1426</td>
+      <td>1426</td>
+      <td>71</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>1426</td>
+      <td>1426</td>
+      <td>71</td>
+      <td>71</td>
     </tr>
     <tr>
       <td></td>
@@ -23011,7 +27867,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -23031,7 +27886,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
+      <td>1312</td>
+      <td>1312</td>
+      <td>219</td>
+      <td>219</td>
+      <td>116</td>
+      <td>116</td>
+      <td>58</td>
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+      <td>37</td>
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+      <td>6</td>
+      <td>6</td>
+      <td>1465</td>
+      <td>1465</td>
+      <td>283</td>
+      <td>283</td>
     </tr>
     <tr>
       <td></td>
@@ -23060,8 +27930,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -23090,12 +27959,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>284</td>
-      <td>329556</td>
+      <td>15624</td>
+      <td>330820</td>
+      <td>1864</td>
+      <td>2438</td>
+      <td>52317</td>
+      <td>513688</td>
+      <td>10198</td>
+      <td>39421</td>
+      <td>1329</td>
+      <td>1645</td>
+      <td>213</td>
+      <td>289</td>
+      <td>69270</td>
+      <td>846153</td>
+      <td>12275</td>
+      <td>42148</td>
     </tr>
     <tr>
       <td></td>
@@ -23124,9 +28008,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -23154,12 +28037,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
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       <td>0</td>
-      <td>117</td>
-      <td>2448</td>
+      <td>1980</td>
+      <td>2697</td>
+      <td>345</td>
+      <td>410</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>1081</td>
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+      <td>44</td>
+      <td>44</td>
+      <td>3061</td>
+      <td>3778</td>
+      <td>389</td>
+      <td>454</td>
     </tr>
     <tr>
       <td></td>
@@ -23222,8 +28120,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>30</td>
+      <td>30</td>
       <td>2</td>
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+      <td>30</td>
       <td>30</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -23252,10 +28164,9 @@
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       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -23282,12 +28193,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
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       <td>0</td>
-      <td>2</td>
-      <td>69</td>
+      <td>62</td>
+      <td>70</td>
+      <td>4</td>
+      <td>4</td>
+      <td>207</td>
+      <td>334</td>
+      <td>27</td>
+      <td>71</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>269</td>
+      <td>404</td>
+      <td>31</td>
+      <td>75</td>
     </tr>
     <tr>
       <td></td>
@@ -23316,10 +28242,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -23346,12 +28271,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
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-      <td>13</td>
-      <td>156</td>
+      <td>144</td>
+      <td>157</td>
+      <td>26</td>
+      <td>30</td>
+      <td>268</td>
+      <td>707</td>
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+      <td>248</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>412</td>
+      <td>864</td>
+      <td>109</td>
+      <td>278</td>
     </tr>
     <tr>
       <td></td>
@@ -23416,6 +28356,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -23458,7 +28412,6 @@
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-      <td>0</td>
       <td>1</td>
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       <td>1</td>
@@ -23474,12 +28427,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
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       <td>0</td>
-      <td>481</td>
-      <td>14683</td>
+      <td>23008</td>
+      <td>23014</td>
+      <td>1060</td>
+      <td>1061</td>
+      <td>16194</td>
+      <td>24490</td>
+      <td>1719</td>
+      <td>2168</td>
+      <td>14898</td>
+      <td>14898</td>
+      <td>436</td>
+      <td>436</td>
+      <td>54100</td>
+      <td>62402</td>
+      <td>3215</td>
+      <td>3665</td>
     </tr>
     <tr>
       <td></td>
@@ -23544,6 +28512,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -23606,7 +28588,21 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>7</td>
+      <td>9</td>
+      <td>3</td>
+      <td>4</td>
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+      <td>10</td>
+      <td>5</td>
+      <td>5</td>
+      <td>15</td>
+      <td>19</td>
+      <td>8</td>
       <td>9</td>
     </tr>
     <tr>
@@ -23670,8 +28666,22 @@
       <td>1</td>
       <td>1</td>
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-      <td>2</td>
+      <td>89</td>
       <td>137</td>
+      <td>4</td>
+      <td>20</td>
+      <td>118</td>
+      <td>6136</td>
+      <td>15</td>
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+      <td>207</td>
+      <td>6273</td>
+      <td>19</td>
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     </tr>
     <tr>
       <td></td>
@@ -23700,10 +28710,9 @@
       <td>1</td>
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       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
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@@ -23730,12 +28739,27 @@
       <td>0</td>
       <td>0</td>
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-      <td>18</td>
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+      <td>147</td>
+      <td>159</td>
+      <td>46</td>
+      <td>48</td>
+      <td>793</td>
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+      <td>940</td>
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     </tr>
     <tr>
       <td></td>
@@ -23798,8 +28822,22 @@
       <td>1</td>
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-      <td>9</td>
-      <td>152</td>
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     </tr>
     <tr>
       <td></td>
@@ -23864,6 +28902,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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+      <td>146</td>
+      <td>1103</td>
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     </tr>
     <tr>
       <td></td>
@@ -23926,8 +28978,22 @@
       <td>1</td>
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-      <td>11</td>
-      <td>339</td>
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     </tr>
     <tr>
       <td></td>
@@ -23992,6 +29058,20 @@
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -24056,6 +29136,20 @@
       <td>0</td>
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     </tr>
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       <td></td>
@@ -24084,8 +29178,7 @@
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       <td>2</td>
-      <td>2</td>
-      <td>2</td>
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@@ -24114,12 +29207,27 @@
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-      <td>817</td>
-      <td>143045</td>
+      <td>172433</td>
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+      <td>1865</td>
+      <td>1951</td>
+      <td>108640</td>
+      <td>122790</td>
+      <td>4266</td>
+      <td>5521</td>
+      <td>20027</td>
+      <td>20027</td>
+      <td>1172</td>
+      <td>1172</td>
+      <td>301100</td>
+      <td>317273</td>
+      <td>7303</td>
+      <td>8644</td>
     </tr>
     <tr>
       <td></td>
@@ -24184,6 +29292,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -24246,8 +29368,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>2</td>
+      <td>2</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -24310,8 +29446,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3</td>
-      <td>85</td>
+      <td>73</td>
+      <td>86</td>
+      <td>5</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>73</td>
+      <td>86</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -24354,7 +29504,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -24370,12 +29519,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>36</td>
-      <td>338</td>
+      <td>743</td>
+      <td>816</td>
+      <td>103</td>
+      <td>141</td>
+      <td>292</td>
+      <td>2868</td>
+      <td>82</td>
+      <td>459</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>1035</td>
+      <td>3684</td>
+      <td>185</td>
+      <td>600</td>
     </tr>
     <tr>
       <td></td>
@@ -24404,8 +29568,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -24434,12 +29597,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>193</td>
-      <td>563676</td>
+      <td>565922</td>
+      <td>566630</td>
+      <td>418</td>
+      <td>441</td>
+      <td>45844</td>
+      <td>107523</td>
+      <td>671</td>
+      <td>4353</td>
+      <td>19828</td>
+      <td>19994</td>
+      <td>100</td>
+      <td>137</td>
+      <td>631594</td>
+      <td>694147</td>
+      <td>1189</td>
+      <td>4931</td>
     </tr>
     <tr>
       <td></td>
@@ -24468,11 +29646,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -24481,7 +29659,6 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -24498,12 +29675,27 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>542</td>
-      <td>28593</td>
+      <td>20905</td>
+      <td>31051</td>
+      <td>1906</td>
+      <td>2128</td>
+      <td>21780</td>
+      <td>132833</td>
+      <td>885</td>
+      <td>3172</td>
+      <td>1524</td>
+      <td>1925</td>
+      <td>122</td>
+      <td>152</td>
+      <td>44209</td>
+      <td>165809</td>
+      <td>2913</td>
+      <td>5452</td>
     </tr>
     <tr>
       <td></td>
@@ -24566,8 +29758,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>632</td>
+      <td>5461</td>
+      <td>155</td>
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+      <td>0</td>
+      <td>632</td>
       <td>5461</td>
+      <td>155</td>
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     </tr>
     <tr>
       <td></td>
@@ -24615,7 +29821,6 @@
       <td>0</td>
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-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -24626,12 +29831,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>200</td>
-      <td>16573</td>
+      <td>14907</td>
+      <td>18971</td>
+      <td>638</td>
+      <td>894</td>
+      <td>2677</td>
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+      <td>230</td>
+      <td>230</td>
+      <td>2313</td>
+      <td>2313</td>
+      <td>83</td>
+      <td>83</td>
+      <td>19897</td>
+      <td>23961</td>
+      <td>951</td>
+      <td>1207</td>
     </tr>
     <tr>
       <td></td>
@@ -24660,11 +29880,10 @@
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-      <td>1</td>
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       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
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       <td>0</td>
@@ -24696,6 +29915,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -24724,8 +29958,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -24754,12 +29987,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>103</td>
-      <td>3966</td>
+      <td>3209</td>
+      <td>4572</td>
+      <td>312</td>
+      <td>442</td>
+      <td>479</td>
+      <td>479</td>
+      <td>79</td>
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+      <td>315</td>
+      <td>315</td>
+      <td>51</td>
+      <td>51</td>
+      <td>4003</td>
+      <td>5366</td>
+      <td>442</td>
+      <td>572</td>
     </tr>
     <tr>
       <td></td>
@@ -24822,8 +30070,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>573</td>
+      <td>573</td>
+      <td>3</td>
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+      <td>0</td>
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+      <td>573</td>
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+      <td>3</td>
+      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -24888,6 +30150,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -24952,6 +30228,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -25016,6 +30306,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>135</td>
+      <td>973</td>
+      <td>50</td>
+      <td>140</td>
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+      <td>973</td>
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     </tr>
     <tr>
       <td></td>
@@ -25080,6 +30384,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>312</td>
+      <td>22</td>
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+      <td>22</td>
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     </tr>
     <tr>
       <td></td>
@@ -25142,8 +30460,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>53</td>
-      <td>895</td>
+      <td>1213</td>
+      <td>1309</td>
+      <td>115</td>
+      <td>124</td>
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+      <td>1213</td>
+      <td>1309</td>
+      <td>115</td>
+      <td>124</td>
     </tr>
     <tr>
       <td></td>
@@ -25172,10 +30504,9 @@
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       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -25202,12 +30533,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
+      <td>9</td>
       <td>11</td>
+      <td>8</td>
+      <td>8</td>
+      <td>17</td>
+      <td>63</td>
+      <td>6</td>
+      <td>19</td>
+      <td>0</td>
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+      <td>26</td>
+      <td>74</td>
+      <td>14</td>
+      <td>27</td>
     </tr>
     <tr>
       <td></td>
@@ -25252,7 +30598,6 @@
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-      <td>0</td>
       <td>1</td>
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@@ -25267,11 +30612,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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-      <td>21</td>
-      <td>185</td>
+      <td>229</td>
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+      <td>32</td>
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     </tr>
     <tr>
       <td></td>
@@ -25316,7 +30676,6 @@
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-      <td>0</td>
       <td>1</td>
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@@ -25331,11 +30690,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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-      <td>56</td>
-      <td>613</td>
+      <td>1020</td>
+      <td>1020</td>
+      <td>176</td>
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+      <td>414</td>
+      <td>414</td>
+      <td>73</td>
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+      <td>20</td>
+      <td>20</td>
+      <td>1711</td>
+      <td>1711</td>
+      <td>269</td>
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     </tr>
     <tr>
       <td></td>
@@ -25400,6 +30774,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -25464,6 +30852,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -25526,8 +30928,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5</td>
+      <td>71</td>
       <td>76</td>
+      <td>9</td>
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+      <td>71</td>
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     </tr>
     <tr>
       <td></td>
@@ -25592,6 +31008,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -25654,8 +31084,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>83</td>
-      <td>652</td>
+      <td>883</td>
+      <td>921</td>
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+      <td>730</td>
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+      <td>49</td>
+      <td>1749</td>
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+      <td>432</td>
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     </tr>
     <tr>
       <td></td>
@@ -25718,8 +31162,22 @@
       <td>5</td>
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       <td>0</td>
-      <td>240</td>
-      <td>1872</td>
+      <td>2801</td>
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+      <td>4522</td>
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+      <td>390</td>
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     </tr>
     <tr>
       <td></td>
@@ -25782,8 +31240,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>44</td>
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+      <td>5</td>
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     </tr>
     <tr>
       <td></td>
@@ -25812,9 +31284,8 @@
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-      <td>4</td>
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@@ -25842,12 +31313,27 @@
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-      <td>78</td>
-      <td>8366</td>
+      <td>9284</td>
+      <td>9694</td>
+      <td>215</td>
+      <td>229</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2358</td>
+      <td>2358</td>
+      <td>49</td>
+      <td>49</td>
+      <td>11642</td>
+      <td>12052</td>
+      <td>264</td>
+      <td>278</td>
     </tr>
     <tr>
       <td></td>
@@ -25910,8 +31396,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>36</td>
+      <td>40</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>36</td>
       <td>40</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -25974,8 +31474,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
-      <td>11</td>
+      <td>12</td>
+      <td>12</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>6</td>
+      <td>6</td>
     </tr>
     <tr>
       <td></td>
@@ -26001,11 +31515,11 @@
       <td>2.5.2</td>
       <td>De-novo assembly, Genome assembly</td>
       <td>Sequencing, Sequence assembly</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>0</td>
@@ -26038,8 +31552,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>84</td>
-      <td>268</td>
+      <td>391</td>
+      <td>391</td>
+      <td>158</td>
+      <td>158</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>391</td>
+      <td>391</td>
+      <td>158</td>
+      <td>158</td>
     </tr>
     <tr>
       <td></td>
@@ -26104,6 +31632,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -26166,8 +31708,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
-      <td>861</td>
+      <td>118</td>
+      <td>863</td>
+      <td>19</td>
+      <td>26</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>118</td>
+      <td>863</td>
+      <td>19</td>
+      <td>26</td>
     </tr>
     <tr>
       <td></td>
@@ -26196,11 +31752,10 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -26231,7 +31786,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>391</td>
       <td>486</td>
+      <td>5</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>391</td>
+      <td>486</td>
+      <td>5</td>
+      <td>11</td>
     </tr>
     <tr>
       <td></td>
@@ -26294,8 +31864,22 @@
       <td>135</td>
       <td>134</td>
       <td>0</td>
-      <td>916</td>
-      <td>105743</td>
+      <td>31121</td>
+      <td>108907</td>
+      <td>3369</td>
+      <td>5029</td>
+      <td>50</td>
+      <td>50</td>
+      <td>15</td>
+      <td>15</td>
+      <td>933</td>
+      <td>933</td>
+      <td>242</td>
+      <td>242</td>
+      <td>32104</td>
+      <td>109890</td>
+      <td>3626</td>
+      <td>5286</td>
     </tr>
     <tr>
       <td></td>
@@ -26358,8 +31942,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>7</td>
-      <td>269</td>
+      <td>261</td>
+      <td>275</td>
+      <td>12</td>
+      <td>12</td>
+      <td>63</td>
+      <td>63</td>
+      <td>22</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>324</td>
+      <td>338</td>
+      <td>34</td>
+      <td>34</td>
     </tr>
     <tr>
       <td></td>
@@ -26422,8 +32020,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>7</td>
-      <td>299</td>
+      <td>322</td>
+      <td>349</td>
+      <td>24</td>
+      <td>29</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>322</td>
+      <td>349</td>
+      <td>24</td>
+      <td>29</td>
     </tr>
     <tr>
       <td></td>
@@ -26488,6 +32100,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>142</td>
+      <td>8</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>142</td>
+      <td>8</td>
+      <td>42</td>
     </tr>
     <tr>
       <td></td>
@@ -26550,8 +32176,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>78</td>
-      <td>3109</td>
+      <td>2807</td>
+      <td>3337</td>
+      <td>178</td>
+      <td>196</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2807</td>
+      <td>3337</td>
+      <td>178</td>
+      <td>196</td>
     </tr>
     <tr>
       <td></td>
@@ -26616,6 +32256,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -26680,6 +32334,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -26708,8 +32376,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -26739,11 +32406,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>19</td>
-      <td>165</td>
+      <td>773</td>
+      <td>773</td>
+      <td>60</td>
+      <td>60</td>
+      <td>495</td>
+      <td>495</td>
+      <td>72</td>
+      <td>72</td>
+      <td>246</td>
+      <td>246</td>
+      <td>17</td>
+      <td>17</td>
+      <td>1514</td>
+      <td>1514</td>
+      <td>149</td>
+      <td>149</td>
     </tr>
     <tr>
       <td></td>
@@ -26808,6 +32490,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -26872,6 +32568,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -26934,8 +32644,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>14</td>
-      <td>82</td>
+      <td>109</td>
+      <td>109</td>
+      <td>29</td>
+      <td>29</td>
+      <td>250</td>
+      <td>250</td>
+      <td>84</td>
+      <td>84</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>359</td>
+      <td>359</td>
+      <td>113</td>
+      <td>113</td>
     </tr>
     <tr>
       <td></td>
@@ -26964,8 +32688,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -26994,12 +32717,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>15</td>
-      <td>632</td>
+      <td>613</td>
+      <td>640</td>
+      <td>48</td>
+      <td>54</td>
+      <td>1381</td>
+      <td>7804</td>
+      <td>201</td>
+      <td>1552</td>
+      <td>756</td>
+      <td>815</td>
+      <td>22</td>
+      <td>30</td>
+      <td>2750</td>
+      <td>9259</td>
+      <td>271</td>
+      <td>1636</td>
     </tr>
     <tr>
       <td></td>
@@ -27028,8 +32766,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -27058,12 +32795,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>169</td>
-      <td>3158</td>
+      <td>3639</td>
+      <td>3774</td>
+      <td>414</td>
+      <td>461</td>
+      <td>9754</td>
+      <td>52522</td>
+      <td>1247</td>
+      <td>4531</td>
+      <td>1893</td>
+      <td>2433</td>
+      <td>191</td>
+      <td>318</td>
+      <td>15286</td>
+      <td>58729</td>
+      <td>1852</td>
+      <td>5310</td>
     </tr>
     <tr>
       <td></td>
@@ -27126,8 +32878,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>21</td>
-      <td>275</td>
+      <td>238</td>
+      <td>283</td>
+      <td>42</td>
+      <td>45</td>
+      <td>0</td>
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+      <td>238</td>
+      <td>283</td>
+      <td>42</td>
+      <td>45</td>
     </tr>
     <tr>
       <td></td>
@@ -27190,8 +32956,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>39</td>
-      <td>1809</td>
+      <td>1408</td>
+      <td>2068</td>
+      <td>94</td>
+      <td>119</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>1408</td>
+      <td>2068</td>
+      <td>94</td>
+      <td>119</td>
     </tr>
     <tr>
       <td></td>
@@ -27256,6 +33036,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -27284,10 +33078,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -27314,12 +33107,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>9</td>
-      <td>73</td>
+      <td>65</td>
+      <td>77</td>
+      <td>19</td>
+      <td>25</td>
+      <td>153</td>
+      <td>886</td>
+      <td>38</td>
+      <td>343</td>
+      <td>142</td>
+      <td>155</td>
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+      <td>10</td>
+      <td>360</td>
+      <td>1118</td>
+      <td>65</td>
+      <td>378</td>
     </tr>
     <tr>
       <td></td>
@@ -27382,8 +33190,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>71</td>
-      <td>1323</td>
+      <td>1342</td>
+      <td>1472</td>
+      <td>184</td>
+      <td>197</td>
+      <td>902</td>
+      <td>902</td>
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+      <td>156</td>
+      <td>630</td>
+      <td>630</td>
+      <td>24</td>
+      <td>24</td>
+      <td>2874</td>
+      <td>3004</td>
+      <td>364</td>
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     </tr>
     <tr>
       <td></td>
@@ -27446,8 +33268,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>37</td>
-      <td>652</td>
+      <td>408</td>
+      <td>664</td>
+      <td>91</td>
+      <td>122</td>
+      <td>627</td>
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+      <td>118</td>
+      <td>605</td>
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+      <td>26</td>
+      <td>26</td>
+      <td>1640</td>
+      <td>1896</td>
+      <td>235</td>
+      <td>266</td>
     </tr>
     <tr>
       <td></td>
@@ -27510,8 +33346,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>79</td>
-      <td>843</td>
+      <td>764</td>
+      <td>879</td>
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+      <td>95</td>
+      <td>95</td>
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+      <td>26</td>
+      <td>26</td>
+      <td>1261</td>
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     </tr>
     <tr>
       <td></td>
@@ -27574,8 +33424,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>6</td>
-      <td>116</td>
+      <td>112</td>
+      <td>120</td>
+      <td>16</td>
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+      <td>4</td>
+      <td>562</td>
+      <td>1</td>
+      <td>140</td>
+      <td>320</td>
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+      <td>7</td>
+      <td>8</td>
+      <td>436</td>
+      <td>1029</td>
+      <td>24</td>
+      <td>164</td>
     </tr>
     <tr>
       <td></td>
@@ -27640,6 +33504,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -27668,10 +33546,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -27698,12 +33575,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>88</td>
-      <td>9989</td>
+      <td>9788</td>
+      <td>10032</td>
+      <td>207</td>
+      <td>244</td>
+      <td>3072</td>
+      <td>8054</td>
+      <td>607</td>
+      <td>1488</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12860</td>
+      <td>18086</td>
+      <td>814</td>
+      <td>1732</td>
     </tr>
     <tr>
       <td></td>
@@ -27766,8 +33658,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>7</td>
-      <td>154</td>
+      <td>129</td>
+      <td>155</td>
+      <td>15</td>
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+      <td>15</td>
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     </tr>
     <tr>
       <td></td>
@@ -27830,8 +33736,22 @@
       <td>6</td>
       <td>6</td>
       <td>0</td>
-      <td>451</td>
-      <td>6428</td>
+      <td>11743</td>
+      <td>12752</td>
+      <td>1137</td>
+      <td>1278</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
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+      <td>11745</td>
+      <td>12754</td>
+      <td>1138</td>
+      <td>1279</td>
     </tr>
     <tr>
       <td></td>
@@ -27894,8 +33814,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>30</td>
-      <td>604</td>
+      <td>465</td>
+      <td>638</td>
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     </tr>
     <tr>
       <td></td>
@@ -27960,6 +33894,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>724</td>
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     </tr>
     <tr>
       <td></td>
@@ -28024,6 +33972,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -28052,8 +34014,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -28082,12 +34043,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>309</td>
-      <td>21353</td>
+      <td>27113</td>
+      <td>27315</td>
+      <td>839</td>
+      <td>850</td>
+      <td>9089</td>
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+      <td>475</td>
+      <td>475</td>
+      <td>5452</td>
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+      <td>171</td>
+      <td>171</td>
+      <td>41654</td>
+      <td>41856</td>
+      <td>1485</td>
+      <td>1496</td>
     </tr>
     <tr>
       <td></td>
@@ -28150,8 +34126,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>90</td>
+      <td>90</td>
+      <td>6</td>
+      <td>6</td>
       <td>0</td>
-      <td>36</td>
+      <td>0</td>
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+      <td>6</td>
+      <td>6</td>
     </tr>
     <tr>
       <td></td>
@@ -28214,8 +34204,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>38</td>
-      <td>1226</td>
+      <td>860</td>
+      <td>1257</td>
+      <td>88</td>
+      <td>98</td>
+      <td>0</td>
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+      <td>1257</td>
+      <td>88</td>
+      <td>98</td>
     </tr>
     <tr>
       <td></td>
@@ -28280,6 +34284,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>49</td>
+      <td>191</td>
+      <td>5</td>
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+      <td>49</td>
+      <td>191</td>
+      <td>5</td>
+      <td>46</td>
     </tr>
     <tr>
       <td></td>
@@ -28344,6 +34362,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -28372,11 +34404,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -28385,7 +34417,6 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -28402,12 +34433,27 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1409</td>
-      <td>137310</td>
+      <td>148572</td>
+      <td>169964</td>
+      <td>3525</td>
+      <td>3682</td>
+      <td>36694</td>
+      <td>113826</td>
+      <td>3910</td>
+      <td>8163</td>
+      <td>9713</td>
+      <td>10577</td>
+      <td>1475</td>
+      <td>1598</td>
+      <td>194979</td>
+      <td>294367</td>
+      <td>8910</td>
+      <td>13443</td>
     </tr>
     <tr>
       <td></td>
@@ -28470,8 +34516,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
-      <td>42</td>
+      <td>39</td>
+      <td>44</td>
+      <td>6</td>
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+      <td>6</td>
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     </tr>
     <tr>
       <td></td>
@@ -28500,8 +34560,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -28530,12 +34589,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>248</td>
-      <td>3750</td>
+      <td>5998</td>
+      <td>5998</td>
+      <td>810</td>
+      <td>810</td>
+      <td>7618</td>
+      <td>7618</td>
+      <td>803</td>
+      <td>803</td>
+      <td>3135</td>
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+      <td>292</td>
+      <td>292</td>
+      <td>16751</td>
+      <td>16751</td>
+      <td>1905</td>
+      <td>1905</td>
     </tr>
     <tr>
       <td></td>
@@ -28564,8 +34638,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -28594,12 +34667,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>189</td>
-      <td>576111</td>
+      <td>577184</td>
+      <td>577312</td>
+      <td>463</td>
+      <td>492</td>
+      <td>43900</td>
+      <td>44233</td>
+      <td>283</td>
+      <td>373</td>
+      <td>2190</td>
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+      <td>112</td>
+      <td>112</td>
+      <td>623274</td>
+      <td>623735</td>
+      <td>858</td>
+      <td>977</td>
     </tr>
     <tr>
       <td></td>
@@ -28664,6 +34752,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -28726,8 +34828,22 @@
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>44</td>
-      <td>628</td>
+      <td>661</td>
+      <td>681</td>
+      <td>78</td>
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+      <td>0</td>
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+      <td>681</td>
+      <td>78</td>
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     </tr>
     <tr>
       <td></td>
@@ -28792,6 +34908,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -28856,6 +34986,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -28918,8 +35062,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>11</td>
-      <td>129</td>
+      <td>137</td>
+      <td>173</td>
+      <td>40</td>
+      <td>49</td>
+      <td>0</td>
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+      <td>137</td>
+      <td>173</td>
+      <td>40</td>
+      <td>49</td>
     </tr>
     <tr>
       <td></td>
@@ -28982,8 +35140,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3</td>
-      <td>164</td>
+      <td>90</td>
+      <td>196</td>
+      <td>9</td>
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+      <td>90</td>
+      <td>196</td>
+      <td>9</td>
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     </tr>
     <tr>
       <td></td>
@@ -29046,8 +35218,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5</td>
-      <td>1358</td>
+      <td>878</td>
+      <td>1363</td>
+      <td>29</td>
+      <td>35</td>
+      <td>0</td>
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+      <td>878</td>
+      <td>1363</td>
+      <td>29</td>
+      <td>35</td>
     </tr>
     <tr>
       <td></td>
@@ -29110,8 +35296,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>6</td>
-      <td>1074</td>
+      <td>1024</td>
+      <td>1077</td>
+      <td>18</td>
+      <td>21</td>
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+      <td>18</td>
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     </tr>
     <tr>
       <td></td>
@@ -29174,8 +35374,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>6</td>
+      <td>6</td>
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+      <td>26</td>
+      <td>26</td>
+      <td>6</td>
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     </tr>
     <tr>
       <td></td>
@@ -29238,8 +35452,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>4</td>
+      <td>23</td>
       <td>33</td>
+      <td>10</td>
+      <td>14</td>
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+      <td>10</td>
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     </tr>
     <tr>
       <td></td>
@@ -29302,8 +35530,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5</td>
-      <td>86</td>
+      <td>65</td>
+      <td>89</td>
+      <td>14</td>
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     </tr>
     <tr>
       <td></td>
@@ -29366,8 +35608,22 @@
       <td>6</td>
       <td>6</td>
       <td>0</td>
-      <td>28</td>
-      <td>43279</td>
+      <td>1156</td>
+      <td>43309</td>
+      <td>93</td>
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     </tr>
     <tr>
       <td></td>
@@ -29396,8 +35652,7 @@
       <td>1</td>
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       <td>1</td>
-      <td>1</td>
-      <td>1</td>
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@@ -29426,12 +35681,27 @@
       <td>0</td>
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-      <td>55</td>
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+      <td>4168</td>
+      <td>165</td>
+      <td>199</td>
+      <td>8399</td>
+      <td>14473</td>
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+      <td>2710</td>
+      <td>3000</td>
+      <td>151</td>
+      <td>175</td>
+      <td>14737</td>
+      <td>21641</td>
+      <td>889</td>
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     </tr>
     <tr>
       <td></td>
@@ -29460,11 +35730,10 @@
       <td>2</td>
       <td>2</td>
       <td>3</td>
-      <td>1</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>3</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -29490,12 +35759,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>969</td>
-      <td>61937</td>
+      <td>73085</td>
+      <td>77081</td>
+      <td>2243</td>
+      <td>2319</td>
+      <td>90634</td>
+      <td>122835</td>
+      <td>3402</td>
+      <td>4726</td>
+      <td>13371</td>
+      <td>15818</td>
+      <td>513</td>
+      <td>586</td>
+      <td>177090</td>
+      <td>215734</td>
+      <td>6158</td>
+      <td>7631</td>
     </tr>
     <tr>
       <td></td>
@@ -29524,75 +35808,12 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
       <td>1</td>
-      <td>0</td>
-      <td>20</td>
-      <td>1189</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>sam_bitwise_flag_filter</td>
-      <td>sam_bw_filter</td>
-      <td>Filter SAM on bitwise flag values</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td></td>
-      <td>SAM</td>
-      <td>sam_bitwise_flag_filter</td>
-      <td>devteam</td>
-      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter</td>
-      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter</td>
-      <td>1.0.1</td>
-      <td>python</td>
-      <td></td>
-      <td></td>
-      <td></td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -29617,13 +35838,104 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
       <td>0</td>
+      <td>1155</td>
+      <td>1251</td>
+      <td>57</td>
+      <td>63</td>
+      <td>2264</td>
+      <td>18187</td>
+      <td>189</td>
+      <td>1748</td>
+      <td>525</td>
+      <td>590</td>
+      <td>10</td>
+      <td>17</td>
+      <td>3944</td>
+      <td>20028</td>
+      <td>256</td>
+      <td>1828</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sam_bitwise_flag_filter</td>
+      <td>sam_bw_filter</td>
+      <td>Filter SAM on bitwise flag values</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>SAM</td>
+      <td>sam_bitwise_flag_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter</td>
+      <td>1.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
       <td>1</td>
+      <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>1</td>
+      <td>0</td>
+      <td>96</td>
       <td>278</td>
+      <td>12</td>
+      <td>26</td>
+      <td>3554</td>
+      <td>76029</td>
+      <td>450</td>
+      <td>6346</td>
+      <td>229</td>
+      <td>345</td>
+      <td>16</td>
+      <td>29</td>
+      <td>3879</td>
+      <td>76652</td>
+      <td>478</td>
+      <td>6401</td>
     </tr>
     <tr>
       <td></td>
@@ -29686,8 +35998,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>297</td>
+      <td>297</td>
+      <td>51</td>
+      <td>51</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>297</td>
+      <td>297</td>
+      <td>51</td>
+      <td>51</td>
     </tr>
     <tr>
       <td></td>
@@ -29716,8 +36042,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -29747,11 +36072,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>149</td>
-      <td>3765</td>
+      <td>3421</td>
+      <td>3859</td>
+      <td>340</td>
+      <td>382</td>
+      <td>883</td>
+      <td>883</td>
+      <td>109</td>
+      <td>109</td>
+      <td>1138</td>
+      <td>1138</td>
+      <td>15</td>
+      <td>15</td>
+      <td>5442</td>
+      <td>5880</td>
+      <td>464</td>
+      <td>506</td>
     </tr>
     <tr>
       <td></td>
@@ -29816,6 +36156,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -29844,8 +36198,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -29874,12 +36227,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>296</td>
-      <td>4948</td>
+      <td>6485</td>
+      <td>6549</td>
+      <td>720</td>
+      <td>726</td>
+      <td>10127</td>
+      <td>10127</td>
+      <td>1518</td>
+      <td>1518</td>
+      <td>238</td>
+      <td>238</td>
+      <td>37</td>
+      <td>37</td>
+      <td>16850</td>
+      <td>16914</td>
+      <td>2275</td>
+      <td>2281</td>
     </tr>
     <tr>
       <td></td>
@@ -29908,8 +36276,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -29938,12 +36305,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1450</td>
-      <td>48426</td>
+      <td>52099</td>
+      <td>55110</td>
+      <td>4053</td>
+      <td>4497</td>
+      <td>73194</td>
+      <td>108684</td>
+      <td>6930</td>
+      <td>9936</td>
+      <td>14771</td>
+      <td>15714</td>
+      <td>1222</td>
+      <td>1419</td>
+      <td>140064</td>
+      <td>179508</td>
+      <td>12205</td>
+      <td>15852</td>
     </tr>
     <tr>
       <td></td>
@@ -29972,10 +36354,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -30002,12 +36383,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>61</td>
-      <td>1677</td>
+      <td>1234</td>
+      <td>1752</td>
+      <td>179</td>
+      <td>261</td>
+      <td>680</td>
+      <td>9223</td>
+      <td>231</td>
+      <td>1927</td>
+      <td>0</td>
+      <td>49</td>
+      <td>0</td>
+      <td>18</td>
+      <td>1914</td>
+      <td>11024</td>
+      <td>410</td>
+      <td>2206</td>
     </tr>
     <tr>
       <td></td>
@@ -30070,8 +36466,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>2276</td>
+      <td>281</td>
+      <td>2284</td>
+      <td>10</td>
+      <td>53</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>281</td>
+      <td>2284</td>
+      <td>10</td>
+      <td>53</td>
     </tr>
     <tr>
       <td></td>
@@ -30134,8 +36544,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>30</td>
-      <td>1276</td>
+      <td>1095</td>
+      <td>1306</td>
+      <td>98</td>
+      <td>113</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1095</td>
+      <td>1306</td>
+      <td>98</td>
+      <td>113</td>
     </tr>
     <tr>
       <td></td>
@@ -30180,7 +36604,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -30195,11 +36618,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>27</td>
-      <td>457</td>
+      <td>305</td>
+      <td>463</td>
+      <td>43</td>
+      <td>50</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>305</td>
+      <td>463</td>
+      <td>43</td>
+      <td>50</td>
     </tr>
     <tr>
       <td></td>
@@ -30228,10 +36666,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -30259,11 +36696,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>71</td>
-      <td>874</td>
+      <td>1053</td>
+      <td>1186</td>
+      <td>137</td>
+      <td>195</td>
+      <td>680</td>
+      <td>680</td>
+      <td>206</td>
+      <td>206</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1733</td>
+      <td>1866</td>
+      <td>343</td>
+      <td>401</td>
     </tr>
     <tr>
       <td></td>
@@ -30292,8 +36744,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -30323,11 +36774,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>306</td>
-      <td>25302</td>
+      <td>30300</td>
+      <td>32553</td>
+      <td>732</td>
+      <td>799</td>
+      <td>21726</td>
+      <td>31891</td>
+      <td>619</td>
+      <td>621</td>
+      <td>2886</td>
+      <td>2886</td>
+      <td>144</td>
+      <td>144</td>
+      <td>54912</td>
+      <td>67330</td>
+      <td>1495</td>
+      <td>1564</td>
     </tr>
     <tr>
       <td></td>
@@ -30372,7 +36838,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -30387,11 +36852,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>82</td>
-      <td>3784</td>
+      <td>4322</td>
+      <td>4714</td>
+      <td>180</td>
+      <td>205</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4322</td>
+      <td>4714</td>
+      <td>180</td>
+      <td>205</td>
     </tr>
     <tr>
       <td></td>
@@ -30436,7 +36916,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -30456,6 +36935,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -30478,7 +36972,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip</td>
       <td>0.0.18</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -30520,6 +37014,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -30542,7 +37050,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename</td>
       <td>0.0.10</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -30564,7 +37072,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -30580,10 +37087,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -30628,7 +37150,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -30648,6 +37169,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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+      <td>3529</td>
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+      <td>2196</td>
+      <td>3529</td>
+      <td>260</td>
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     </tr>
     <tr>
       <td></td>
@@ -30712,6 +37248,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -30774,8 +37324,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>13</td>
+      <td>145</td>
       <td>163</td>
+      <td>25</td>
+      <td>30</td>
+      <td>196</td>
+      <td>3360</td>
+      <td>23</td>
+      <td>711</td>
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+      <td>341</td>
+      <td>3523</td>
+      <td>48</td>
+      <td>741</td>
     </tr>
     <tr>
       <td></td>
@@ -30838,8 +37402,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>21</td>
+      <td>175</td>
       <td>220</td>
+      <td>51</td>
+      <td>60</td>
+      <td>350</td>
+      <td>6657</td>
+      <td>85</td>
+      <td>1602</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>525</td>
+      <td>6877</td>
+      <td>136</td>
+      <td>1662</td>
     </tr>
     <tr>
       <td></td>
@@ -30868,11 +37446,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -30881,7 +37459,6 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -30898,12 +37475,27 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>704</td>
-      <td>32112</td>
+      <td>27232</td>
+      <td>36366</td>
+      <td>2184</td>
+      <td>2789</td>
+      <td>16648</td>
+      <td>84460</td>
+      <td>4191</td>
+      <td>18767</td>
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+      <td>3276</td>
+      <td>373</td>
+      <td>452</td>
+      <td>46665</td>
+      <td>124102</td>
+      <td>6748</td>
+      <td>22008</td>
     </tr>
     <tr>
       <td></td>
@@ -30932,11 +37524,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
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       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -30945,7 +37537,6 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -30962,12 +37553,27 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>128</td>
-      <td>2513</td>
+      <td>1620</td>
+      <td>2660</td>
+      <td>378</td>
+      <td>589</td>
+      <td>10551</td>
+      <td>24579</td>
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+      <td>284</td>
+      <td>398</td>
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+      <td>83</td>
+      <td>12455</td>
+      <td>27637</td>
+      <td>1127</td>
+      <td>2523</td>
     </tr>
     <tr>
       <td></td>
@@ -30996,8 +37602,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -31026,12 +37631,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
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+      <td>379</td>
+      <td>30</td>
+      <td>42</td>
+      <td>972</td>
+      <td>9053</td>
+      <td>146</td>
+      <td>1008</td>
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+      <td>689</td>
       <td>5</td>
-      <td>374</td>
+      <td>7</td>
+      <td>1892</td>
+      <td>10121</td>
+      <td>181</td>
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     </tr>
     <tr>
       <td></td>
@@ -31060,11 +37680,11 @@
       <td>30</td>
       <td>14</td>
       <td>31</td>
-      <td>16</td>
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       <td>30</td>
       <td>14</td>
       <td>31</td>
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@@ -31094,8 +37714,22 @@
       <td>31</td>
       <td>27</td>
       <td>0</td>
-      <td>958</td>
-      <td>113932</td>
+      <td>82169</td>
+      <td>116810</td>
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+      <td>2666</td>
+      <td>18101</td>
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+      <td>2375</td>
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+      <td>321</td>
+      <td>117819</td>
+      <td>152460</td>
+      <td>5098</td>
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     </tr>
     <tr>
       <td></td>
@@ -31158,8 +37792,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>7</td>
-      <td>37</td>
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+      <td>10</td>
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     </tr>
     <tr>
       <td></td>
@@ -31188,8 +37836,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
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       <td>1</td>
@@ -31218,12 +37865,27 @@
       <td>0</td>
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       <td>0</td>
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+      <td>1126</td>
+      <td>3141</td>
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+      <td>26310</td>
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+      <td>1564</td>
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     </tr>
     <tr>
       <td></td>
@@ -31252,8 +37914,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
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@@ -31283,11 +37944,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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+      <td>8171</td>
+      <td>8437</td>
+      <td>721</td>
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     </tr>
     <tr>
       <td></td>
@@ -31316,8 +37992,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
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       <td>1</td>
@@ -31346,12 +38021,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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+      <td>29688</td>
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     <tr>
       <td></td>
@@ -31396,7 +38086,6 @@
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@@ -31416,6 +38105,21 @@
       <td>0</td>
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       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -31460,7 +38164,6 @@
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@@ -31475,11 +38178,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -31542,8 +38260,22 @@
       <td>1</td>
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       <td>0</td>
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       <td></td>
@@ -31606,8 +38338,22 @@
       <td>1</td>
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       <td>0</td>
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     <tr>
       <td></td>
@@ -31670,8 +38416,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -31736,6 +38496,20 @@
       <td>0</td>
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       <td>0</td>
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     <tr>
       <td></td>
@@ -31800,6 +38574,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td></td>
@@ -31828,8 +38616,7 @@
       <td>1</td>
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       <td>1</td>
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       <td>1</td>
@@ -31858,12 +38645,27 @@
       <td>0</td>
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+      <td>637145</td>
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     </tr>
     <tr>
       <td></td>
@@ -31892,11 +38694,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
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@@ -31926,8 +38728,22 @@
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       <td>0</td>
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-      <td>1019</td>
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+      <td>38</td>
+      <td>5146</td>
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     </tr>
     <tr>
       <td></td>
@@ -31972,7 +38788,6 @@
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@@ -31986,12 +38801,27 @@
       <td>0</td>
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@@ -32036,7 +38866,6 @@
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@@ -32050,12 +38879,27 @@
       <td>0</td>
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       <td></td>
@@ -32084,11 +38928,11 @@
       <td>1</td>
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       <td>1</td>
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       <td>0</td>
@@ -32118,8 +38962,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>6</td>
-      <td>210</td>
+      <td>141</td>
+      <td>215</td>
+      <td>20</td>
+      <td>31</td>
+      <td>520</td>
+      <td>1166</td>
+      <td>79</td>
+      <td>274</td>
+      <td>1025</td>
+      <td>1118</td>
+      <td>11</td>
+      <td>12</td>
+      <td>1686</td>
+      <td>2499</td>
+      <td>110</td>
+      <td>317</td>
     </tr>
     <tr>
       <td></td>
@@ -32184,6 +39042,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16526</td>
+      <td>64515</td>
+      <td>2803</td>
+      <td>7456</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16526</td>
+      <td>64515</td>
+      <td>2803</td>
+      <td>7456</td>
     </tr>
     <tr>
       <td></td>
@@ -32212,10 +39084,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -32242,12 +39113,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>14</td>
-      <td>2207</td>
+      <td>2188</td>
+      <td>2220</td>
+      <td>33</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2188</td>
+      <td>2220</td>
+      <td>33</td>
+      <td>38</td>
     </tr>
     <tr>
       <td></td>
@@ -32276,8 +39162,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -32306,12 +39191,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>601</td>
-      <td>319334</td>
+      <td>329032</td>
+      <td>333057</td>
+      <td>1489</td>
+      <td>1702</td>
+      <td>79033</td>
+      <td>215770</td>
+      <td>2441</td>
+      <td>8587</td>
+      <td>27876</td>
+      <td>33727</td>
+      <td>296</td>
+      <td>360</td>
+      <td>435941</td>
+      <td>582554</td>
+      <td>4226</td>
+      <td>10649</td>
     </tr>
     <tr>
       <td></td>
@@ -32374,8 +39274,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>19</td>
+      <td>19</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>19</td>
+      <td>6</td>
+      <td>6</td>
     </tr>
     <tr>
       <td></td>
@@ -32438,8 +39352,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>37</td>
-      <td>713</td>
+      <td>827</td>
+      <td>838</td>
+      <td>89</td>
+      <td>92</td>
+      <td>114</td>
+      <td>114</td>
+      <td>41</td>
+      <td>41</td>
+      <td>900</td>
+      <td>900</td>
+      <td>29</td>
+      <td>29</td>
+      <td>1841</td>
+      <td>1852</td>
+      <td>159</td>
+      <td>162</td>
     </tr>
     <tr>
       <td></td>
@@ -32468,8 +39396,7 @@
       <td>20</td>
       <td>20</td>
       <td>20</td>
-      <td>20</td>
-      <td>20</td>
+      <td>0</td>
       <td>20</td>
       <td>20</td>
       <td>20</td>
@@ -32498,12 +39425,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>19</td>
       <td>19</td>
       <td>19</td>
       <td>0</td>
-      <td>15048</td>
-      <td>3864895</td>
+      <td>3898014</td>
+      <td>4015573</td>
+      <td>37698</td>
+      <td>42095</td>
+      <td>648268</td>
+      <td>915282</td>
+      <td>47636</td>
+      <td>69828</td>
+      <td>103365</td>
+      <td>105214</td>
+      <td>7778</td>
+      <td>7953</td>
+      <td>4649647</td>
+      <td>5036069</td>
+      <td>93112</td>
+      <td>119876</td>
     </tr>
     <tr>
       <td></td>
@@ -32566,8 +39508,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>36</td>
-      <td>460</td>
+      <td>547</td>
+      <td>547</td>
+      <td>51</td>
+      <td>51</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>547</td>
+      <td>547</td>
+      <td>51</td>
+      <td>51</td>
     </tr>
     <tr>
       <td></td>
@@ -32630,8 +39586,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>8</td>
+      <td>8</td>
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+      <td>0</td>
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+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>8</td>
+      <td>8</td>
     </tr>
     <tr>
       <td></td>
@@ -32694,8 +39664,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>15</td>
       <td>445</td>
+      <td>445</td>
+      <td>25</td>
+      <td>25</td>
+      <td>71</td>
+      <td>71</td>
+      <td>32</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>516</td>
+      <td>516</td>
+      <td>57</td>
+      <td>57</td>
     </tr>
     <tr>
       <td></td>
@@ -32750,7 +39734,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -32759,7 +39742,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>158</td>
+      <td>66524</td>
+      <td>28</td>
+      <td>7228</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>66525</td>
+      <td>28</td>
+      <td>7229</td>
     </tr>
     <tr>
       <td></td>
@@ -32802,7 +39800,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -32818,12 +39815,27 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>312</td>
-      <td>24167</td>
+      <td>15496</td>
+      <td>26623</td>
+      <td>1076</td>
+      <td>1664</td>
+      <td>83063</td>
+      <td>343017</td>
+      <td>8372</td>
+      <td>27829</td>
+      <td>5388</td>
+      <td>14057</td>
+      <td>508</td>
+      <td>1012</td>
+      <td>103947</td>
+      <td>383697</td>
+      <td>9956</td>
+      <td>30505</td>
     </tr>
     <tr>
       <td></td>
@@ -32886,8 +39898,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>15</td>
-      <td>216</td>
+      <td>220</td>
+      <td>242</td>
+      <td>41</td>
+      <td>46</td>
+      <td>6</td>
+      <td>814</td>
+      <td>2</td>
+      <td>191</td>
+      <td>100</td>
+      <td>120</td>
+      <td>8</td>
+      <td>12</td>
+      <td>326</td>
+      <td>1176</td>
+      <td>51</td>
+      <td>249</td>
     </tr>
     <tr>
       <td></td>
@@ -32916,8 +39942,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -32946,12 +39971,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2334</td>
-      <td>238699</td>
+      <td>229489</td>
+      <td>275008</td>
+      <td>5733</td>
+      <td>6500</td>
+      <td>228708</td>
+      <td>324716</td>
+      <td>11708</td>
+      <td>16638</td>
+      <td>22644</td>
+      <td>23869</td>
+      <td>1439</td>
+      <td>1527</td>
+      <td>480841</td>
+      <td>623593</td>
+      <td>18880</td>
+      <td>24665</td>
     </tr>
     <tr>
       <td></td>
@@ -32980,11 +40020,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -32993,7 +40033,6 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -33010,12 +40049,27 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>188</td>
-      <td>6058</td>
+      <td>5304</td>
+      <td>7438</td>
+      <td>447</td>
+      <td>512</td>
+      <td>15698</td>
+      <td>108672</td>
+      <td>658</td>
+      <td>2946</td>
+      <td>266</td>
+      <td>822</td>
+      <td>53</td>
+      <td>81</td>
+      <td>21268</td>
+      <td>116932</td>
+      <td>1158</td>
+      <td>3539</td>
     </tr>
     <tr>
       <td></td>
@@ -33059,7 +40113,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -33075,11 +40128,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>236</td>
-      <td>2935</td>
+      <td>4361</td>
+      <td>4601</td>
+      <td>741</td>
+      <td>807</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2469</td>
+      <td>2469</td>
+      <td>190</td>
+      <td>190</td>
+      <td>6830</td>
+      <td>7070</td>
+      <td>931</td>
+      <td>997</td>
     </tr>
     <tr>
       <td></td>
@@ -33142,8 +40210,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>45</td>
-      <td>394</td>
+      <td>373</td>
+      <td>463</td>
+      <td>134</td>
+      <td>151</td>
+      <td>2249</td>
+      <td>18611</td>
+      <td>638</td>
+      <td>4080</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2622</td>
+      <td>19074</td>
+      <td>772</td>
+      <td>4231</td>
     </tr>
     <tr>
       <td></td>
@@ -33206,8 +40288,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>132</td>
-      <td>2406</td>
+      <td>2117</td>
+      <td>2725</td>
+      <td>341</td>
+      <td>412</td>
+      <td>3111</td>
+      <td>5779</td>
+      <td>594</td>
+      <td>1011</td>
+      <td>806</td>
+      <td>806</td>
+      <td>50</td>
+      <td>50</td>
+      <td>6034</td>
+      <td>9310</td>
+      <td>985</td>
+      <td>1473</td>
     </tr>
     <tr>
       <td></td>
@@ -33236,8 +40332,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -33267,11 +40362,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>246</td>
-      <td>5191</td>
+      <td>5058</td>
+      <td>6139</td>
+      <td>606</td>
+      <td>699</td>
+      <td>17232</td>
+      <td>53268</td>
+      <td>2965</td>
+      <td>5686</td>
+      <td>2298</td>
+      <td>2656</td>
+      <td>424</td>
+      <td>482</td>
+      <td>24588</td>
+      <td>62063</td>
+      <td>3995</td>
+      <td>6867</td>
     </tr>
     <tr>
       <td></td>
@@ -33334,8 +40444,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>15</td>
-      <td>206</td>
+      <td>191</td>
+      <td>221</td>
+      <td>57</td>
+      <td>65</td>
+      <td>1399</td>
+      <td>2700</td>
+      <td>209</td>
+      <td>584</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>1590</td>
+      <td>2921</td>
+      <td>266</td>
+      <td>649</td>
     </tr>
     <tr>
       <td></td>
@@ -33400,6 +40524,20 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
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+      <td>340</td>
+      <td>31</td>
+      <td>54</td>
+      <td>263</td>
+      <td>342</td>
+      <td>31</td>
+      <td>56</td>
     </tr>
     <tr>
       <td></td>
@@ -33444,7 +40582,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -33464,6 +40601,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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+      <td>6</td>
+      <td>9</td>
     </tr>
     <tr>
       <td></td>
@@ -33526,8 +40678,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>63</td>
-      <td>388</td>
+      <td>400</td>
+      <td>455</td>
+      <td>129</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>238</td>
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+      <td>19</td>
+      <td>56</td>
+      <td>638</td>
+      <td>1061</td>
+      <td>148</td>
+      <td>196</td>
     </tr>
     <tr>
       <td></td>
@@ -33571,7 +40737,6 @@
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-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -33591,7 +40756,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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+      <td>463</td>
       <td>19</td>
+      <td>28</td>
+      <td>335</td>
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+      <td>19</td>
+      <td>31</td>
     </tr>
     <tr>
       <td></td>
@@ -33620,10 +40800,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -33650,12 +40829,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
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-      <td>24</td>
-      <td>171</td>
+      <td>155</td>
+      <td>192</td>
+      <td>81</td>
+      <td>90</td>
+      <td>1853</td>
+      <td>3943</td>
+      <td>581</td>
+      <td>1280</td>
+      <td>144</td>
+      <td>156</td>
+      <td>13</td>
+      <td>16</td>
+      <td>2152</td>
+      <td>4291</td>
+      <td>675</td>
+      <td>1386</td>
     </tr>
     <tr>
       <td></td>
@@ -33718,8 +40912,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>34</td>
-      <td>531</td>
+      <td>440</td>
+      <td>594</td>
+      <td>127</td>
+      <td>142</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>0</td>
+      <td>12</td>
+      <td>440</td>
+      <td>610</td>
+      <td>127</td>
+      <td>154</td>
     </tr>
     <tr>
       <td></td>
@@ -33764,7 +40972,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -33784,6 +40991,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -33828,7 +41050,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -33842,12 +41063,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>35</td>
-      <td>498</td>
+      <td>379</td>
+      <td>537</td>
+      <td>104</td>
+      <td>118</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>39</td>
+      <td>496</td>
+      <td>28</td>
+      <td>48</td>
+      <td>418</td>
+      <td>1034</td>
+      <td>132</td>
+      <td>167</td>
     </tr>
     <tr>
       <td></td>
@@ -33910,8 +41146,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>68</td>
-      <td>953</td>
+      <td>817</td>
+      <td>1084</td>
+      <td>244</td>
+      <td>273</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>93</td>
+      <td>448</td>
+      <td>44</td>
+      <td>60</td>
+      <td>910</td>
+      <td>1532</td>
+      <td>288</td>
+      <td>333</td>
     </tr>
     <tr>
       <td></td>
@@ -33940,10 +41190,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -33970,12 +41219,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>24</td>
-      <td>411</td>
+      <td>410</td>
+      <td>423</td>
+      <td>56</td>
+      <td>60</td>
+      <td>6261</td>
+      <td>8115</td>
+      <td>133</td>
+      <td>362</td>
+      <td>127</td>
+      <td>157</td>
+      <td>10</td>
+      <td>19</td>
+      <td>6798</td>
+      <td>8695</td>
+      <td>199</td>
+      <td>441</td>
     </tr>
     <tr>
       <td></td>
@@ -34038,8 +41302,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>17</td>
-      <td>137</td>
+      <td>134</td>
+      <td>142</td>
+      <td>46</td>
+      <td>49</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>120</td>
+      <td>142</td>
+      <td>12</td>
+      <td>19</td>
+      <td>254</td>
+      <td>284</td>
+      <td>58</td>
+      <td>68</td>
     </tr>
     <tr>
       <td></td>
@@ -34062,16 +41340,15 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list</td>
       <td>0.1.2</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -34099,11 +41376,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>248</td>
-      <td>5067</td>
+      <td>4519</td>
+      <td>5476</td>
+      <td>667</td>
+      <td>730</td>
+      <td>9858</td>
+      <td>18420</td>
+      <td>986</td>
+      <td>2010</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14377</td>
+      <td>23896</td>
+      <td>1653</td>
+      <td>2740</td>
     </tr>
     <tr>
       <td></td>
@@ -34166,8 +41458,22 @@
       <td>21</td>
       <td>21</td>
       <td>0</td>
-      <td>123</td>
-      <td>7864</td>
+      <td>3197</td>
+      <td>8107</td>
+      <td>344</td>
+      <td>415</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3197</td>
+      <td>8107</td>
+      <td>344</td>
+      <td>415</td>
     </tr>
     <tr>
       <td></td>
@@ -34232,6 +41538,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -34296,6 +41616,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>227</td>
+      <td>2307</td>
+      <td>17</td>
+      <td>75</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>227</td>
+      <td>2307</td>
+      <td>17</td>
+      <td>75</td>
     </tr>
     <tr>
       <td></td>
@@ -34358,8 +41692,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>96</td>
+      <td>96</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>96</td>
+      <td>96</td>
+      <td>13</td>
+      <td>13</td>
     </tr>
     <tr>
       <td></td>
@@ -34424,6 +41772,20 @@
       <td>0</td>
       <td>0</td>
       <td>11</td>
+      <td>0</td>
+      <td>2</td>
+      <td>171</td>
+      <td>3961</td>
+      <td>34</td>
+      <td>328</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>171</td>
+      <td>3972</td>
+      <td>34</td>
+      <td>330</td>
     </tr>
     <tr>
       <td></td>
@@ -34486,8 +41848,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -34516,10 +41892,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -34547,11 +41922,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>116</td>
-      <td>1660</td>
+      <td>1619</td>
+      <td>1715</td>
+      <td>337</td>
+      <td>376</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1619</td>
+      <td>1715</td>
+      <td>337</td>
+      <td>376</td>
     </tr>
     <tr>
       <td></td>
@@ -34580,8 +41970,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -34592,8 +41981,8 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -34610,12 +41999,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>344</td>
-      <td>5892</td>
+      <td>4490</td>
+      <td>6169</td>
+      <td>768</td>
+      <td>889</td>
+      <td>6120</td>
+      <td>15516</td>
+      <td>1921</td>
+      <td>3653</td>
+      <td>2033</td>
+      <td>2212</td>
+      <td>556</td>
+      <td>590</td>
+      <td>12643</td>
+      <td>23897</td>
+      <td>3245</td>
+      <td>5132</td>
     </tr>
     <tr>
       <td></td>
@@ -34678,8 +42082,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
-      <td>42</td>
+      <td>43</td>
+      <td>43</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>20</td>
+      <td>20</td>
     </tr>
     <tr>
       <td></td>
@@ -34708,8 +42126,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -34738,12 +42155,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>1764</td>
-      <td>496717</td>
+      <td>619817</td>
+      <td>622353</td>
+      <td>4097</td>
+      <td>4130</td>
+      <td>320454</td>
+      <td>320454</td>
+      <td>2915</td>
+      <td>2915</td>
+      <td>496156</td>
+      <td>503743</td>
+      <td>2012</td>
+      <td>2227</td>
+      <td>1436427</td>
+      <td>1446550</td>
+      <td>9024</td>
+      <td>9272</td>
     </tr>
     <tr>
       <td></td>
@@ -34806,8 +42238,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>109</td>
+      <td>109</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>109</td>
+      <td>109</td>
     </tr>
     <tr>
       <td></td>
@@ -34836,9 +42282,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -34866,12 +42311,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>391</td>
-      <td>4278</td>
+      <td>5543</td>
+      <td>5543</td>
+      <td>1042</td>
+      <td>1042</td>
+      <td>1301</td>
+      <td>1305</td>
+      <td>413</td>
+      <td>414</td>
+      <td>2030</td>
+      <td>2030</td>
+      <td>299</td>
+      <td>299</td>
+      <td>8874</td>
+      <td>8878</td>
+      <td>1754</td>
+      <td>1755</td>
     </tr>
     <tr>
       <td></td>
@@ -34934,8 +42394,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>37</td>
-      <td>217</td>
+      <td>348</td>
+      <td>348</td>
+      <td>62</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>348</td>
+      <td>348</td>
+      <td>62</td>
+      <td>62</td>
     </tr>
     <tr>
       <td></td>
@@ -34980,7 +42454,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -34995,11 +42468,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>91</td>
-      <td>83150</td>
+      <td>76834</td>
+      <td>86002</td>
+      <td>227</td>
+      <td>246</td>
+      <td>20174</td>
+      <td>20953</td>
+      <td>312</td>
+      <td>395</td>
+      <td>11</td>
+      <td>11</td>
+      <td>2</td>
+      <td>2</td>
+      <td>97019</td>
+      <td>106966</td>
+      <td>541</td>
+      <td>643</td>
     </tr>
     <tr>
       <td></td>
@@ -35028,11 +42516,11 @@
       <td>1</td>
       <td>4</td>
       <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>1</td>
       <td>4</td>
       <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -35062,8 +42550,22 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>47</td>
-      <td>168</td>
+      <td>200</td>
+      <td>200</td>
+      <td>77</td>
+      <td>77</td>
+      <td>83</td>
+      <td>83</td>
+      <td>39</td>
+      <td>39</td>
+      <td>1747</td>
+      <td>1747</td>
+      <td>44</td>
+      <td>44</td>
+      <td>2030</td>
+      <td>2030</td>
+      <td>160</td>
+      <td>160</td>
     </tr>
     <tr>
       <td></td>
@@ -35126,8 +42628,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>13</td>
-      <td>129</td>
+      <td>262</td>
+      <td>262</td>
+      <td>36</td>
+      <td>36</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>262</td>
+      <td>262</td>
+      <td>36</td>
+      <td>36</td>
     </tr>
     <tr>
       <td></td>
@@ -35172,7 +42688,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -35192,6 +42707,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -35254,8 +42784,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>12</td>
-      <td>53</td>
+      <td>81</td>
+      <td>81</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>81</td>
+      <td>81</td>
+      <td>17</td>
+      <td>17</td>
     </tr>
     <tr>
       <td></td>
@@ -35318,8 +42862,22 @@
       <td>19</td>
       <td>0</td>
       <td>0</td>
-      <td>42</td>
-      <td>267</td>
+      <td>1213</td>
+      <td>1213</td>
+      <td>155</td>
+      <td>155</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1213</td>
+      <td>1213</td>
+      <td>155</td>
+      <td>155</td>
     </tr>
     <tr>
       <td></td>
@@ -35348,10 +42906,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -35383,7 +42940,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>591</td>
+      <td>5734</td>
+      <td>5734</td>
+      <td>334</td>
+      <td>334</td>
+      <td>1035</td>
+      <td>1035</td>
+      <td>106</td>
+      <td>106</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6769</td>
+      <td>6769</td>
+      <td>440</td>
+      <td>440</td>
     </tr>
     <tr>
       <td></td>
@@ -35446,7 +43018,21 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
+      <td>26</td>
+      <td>26</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>7</td>
       <td>7</td>
     </tr>
     <tr>
@@ -35510,8 +43096,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>625</td>
-      <td>35620</td>
+      <td>43047</td>
+      <td>43139</td>
+      <td>1826</td>
+      <td>1827</td>
+      <td>17240</td>
+      <td>17240</td>
+      <td>878</td>
+      <td>878</td>
+      <td>9309</td>
+      <td>9309</td>
+      <td>298</td>
+      <td>298</td>
+      <td>69596</td>
+      <td>69688</td>
+      <td>3002</td>
+      <td>3003</td>
     </tr>
     <tr>
       <td></td>
@@ -35540,8 +43140,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -35570,12 +43169,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1175</td>
-      <td>25975</td>
+      <td>29266</td>
+      <td>30655</td>
+      <td>2849</td>
+      <td>2973</td>
+      <td>59299</td>
+      <td>66180</td>
+      <td>5917</td>
+      <td>6355</td>
+      <td>5644</td>
+      <td>5644</td>
+      <td>1049</td>
+      <td>1049</td>
+      <td>94209</td>
+      <td>102479</td>
+      <td>9815</td>
+      <td>10377</td>
     </tr>
     <tr>
       <td></td>
@@ -35604,11 +43218,25 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -35702,8 +43330,22 @@
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>38</td>
-      <td>3528</td>
+      <td>3670</td>
+      <td>3670</td>
+      <td>71</td>
+      <td>71</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>234</td>
+      <td>234</td>
+      <td>10</td>
+      <td>10</td>
+      <td>3907</td>
+      <td>3907</td>
+      <td>83</td>
+      <td>83</td>
     </tr>
     <tr>
       <td></td>
@@ -35748,7 +43390,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -35767,7 +43408,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>140</td>
+      <td>140</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>140</td>
+      <td>140</td>
+      <td>9</td>
+      <td>9</td>
     </tr>
     <tr>
       <td></td>
@@ -35812,7 +43468,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -35826,12 +43481,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>2</td>
       <td>1</td>
       <td>0</td>
-      <td>123</td>
-      <td>8175</td>
+      <td>9021</td>
+      <td>9021</td>
+      <td>238</td>
+      <td>238</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9021</td>
+      <td>9021</td>
+      <td>238</td>
+      <td>238</td>
     </tr>
     <tr>
       <td></td>
@@ -35860,11 +43530,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -35943,7 +43627,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -35954,12 +43637,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>151</td>
+      <td>151</td>
+      <td>5</td>
+      <td>5</td>
+      <td>151</td>
+      <td>151</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -35988,8 +43686,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -36018,12 +43715,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>685</td>
-      <td>11245</td>
+      <td>12890</td>
+      <td>13988</td>
+      <td>1826</td>
+      <td>1988</td>
+      <td>14901</td>
+      <td>14901</td>
+      <td>2633</td>
+      <td>2633</td>
+      <td>6187</td>
+      <td>6187</td>
+      <td>511</td>
+      <td>511</td>
+      <td>33978</td>
+      <td>35076</td>
+      <td>4970</td>
+      <td>5132</td>
     </tr>
     <tr>
       <td></td>
@@ -36086,8 +43798,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>12</td>
-      <td>345</td>
+      <td>369</td>
+      <td>369</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>369</td>
+      <td>369</td>
+      <td>19</td>
+      <td>19</td>
     </tr>
     <tr>
       <td></td>
@@ -36116,8 +43842,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -36147,11 +43872,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>151</td>
-      <td>2982</td>
+      <td>11117</td>
+      <td>11117</td>
+      <td>534</td>
+      <td>534</td>
+      <td>19</td>
+      <td>19</td>
+      <td>1</td>
+      <td>1</td>
+      <td>9601</td>
+      <td>9601</td>
+      <td>167</td>
+      <td>167</td>
+      <td>20737</td>
+      <td>20737</td>
+      <td>702</td>
+      <td>702</td>
     </tr>
     <tr>
       <td></td>
@@ -36214,8 +43954,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>4</td>
-      <td>128</td>
+      <td>83</td>
+      <td>131</td>
+      <td>15</td>
+      <td>20</td>
+      <td>329</td>
+      <td>785</td>
+      <td>50</td>
+      <td>210</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>412</td>
+      <td>916</td>
+      <td>65</td>
+      <td>230</td>
     </tr>
     <tr>
       <td></td>
@@ -36244,8 +43998,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -36274,12 +44027,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>208</td>
-      <td>14021</td>
+      <td>14693</td>
+      <td>15620</td>
+      <td>653</td>
+      <td>721</td>
+      <td>61872</td>
+      <td>101400</td>
+      <td>1656</td>
+      <td>5678</td>
+      <td>39</td>
+      <td>39</td>
+      <td>3</td>
+      <td>3</td>
+      <td>76604</td>
+      <td>117059</td>
+      <td>2312</td>
+      <td>6402</td>
     </tr>
     <tr>
       <td></td>
@@ -36308,8 +44076,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -36338,12 +44105,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1195</td>
-      <td>114863</td>
+      <td>115954</td>
+      <td>124795</td>
+      <td>2994</td>
+      <td>3180</td>
+      <td>95433</td>
+      <td>142254</td>
+      <td>6712</td>
+      <td>10660</td>
+      <td>5793</td>
+      <td>5793</td>
+      <td>497</td>
+      <td>497</td>
+      <td>217180</td>
+      <td>272842</td>
+      <td>10203</td>
+      <td>14337</td>
     </tr>
     <tr>
       <td></td>
@@ -36388,7 +44170,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -36403,11 +44184,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>197</td>
-      <td>4328</td>
+      <td>9073</td>
+      <td>9073</td>
+      <td>401</td>
+      <td>401</td>
+      <td>2746</td>
+      <td>2746</td>
+      <td>224</td>
+      <td>224</td>
+      <td>103</td>
+      <td>103</td>
+      <td>10</td>
+      <td>10</td>
+      <td>11922</td>
+      <td>11922</td>
+      <td>635</td>
+      <td>635</td>
     </tr>
     <tr>
       <td></td>
@@ -36470,8 +44266,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
-      <td>39</td>
+      <td>45</td>
+      <td>45</td>
+      <td>20</td>
+      <td>20</td>
+      <td>69</td>
+      <td>69</td>
+      <td>21</td>
+      <td>21</td>
+      <td>258</td>
+      <td>258</td>
+      <td>1</td>
+      <td>1</td>
+      <td>372</td>
+      <td>372</td>
+      <td>42</td>
+      <td>42</td>
     </tr>
     <tr>
       <td></td>
@@ -36500,8 +44310,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -36530,12 +44339,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>2016</td>
-      <td>44390</td>
+      <td>55392</td>
+      <td>56095</td>
+      <td>4951</td>
+      <td>5035</td>
+      <td>47603</td>
+      <td>47603</td>
+      <td>4916</td>
+      <td>4916</td>
+      <td>18089</td>
+      <td>18089</td>
+      <td>3121</td>
+      <td>3121</td>
+      <td>121084</td>
+      <td>121787</td>
+      <td>12988</td>
+      <td>13072</td>
     </tr>
     <tr>
       <td></td>
@@ -36600,6 +44424,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -36662,8 +44500,22 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>71</td>
+      <td>111</td>
+      <td>111</td>
+      <td>8</td>
+      <td>8</td>
+      <td>29</td>
+      <td>29</td>
+      <td>10</td>
+      <td>10</td>
+      <td>21</td>
+      <td>21</td>
+      <td>4</td>
+      <td>4</td>
+      <td>161</td>
+      <td>161</td>
+      <td>22</td>
+      <td>22</td>
     </tr>
     <tr>
       <td></td>
@@ -36692,9 +44544,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -36723,11 +44574,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>160</td>
-      <td>3938</td>
+      <td>6041</td>
+      <td>6041</td>
+      <td>316</td>
+      <td>316</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6723</td>
+      <td>7273</td>
+      <td>240</td>
+      <td>322</td>
+      <td>12764</td>
+      <td>13314</td>
+      <td>556</td>
+      <td>638</td>
     </tr>
     <tr>
       <td></td>
@@ -36772,7 +44638,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -36786,12 +44651,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>35</td>
-      <td>266</td>
+      <td>306</td>
+      <td>311</td>
+      <td>82</td>
+      <td>83</td>
+      <td>467</td>
+      <td>467</td>
+      <td>99</td>
+      <td>99</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>773</td>
+      <td>778</td>
+      <td>181</td>
+      <td>182</td>
     </tr>
     <tr>
       <td></td>
@@ -36854,8 +44734,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>8</td>
-      <td>200</td>
+      <td>208</td>
+      <td>208</td>
+      <td>26</td>
+      <td>26</td>
+      <td>210</td>
+      <td>210</td>
+      <td>30</td>
+      <td>30</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>418</td>
+      <td>418</td>
+      <td>56</td>
+      <td>56</td>
     </tr>
     <tr>
       <td></td>
@@ -36918,8 +44812,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>8</td>
-      <td>64</td>
+      <td>90</td>
+      <td>90</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>90</td>
+      <td>90</td>
+      <td>28</td>
+      <td>28</td>
     </tr>
     <tr>
       <td></td>
@@ -36982,8 +44890,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>7</td>
+      <td>7</td>
+      <td>175</td>
+      <td>175</td>
+      <td>26</td>
+      <td>26</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>217</td>
+      <td>217</td>
+      <td>33</td>
+      <td>33</td>
     </tr>
     <tr>
       <td></td>
@@ -37028,7 +44950,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -37043,11 +44964,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>420</td>
-      <td>6381</td>
+      <td>11989</td>
+      <td>11989</td>
+      <td>768</td>
+      <td>768</td>
+      <td>4458</td>
+      <td>4458</td>
+      <td>652</td>
+      <td>652</td>
+      <td>2507</td>
+      <td>2507</td>
+      <td>80</td>
+      <td>80</td>
+      <td>18954</td>
+      <td>18954</td>
+      <td>1500</td>
+      <td>1500</td>
     </tr>
     <tr>
       <td></td>
@@ -37112,6 +45048,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -37174,8 +45124,22 @@
       <td>7</td>
       <td>7</td>
       <td>0</td>
-      <td>87</td>
-      <td>2895</td>
+      <td>2352</td>
+      <td>3092</td>
+      <td>234</td>
+      <td>265</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2352</td>
+      <td>3092</td>
+      <td>234</td>
+      <td>265</td>
     </tr>
     <tr>
       <td></td>
@@ -37238,8 +45202,22 @@
       <td>3</td>
       <td>0</td>
       <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>9</td>
+      <td>9</td>
       <td>0</td>
-      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>9</td>
+      <td>9</td>
     </tr>
     <tr>
       <td></td>
@@ -37302,8 +45280,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>22</td>
+      <td>22</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>22</td>
+      <td>22</td>
+      <td>7</td>
+      <td>7</td>
     </tr>
     <tr>
       <td></td>
@@ -37348,7 +45340,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -37363,11 +45354,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>10</td>
-      <td>54</td>
+      <td>88</td>
+      <td>88</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>88</td>
+      <td>88</td>
+      <td>28</td>
+      <td>28</td>
     </tr>
     <tr>
       <td></td>
@@ -37430,8 +45436,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>10</td>
-      <td>28</td>
+      <td>93</td>
+      <td>93</td>
+      <td>36</td>
+      <td>36</td>
+      <td>181</td>
+      <td>181</td>
+      <td>62</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>274</td>
+      <td>274</td>
+      <td>98</td>
+      <td>98</td>
     </tr>
     <tr>
       <td></td>
@@ -37460,8 +45480,7 @@
       <td>37</td>
       <td>37</td>
       <td>37</td>
-      <td>37</td>
-      <td>37</td>
+      <td>0</td>
       <td>37</td>
       <td>37</td>
       <td>37</td>
@@ -37490,12 +45509,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>37</td>
       <td>37</td>
       <td>37</td>
       <td>0</td>
-      <td>5844</td>
-      <td>901750</td>
+      <td>916111</td>
+      <td>962278</td>
+      <td>13235</td>
+      <td>14525</td>
+      <td>407944</td>
+      <td>647621</td>
+      <td>25849</td>
+      <td>41751</td>
+      <td>84008</td>
+      <td>89233</td>
+      <td>2486</td>
+      <td>2832</td>
+      <td>1408063</td>
+      <td>1699132</td>
+      <td>41570</td>
+      <td>59108</td>
     </tr>
     <tr>
       <td></td>
@@ -37558,8 +45592,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>123</td>
-      <td>1194</td>
+      <td>1611</td>
+      <td>1611</td>
+      <td>262</td>
+      <td>262</td>
+      <td>763</td>
+      <td>763</td>
+      <td>67</td>
+      <td>67</td>
+      <td>543</td>
+      <td>543</td>
+      <td>30</td>
+      <td>30</td>
+      <td>2917</td>
+      <td>2917</td>
+      <td>359</td>
+      <td>359</td>
     </tr>
     <tr>
       <td></td>
@@ -37624,6 +45672,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>617</td>
+      <td>617</td>
+      <td>63</td>
+      <td>63</td>
+      <td>617</td>
+      <td>617</td>
+      <td>63</td>
+      <td>63</td>
     </tr>
     <tr>
       <td></td>
@@ -37686,8 +45748,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>544</td>
+      <td>544</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>544</td>
+      <td>544</td>
+      <td>20</td>
+      <td>20</td>
     </tr>
     <tr>
       <td></td>
@@ -37750,8 +45826,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>5</td>
+      <td>5</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -37796,7 +45886,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -37811,11 +45900,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>21</td>
-      <td>81</td>
+      <td>126</td>
+      <td>126</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>126</td>
+      <td>126</td>
+      <td>42</td>
+      <td>42</td>
     </tr>
     <tr>
       <td></td>
@@ -37860,7 +45964,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -37875,11 +45978,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>363</td>
-      <td>15228</td>
+      <td>17413</td>
+      <td>17413</td>
+      <td>822</td>
+      <td>822</td>
+      <td>15349</td>
+      <td>15349</td>
+      <td>2020</td>
+      <td>2020</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>32764</td>
+      <td>32764</td>
+      <td>2843</td>
+      <td>2843</td>
     </tr>
     <tr>
       <td></td>
@@ -37942,8 +46060,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>1137</td>
+      <td>1137</td>
+      <td>97</td>
+      <td>97</td>
+      <td>1029</td>
+      <td>1029</td>
       <td>71</td>
-      <td>978</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2166</td>
+      <td>2166</td>
+      <td>168</td>
+      <td>168</td>
     </tr>
     <tr>
       <td></td>
@@ -37987,7 +46119,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -38002,12 +46133,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>98</td>
-      <td>3906</td>
+      <td>12725</td>
+      <td>12725</td>
+      <td>297</td>
+      <td>297</td>
+      <td>2851</td>
+      <td>5049</td>
+      <td>450</td>
+      <td>638</td>
+      <td>2171</td>
+      <td>2371</td>
+      <td>214</td>
+      <td>239</td>
+      <td>17747</td>
+      <td>20145</td>
+      <td>961</td>
+      <td>1174</td>
     </tr>
     <tr>
       <td></td>
@@ -38036,8 +46182,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -38067,11 +46212,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>240</td>
-      <td>6736</td>
+      <td>7738</td>
+      <td>7931</td>
+      <td>478</td>
+      <td>508</td>
+      <td>8301</td>
+      <td>8301</td>
+      <td>849</td>
+      <td>849</td>
+      <td>1369</td>
+      <td>1369</td>
+      <td>154</td>
+      <td>154</td>
+      <td>17408</td>
+      <td>17601</td>
+      <td>1481</td>
+      <td>1511</td>
     </tr>
     <tr>
       <td></td>
@@ -38136,6 +46296,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6243</td>
+      <td>6243</td>
+      <td>375</td>
+      <td>375</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6243</td>
+      <td>6243</td>
+      <td>375</td>
+      <td>375</td>
     </tr>
     <tr>
       <td></td>
@@ -38198,8 +46372,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1</td>
       <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>3</td>
+      <td>3</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -38262,8 +46450,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>78</td>
-      <td>511</td>
+      <td>738</td>
+      <td>738</td>
+      <td>151</td>
+      <td>151</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>740</td>
+      <td>740</td>
+      <td>152</td>
+      <td>152</td>
     </tr>
     <tr>
       <td></td>
@@ -38326,8 +46528,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>24</td>
-      <td>185</td>
+      <td>585</td>
+      <td>585</td>
+      <td>102</td>
+      <td>102</td>
+      <td>172</td>
+      <td>172</td>
+      <td>63</td>
+      <td>63</td>
+      <td>135</td>
+      <td>135</td>
+      <td>16</td>
+      <td>16</td>
+      <td>892</td>
+      <td>892</td>
+      <td>181</td>
+      <td>181</td>
     </tr>
     <tr>
       <td></td>
@@ -38356,8 +46572,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -38386,12 +46601,27 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5136</td>
-      <td>380252</td>
+      <td>397893</td>
+      <td>427447</td>
+      <td>12133</td>
+      <td>13176</td>
+      <td>577209</td>
+      <td>903193</td>
+      <td>33086</td>
+      <td>52020</td>
+      <td>60105</td>
+      <td>67495</td>
+      <td>3779</td>
+      <td>4271</td>
+      <td>1035207</td>
+      <td>1398135</td>
+      <td>48998</td>
+      <td>69467</td>
     </tr>
     <tr>
       <td></td>
@@ -38420,8 +46650,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -38451,11 +46680,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>326</td>
-      <td>18351</td>
+      <td>51378</td>
+      <td>51378</td>
+      <td>775</td>
+      <td>775</td>
+      <td>3298</td>
+      <td>3298</td>
+      <td>160</td>
+      <td>160</td>
+      <td>1660</td>
+      <td>1660</td>
+      <td>63</td>
+      <td>63</td>
+      <td>56336</td>
+      <td>56336</td>
+      <td>998</td>
+      <td>998</td>
     </tr>
     <tr>
       <td></td>
@@ -38499,7 +46743,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -38515,11 +46758,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>50</td>
-      <td>1871</td>
+      <td>2976</td>
+      <td>2976</td>
+      <td>98</td>
+      <td>98</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>884</td>
+      <td>884</td>
+      <td>70</td>
+      <td>70</td>
+      <td>3860</td>
+      <td>3860</td>
+      <td>168</td>
+      <td>168</td>
     </tr>
     <tr>
       <td></td>
@@ -38582,8 +46840,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>6</td>
+      <td>6</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>3</td>
+      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -38612,8 +46884,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -38642,12 +46913,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1804</td>
-      <td>86180</td>
+      <td>102717</td>
+      <td>103051</td>
+      <td>3877</td>
+      <td>3926</td>
+      <td>34251</td>
+      <td>34251</td>
+      <td>3506</td>
+      <td>3506</td>
+      <td>33192</td>
+      <td>34369</td>
+      <td>2439</td>
+      <td>2525</td>
+      <td>170160</td>
+      <td>171671</td>
+      <td>9822</td>
+      <td>9957</td>
     </tr>
     <tr>
       <td></td>
@@ -38676,8 +46962,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -38706,12 +46991,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>5295</td>
-      <td>981251</td>
+      <td>976935</td>
+      <td>1017671</td>
+      <td>13526</td>
+      <td>14401</td>
+      <td>474702</td>
+      <td>681286</td>
+      <td>32627</td>
+      <td>47624</td>
+      <td>79802</td>
+      <td>87191</td>
+      <td>4219</td>
+      <td>4954</td>
+      <td>1531439</td>
+      <td>1786148</td>
+      <td>50372</td>
+      <td>66979</td>
     </tr>
     <tr>
       <td></td>
@@ -38740,8 +47040,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -38771,11 +47070,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1220</td>
-      <td>44386</td>
+      <td>56619</td>
+      <td>56619</td>
+      <td>2324</td>
+      <td>2324</td>
+      <td>36631</td>
+      <td>36631</td>
+      <td>2808</td>
+      <td>2808</td>
+      <td>18121</td>
+      <td>18121</td>
+      <td>713</td>
+      <td>713</td>
+      <td>111371</td>
+      <td>111371</td>
+      <td>5845</td>
+      <td>5845</td>
     </tr>
     <tr>
       <td></td>
@@ -38823,7 +47137,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -38834,12 +47147,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>201</td>
-      <td>10619</td>
+      <td>7970</td>
+      <td>11724</td>
+      <td>643</td>
+      <td>826</td>
+      <td>5524</td>
+      <td>5524</td>
+      <td>611</td>
+      <td>611</td>
+      <td>1242</td>
+      <td>1242</td>
+      <td>114</td>
+      <td>114</td>
+      <td>14736</td>
+      <td>18490</td>
+      <td>1368</td>
+      <td>1551</td>
     </tr>
     <tr>
       <td></td>
@@ -38868,11 +47196,11 @@
       <td>0</td>
       <td>2</td>
       <td>2</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>2</td>
       <td>2</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -38902,8 +47230,22 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>26</td>
-      <td>234</td>
+      <td>299</td>
+      <td>299</td>
+      <td>61</td>
+      <td>61</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1339</td>
+      <td>1339</td>
+      <td>95</td>
+      <td>95</td>
+      <td>1638</td>
+      <td>1638</td>
+      <td>156</td>
+      <td>156</td>
     </tr>
     <tr>
       <td></td>
@@ -38968,6 +47310,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -39030,8 +47386,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
       <td>1393</td>
+      <td>1393</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1393</td>
+      <td>1393</td>
+      <td>10</td>
+      <td>10</td>
     </tr>
     <tr>
       <td></td>
@@ -39094,8 +47464,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>195</td>
+      <td>195</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>195</td>
+      <td>195</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -39140,7 +47524,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -39154,12 +47537,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>268</td>
-      <td>2878</td>
+      <td>3835</td>
+      <td>3835</td>
+      <td>597</td>
+      <td>597</td>
+      <td>1359</td>
+      <td>1359</td>
+      <td>467</td>
+      <td>467</td>
+      <td>646</td>
+      <td>646</td>
+      <td>98</td>
+      <td>98</td>
+      <td>5840</td>
+      <td>5840</td>
+      <td>1162</td>
+      <td>1162</td>
     </tr>
     <tr>
       <td></td>
@@ -39188,10 +47586,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -39219,11 +47616,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>280</td>
-      <td>4474</td>
+      <td>10414</td>
+      <td>10414</td>
+      <td>510</td>
+      <td>510</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>10418</td>
+      <td>10418</td>
+      <td>512</td>
+      <td>512</td>
     </tr>
     <tr>
       <td></td>
@@ -39286,8 +47698,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
-      <td>98</td>
+      <td>225</td>
+      <td>225</td>
+      <td>32</td>
+      <td>32</td>
+      <td>271</td>
+      <td>271</td>
+      <td>61</td>
+      <td>61</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>496</td>
+      <td>496</td>
+      <td>93</td>
+      <td>93</td>
     </tr>
     <tr>
       <td></td>
@@ -39350,8 +47776,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>287</td>
-      <td>3589</td>
+      <td>3383</td>
+      <td>4001</td>
+      <td>1576</td>
+      <td>1822</td>
+      <td>7870</td>
+      <td>13727</td>
+      <td>3823</td>
+      <td>6880</td>
+      <td>249</td>
+      <td>350</td>
+      <td>108</td>
+      <td>145</td>
+      <td>11502</td>
+      <td>18078</td>
+      <td>5507</td>
+      <td>8847</td>
     </tr>
     <tr>
       <td></td>
@@ -39380,9 +47820,8 @@
       <td>0</td>
       <td>10</td>
       <td>10</td>
-      <td>10</td>
       <td>0</td>
-      <td>10</td>
+      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
@@ -39411,11 +47850,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>10</td>
       <td>0</td>
       <td>0</td>
-      <td>390</td>
-      <td>5165</td>
+      <td>7500</td>
+      <td>7500</td>
+      <td>930</td>
+      <td>930</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7500</td>
+      <td>7500</td>
+      <td>930</td>
+      <td>930</td>
     </tr>
     <tr>
       <td></td>
@@ -39478,8 +47932,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
+      <td>207</td>
+      <td>207</td>
       <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>207</td>
       <td>207</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -39542,8 +48010,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>727</td>
+      <td>727</td>
+      <td>76</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>727</td>
+      <td>727</td>
+      <td>76</td>
+      <td>76</td>
     </tr>
     <tr>
       <td></td>
@@ -39606,8 +48088,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>97</td>
-      <td>6418</td>
+      <td>16542</td>
+      <td>16542</td>
+      <td>287</td>
+      <td>287</td>
+      <td>1061</td>
+      <td>1061</td>
+      <td>102</td>
+      <td>102</td>
+      <td>27</td>
+      <td>27</td>
+      <td>5</td>
+      <td>5</td>
+      <td>17630</td>
+      <td>17630</td>
+      <td>394</td>
+      <td>394</td>
     </tr>
     <tr>
       <td></td>
@@ -39672,6 +48168,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>6</td>
+      <td>6</td>
     </tr>
     <tr>
       <td></td>
@@ -39700,9 +48210,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -39730,12 +48239,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>182</td>
-      <td>2130</td>
+      <td>2696</td>
+      <td>2696</td>
+      <td>398</td>
+      <td>398</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1235</td>
+      <td>1235</td>
+      <td>186</td>
+      <td>186</td>
+      <td>3931</td>
+      <td>3931</td>
+      <td>584</td>
+      <td>584</td>
     </tr>
     <tr>
       <td></td>
@@ -39798,8 +48322,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>16</td>
-      <td>269</td>
+      <td>524</td>
+      <td>524</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>524</td>
+      <td>524</td>
+      <td>32</td>
+      <td>32</td>
     </tr>
     <tr>
       <td></td>
@@ -39828,8 +48366,7 @@
       <td>11</td>
       <td>11</td>
       <td>11</td>
-      <td>11</td>
-      <td>11</td>
+      <td>0</td>
       <td>11</td>
       <td>11</td>
       <td>11</td>
@@ -39858,12 +48395,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>11</td>
       <td>11</td>
       <td>11</td>
       <td>0</td>
-      <td>1018</td>
-      <td>21305</td>
+      <td>26265</td>
+      <td>26265</td>
+      <td>2483</td>
+      <td>2483</td>
+      <td>31332</td>
+      <td>31332</td>
+      <td>3535</td>
+      <td>3535</td>
+      <td>26359</td>
+      <td>26359</td>
+      <td>999</td>
+      <td>999</td>
+      <td>83956</td>
+      <td>83956</td>
+      <td>7017</td>
+      <td>7017</td>
     </tr>
     <tr>
       <td></td>
@@ -39926,8 +48478,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>21</td>
+      <td>21</td>
+      <td>4</td>
+      <td>4</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
       <td>18</td>
+      <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td>48</td>
+      <td>48</td>
+      <td>10</td>
+      <td>10</td>
     </tr>
     <tr>
       <td></td>
@@ -39972,7 +48538,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -39987,11 +48552,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>68</td>
-      <td>1856</td>
+      <td>3388</td>
+      <td>3388</td>
+      <td>187</td>
+      <td>187</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>3390</td>
+      <td>3390</td>
+      <td>189</td>
+      <td>189</td>
     </tr>
     <tr>
       <td></td>
@@ -40020,8 +48600,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -40050,12 +48629,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>651</td>
-      <td>46793</td>
+      <td>79867</td>
+      <td>80817</td>
+      <td>1675</td>
+      <td>1785</td>
+      <td>49493</td>
+      <td>87884</td>
+      <td>3703</td>
+      <td>7380</td>
+      <td>8797</td>
+      <td>9713</td>
+      <td>670</td>
+      <td>728</td>
+      <td>138157</td>
+      <td>178414</td>
+      <td>6048</td>
+      <td>9893</td>
     </tr>
     <tr>
       <td></td>
@@ -40118,8 +48712,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -40182,8 +48790,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -40246,8 +48868,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -40310,8 +48946,22 @@
       <td>17</td>
       <td>0</td>
       <td>0</td>
-      <td>45</td>
-      <td>370</td>
+      <td>618</td>
+      <td>618</td>
+      <td>177</td>
+      <td>177</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>618</td>
+      <td>618</td>
+      <td>177</td>
+      <td>177</td>
     </tr>
     <tr>
       <td></td>
@@ -40374,8 +49024,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>29</td>
-      <td>60901</td>
+      <td>61197</td>
+      <td>61220</td>
+      <td>64</td>
+      <td>65</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>61197</td>
+      <td>61220</td>
+      <td>64</td>
+      <td>65</td>
     </tr>
     <tr>
       <td></td>
@@ -40438,8 +49102,22 @@
       <td>3</td>
       <td>0</td>
       <td>0</td>
+      <td>2758</td>
+      <td>2758</td>
+      <td>22</td>
+      <td>22</td>
+      <td>20</td>
       <td>20</td>
-      <td>2757</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2778</td>
+      <td>2778</td>
+      <td>32</td>
+      <td>32</td>
     </tr>
     <tr>
       <td></td>
@@ -40504,6 +49182,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6771</td>
+      <td>6771</td>
+      <td>50</td>
+      <td>50</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6771</td>
+      <td>6771</td>
+      <td>50</td>
+      <td>50</td>
     </tr>
     <tr>
       <td></td>
@@ -40517,14 +49209,14 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://colibread.inria.fr/</td>
       <td>Sequence Analysis, Variant Analysis</td>
       <td>colibread</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread</td>
-      <td>24.7.14+galaxy0</td>
+      <td>24.7.14</td>
       <td>commet</td>
       <td>24.7.14</td>
       <td></td>
@@ -40532,10 +49224,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -40562,12 +49253,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>18</td>
-      <td>251</td>
+      <td>273</td>
+      <td>273</td>
+      <td>40</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>273</td>
+      <td>273</td>
+      <td>40</td>
+      <td>40</td>
     </tr>
     <tr>
       <td></td>
@@ -40596,8 +49302,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -40626,12 +49331,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1483</td>
-      <td>20857</td>
+      <td>23979</td>
+      <td>25337</td>
+      <td>3827</td>
+      <td>4011</td>
+      <td>21671</td>
+      <td>25163</td>
+      <td>4645</td>
+      <td>5045</td>
+      <td>2939</td>
+      <td>3036</td>
+      <td>688</td>
+      <td>701</td>
+      <td>48589</td>
+      <td>53536</td>
+      <td>9160</td>
+      <td>9757</td>
     </tr>
     <tr>
       <td></td>
@@ -40660,8 +49380,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -40690,12 +49409,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>912</td>
-      <td>5059</td>
+      <td>6905</td>
+      <td>7102</td>
+      <td>1620</td>
+      <td>1630</td>
+      <td>7761</td>
+      <td>7761</td>
+      <td>1897</td>
+      <td>1897</td>
+      <td>1157</td>
+      <td>1157</td>
+      <td>243</td>
+      <td>243</td>
+      <td>15823</td>
+      <td>16020</td>
+      <td>3760</td>
+      <td>3770</td>
     </tr>
     <tr>
       <td></td>
@@ -40724,8 +49458,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -40754,12 +49487,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2379</td>
-      <td>3883271</td>
+      <td>2940752</td>
+      <td>3907183</td>
+      <td>5422</td>
+      <td>6121</td>
+      <td>263254</td>
+      <td>737503</td>
+      <td>6095</td>
+      <td>13728</td>
+      <td>96478</td>
+      <td>97667</td>
+      <td>884</td>
+      <td>974</td>
+      <td>3300484</td>
+      <td>4742353</td>
+      <td>12401</td>
+      <td>20823</td>
     </tr>
     <tr>
       <td></td>
@@ -40788,10 +49536,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -40818,12 +49565,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>80</td>
-      <td>3258</td>
+      <td>3735</td>
+      <td>3891</td>
+      <td>268</td>
+      <td>297</td>
+      <td>1923</td>
+      <td>1923</td>
+      <td>381</td>
+      <td>381</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5658</td>
+      <td>5814</td>
+      <td>649</td>
+      <td>678</td>
     </tr>
     <tr>
       <td></td>
@@ -40852,8 +49614,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -40882,12 +49643,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>199</td>
-      <td>8424</td>
+      <td>8331</td>
+      <td>8917</td>
+      <td>613</td>
+      <td>662</td>
+      <td>5206</td>
+      <td>5206</td>
+      <td>716</td>
+      <td>716</td>
+      <td>1976</td>
+      <td>1976</td>
+      <td>27</td>
+      <td>27</td>
+      <td>15513</td>
+      <td>16099</td>
+      <td>1356</td>
+      <td>1405</td>
     </tr>
     <tr>
       <td></td>
@@ -40916,8 +49692,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -40951,7 +49726,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>266</td>
+      <td>266</td>
+      <td>39</td>
+      <td>39</td>
+      <td>28</td>
+      <td>28</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>294</td>
+      <td>294</td>
+      <td>54</td>
+      <td>54</td>
     </tr>
     <tr>
       <td></td>
@@ -40980,8 +49770,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -41010,12 +49799,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>375</td>
-      <td>35084</td>
+      <td>45827</td>
+      <td>45831</td>
+      <td>689</td>
+      <td>691</td>
+      <td>7721</td>
+      <td>7721</td>
+      <td>303</td>
+      <td>303</td>
+      <td>1481</td>
+      <td>1481</td>
+      <td>121</td>
+      <td>121</td>
+      <td>55029</td>
+      <td>55033</td>
+      <td>1113</td>
+      <td>1115</td>
     </tr>
     <tr>
       <td></td>
@@ -41078,8 +49882,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>164</td>
+      <td>6343</td>
+      <td>6343</td>
+      <td>290</td>
+      <td>290</td>
       <td>3674</td>
+      <td>3674</td>
+      <td>286</td>
+      <td>286</td>
+      <td>11832</td>
+      <td>11832</td>
+      <td>59</td>
+      <td>59</td>
+      <td>21849</td>
+      <td>21849</td>
+      <td>635</td>
+      <td>635</td>
     </tr>
     <tr>
       <td></td>
@@ -41108,10 +49926,9 @@
       <td>0</td>
       <td>0</td>
       <td>5</td>
-      <td>5</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -41139,11 +49956,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
-      <td>92</td>
-      <td>786</td>
+      <td>2105</td>
+      <td>2105</td>
+      <td>155</td>
+      <td>155</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2105</td>
+      <td>2105</td>
+      <td>155</td>
+      <td>155</td>
     </tr>
     <tr>
       <td></td>
@@ -41208,6 +50040,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -41252,7 +50098,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -41272,6 +50117,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -41300,10 +50160,9 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -41331,11 +50190,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>72</td>
-      <td>529</td>
+      <td>1081</td>
+      <td>1081</td>
+      <td>151</td>
+      <td>151</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1081</td>
+      <td>1081</td>
+      <td>151</td>
+      <td>151</td>
     </tr>
     <tr>
       <td></td>
@@ -41398,8 +50272,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>30</td>
-      <td>636</td>
+      <td>1052</td>
+      <td>1053</td>
+      <td>75</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1052</td>
+      <td>1053</td>
+      <td>75</td>
+      <td>76</td>
     </tr>
     <tr>
       <td></td>
@@ -41462,8 +50350,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>17</td>
-      <td>347</td>
+      <td>276</td>
+      <td>390</td>
+      <td>61</td>
+      <td>76</td>
+      <td>131</td>
+      <td>131</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>407</td>
+      <td>521</td>
+      <td>103</td>
+      <td>118</td>
     </tr>
     <tr>
       <td></td>
@@ -41515,19 +50417,33 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>6</td>
       <td>5</td>
       <td>0</td>
-      <td>116</td>
-      <td>1968</td>
+      <td>2182</td>
+      <td>2182</td>
+      <td>331</td>
+      <td>331</td>
+      <td>5251</td>
+      <td>5251</td>
+      <td>903</td>
+      <td>903</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7433</td>
+      <td>7433</td>
+      <td>1234</td>
+      <td>1234</td>
     </tr>
     <tr>
       <td></td>
@@ -41556,8 +50472,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -41586,12 +50501,27 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>65</td>
-      <td>1130</td>
+      <td>768</td>
+      <td>1199</td>
+      <td>171</td>
+      <td>300</td>
+      <td>2205</td>
+      <td>24981</td>
+      <td>754</td>
+      <td>5750</td>
+      <td>251</td>
+      <td>493</td>
+      <td>46</td>
+      <td>98</td>
+      <td>3224</td>
+      <td>26673</td>
+      <td>971</td>
+      <td>6148</td>
     </tr>
     <tr>
       <td></td>
@@ -41635,7 +50565,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -41650,12 +50579,27 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>228</td>
-      <td>5831</td>
+      <td>4176</td>
+      <td>6065</td>
+      <td>564</td>
+      <td>725</td>
+      <td>24284</td>
+      <td>117007</td>
+      <td>4952</td>
+      <td>20249</td>
+      <td>971</td>
+      <td>4231</td>
+      <td>193</td>
+      <td>616</td>
+      <td>29431</td>
+      <td>127303</td>
+      <td>5709</td>
+      <td>21590</td>
     </tr>
     <tr>
       <td></td>
@@ -41684,8 +50628,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -41714,12 +50657,27 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>319</td>
-      <td>32218</td>
+      <td>26122</td>
+      <td>33320</td>
+      <td>870</td>
+      <td>1213</td>
+      <td>70653</td>
+      <td>349091</td>
+      <td>6984</td>
+      <td>27076</td>
+      <td>3963</td>
+      <td>10315</td>
+      <td>440</td>
+      <td>836</td>
+      <td>100738</td>
+      <td>392726</td>
+      <td>8294</td>
+      <td>29125</td>
     </tr>
     <tr>
       <td></td>
@@ -41748,8 +50706,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -41778,12 +50735,27 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>122</td>
-      <td>3292</td>
+      <td>2406</td>
+      <td>3448</td>
+      <td>351</td>
+      <td>637</td>
+      <td>20978</td>
+      <td>67769</td>
+      <td>3641</td>
+      <td>13764</td>
+      <td>1209</td>
+      <td>3057</td>
+      <td>227</td>
+      <td>573</td>
+      <td>24593</td>
+      <td>74274</td>
+      <td>4219</td>
+      <td>14974</td>
     </tr>
     <tr>
       <td></td>
@@ -41835,19 +50807,33 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>27</td>
-      <td>660</td>
+      <td>374</td>
+      <td>701</td>
+      <td>81</td>
+      <td>114</td>
+      <td>1032</td>
+      <td>13499</td>
+      <td>273</td>
+      <td>1166</td>
+      <td>262</td>
+      <td>322</td>
+      <td>53</td>
+      <td>70</td>
+      <td>1668</td>
+      <td>14522</td>
+      <td>407</td>
+      <td>1350</td>
     </tr>
     <tr>
       <td></td>
@@ -41899,19 +50885,33 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>18</td>
-      <td>688</td>
+      <td>408</td>
+      <td>732</td>
+      <td>54</td>
+      <td>71</td>
+      <td>1964</td>
+      <td>15883</td>
+      <td>267</td>
+      <td>1310</td>
+      <td>308</td>
+      <td>422</td>
+      <td>26</td>
+      <td>46</td>
+      <td>2680</td>
+      <td>17037</td>
+      <td>347</td>
+      <td>1427</td>
     </tr>
     <tr>
       <td></td>
@@ -41940,8 +50940,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -41973,9 +50972,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>5090</td>
-      <td>232004</td>
+      <td>259754</td>
+      <td>272370</td>
+      <td>11716</td>
+      <td>12601</td>
+      <td>334550</td>
+      <td>362356</td>
+      <td>18618</td>
+      <td>20162</td>
+      <td>64377</td>
+      <td>65986</td>
+      <td>3507</td>
+      <td>3627</td>
+      <td>658681</td>
+      <td>700712</td>
+      <td>33841</td>
+      <td>36390</td>
     </tr>
     <tr>
       <td></td>
@@ -42038,8 +51052,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>17</td>
-      <td>235</td>
+      <td>260</td>
+      <td>260</td>
+      <td>43</td>
+      <td>43</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>119</td>
+      <td>8</td>
+      <td>8</td>
+      <td>379</td>
+      <td>379</td>
+      <td>51</td>
+      <td>51</td>
     </tr>
     <tr>
       <td></td>
@@ -42104,6 +51132,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>173</td>
+      <td>280</td>
+      <td>41</td>
+      <td>83</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>173</td>
+      <td>280</td>
+      <td>41</td>
+      <td>83</td>
     </tr>
     <tr>
       <td></td>
@@ -42132,8 +51174,7 @@
       <td>10</td>
       <td>10</td>
       <td>10</td>
-      <td>10</td>
-      <td>10</td>
+      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>10</td>
@@ -42162,12 +51203,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
-      <td>1263</td>
-      <td>66609</td>
+      <td>92240</td>
+      <td>92240</td>
+      <td>2716</td>
+      <td>2716</td>
+      <td>179176</td>
+      <td>179176</td>
+      <td>5317</td>
+      <td>5317</td>
+      <td>12478</td>
+      <td>12478</td>
+      <td>394</td>
+      <td>394</td>
+      <td>283894</td>
+      <td>283894</td>
+      <td>8427</td>
+      <td>8427</td>
     </tr>
     <tr>
       <td></td>
@@ -42196,11 +51252,11 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -42230,8 +51286,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>24</td>
-      <td>706</td>
+      <td>1323</td>
+      <td>1323</td>
+      <td>47</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1323</td>
+      <td>1323</td>
+      <td>47</td>
+      <td>47</td>
     </tr>
     <tr>
       <td></td>
@@ -42296,6 +51366,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -42324,8 +51408,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -42354,12 +51437,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>3066</td>
-      <td>739298</td>
+      <td>748586</td>
+      <td>760943</td>
+      <td>7066</td>
+      <td>7307</td>
+      <td>98089</td>
+      <td>112831</td>
+      <td>5306</td>
+      <td>6131</td>
+      <td>16235</td>
+      <td>16317</td>
+      <td>2161</td>
+      <td>2171</td>
+      <td>862910</td>
+      <td>890091</td>
+      <td>14533</td>
+      <td>15609</td>
     </tr>
     <tr>
       <td></td>
@@ -42422,8 +51520,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>15</td>
-      <td>99</td>
+      <td>121</td>
+      <td>121</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>28</td>
+      <td>28</td>
     </tr>
     <tr>
       <td></td>
@@ -42486,8 +51598,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
-      <td>501</td>
+      <td>558</td>
+      <td>558</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>558</td>
+      <td>558</td>
+      <td>7</td>
+      <td>7</td>
     </tr>
     <tr>
       <td></td>
@@ -42516,10 +51642,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -42551,7 +51676,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
+      <td>65</td>
+      <td>65</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>37</td>
+      <td>37</td>
     </tr>
     <tr>
       <td></td>
@@ -42614,8 +51754,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>182</td>
-      <td>1889</td>
+      <td>2561</td>
+      <td>2561</td>
+      <td>325</td>
+      <td>325</td>
+      <td>2916</td>
+      <td>2916</td>
+      <td>460</td>
+      <td>460</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5477</td>
+      <td>5477</td>
+      <td>785</td>
+      <td>785</td>
     </tr>
     <tr>
       <td></td>
@@ -42644,8 +51798,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -42674,12 +51827,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1774</td>
-      <td>19910</td>
+      <td>22774</td>
+      <td>23146</td>
+      <td>4084</td>
+      <td>4155</td>
+      <td>33972</td>
+      <td>33972</td>
+      <td>5372</td>
+      <td>5372</td>
+      <td>4236</td>
+      <td>4236</td>
+      <td>846</td>
+      <td>846</td>
+      <td>60982</td>
+      <td>61354</td>
+      <td>10302</td>
+      <td>10373</td>
     </tr>
     <tr>
       <td></td>
@@ -42723,7 +51891,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -42738,12 +51905,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>6</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
-      <td>124</td>
-      <td>1135</td>
+      <td>1451</td>
+      <td>1451</td>
+      <td>288</td>
+      <td>288</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1451</td>
+      <td>1451</td>
+      <td>288</td>
+      <td>288</td>
     </tr>
     <tr>
       <td></td>
@@ -42772,8 +51954,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -42805,9 +51986,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>4990</td>
-      <td>95752</td>
+      <td>97434</td>
+      <td>109474</td>
+      <td>11355</td>
+      <td>12514</td>
+      <td>183905</td>
+      <td>246475</td>
+      <td>24951</td>
+      <td>31957</td>
+      <td>18551</td>
+      <td>20166</td>
+      <td>2647</td>
+      <td>2905</td>
+      <td>299890</td>
+      <td>376115</td>
+      <td>38953</td>
+      <td>47376</td>
     </tr>
     <tr>
       <td></td>
@@ -42836,8 +52032,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -42866,12 +52061,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>218</td>
-      <td>16064</td>
+      <td>14874</td>
+      <td>16927</td>
+      <td>533</td>
+      <td>837</td>
+      <td>18475</td>
+      <td>28854</td>
+      <td>1403</td>
+      <td>2568</td>
+      <td>3854</td>
+      <td>4271</td>
+      <td>141</td>
+      <td>163</td>
+      <td>37203</td>
+      <td>50052</td>
+      <td>2077</td>
+      <td>3568</td>
     </tr>
     <tr>
       <td></td>
@@ -42900,8 +52110,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -42931,11 +52140,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>963</td>
-      <td>49711</td>
+      <td>61376</td>
+      <td>61746</td>
+      <td>1847</td>
+      <td>1895</td>
+      <td>23164</td>
+      <td>28729</td>
+      <td>1140</td>
+      <td>1556</td>
+      <td>63034</td>
+      <td>63034</td>
+      <td>522</td>
+      <td>522</td>
+      <td>147574</td>
+      <td>153509</td>
+      <td>3509</td>
+      <td>3973</td>
     </tr>
     <tr>
       <td></td>
@@ -42964,11 +52188,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -42998,8 +52222,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>250</td>
-      <td>6264</td>
+      <td>7092</td>
+      <td>7663</td>
+      <td>606</td>
+      <td>652</td>
+      <td>14367</td>
+      <td>18624</td>
+      <td>1360</td>
+      <td>1916</td>
+      <td>1477</td>
+      <td>1640</td>
+      <td>69</td>
+      <td>84</td>
+      <td>22936</td>
+      <td>27927</td>
+      <td>2035</td>
+      <td>2652</td>
     </tr>
     <tr>
       <td></td>
@@ -43064,6 +52302,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -43108,7 +52360,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -43122,12 +52373,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>42</td>
-      <td>369</td>
+      <td>358</td>
+      <td>406</td>
+      <td>124</td>
+      <td>139</td>
+      <td>1361</td>
+      <td>1361</td>
+      <td>384</td>
+      <td>384</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1719</td>
+      <td>1767</td>
+      <td>508</td>
+      <td>523</td>
     </tr>
     <tr>
       <td></td>
@@ -43192,6 +52458,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -43256,6 +52536,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -43318,8 +52612,22 @@
       <td>5</td>
       <td>0</td>
       <td>0</td>
-      <td>39</td>
-      <td>6886</td>
+      <td>7358</td>
+      <td>7358</td>
+      <td>88</td>
+      <td>88</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7358</td>
+      <td>7358</td>
+      <td>88</td>
+      <td>88</td>
     </tr>
     <tr>
       <td></td>
@@ -43348,10 +52656,9 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -43378,12 +52685,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>46</td>
-      <td>646</td>
+      <td>916</td>
+      <td>916</td>
+      <td>113</td>
+      <td>113</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>916</td>
+      <td>916</td>
+      <td>113</td>
+      <td>113</td>
     </tr>
     <tr>
       <td></td>
@@ -43412,8 +52734,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -43442,12 +52763,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>126</td>
-      <td>3934</td>
+      <td>4413</td>
+      <td>4442</td>
+      <td>430</td>
+      <td>431</td>
+      <td>4403</td>
+      <td>4403</td>
+      <td>255</td>
+      <td>255</td>
+      <td>1816</td>
+      <td>1816</td>
+      <td>33</td>
+      <td>33</td>
+      <td>10632</td>
+      <td>10661</td>
+      <td>718</td>
+      <td>719</td>
     </tr>
     <tr>
       <td></td>
@@ -43510,8 +52846,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>52</td>
-      <td>382</td>
+      <td>276</td>
+      <td>406</td>
+      <td>133</td>
+      <td>163</td>
+      <td>1421</td>
+      <td>1421</td>
+      <td>547</td>
+      <td>547</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1697</td>
+      <td>1827</td>
+      <td>680</td>
+      <td>710</td>
     </tr>
     <tr>
       <td></td>
@@ -43540,8 +52890,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -43570,12 +52919,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>945</td>
-      <td>18117</td>
+      <td>19294</td>
+      <td>20905</td>
+      <td>2423</td>
+      <td>2618</td>
+      <td>48876</td>
+      <td>58723</td>
+      <td>6341</td>
+      <td>7527</td>
+      <td>8010</td>
+      <td>8705</td>
+      <td>846</td>
+      <td>892</td>
+      <td>76180</td>
+      <td>88333</td>
+      <td>9610</td>
+      <td>11037</td>
     </tr>
     <tr>
       <td></td>
@@ -43638,8 +53002,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>177</td>
-      <td>2524</td>
+      <td>2809</td>
+      <td>3060</td>
+      <td>371</td>
+      <td>402</td>
+      <td>5179</td>
+      <td>5179</td>
+      <td>759</td>
+      <td>759</td>
+      <td>1931</td>
+      <td>1931</td>
+      <td>226</td>
+      <td>226</td>
+      <td>9919</td>
+      <td>10170</td>
+      <td>1356</td>
+      <td>1387</td>
     </tr>
     <tr>
       <td></td>
@@ -43668,8 +53046,7 @@
       <td>107</td>
       <td>107</td>
       <td>107</td>
-      <td>107</td>
-      <td>107</td>
+      <td>0</td>
       <td>107</td>
       <td>107</td>
       <td>107</td>
@@ -43698,12 +53075,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>107</td>
       <td>107</td>
       <td>107</td>
       <td>0</td>
-      <td>1816</td>
-      <td>89530</td>
+      <td>143762</td>
+      <td>148864</td>
+      <td>4481</td>
+      <td>5039</td>
+      <td>151989</td>
+      <td>296028</td>
+      <td>13224</td>
+      <td>31140</td>
+      <td>24955</td>
+      <td>27001</td>
+      <td>2397</td>
+      <td>2705</td>
+      <td>320706</td>
+      <td>471893</td>
+      <td>20102</td>
+      <td>38884</td>
     </tr>
     <tr>
       <td></td>
@@ -43732,9 +53124,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -43762,12 +53153,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>366</td>
+      <td>366</td>
+      <td>41</td>
+      <td>41</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1302</td>
+      <td>1302</td>
       <td>14</td>
-      <td>208</td>
+      <td>14</td>
+      <td>1668</td>
+      <td>1668</td>
+      <td>55</td>
+      <td>55</td>
     </tr>
     <tr>
       <td></td>
@@ -43811,7 +53217,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>4</td>
       <td>0</td>
@@ -43827,11 +53232,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>126</td>
-      <td>2257</td>
+      <td>1989</td>
+      <td>2302</td>
+      <td>367</td>
+      <td>453</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1989</td>
+      <td>2302</td>
+      <td>367</td>
+      <td>453</td>
     </tr>
     <tr>
       <td></td>
@@ -43894,8 +53314,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>119</td>
-      <td>2653</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>171</td>
+      <td>171</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>171</td>
+      <td>171</td>
     </tr>
     <tr>
       <td></td>
@@ -43958,8 +53392,22 @@
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>20</td>
-      <td>736</td>
+      <td>880</td>
+      <td>880</td>
+      <td>80</td>
+      <td>80</td>
+      <td>221</td>
+      <td>221</td>
+      <td>37</td>
+      <td>37</td>
+      <td>49</td>
+      <td>49</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1150</td>
+      <td>1150</td>
+      <td>120</td>
+      <td>120</td>
     </tr>
     <tr>
       <td></td>
@@ -44024,6 +53472,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -44086,8 +53548,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>29</td>
-      <td>410</td>
+      <td>517</td>
+      <td>517</td>
+      <td>61</td>
+      <td>61</td>
+      <td>2995</td>
+      <td>2995</td>
+      <td>184</td>
+      <td>184</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3512</td>
+      <td>3512</td>
+      <td>245</td>
+      <td>245</td>
     </tr>
     <tr>
       <td></td>
@@ -44116,8 +53592,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -44146,12 +53621,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>59</td>
-      <td>988</td>
+      <td>1030</td>
+      <td>1072</td>
+      <td>185</td>
+      <td>188</td>
+      <td>1058</td>
+      <td>1058</td>
+      <td>189</td>
+      <td>189</td>
+      <td>922</td>
+      <td>922</td>
+      <td>35</td>
+      <td>35</td>
+      <td>3010</td>
+      <td>3052</td>
+      <td>409</td>
+      <td>412</td>
     </tr>
     <tr>
       <td></td>
@@ -44180,8 +53670,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -44210,12 +53699,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>200</td>
-      <td>5265</td>
+      <td>5396</td>
+      <td>5938</td>
+      <td>580</td>
+      <td>607</td>
+      <td>628</td>
+      <td>628</td>
+      <td>168</td>
+      <td>168</td>
+      <td>519</td>
+      <td>519</td>
+      <td>107</td>
+      <td>107</td>
+      <td>6543</td>
+      <td>7085</td>
+      <td>855</td>
+      <td>882</td>
     </tr>
     <tr>
       <td></td>
@@ -44258,7 +53762,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -44274,12 +53777,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>285</td>
-      <td>11846</td>
+      <td>9409</td>
+      <td>12735</td>
+      <td>813</td>
+      <td>923</td>
+      <td>20180</td>
+      <td>259099</td>
+      <td>2072</td>
+      <td>11791</td>
+      <td>168</td>
+      <td>611</td>
+      <td>20</td>
+      <td>63</td>
+      <td>29757</td>
+      <td>272445</td>
+      <td>2905</td>
+      <td>12777</td>
     </tr>
     <tr>
       <td></td>
@@ -44342,8 +53860,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>4298</td>
+      <td>4298</td>
+      <td>34</td>
+      <td>34</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4298</td>
+      <td>4298</td>
+      <td>34</td>
+      <td>34</td>
     </tr>
     <tr>
       <td></td>
@@ -44388,7 +53920,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -44402,12 +53933,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>52</td>
-      <td>459</td>
+      <td>601</td>
+      <td>601</td>
+      <td>128</td>
+      <td>128</td>
+      <td>1165</td>
+      <td>1165</td>
+      <td>232</td>
+      <td>232</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1766</td>
+      <td>1766</td>
+      <td>360</td>
+      <td>360</td>
     </tr>
     <tr>
       <td></td>
@@ -44436,8 +53982,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -44466,12 +54011,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>242</td>
-      <td>2644</td>
+      <td>3278</td>
+      <td>3361</td>
+      <td>460</td>
+      <td>478</td>
+      <td>6144</td>
+      <td>6144</td>
+      <td>595</td>
+      <td>595</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>183</td>
+      <td>183</td>
+      <td>10561</td>
+      <td>10644</td>
+      <td>1238</td>
+      <td>1256</td>
     </tr>
     <tr>
       <td></td>
@@ -44516,7 +54076,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -44536,6 +54095,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5191</td>
+      <td>5367</td>
+      <td>104</td>
+      <td>130</td>
+      <td>5191</td>
+      <td>5367</td>
+      <td>104</td>
+      <td>130</td>
     </tr>
     <tr>
       <td></td>
@@ -44564,8 +54138,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -44594,12 +54167,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>68</td>
-      <td>2912</td>
+      <td>5235</td>
+      <td>5486</td>
+      <td>237</td>
+      <td>288</td>
+      <td>4060</td>
+      <td>25609</td>
+      <td>480</td>
+      <td>2039</td>
+      <td>816</td>
+      <td>1093</td>
+      <td>73</td>
+      <td>89</td>
+      <td>10111</td>
+      <td>32188</td>
+      <td>790</td>
+      <td>2416</td>
     </tr>
     <tr>
       <td></td>
@@ -44628,8 +54216,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -44658,12 +54245,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>29</td>
-      <td>774</td>
+      <td>497</td>
+      <td>808</td>
+      <td>71</td>
+      <td>108</td>
+      <td>2249</td>
+      <td>5479</td>
+      <td>216</td>
+      <td>703</td>
+      <td>415</td>
+      <td>437</td>
+      <td>18</td>
+      <td>20</td>
+      <td>3161</td>
+      <td>6724</td>
+      <td>305</td>
+      <td>831</td>
     </tr>
     <tr>
       <td></td>
@@ -44726,8 +54328,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>15</td>
-      <td>160</td>
+      <td>164</td>
+      <td>179</td>
+      <td>42</td>
+      <td>47</td>
+      <td>758</td>
+      <td>905</td>
+      <td>128</td>
+      <td>170</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>922</td>
+      <td>1084</td>
+      <td>170</td>
+      <td>217</td>
     </tr>
     <tr>
       <td></td>
@@ -44756,8 +54372,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -44786,12 +54401,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1080</td>
-      <td>35336</td>
+      <td>43726</td>
+      <td>44512</td>
+      <td>3104</td>
+      <td>3259</td>
+      <td>19941</td>
+      <td>19941</td>
+      <td>3693</td>
+      <td>3693</td>
+      <td>16788</td>
+      <td>18589</td>
+      <td>2467</td>
+      <td>2650</td>
+      <td>80455</td>
+      <td>83042</td>
+      <td>9264</td>
+      <td>9602</td>
     </tr>
     <tr>
       <td></td>
@@ -44820,10 +54450,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -44850,12 +54479,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>250</td>
-      <td>3498</td>
+      <td>6685</td>
+      <td>6685</td>
+      <td>603</td>
+      <td>603</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6685</td>
+      <td>6685</td>
+      <td>603</td>
+      <td>603</td>
     </tr>
     <tr>
       <td></td>
@@ -44918,8 +54562,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>136</td>
+      <td>136</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>136</td>
+      <td>136</td>
+      <td>11</td>
+      <td>11</td>
     </tr>
     <tr>
       <td></td>
@@ -44948,8 +54606,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -44978,12 +54635,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>2803</td>
-      <td>1055760</td>
+      <td>1126086</td>
+      <td>1127111</td>
+      <td>6847</td>
+      <td>6909</td>
+      <td>422259</td>
+      <td>422259</td>
+      <td>10722</td>
+      <td>10722</td>
+      <td>76462</td>
+      <td>76462</td>
+      <td>2242</td>
+      <td>2242</td>
+      <td>1624807</td>
+      <td>1625832</td>
+      <td>19811</td>
+      <td>19873</td>
     </tr>
     <tr>
       <td></td>
@@ -44997,7 +54669,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation, Fasta Manipulation</td>
       <td>fastq_combiner</td>
@@ -45006,14 +54678,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45042,12 +54713,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>66</td>
-      <td>8676</td>
+      <td>8604</td>
+      <td>8799</td>
+      <td>215</td>
+      <td>240</td>
+      <td>54200</td>
+      <td>75329</td>
+      <td>919</td>
+      <td>2957</td>
+      <td>1562</td>
+      <td>1680</td>
+      <td>76</td>
+      <td>85</td>
+      <td>64366</td>
+      <td>85808</td>
+      <td>1210</td>
+      <td>3282</td>
     </tr>
     <tr>
       <td></td>
@@ -45061,7 +54747,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_filter</td>
@@ -45070,14 +54756,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45106,12 +54791,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>266</td>
-      <td>14222</td>
+      <td>15582</td>
+      <td>18350</td>
+      <td>690</td>
+      <td>771</td>
+      <td>40489</td>
+      <td>121585</td>
+      <td>2715</td>
+      <td>9239</td>
+      <td>4657</td>
+      <td>5793</td>
+      <td>214</td>
+      <td>287</td>
+      <td>60728</td>
+      <td>145728</td>
+      <td>3619</td>
+      <td>10297</td>
     </tr>
     <tr>
       <td></td>
@@ -45125,7 +54825,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_groomer</td>
@@ -45134,14 +54834,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45170,12 +54869,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1028</td>
-      <td>94802</td>
+      <td>92594</td>
+      <td>102535</td>
+      <td>2576</td>
+      <td>2995</td>
+      <td>179461</td>
+      <td>897457</td>
+      <td>9437</td>
+      <td>44701</td>
+      <td>15434</td>
+      <td>25533</td>
+      <td>664</td>
+      <td>1073</td>
+      <td>287489</td>
+      <td>1025525</td>
+      <td>12677</td>
+      <td>48769</td>
     </tr>
     <tr>
       <td></td>
@@ -45189,7 +54903,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_manipulation</td>
@@ -45198,14 +54912,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45234,12 +54947,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>69</td>
-      <td>2503</td>
+      <td>2488</td>
+      <td>3132</td>
+      <td>215</td>
+      <td>267</td>
+      <td>6241</td>
+      <td>14508</td>
+      <td>834</td>
+      <td>2121</td>
+      <td>4121</td>
+      <td>4592</td>
+      <td>131</td>
+      <td>158</td>
+      <td>12850</td>
+      <td>22232</td>
+      <td>1180</td>
+      <td>2546</td>
     </tr>
     <tr>
       <td></td>
@@ -45253,7 +54981,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_masker_by_quality</td>
@@ -45262,14 +54990,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45298,12 +55025,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>16</td>
-      <td>170</td>
+      <td>234</td>
+      <td>249</td>
+      <td>43</td>
+      <td>44</td>
+      <td>2648</td>
+      <td>8092</td>
+      <td>288</td>
+      <td>983</td>
+      <td>442</td>
+      <td>466</td>
+      <td>12</td>
+      <td>17</td>
+      <td>3324</td>
+      <td>8807</td>
+      <td>343</td>
+      <td>1044</td>
     </tr>
     <tr>
       <td></td>
@@ -45317,7 +55059,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_paired_end_deinterlacer</td>
@@ -45326,14 +55068,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45362,12 +55103,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>122</td>
-      <td>8410</td>
+      <td>5873</td>
+      <td>8936</td>
+      <td>532</td>
+      <td>657</td>
+      <td>14738</td>
+      <td>20229</td>
+      <td>1889</td>
+      <td>2366</td>
+      <td>2316</td>
+      <td>2711</td>
+      <td>225</td>
+      <td>261</td>
+      <td>22927</td>
+      <td>31876</td>
+      <td>2646</td>
+      <td>3284</td>
     </tr>
     <tr>
       <td></td>
@@ -45381,7 +55137,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_paired_end_interlacer</td>
@@ -45390,14 +55146,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45426,12 +55181,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1087</td>
-      <td>17024</td>
+      <td>18216</td>
+      <td>19573</td>
+      <td>2348</td>
+      <td>2492</td>
+      <td>23484</td>
+      <td>25936</td>
+      <td>3482</td>
+      <td>3851</td>
+      <td>6207</td>
+      <td>6551</td>
+      <td>1402</td>
+      <td>1442</td>
+      <td>47907</td>
+      <td>52060</td>
+      <td>7232</td>
+      <td>7785</td>
     </tr>
     <tr>
       <td></td>
@@ -45445,7 +55215,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_paired_end_joiner</td>
@@ -45454,14 +55224,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45490,12 +55259,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>245</td>
-      <td>16635</td>
+      <td>15628</td>
+      <td>17130</td>
+      <td>536</td>
+      <td>679</td>
+      <td>24157</td>
+      <td>58368</td>
+      <td>1954</td>
+      <td>5716</td>
+      <td>1941</td>
+      <td>2266</td>
+      <td>172</td>
+      <td>214</td>
+      <td>41726</td>
+      <td>77764</td>
+      <td>2662</td>
+      <td>6609</td>
     </tr>
     <tr>
       <td></td>
@@ -45509,7 +55293,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_paired_end_splitter</td>
@@ -45518,14 +55302,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45554,12 +55337,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>196</td>
-      <td>3092</td>
+      <td>3169</td>
+      <td>3521</td>
+      <td>459</td>
+      <td>535</td>
+      <td>19309</td>
+      <td>30747</td>
+      <td>1410</td>
+      <td>3441</td>
+      <td>807</td>
+      <td>1023</td>
+      <td>219</td>
+      <td>247</td>
+      <td>23285</td>
+      <td>35291</td>
+      <td>2088</td>
+      <td>4223</td>
     </tr>
     <tr>
       <td></td>
@@ -45588,8 +55386,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45618,12 +55415,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>1271</td>
+      <td>1393</td>
+      <td>131</td>
+      <td>176</td>
+      <td>12763</td>
+      <td>58819</td>
+      <td>2073</td>
+      <td>8850</td>
+      <td>430</td>
+      <td>479</td>
+      <td>32</td>
       <td>51</td>
-      <td>1178</td>
+      <td>14464</td>
+      <td>60691</td>
+      <td>2236</td>
+      <td>9077</td>
     </tr>
     <tr>
       <td></td>
@@ -45652,8 +55464,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45682,12 +55493,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>11</td>
-      <td>220</td>
+      <td>335</td>
+      <td>352</td>
+      <td>44</td>
+      <td>47</td>
+      <td>1583</td>
+      <td>9696</td>
+      <td>269</td>
+      <td>2229</td>
+      <td>1131</td>
+      <td>1254</td>
+      <td>15</td>
+      <td>27</td>
+      <td>3049</td>
+      <td>11302</td>
+      <td>328</td>
+      <td>2303</td>
     </tr>
     <tr>
       <td></td>
@@ -45716,8 +55542,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45746,12 +55571,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1509</td>
-      <td>15172</td>
+      <td>17279</td>
+      <td>18386</td>
+      <td>3826</td>
+      <td>4062</td>
+      <td>55268</td>
+      <td>136888</td>
+      <td>6055</td>
+      <td>12590</td>
+      <td>7685</td>
+      <td>9356</td>
+      <td>1854</td>
+      <td>2043</td>
+      <td>80232</td>
+      <td>164630</td>
+      <td>11735</td>
+      <td>18695</td>
     </tr>
     <tr>
       <td></td>
@@ -45765,7 +55605,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_stats</td>
@@ -45774,14 +55614,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45810,12 +55649,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>221</td>
-      <td>4246</td>
+      <td>3858</td>
+      <td>4595</td>
+      <td>680</td>
+      <td>815</td>
+      <td>15213</td>
+      <td>81513</td>
+      <td>3159</td>
+      <td>14109</td>
+      <td>3855</td>
+      <td>4163</td>
+      <td>184</td>
+      <td>256</td>
+      <td>22926</td>
+      <td>90271</td>
+      <td>4023</td>
+      <td>15180</td>
     </tr>
     <tr>
       <td></td>
@@ -45844,8 +55698,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45874,12 +55727,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>419</td>
-      <td>13599</td>
+      <td>36069</td>
+      <td>37805</td>
+      <td>1151</td>
+      <td>1234</td>
+      <td>45213</td>
+      <td>99852</td>
+      <td>2691</td>
+      <td>6370</td>
+      <td>8457</td>
+      <td>13335</td>
+      <td>408</td>
+      <td>609</td>
+      <td>89739</td>
+      <td>150992</td>
+      <td>4250</td>
+      <td>8213</td>
     </tr>
     <tr>
       <td></td>
@@ -45893,7 +55761,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_to_tabular</td>
@@ -45902,14 +55770,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -45938,12 +55805,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>93</td>
-      <td>12593</td>
+      <td>12895</td>
+      <td>14110</td>
+      <td>269</td>
+      <td>297</td>
+      <td>13315</td>
+      <td>30673</td>
+      <td>612</td>
+      <td>1810</td>
+      <td>5125</td>
+      <td>5373</td>
+      <td>64</td>
+      <td>87</td>
+      <td>31335</td>
+      <td>50156</td>
+      <td>945</td>
+      <td>2194</td>
     </tr>
     <tr>
       <td></td>
@@ -45957,7 +55839,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_trimmer</td>
@@ -45966,14 +55848,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46002,12 +55883,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>210</td>
-      <td>9757</td>
+      <td>10114</td>
+      <td>11383</td>
+      <td>582</td>
+      <td>665</td>
+      <td>23906</td>
+      <td>92351</td>
+      <td>1986</td>
+      <td>8818</td>
+      <td>1588</td>
+      <td>2607</td>
+      <td>108</td>
+      <td>212</td>
+      <td>35608</td>
+      <td>106341</td>
+      <td>2676</td>
+      <td>9695</td>
     </tr>
     <tr>
       <td></td>
@@ -46036,8 +55932,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46069,9 +55964,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>17447</td>
-      <td>1556625</td>
+      <td>1784056</td>
+      <td>1913280</td>
+      <td>41344</td>
+      <td>43940</td>
+      <td>2269843</td>
+      <td>3195869</td>
+      <td>90828</td>
+      <td>140008</td>
+      <td>410004</td>
+      <td>445555</td>
+      <td>14195</td>
+      <td>16026</td>
+      <td>4463903</td>
+      <td>5554704</td>
+      <td>146367</td>
+      <td>199974</td>
     </tr>
     <tr>
       <td></td>
@@ -46100,8 +56010,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46130,12 +56039,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1266</td>
-      <td>4333</td>
+      <td>5162</td>
+      <td>5162</td>
+      <td>2350</td>
+      <td>2350</td>
+      <td>10176</td>
+      <td>10176</td>
+      <td>4714</td>
+      <td>4714</td>
+      <td>2610</td>
+      <td>2610</td>
+      <td>991</td>
+      <td>991</td>
+      <td>17948</td>
+      <td>17948</td>
+      <td>8055</td>
+      <td>8055</td>
     </tr>
     <tr>
       <td></td>
@@ -46149,7 +56073,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastqtofasta</td>
@@ -46158,7 +56082,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -46180,7 +56104,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -46194,12 +56117,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1371</td>
-      <td>178178</td>
+      <td>208349</td>
+      <td>217568</td>
+      <td>3421</td>
+      <td>3732</td>
+      <td>131388</td>
+      <td>245005</td>
+      <td>5108</td>
+      <td>13227</td>
+      <td>18655</td>
+      <td>18655</td>
+      <td>679</td>
+      <td>679</td>
+      <td>358392</td>
+      <td>481228</td>
+      <td>9208</td>
+      <td>17638</td>
     </tr>
     <tr>
       <td></td>
@@ -46228,8 +56166,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46258,12 +56195,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>379</td>
-      <td>55434</td>
+      <td>65542</td>
+      <td>65631</td>
+      <td>1049</td>
+      <td>1071</td>
+      <td>25992</td>
+      <td>25992</td>
+      <td>2147</td>
+      <td>2147</td>
+      <td>6733</td>
+      <td>7339</td>
+      <td>649</td>
+      <td>745</td>
+      <td>98267</td>
+      <td>98962</td>
+      <td>3845</td>
+      <td>3963</td>
     </tr>
     <tr>
       <td></td>
@@ -46292,8 +56244,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46322,12 +56273,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>27</td>
-      <td>1810</td>
+      <td>1769</td>
+      <td>2020</td>
+      <td>88</td>
+      <td>101</td>
+      <td>6948</td>
+      <td>24960</td>
+      <td>358</td>
+      <td>2424</td>
+      <td>623</td>
+      <td>998</td>
+      <td>32</td>
+      <td>50</td>
+      <td>9340</td>
+      <td>27978</td>
+      <td>478</td>
+      <td>2575</td>
     </tr>
     <tr>
       <td></td>
@@ -46356,8 +56322,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46386,12 +56351,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>128</td>
-      <td>16591</td>
+      <td>16957</td>
+      <td>18124</td>
+      <td>225</td>
+      <td>260</td>
+      <td>37001</td>
+      <td>89126</td>
+      <td>919</td>
+      <td>2720</td>
+      <td>863</td>
+      <td>989</td>
+      <td>56</td>
+      <td>68</td>
+      <td>54821</td>
+      <td>108239</td>
+      <td>1200</td>
+      <td>3048</td>
     </tr>
     <tr>
       <td></td>
@@ -46420,8 +56400,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46450,12 +56429,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>96</td>
-      <td>3333</td>
+      <td>3140</td>
+      <td>3520</td>
+      <td>178</td>
+      <td>212</td>
+      <td>13975</td>
+      <td>117900</td>
+      <td>1198</td>
+      <td>6006</td>
+      <td>409</td>
+      <td>712</td>
+      <td>36</td>
+      <td>55</td>
+      <td>17524</td>
+      <td>122132</td>
+      <td>1412</td>
+      <td>6273</td>
     </tr>
     <tr>
       <td></td>
@@ -46484,8 +56478,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46514,12 +56507,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>114</td>
-      <td>61218</td>
+      <td>64187</td>
+      <td>67981</td>
+      <td>326</td>
+      <td>349</td>
+      <td>87477</td>
+      <td>185555</td>
+      <td>781</td>
+      <td>3067</td>
+      <td>16563</td>
+      <td>17125</td>
+      <td>58</td>
+      <td>78</td>
+      <td>168227</td>
+      <td>270661</td>
+      <td>1165</td>
+      <td>3494</td>
     </tr>
     <tr>
       <td></td>
@@ -46548,8 +56556,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46578,12 +56585,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>25</td>
-      <td>249</td>
+      <td>174</td>
+      <td>272</td>
+      <td>61</td>
+      <td>92</td>
+      <td>4295</td>
+      <td>25068</td>
+      <td>1056</td>
+      <td>4180</td>
+      <td>1127</td>
+      <td>1171</td>
+      <td>70</td>
+      <td>89</td>
+      <td>5596</td>
+      <td>26511</td>
+      <td>1187</td>
+      <td>4361</td>
     </tr>
     <tr>
       <td></td>
@@ -46612,8 +56634,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46642,12 +56663,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>63</td>
-      <td>2176</td>
+      <td>2218</td>
+      <td>2344</td>
+      <td>168</td>
+      <td>206</td>
+      <td>20551</td>
+      <td>60032</td>
+      <td>3784</td>
+      <td>9866</td>
+      <td>2347</td>
+      <td>2460</td>
+      <td>234</td>
+      <td>256</td>
+      <td>25116</td>
+      <td>64836</td>
+      <td>4186</td>
+      <td>10328</td>
     </tr>
     <tr>
       <td></td>
@@ -46676,8 +56712,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46706,12 +56741,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>68</td>
-      <td>2280</td>
+      <td>2364</td>
+      <td>2526</td>
+      <td>180</td>
+      <td>214</td>
+      <td>6572</td>
+      <td>11745</td>
+      <td>303</td>
+      <td>1024</td>
+      <td>462</td>
+      <td>696</td>
+      <td>49</td>
+      <td>64</td>
+      <td>9398</td>
+      <td>14967</td>
+      <td>532</td>
+      <td>1302</td>
     </tr>
     <tr>
       <td></td>
@@ -46740,8 +56790,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46770,12 +56819,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>156</td>
-      <td>10832</td>
+      <td>10707</td>
+      <td>12597</td>
+      <td>356</td>
+      <td>415</td>
+      <td>21568</td>
+      <td>67304</td>
+      <td>574</td>
+      <td>1527</td>
+      <td>719</td>
+      <td>861</td>
+      <td>61</td>
+      <td>78</td>
+      <td>32994</td>
+      <td>80762</td>
+      <td>991</td>
+      <td>2020</td>
     </tr>
     <tr>
       <td></td>
@@ -46804,8 +56868,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46834,12 +56897,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>205</td>
-      <td>13149</td>
+      <td>13584</td>
+      <td>14557</td>
+      <td>550</td>
+      <td>641</td>
+      <td>123676</td>
+      <td>206733</td>
+      <td>2034</td>
+      <td>8390</td>
+      <td>2819</td>
+      <td>4757</td>
+      <td>229</td>
+      <td>267</td>
+      <td>140079</td>
+      <td>226047</td>
+      <td>2813</td>
+      <td>9298</td>
     </tr>
     <tr>
       <td></td>
@@ -46902,8 +56980,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>22</td>
-      <td>285</td>
+      <td>385</td>
+      <td>385</td>
+      <td>46</td>
+      <td>46</td>
+      <td>587</td>
+      <td>587</td>
+      <td>107</td>
+      <td>107</td>
+      <td>58</td>
+      <td>58</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1030</td>
+      <td>1030</td>
+      <td>158</td>
+      <td>158</td>
     </tr>
     <tr>
       <td></td>
@@ -46932,8 +57024,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -46965,9 +57056,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>4679</td>
-      <td>696399</td>
+      <td>740719</td>
+      <td>770524</td>
+      <td>11699</td>
+      <td>12547</td>
+      <td>643892</td>
+      <td>784396</td>
+      <td>23272</td>
+      <td>27598</td>
+      <td>66108</td>
+      <td>68867</td>
+      <td>2348</td>
+      <td>2463</td>
+      <td>1450719</td>
+      <td>1623787</td>
+      <td>37319</td>
+      <td>42608</td>
     </tr>
     <tr>
       <td></td>
@@ -46996,8 +57102,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -47026,12 +57131,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>46</td>
-      <td>1191</td>
+      <td>1375</td>
+      <td>1500</td>
+      <td>95</td>
+      <td>99</td>
+      <td>797</td>
+      <td>797</td>
+      <td>116</td>
+      <td>116</td>
+      <td>59</td>
+      <td>59</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2231</td>
+      <td>2356</td>
+      <td>214</td>
+      <td>218</td>
     </tr>
     <tr>
       <td></td>
@@ -47096,6 +57216,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -47124,8 +57258,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -47154,12 +57287,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>307</td>
-      <td>5240</td>
+      <td>5618</td>
+      <td>5820</td>
+      <td>582</td>
+      <td>607</td>
+      <td>21673</td>
+      <td>21673</td>
+      <td>938</td>
+      <td>938</td>
+      <td>869</td>
+      <td>869</td>
+      <td>110</td>
+      <td>110</td>
+      <td>28160</td>
+      <td>28362</td>
+      <td>1630</td>
+      <td>1655</td>
     </tr>
     <tr>
       <td></td>
@@ -47188,8 +57336,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -47218,12 +57365,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>617</td>
-      <td>30483</td>
+      <td>53310</td>
+      <td>53944</td>
+      <td>1499</td>
+      <td>1575</td>
+      <td>25043</td>
+      <td>25043</td>
+      <td>726</td>
+      <td>726</td>
+      <td>10824</td>
+      <td>10824</td>
+      <td>593</td>
+      <td>593</td>
+      <td>89177</td>
+      <td>89811</td>
+      <td>2818</td>
+      <td>2894</td>
     </tr>
     <tr>
       <td></td>
@@ -47286,8 +57448,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>14</td>
-      <td>331</td>
+      <td>1985</td>
+      <td>1985</td>
+      <td>41</td>
+      <td>41</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1985</td>
+      <td>1985</td>
+      <td>41</td>
+      <td>41</td>
     </tr>
     <tr>
       <td></td>
@@ -47332,7 +57508,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -47346,12 +57521,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>74</td>
-      <td>13759</td>
+      <td>22017</td>
+      <td>22304</td>
+      <td>239</td>
+      <td>255</td>
+      <td>9399</td>
+      <td>14886</td>
+      <td>462</td>
+      <td>709</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>31420</td>
+      <td>37194</td>
+      <td>702</td>
+      <td>965</td>
     </tr>
     <tr>
       <td></td>
@@ -47380,9 +57570,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -47410,12 +57599,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>68</td>
-      <td>1102</td>
+      <td>1257</td>
+      <td>1450</td>
+      <td>150</td>
+      <td>162</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1052</td>
+      <td>1052</td>
+      <td>45</td>
+      <td>45</td>
+      <td>2309</td>
+      <td>2502</td>
+      <td>195</td>
+      <td>207</td>
     </tr>
     <tr>
       <td></td>
@@ -47444,8 +57648,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -47474,12 +57677,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>3059</td>
-      <td>155087</td>
+      <td>149715</td>
+      <td>171093</td>
+      <td>8158</td>
+      <td>8794</td>
+      <td>144708</td>
+      <td>256315</td>
+      <td>15996</td>
+      <td>25107</td>
+      <td>19156</td>
+      <td>21936</td>
+      <td>2251</td>
+      <td>2571</td>
+      <td>313579</td>
+      <td>449344</td>
+      <td>26405</td>
+      <td>36472</td>
     </tr>
     <tr>
       <td></td>
@@ -47542,8 +57760,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>44</td>
-      <td>665</td>
+      <td>748</td>
+      <td>748</td>
+      <td>91</td>
+      <td>91</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1</td>
+      <td>1</td>
+      <td>760</td>
+      <td>760</td>
+      <td>92</td>
+      <td>92</td>
     </tr>
     <tr>
       <td></td>
@@ -47588,7 +57820,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -47603,11 +57834,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>55</td>
-      <td>20021</td>
+      <td>21757</td>
+      <td>21757</td>
+      <td>101</td>
+      <td>101</td>
+      <td>217</td>
+      <td>217</td>
+      <td>21</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21974</td>
+      <td>21974</td>
+      <td>122</td>
+      <td>122</td>
     </tr>
     <tr>
       <td></td>
@@ -47672,6 +57918,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>578</td>
+      <td>578</td>
+      <td>34</td>
+      <td>34</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>578</td>
+      <td>578</td>
+      <td>34</td>
+      <td>34</td>
     </tr>
     <tr>
       <td></td>
@@ -47700,11 +57960,11 @@
       <td>3</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>3</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -47734,8 +57994,22 @@
       <td>5</td>
       <td>0</td>
       <td>0</td>
-      <td>900</td>
-      <td>5906</td>
+      <td>8648</td>
+      <td>8648</td>
+      <td>1408</td>
+      <td>1408</td>
+      <td>32</td>
+      <td>32</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6406</td>
+      <td>6406</td>
+      <td>597</td>
+      <td>597</td>
+      <td>15086</td>
+      <td>15086</td>
+      <td>2011</td>
+      <td>2011</td>
     </tr>
     <tr>
       <td></td>
@@ -47779,7 +58053,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -47794,12 +58067,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>181</td>
-      <td>2483</td>
+      <td>3463</td>
+      <td>3463</td>
+      <td>452</td>
+      <td>452</td>
+      <td>9040</td>
+      <td>9040</td>
+      <td>1639</td>
+      <td>1639</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12503</td>
+      <td>12503</td>
+      <td>2091</td>
+      <td>2091</td>
     </tr>
     <tr>
       <td></td>
@@ -47844,7 +58132,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -47858,12 +58145,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -47908,7 +58210,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -47922,12 +58223,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>112</td>
-      <td>519</td>
+      <td>723</td>
+      <td>723</td>
+      <td>235</td>
+      <td>235</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>786</td>
+      <td>786</td>
+      <td>95</td>
+      <td>95</td>
+      <td>1509</td>
+      <td>1509</td>
+      <td>330</td>
+      <td>330</td>
     </tr>
     <tr>
       <td></td>
@@ -47956,11 +58272,11 @@
       <td>1</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>1</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -47990,8 +58306,22 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>662</td>
-      <td>4916</td>
+      <td>4967</td>
+      <td>5475</td>
+      <td>1863</td>
+      <td>1992</td>
+      <td>992</td>
+      <td>1118</td>
+      <td>279</td>
+      <td>370</td>
+      <td>3756</td>
+      <td>3811</td>
+      <td>423</td>
+      <td>425</td>
+      <td>9715</td>
+      <td>10404</td>
+      <td>2565</td>
+      <td>2787</td>
     </tr>
     <tr>
       <td></td>
@@ -48020,12 +58350,12 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -48033,7 +58363,6 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -48053,9 +58382,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>4</td>
+      <td>4</td>
+      <td>2</td>
+      <td>2</td>
+      <td>221</td>
+      <td>2905</td>
+      <td>23</td>
+      <td>279</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>225</td>
+      <td>2909</td>
+      <td>25</td>
+      <td>281</td>
     </tr>
     <tr>
       <td></td>
@@ -48120,6 +58464,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -48182,8 +58540,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
-      <td>67</td>
+      <td>101</td>
+      <td>101</td>
+      <td>25</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59</td>
+      <td>59</td>
+      <td>6</td>
+      <td>6</td>
+      <td>160</td>
+      <td>160</td>
+      <td>31</td>
+      <td>31</td>
     </tr>
     <tr>
       <td></td>
@@ -48248,6 +58620,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>445</td>
+      <td>660</td>
+      <td>104</td>
+      <td>197</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>445</td>
+      <td>660</td>
+      <td>104</td>
+      <td>197</td>
     </tr>
     <tr>
       <td></td>
@@ -48276,8 +58662,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -48307,11 +58692,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>329</td>
-      <td>2118</td>
+      <td>3181</td>
+      <td>3181</td>
+      <td>665</td>
+      <td>665</td>
+      <td>2112</td>
+      <td>2112</td>
+      <td>435</td>
+      <td>435</td>
+      <td>1622</td>
+      <td>1622</td>
+      <td>148</td>
+      <td>148</td>
+      <td>6915</td>
+      <td>6915</td>
+      <td>1248</td>
+      <td>1248</td>
     </tr>
     <tr>
       <td></td>
@@ -48374,8 +58774,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>11</td>
-      <td>46</td>
+      <td>47</td>
+      <td>47</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>47</td>
+      <td>47</td>
+      <td>13</td>
+      <td>13</td>
     </tr>
     <tr>
       <td></td>
@@ -48438,8 +58852,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>79</td>
-      <td>3515</td>
+      <td>3534</td>
+      <td>3577</td>
+      <td>402</td>
+      <td>405</td>
+      <td>2840</td>
+      <td>2840</td>
+      <td>419</td>
+      <td>419</td>
+      <td>571</td>
+      <td>571</td>
+      <td>31</td>
+      <td>31</td>
+      <td>6945</td>
+      <td>6988</td>
+      <td>852</td>
+      <td>855</td>
     </tr>
     <tr>
       <td></td>
@@ -48502,8 +58930,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>4</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -48566,8 +59008,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>18</td>
-      <td>495</td>
+      <td>1542</td>
+      <td>1542</td>
+      <td>159</td>
+      <td>159</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>587</td>
+      <td>587</td>
+      <td>64</td>
+      <td>64</td>
+      <td>2129</td>
+      <td>2129</td>
+      <td>223</td>
+      <td>223</td>
     </tr>
     <tr>
       <td></td>
@@ -48596,8 +59052,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -48626,12 +59081,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>332</td>
-      <td>8274</td>
+      <td>9664</td>
+      <td>9775</td>
+      <td>763</td>
+      <td>765</td>
+      <td>5623</td>
+      <td>5623</td>
+      <td>493</td>
+      <td>493</td>
+      <td>1000</td>
+      <td>1000</td>
+      <td>135</td>
+      <td>135</td>
+      <td>16287</td>
+      <td>16398</td>
+      <td>1391</td>
+      <td>1393</td>
     </tr>
     <tr>
       <td></td>
@@ -48660,11 +59130,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -48694,8 +59164,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>806</td>
+      <td>812</td>
+      <td>68</td>
+      <td>68</td>
+      <td>197</td>
+      <td>197</td>
+      <td>37</td>
+      <td>37</td>
+      <td>132</td>
+      <td>132</td>
       <td>12</td>
-      <td>135</td>
+      <td>12</td>
+      <td>1135</td>
+      <td>1141</td>
+      <td>117</td>
+      <td>117</td>
     </tr>
     <tr>
       <td></td>
@@ -48724,8 +59208,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -48754,12 +59237,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>381</td>
-      <td>3477</td>
+      <td>3560</td>
+      <td>3980</td>
+      <td>916</td>
+      <td>999</td>
+      <td>5281</td>
+      <td>8000</td>
+      <td>1713</td>
+      <td>2521</td>
+      <td>1468</td>
+      <td>1642</td>
+      <td>208</td>
+      <td>225</td>
+      <td>10309</td>
+      <td>13622</td>
+      <td>2837</td>
+      <td>3745</td>
     </tr>
     <tr>
       <td></td>
@@ -48788,8 +59286,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -48818,12 +59315,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>680</td>
-      <td>10995</td>
+      <td>12828</td>
+      <td>13716</td>
+      <td>1740</td>
+      <td>1829</td>
+      <td>15217</td>
+      <td>23818</td>
+      <td>2588</td>
+      <td>3486</td>
+      <td>4423</td>
+      <td>4423</td>
+      <td>732</td>
+      <td>732</td>
+      <td>32468</td>
+      <td>41957</td>
+      <td>5060</td>
+      <td>6047</td>
     </tr>
     <tr>
       <td></td>
@@ -48852,8 +59364,7 @@
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
@@ -48882,12 +59393,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>1388</td>
-      <td>22148</td>
+      <td>24606</td>
+      <td>25662</td>
+      <td>3463</td>
+      <td>3630</td>
+      <td>26805</td>
+      <td>26808</td>
+      <td>5143</td>
+      <td>5144</td>
+      <td>8174</td>
+      <td>8237</td>
+      <td>1259</td>
+      <td>1279</td>
+      <td>59585</td>
+      <td>60707</td>
+      <td>9865</td>
+      <td>10053</td>
     </tr>
     <tr>
       <td></td>
@@ -48952,6 +59478,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -49014,8 +59554,22 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>187</td>
-      <td>3965</td>
+      <td>4343</td>
+      <td>4343</td>
+      <td>407</td>
+      <td>407</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4343</td>
+      <td>4343</td>
+      <td>407</td>
+      <td>407</td>
     </tr>
     <tr>
       <td></td>
@@ -49044,8 +59598,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -49074,12 +59627,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>408</td>
-      <td>5484</td>
+      <td>5800</td>
+      <td>6212</td>
+      <td>826</td>
+      <td>871</td>
+      <td>7756</td>
+      <td>7756</td>
+      <td>1048</td>
+      <td>1048</td>
+      <td>1149</td>
+      <td>1149</td>
+      <td>215</td>
+      <td>215</td>
+      <td>14705</td>
+      <td>15117</td>
+      <td>2089</td>
+      <td>2134</td>
     </tr>
     <tr>
       <td></td>
@@ -49108,8 +59676,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -49138,12 +59705,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1210</td>
-      <td>19167</td>
+      <td>20207</td>
+      <td>21960</td>
+      <td>2807</td>
+      <td>3139</td>
+      <td>24488</td>
+      <td>26198</td>
+      <td>3066</td>
+      <td>3321</td>
+      <td>4155</td>
+      <td>4155</td>
+      <td>545</td>
+      <td>545</td>
+      <td>48850</td>
+      <td>52313</td>
+      <td>6418</td>
+      <td>7005</td>
     </tr>
     <tr>
       <td></td>
@@ -49206,8 +59788,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>196</td>
-      <td>3443</td>
+      <td>4001</td>
+      <td>4001</td>
+      <td>614</td>
+      <td>614</td>
+      <td>7882</td>
+      <td>7882</td>
+      <td>1238</td>
+      <td>1238</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11883</td>
+      <td>11883</td>
+      <td>1852</td>
+      <td>1852</td>
     </tr>
     <tr>
       <td></td>
@@ -49270,8 +59866,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
-      <td>63</td>
+      <td>78</td>
+      <td>78</td>
+      <td>6</td>
+      <td>6</td>
+      <td>120</td>
+      <td>120</td>
+      <td>43</td>
+      <td>43</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>198</td>
+      <td>198</td>
+      <td>49</td>
+      <td>49</td>
     </tr>
     <tr>
       <td></td>
@@ -49300,8 +59910,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -49330,12 +59939,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>432</td>
-      <td>9277</td>
+      <td>9816</td>
+      <td>10927</td>
+      <td>1285</td>
+      <td>1350</td>
+      <td>1273</td>
+      <td>1273</td>
+      <td>368</td>
+      <td>368</td>
+      <td>1104</td>
+      <td>1104</td>
+      <td>242</td>
+      <td>242</td>
+      <td>12193</td>
+      <td>13304</td>
+      <td>1895</td>
+      <td>1960</td>
     </tr>
     <tr>
       <td></td>
@@ -49400,6 +60024,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -49428,9 +60066,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -49463,7 +60100,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>476</td>
+      <td>476</td>
+      <td>87</td>
+      <td>87</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>588</td>
+      <td>588</td>
+      <td>74</td>
+      <td>74</td>
+      <td>1064</td>
+      <td>1064</td>
+      <td>161</td>
+      <td>161</td>
     </tr>
     <tr>
       <td></td>
@@ -49492,8 +60144,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -49522,12 +60173,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1200</td>
-      <td>8107</td>
+      <td>8329</td>
+      <td>9363</td>
+      <td>3336</td>
+      <td>3828</td>
+      <td>8009</td>
+      <td>8009</td>
+      <td>3130</td>
+      <td>3130</td>
+      <td>1577</td>
+      <td>1577</td>
+      <td>344</td>
+      <td>344</td>
+      <td>17915</td>
+      <td>18949</td>
+      <td>6810</td>
+      <td>7302</td>
     </tr>
     <tr>
       <td></td>
@@ -49572,7 +60238,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -49586,12 +60251,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>145</td>
-      <td>3340</td>
+      <td>3690</td>
+      <td>3811</td>
+      <td>326</td>
+      <td>336</td>
+      <td>3323</td>
+      <td>3323</td>
+      <td>235</td>
+      <td>235</td>
+      <td>1895</td>
+      <td>2429</td>
+      <td>234</td>
+      <td>258</td>
+      <td>8908</td>
+      <td>9563</td>
+      <td>795</td>
+      <td>829</td>
     </tr>
     <tr>
       <td></td>
@@ -49656,6 +60336,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -49720,6 +60414,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -49748,10 +60456,9 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -49779,11 +60486,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>117</td>
-      <td>4459</td>
+      <td>7303</td>
+      <td>7303</td>
+      <td>222</td>
+      <td>222</td>
+      <td>20</td>
+      <td>20</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7323</td>
+      <td>7323</td>
+      <td>224</td>
+      <td>224</td>
     </tr>
     <tr>
       <td></td>
@@ -49846,8 +60568,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>18</td>
-      <td>339</td>
+      <td>349</td>
+      <td>359</td>
+      <td>32</td>
+      <td>33</td>
+      <td>364</td>
+      <td>364</td>
+      <td>53</td>
+      <td>53</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>713</td>
+      <td>723</td>
+      <td>85</td>
+      <td>86</td>
     </tr>
     <tr>
       <td></td>
@@ -49912,6 +60648,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>103</td>
+      <td>103</td>
+      <td>4</td>
+      <td>4</td>
+      <td>103</td>
+      <td>103</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -49940,10 +60690,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -49971,11 +60720,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>36</td>
-      <td>295</td>
+      <td>502</td>
+      <td>502</td>
+      <td>66</td>
+      <td>66</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>502</td>
+      <td>502</td>
+      <td>66</td>
+      <td>66</td>
     </tr>
     <tr>
       <td></td>
@@ -50040,6 +60804,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -50068,8 +60846,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -50101,9 +60878,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>1953</td>
-      <td>44240</td>
+      <td>46700</td>
+      <td>50808</td>
+      <td>4645</td>
+      <td>5114</td>
+      <td>64214</td>
+      <td>70429</td>
+      <td>5799</td>
+      <td>6830</td>
+      <td>7783</td>
+      <td>7912</td>
+      <td>704</td>
+      <td>724</td>
+      <td>118697</td>
+      <td>129149</td>
+      <td>11148</td>
+      <td>12668</td>
     </tr>
     <tr>
       <td></td>
@@ -50111,7 +60903,7 @@
       <td>heinz_bum, heinz, heinz_scoring, heinz_visualization</td>
       <td>An algorithm for identification of the optimal scoring subnetwork.</td>
       <td>heinz</td>
-      <td>heinz, bionet</td>
+      <td>bionet, heinz</td>
       <td></td>
       <td>Heinz</td>
       <td>Tool for single-species active module discovery.</td>
@@ -50166,8 +60958,22 @@
       <td>4</td>
       <td>4</td>
       <td>0</td>
-      <td>242</td>
-      <td>1186</td>
+      <td>1281</td>
+      <td>1434</td>
+      <td>367</td>
+      <td>442</td>
+      <td>1559</td>
+      <td>1559</td>
+      <td>636</td>
+      <td>636</td>
+      <td>678</td>
+      <td>678</td>
+      <td>52</td>
+      <td>52</td>
+      <td>3518</td>
+      <td>3671</td>
+      <td>1055</td>
+      <td>1130</td>
     </tr>
     <tr>
       <td></td>
@@ -50230,8 +61036,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>6346</td>
+      <td>6346</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>6346</td>
+      <td>6346</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -50260,11 +61080,10 @@
       <td>38</td>
       <td>38</td>
       <td>38</td>
-      <td>4</td>
+      <td>0</td>
       <td>38</td>
       <td>38</td>
       <td>38</td>
-      <td>4</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -50290,12 +61109,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>33</td>
       <td>36</td>
       <td>33</td>
       <td>0</td>
-      <td>1085</td>
-      <td>66003</td>
+      <td>44449</td>
+      <td>68602</td>
+      <td>3236</td>
+      <td>4177</td>
+      <td>46</td>
+      <td>46</td>
+      <td>21</td>
+      <td>21</td>
+      <td>1328</td>
+      <td>1328</td>
+      <td>67</td>
+      <td>67</td>
+      <td>45823</td>
+      <td>69976</td>
+      <td>3324</td>
+      <td>4265</td>
     </tr>
     <tr>
       <td></td>
@@ -50360,6 +61194,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -50388,8 +61236,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -50419,11 +61266,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>297</td>
-      <td>1410</td>
+      <td>1819</td>
+      <td>1819</td>
+      <td>539</td>
+      <td>539</td>
+      <td>1334</td>
+      <td>1334</td>
+      <td>389</td>
+      <td>389</td>
+      <td>2472</td>
+      <td>2472</td>
+      <td>137</td>
+      <td>137</td>
+      <td>5625</td>
+      <td>5625</td>
+      <td>1065</td>
+      <td>1065</td>
     </tr>
     <tr>
       <td></td>
@@ -50486,8 +61348,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>12</td>
-      <td>137</td>
+      <td>156</td>
+      <td>156</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>220</td>
+      <td>220</td>
+      <td>11</td>
+      <td>11</td>
+      <td>376</td>
+      <td>376</td>
+      <td>31</td>
+      <td>31</td>
     </tr>
     <tr>
       <td></td>
@@ -50516,8 +61392,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -50546,12 +61421,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>4183</td>
-      <td>299104</td>
+      <td>337151</td>
+      <td>353499</td>
+      <td>10046</td>
+      <td>10719</td>
+      <td>699868</td>
+      <td>896164</td>
+      <td>26656</td>
+      <td>34018</td>
+      <td>87016</td>
+      <td>94859</td>
+      <td>5302</td>
+      <td>5695</td>
+      <td>1124035</td>
+      <td>1344522</td>
+      <td>42004</td>
+      <td>50432</td>
     </tr>
     <tr>
       <td></td>
@@ -50616,6 +61506,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -50644,9 +61548,8 @@
       <td>0</td>
       <td>12</td>
       <td>12</td>
-      <td>12</td>
       <td>0</td>
-      <td>12</td>
+      <td>0</td>
       <td>12</td>
       <td>12</td>
       <td>0</td>
@@ -50674,12 +61577,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>12</td>
       <td>12</td>
       <td>12</td>
       <td>0</td>
-      <td>439</td>
-      <td>33702</td>
+      <td>35919</td>
+      <td>36952</td>
+      <td>1283</td>
+      <td>1321</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3023</td>
+      <td>3023</td>
+      <td>180</td>
+      <td>180</td>
+      <td>38942</td>
+      <td>39975</td>
+      <td>1463</td>
+      <td>1501</td>
     </tr>
     <tr>
       <td></td>
@@ -50708,11 +61626,10 @@
       <td>0</td>
       <td>0</td>
       <td>5</td>
-      <td>4</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>5</td>
-      <td>4</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -50739,11 +61656,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
-      <td>394</td>
-      <td>6937</td>
+      <td>8531</td>
+      <td>8531</td>
+      <td>633</td>
+      <td>633</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8531</td>
+      <td>8531</td>
+      <td>633</td>
+      <td>633</td>
     </tr>
     <tr>
       <td></td>
@@ -50772,8 +61704,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -50802,12 +61733,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1419</td>
-      <td>154533</td>
+      <td>144907</td>
+      <td>168824</td>
+      <td>3703</td>
+      <td>4366</td>
+      <td>213407</td>
+      <td>346792</td>
+      <td>10798</td>
+      <td>16485</td>
+      <td>27209</td>
+      <td>33124</td>
+      <td>2613</td>
+      <td>2854</td>
+      <td>385523</td>
+      <td>548740</td>
+      <td>17114</td>
+      <td>23705</td>
     </tr>
     <tr>
       <td></td>
@@ -50836,11 +61782,10 @@
       <td>6</td>
       <td>10</td>
       <td>10</td>
-      <td>10</td>
+      <td>0</td>
       <td>6</td>
       <td>10</td>
       <td>10</td>
-      <td>10</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -50866,12 +61811,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
-      <td>1037</td>
-      <td>19490</td>
+      <td>26659</td>
+      <td>26659</td>
+      <td>2067</td>
+      <td>2067</td>
+      <td>865</td>
+      <td>865</td>
+      <td>174</td>
+      <td>174</td>
+      <td>3238</td>
+      <td>3238</td>
+      <td>351</td>
+      <td>351</td>
+      <td>30762</td>
+      <td>30762</td>
+      <td>2592</td>
+      <td>2592</td>
     </tr>
     <tr>
       <td></td>
@@ -50934,8 +61894,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1571</td>
+      <td>1571</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>144</td>
+      <td>144</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1715</td>
+      <td>1715</td>
+      <td>7</td>
+      <td>7</td>
     </tr>
     <tr>
       <td></td>
@@ -50964,11 +61938,10 @@
       <td>17</td>
       <td>2</td>
       <td>17</td>
-      <td>2</td>
+      <td>0</td>
       <td>17</td>
       <td>2</td>
       <td>17</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -50994,12 +61967,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>12</td>
       <td>17</td>
       <td>12</td>
       <td>0</td>
-      <td>161</td>
-      <td>10370</td>
+      <td>11429</td>
+      <td>11429</td>
+      <td>428</td>
+      <td>428</td>
+      <td>7751</td>
+      <td>7751</td>
+      <td>676</td>
+      <td>676</td>
+      <td>715</td>
+      <td>715</td>
+      <td>58</td>
+      <td>58</td>
+      <td>19895</td>
+      <td>19895</td>
+      <td>1162</td>
+      <td>1162</td>
     </tr>
     <tr>
       <td></td>
@@ -51062,8 +62050,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>39</td>
-      <td>354</td>
+      <td>473</td>
+      <td>473</td>
+      <td>93</td>
+      <td>93</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>473</td>
+      <td>93</td>
+      <td>93</td>
     </tr>
     <tr>
       <td></td>
@@ -51108,7 +62110,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -51128,6 +62129,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -51156,10 +62172,9 @@
       <td>3</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
       <td>0</td>
       <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -51186,12 +62201,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>69</td>
-      <td>1127</td>
+      <td>1200</td>
+      <td>1220</td>
+      <td>187</td>
+      <td>195</td>
+      <td>1588</td>
+      <td>1588</td>
+      <td>267</td>
+      <td>267</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2788</td>
+      <td>2808</td>
+      <td>454</td>
+      <td>462</td>
     </tr>
     <tr>
       <td></td>
@@ -51243,19 +62273,33 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>30</td>
-      <td>2873</td>
+      <td>2953</td>
+      <td>3027</td>
+      <td>109</td>
+      <td>114</td>
+      <td>1710</td>
+      <td>1710</td>
+      <td>199</td>
+      <td>199</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4663</td>
+      <td>4737</td>
+      <td>308</td>
+      <td>313</td>
     </tr>
     <tr>
       <td></td>
@@ -51284,11 +62328,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -51318,8 +62362,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>10</td>
-      <td>361</td>
+      <td>404</td>
+      <td>404</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>24</td>
+      <td>1</td>
+      <td>1</td>
+      <td>428</td>
+      <td>428</td>
+      <td>38</td>
+      <td>38</td>
     </tr>
     <tr>
       <td></td>
@@ -51382,8 +62440,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>12</td>
-      <td>1506</td>
+      <td>1539</td>
+      <td>1539</td>
+      <td>35</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1539</td>
+      <td>1539</td>
+      <td>35</td>
+      <td>35</td>
     </tr>
     <tr>
       <td></td>
@@ -51446,8 +62518,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -51510,8 +62596,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
-      <td>94</td>
+      <td>102</td>
+      <td>102</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>102</td>
+      <td>102</td>
+      <td>16</td>
+      <td>16</td>
     </tr>
     <tr>
       <td></td>
@@ -51540,8 +62640,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -51571,11 +62670,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>58</td>
-      <td>52965</td>
+      <td>55149</td>
+      <td>55149</td>
+      <td>161</td>
+      <td>161</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6085</td>
+      <td>6085</td>
+      <td>73</td>
+      <td>73</td>
+      <td>61234</td>
+      <td>61234</td>
+      <td>234</td>
+      <td>234</td>
     </tr>
     <tr>
       <td></td>
@@ -51638,8 +62752,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>37</td>
+      <td>46</td>
+      <td>6</td>
+      <td>12</td>
+      <td>72</td>
+      <td>87</td>
+      <td>13</td>
+      <td>15</td>
+      <td>108</td>
+      <td>108</td>
       <td>1</td>
-      <td>44</td>
+      <td>1</td>
+      <td>217</td>
+      <td>241</td>
+      <td>20</td>
+      <td>28</td>
     </tr>
     <tr>
       <td></td>
@@ -51668,8 +62796,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -51698,12 +62825,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>677</td>
-      <td>35243</td>
+      <td>34689</td>
+      <td>55189</td>
+      <td>1634</td>
+      <td>1713</td>
+      <td>65</td>
+      <td>65</td>
+      <td>15</td>
+      <td>15</td>
+      <td>10897</td>
+      <td>10897</td>
+      <td>607</td>
+      <td>607</td>
+      <td>45651</td>
+      <td>66151</td>
+      <td>2256</td>
+      <td>2335</td>
     </tr>
     <tr>
       <td></td>
@@ -51732,14 +62874,13 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -51765,9 +62906,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>5</td>
-      <td>105</td>
+      <td>32</td>
+      <td>107</td>
+      <td>7</td>
+      <td>10</td>
+      <td>758</td>
+      <td>19538</td>
+      <td>87</td>
+      <td>1246</td>
+      <td>16</td>
+      <td>24</td>
+      <td>2</td>
+      <td>2</td>
+      <td>806</td>
+      <td>19669</td>
+      <td>96</td>
+      <td>1258</td>
     </tr>
     <tr>
       <td></td>
@@ -51830,8 +62986,22 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>136</td>
-      <td>1497</td>
+      <td>1557</td>
+      <td>1607</td>
+      <td>278</td>
+      <td>292</td>
+      <td>4458</td>
+      <td>4458</td>
+      <td>458</td>
+      <td>458</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6015</td>
+      <td>6065</td>
+      <td>736</td>
+      <td>750</td>
     </tr>
     <tr>
       <td></td>
@@ -51874,7 +63044,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -51890,12 +63059,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>681</td>
-      <td>21598</td>
+      <td>28279</td>
+      <td>28481</td>
+      <td>1623</td>
+      <td>1646</td>
+      <td>24662</td>
+      <td>24662</td>
+      <td>2093</td>
+      <td>2093</td>
+      <td>9780</td>
+      <td>10086</td>
+      <td>979</td>
+      <td>992</td>
+      <td>62721</td>
+      <td>63229</td>
+      <td>4695</td>
+      <td>4731</td>
     </tr>
     <tr>
       <td></td>
@@ -51958,8 +63142,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>4</td>
       <td>29</td>
+      <td>29</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>8</td>
+      <td>8</td>
     </tr>
     <tr>
       <td></td>
@@ -51988,8 +63186,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -52019,11 +63216,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>50</td>
-      <td>57581</td>
+      <td>59386</td>
+      <td>59386</td>
+      <td>151</td>
+      <td>151</td>
+      <td>56</td>
+      <td>56</td>
+      <td>1</td>
+      <td>1</td>
+      <td>4741</td>
+      <td>4741</td>
+      <td>59</td>
+      <td>59</td>
+      <td>64183</td>
+      <td>64183</td>
+      <td>211</td>
+      <td>211</td>
     </tr>
     <tr>
       <td></td>
@@ -52052,8 +63264,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -52083,11 +63294,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>29</td>
-      <td>822</td>
+      <td>1301</td>
+      <td>1301</td>
+      <td>59</td>
+      <td>59</td>
+      <td>1331</td>
+      <td>1331</td>
+      <td>60</td>
+      <td>60</td>
+      <td>507</td>
+      <td>507</td>
+      <td>9</td>
+      <td>9</td>
+      <td>3139</td>
+      <td>3139</td>
+      <td>128</td>
+      <td>128</td>
     </tr>
     <tr>
       <td></td>
@@ -52116,8 +63342,7 @@
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
@@ -52146,12 +63371,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>1171</td>
-      <td>1224275</td>
+      <td>1252220</td>
+      <td>1252220</td>
+      <td>2366</td>
+      <td>2366</td>
+      <td>126027</td>
+      <td>126027</td>
+      <td>2496</td>
+      <td>2496</td>
+      <td>41901</td>
+      <td>41901</td>
+      <td>993</td>
+      <td>993</td>
+      <td>1420148</td>
+      <td>1420148</td>
+      <td>5855</td>
+      <td>5855</td>
     </tr>
     <tr>
       <td></td>
@@ -52214,8 +63454,22 @@
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>3</td>
-      <td>542</td>
+      <td>675</td>
+      <td>690</td>
+      <td>27</td>
+      <td>28</td>
+      <td>159</td>
+      <td>251</td>
+      <td>29</td>
+      <td>49</td>
+      <td>383</td>
+      <td>383</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1217</td>
+      <td>1324</td>
+      <td>68</td>
+      <td>89</td>
     </tr>
     <tr>
       <td></td>
@@ -52278,8 +63532,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3</td>
-      <td>30</td>
+      <td>32</td>
+      <td>32</td>
+      <td>9</td>
+      <td>9</td>
+      <td>53</td>
+      <td>53</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>85</td>
+      <td>85</td>
+      <td>28</td>
+      <td>28</td>
     </tr>
     <tr>
       <td></td>
@@ -52308,8 +63576,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -52338,12 +63605,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>2346</td>
-      <td>18229</td>
+      <td>21153</td>
+      <td>22174</td>
+      <td>5514</td>
+      <td>5779</td>
+      <td>17428</td>
+      <td>17428</td>
+      <td>6458</td>
+      <td>6458</td>
+      <td>15673</td>
+      <td>17267</td>
+      <td>3248</td>
+      <td>3786</td>
+      <td>54254</td>
+      <td>56869</td>
+      <td>15220</td>
+      <td>16023</td>
     </tr>
     <tr>
       <td></td>
@@ -52372,8 +63654,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -52402,12 +63683,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>255</td>
-      <td>2469</td>
+      <td>2747</td>
+      <td>2926</td>
+      <td>596</td>
+      <td>637</td>
+      <td>2311</td>
+      <td>2311</td>
+      <td>741</td>
+      <td>741</td>
+      <td>1145</td>
+      <td>1145</td>
+      <td>469</td>
+      <td>469</td>
+      <td>6203</td>
+      <td>6382</td>
+      <td>1806</td>
+      <td>1847</td>
     </tr>
     <tr>
       <td></td>
@@ -52436,9 +63732,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -52467,11 +63762,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>91</td>
-      <td>1138</td>
+      <td>1825</td>
+      <td>1825</td>
+      <td>237</td>
+      <td>237</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>971</td>
+      <td>971</td>
+      <td>56</td>
+      <td>56</td>
+      <td>2796</td>
+      <td>2796</td>
+      <td>293</td>
+      <td>293</td>
     </tr>
     <tr>
       <td></td>
@@ -52516,7 +63826,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -52536,6 +63845,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -52564,8 +63888,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -52594,12 +63917,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>21</td>
-      <td>2312</td>
+      <td>660</td>
+      <td>2374</td>
+      <td>61</td>
+      <td>63</td>
+      <td>336</td>
+      <td>336</td>
+      <td>82</td>
+      <td>82</td>
+      <td>281</td>
+      <td>281</td>
+      <td>11</td>
+      <td>11</td>
+      <td>1277</td>
+      <td>2991</td>
+      <td>154</td>
+      <td>156</td>
     </tr>
     <tr>
       <td></td>
@@ -52644,7 +63982,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -52659,11 +63996,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>249</td>
-      <td>6285</td>
+      <td>7179</td>
+      <td>7179</td>
+      <td>509</td>
+      <td>509</td>
+      <td>11138</td>
+      <td>11138</td>
+      <td>1145</td>
+      <td>1145</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18317</td>
+      <td>18317</td>
+      <td>1654</td>
+      <td>1654</td>
     </tr>
     <tr>
       <td></td>
@@ -52692,8 +64044,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -52722,12 +64073,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>299</td>
-      <td>24155</td>
+      <td>28398</td>
+      <td>29031</td>
+      <td>932</td>
+      <td>965</td>
+      <td>73705</td>
+      <td>80087</td>
+      <td>2603</td>
+      <td>3025</td>
+      <td>5333</td>
+      <td>5567</td>
+      <td>218</td>
+      <td>230</td>
+      <td>107436</td>
+      <td>114685</td>
+      <td>3753</td>
+      <td>4220</td>
     </tr>
     <tr>
       <td></td>
@@ -52790,8 +64156,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>19</td>
-      <td>363</td>
+      <td>379</td>
+      <td>379</td>
+      <td>53</td>
+      <td>53</td>
+      <td>8259</td>
+      <td>8259</td>
+      <td>271</td>
+      <td>271</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8638</td>
+      <td>8638</td>
+      <td>324</td>
+      <td>324</td>
     </tr>
     <tr>
       <td></td>
@@ -52835,7 +64215,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -52850,12 +64229,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
-      <td>63</td>
-      <td>2022</td>
+      <td>1995</td>
+      <td>2091</td>
+      <td>174</td>
+      <td>193</td>
+      <td>1430</td>
+      <td>1430</td>
+      <td>389</td>
+      <td>389</td>
+      <td>1580</td>
+      <td>1580</td>
+      <td>56</td>
+      <td>56</td>
+      <td>5005</td>
+      <td>5101</td>
+      <td>619</td>
+      <td>638</td>
     </tr>
     <tr>
       <td></td>
@@ -52918,8 +64312,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
-      <td>5</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -52942,7 +64350,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate</td>
       <td>2.3.2</td>
       <td>kleborate</td>
-      <td>3.0.9</td>
+      <td>3.1.0</td>
       <td>Multilocus sequence typing, Genome assembly, Virulence prediction</td>
       <td>Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing</td>
       <td>0</td>
@@ -52964,7 +64372,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -52979,11 +64386,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>38</td>
-      <td>319</td>
+      <td>503</td>
+      <td>503</td>
+      <td>58</td>
+      <td>58</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>503</td>
+      <td>503</td>
+      <td>58</td>
+      <td>58</td>
     </tr>
     <tr>
       <td></td>
@@ -53046,8 +64468,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -53076,10 +64512,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -53106,12 +64541,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>33</td>
-      <td>594</td>
+      <td>1342</td>
+      <td>1342</td>
+      <td>63</td>
+      <td>63</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1342</td>
+      <td>1342</td>
+      <td>63</td>
+      <td>63</td>
     </tr>
     <tr>
       <td></td>
@@ -53140,8 +64590,7 @@
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
@@ -53153,7 +64602,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>0</td>
@@ -53170,12 +64619,27 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>1209</td>
-      <td>33778</td>
+      <td>48136</td>
+      <td>48164</td>
+      <td>2754</td>
+      <td>2760</td>
+      <td>59952</td>
+      <td>130398</td>
+      <td>5869</td>
+      <td>8654</td>
+      <td>29008</td>
+      <td>31148</td>
+      <td>1936</td>
+      <td>2200</td>
+      <td>137096</td>
+      <td>209710</td>
+      <td>10559</td>
+      <td>13614</td>
     </tr>
     <tr>
       <td></td>
@@ -53204,8 +64668,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -53234,12 +64697,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2367</td>
-      <td>185308</td>
+      <td>271367</td>
+      <td>271786</td>
+      <td>6384</td>
+      <td>6409</td>
+      <td>101752</td>
+      <td>101752</td>
+      <td>4662</td>
+      <td>4662</td>
+      <td>53562</td>
+      <td>53562</td>
+      <td>1663</td>
+      <td>1663</td>
+      <td>426681</td>
+      <td>427100</td>
+      <td>12709</td>
+      <td>12734</td>
     </tr>
     <tr>
       <td></td>
@@ -53268,9 +64746,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -53299,11 +64776,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>182</td>
-      <td>1444</td>
+      <td>3185</td>
+      <td>3185</td>
+      <td>495</td>
+      <td>495</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>385</td>
+      <td>385</td>
+      <td>48</td>
+      <td>48</td>
+      <td>3570</td>
+      <td>3570</td>
+      <td>543</td>
+      <td>543</td>
     </tr>
     <tr>
       <td></td>
@@ -53366,8 +64858,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>354</td>
-      <td>2527</td>
+      <td>3981</td>
+      <td>3986</td>
+      <td>769</td>
+      <td>771</td>
+      <td>4087</td>
+      <td>5610</td>
+      <td>991</td>
+      <td>1284</td>
+      <td>88</td>
+      <td>88</td>
+      <td>41</td>
+      <td>41</td>
+      <td>8156</td>
+      <td>9684</td>
+      <td>1801</td>
+      <td>2096</td>
     </tr>
     <tr>
       <td></td>
@@ -53396,8 +64902,7 @@
       <td>6</td>
       <td>6</td>
       <td>6</td>
-      <td>6</td>
-      <td>6</td>
+      <td>0</td>
       <td>6</td>
       <td>6</td>
       <td>6</td>
@@ -53427,11 +64932,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
-      <td>703</td>
-      <td>16525</td>
+      <td>48516</td>
+      <td>48516</td>
+      <td>2373</td>
+      <td>2373</td>
+      <td>8787</td>
+      <td>8787</td>
+      <td>943</td>
+      <td>943</td>
+      <td>4369</td>
+      <td>4369</td>
+      <td>393</td>
+      <td>393</td>
+      <td>61672</td>
+      <td>61672</td>
+      <td>3709</td>
+      <td>3709</td>
     </tr>
     <tr>
       <td></td>
@@ -53476,7 +64996,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -53496,6 +65015,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -53524,11 +65058,11 @@
       <td>0</td>
       <td>0</td>
       <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -53558,8 +65092,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>41</td>
-      <td>227</td>
+      <td>329</td>
+      <td>329</td>
+      <td>94</td>
+      <td>94</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>329</td>
+      <td>329</td>
+      <td>94</td>
+      <td>94</td>
     </tr>
     <tr>
       <td></td>
@@ -53588,8 +65136,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -53618,12 +65165,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>188</td>
-      <td>83331</td>
+      <td>77409</td>
+      <td>84356</td>
+      <td>447</td>
+      <td>475</td>
+      <td>156658</td>
+      <td>193590</td>
+      <td>870</td>
+      <td>3511</td>
+      <td>38579</td>
+      <td>38780</td>
+      <td>173</td>
+      <td>203</td>
+      <td>272646</td>
+      <td>316726</td>
+      <td>1490</td>
+      <td>4189</td>
     </tr>
     <tr>
       <td></td>
@@ -53688,6 +65250,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -53750,8 +65326,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>7</td>
-      <td>55</td>
+      <td>92</td>
+      <td>92</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>92</td>
+      <td>92</td>
+      <td>8</td>
+      <td>8</td>
     </tr>
     <tr>
       <td></td>
@@ -53780,8 +65370,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -53810,12 +65399,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>322</td>
-      <td>4090</td>
+      <td>4349</td>
+      <td>4466</td>
+      <td>666</td>
+      <td>698</td>
+      <td>2093</td>
+      <td>2286</td>
+      <td>928</td>
+      <td>998</td>
+      <td>201</td>
+      <td>201</td>
+      <td>77</td>
+      <td>77</td>
+      <td>6643</td>
+      <td>6953</td>
+      <td>1671</td>
+      <td>1773</td>
     </tr>
     <tr>
       <td></td>
@@ -53844,11 +65448,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -53878,8 +65482,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1012</td>
-      <td>20344</td>
+      <td>23442</td>
+      <td>24466</td>
+      <td>2379</td>
+      <td>2475</td>
+      <td>45734</td>
+      <td>49342</td>
+      <td>4565</td>
+      <td>5032</td>
+      <td>9327</td>
+      <td>9517</td>
+      <td>835</td>
+      <td>842</td>
+      <td>78503</td>
+      <td>83325</td>
+      <td>7779</td>
+      <td>8349</td>
     </tr>
     <tr>
       <td></td>
@@ -53942,8 +65560,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>37</td>
+      <td>39</td>
+      <td>39</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>39</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -53988,7 +65620,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -54003,11 +65634,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>77</td>
-      <td>405</td>
+      <td>512</td>
+      <td>512</td>
+      <td>126</td>
+      <td>126</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>480</td>
+      <td>480</td>
+      <td>65</td>
+      <td>65</td>
+      <td>992</td>
+      <td>992</td>
+      <td>191</td>
+      <td>191</td>
     </tr>
     <tr>
       <td></td>
@@ -54036,11 +65682,10 @@
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>4</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>4</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -54066,12 +65711,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>1791</td>
-      <td>4150903</td>
+      <td>4176367</td>
+      <td>4176367</td>
+      <td>4301</td>
+      <td>4301</td>
+      <td>509615</td>
+      <td>509615</td>
+      <td>8213</td>
+      <td>8213</td>
+      <td>106342</td>
+      <td>106342</td>
+      <td>1815</td>
+      <td>1815</td>
+      <td>4792324</td>
+      <td>4792324</td>
+      <td>14329</td>
+      <td>14329</td>
     </tr>
     <tr>
       <td></td>
@@ -54134,8 +65794,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
-      <td>647</td>
+      <td>822</td>
+      <td>822</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>822</td>
+      <td>822</td>
+      <td>14</td>
+      <td>14</td>
     </tr>
     <tr>
       <td></td>
@@ -54198,8 +65872,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>105</td>
-      <td>1164</td>
+      <td>1534</td>
+      <td>1534</td>
+      <td>199</td>
+      <td>199</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1534</td>
+      <td>1534</td>
+      <td>199</td>
+      <td>199</td>
     </tr>
     <tr>
       <td></td>
@@ -54262,8 +65950,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>44</td>
+      <td>44</td>
+      <td>11</td>
+      <td>11</td>
       <td>0</td>
-      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>44</td>
+      <td>44</td>
+      <td>11</td>
+      <td>11</td>
     </tr>
     <tr>
       <td></td>
@@ -54326,8 +66028,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>29</td>
-      <td>188</td>
+      <td>2835</td>
+      <td>2835</td>
+      <td>59</td>
+      <td>59</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2835</td>
+      <td>2835</td>
+      <td>59</td>
+      <td>59</td>
     </tr>
     <tr>
       <td></td>
@@ -54356,8 +66072,7 @@
       <td>9</td>
       <td>9</td>
       <td>9</td>
-      <td>9</td>
-      <td>9</td>
+      <td>0</td>
       <td>9</td>
       <td>9</td>
       <td>9</td>
@@ -54386,12 +66101,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>9</td>
       <td>9</td>
       <td>9</td>
       <td>0</td>
-      <td>1969</td>
-      <td>84521</td>
+      <td>87810</td>
+      <td>96069</td>
+      <td>4980</td>
+      <td>5629</td>
+      <td>153500</td>
+      <td>227569</td>
+      <td>12946</td>
+      <td>18825</td>
+      <td>10988</td>
+      <td>12301</td>
+      <td>692</td>
+      <td>807</td>
+      <td>252298</td>
+      <td>335939</td>
+      <td>18618</td>
+      <td>25261</td>
     </tr>
     <tr>
       <td></td>
@@ -54420,11 +66150,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>0</td>
@@ -54433,7 +66163,6 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -54453,9 +66182,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>3</td>
+      <td>15</td>
       <td>21</td>
+      <td>7</td>
+      <td>9</td>
+      <td>227</td>
+      <td>2470</td>
+      <td>52</td>
+      <td>464</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>243</td>
+      <td>2492</td>
+      <td>60</td>
+      <td>474</td>
     </tr>
     <tr>
       <td></td>
@@ -54520,6 +66264,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -54548,11 +66306,10 @@
       <td>3</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>3</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -54578,12 +66335,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>587</td>
-      <td>10503</td>
+      <td>11761</td>
+      <td>12093</td>
+      <td>873</td>
+      <td>889</td>
+      <td>5762</td>
+      <td>5762</td>
+      <td>473</td>
+      <td>473</td>
+      <td>5610</td>
+      <td>5610</td>
+      <td>343</td>
+      <td>343</td>
+      <td>23133</td>
+      <td>23465</td>
+      <td>1689</td>
+      <td>1705</td>
     </tr>
     <tr>
       <td></td>
@@ -54612,8 +66384,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -54642,12 +66413,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>554</td>
-      <td>5591</td>
+      <td>6417</td>
+      <td>6861</td>
+      <td>1315</td>
+      <td>1366</td>
+      <td>7235</td>
+      <td>7235</td>
+      <td>1858</td>
+      <td>1858</td>
+      <td>4112</td>
+      <td>4112</td>
+      <td>902</td>
+      <td>902</td>
+      <td>17764</td>
+      <td>18208</td>
+      <td>4075</td>
+      <td>4126</td>
     </tr>
     <tr>
       <td></td>
@@ -54710,8 +66496,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>6</td>
-      <td>22</td>
+      <td>24</td>
+      <td>24</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>24</td>
+      <td>9</td>
+      <td>9</td>
     </tr>
     <tr>
       <td></td>
@@ -54774,8 +66574,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
-      <td>1528</td>
+      <td>3780</td>
+      <td>3780</td>
+      <td>67</td>
+      <td>67</td>
+      <td>1012</td>
+      <td>1012</td>
+      <td>57</td>
+      <td>57</td>
+      <td>105</td>
+      <td>105</td>
+      <td>3</td>
+      <td>3</td>
+      <td>4897</td>
+      <td>4897</td>
+      <td>127</td>
+      <td>127</td>
     </tr>
     <tr>
       <td></td>
@@ -54820,7 +66634,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -54835,11 +66648,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>167</td>
+      <td>7871</td>
+      <td>7871</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7871</td>
+      <td>7871</td>
+      <td>32</td>
+      <td>32</td>
     </tr>
     <tr>
       <td></td>
@@ -54868,8 +66696,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -54898,12 +66725,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>27</td>
-      <td>9763</td>
+      <td>10119</td>
+      <td>10119</td>
+      <td>61</td>
+      <td>61</td>
+      <td>19</td>
+      <td>19</td>
+      <td>9</td>
+      <td>9</td>
+      <td>647</td>
+      <td>647</td>
+      <td>7</td>
+      <td>7</td>
+      <td>10785</td>
+      <td>10785</td>
+      <td>77</td>
+      <td>77</td>
     </tr>
     <tr>
       <td></td>
@@ -54966,8 +66808,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>894</td>
+      <td>894</td>
+      <td>12</td>
+      <td>12</td>
+      <td>81</td>
+      <td>81</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>975</td>
+      <td>975</td>
+      <td>17</td>
+      <td>17</td>
     </tr>
     <tr>
       <td></td>
@@ -55030,8 +66886,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>13</td>
-      <td>576</td>
+      <td>471</td>
+      <td>582</td>
+      <td>35</td>
+      <td>40</td>
+      <td>589</td>
+      <td>589</td>
+      <td>80</td>
+      <td>80</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1060</td>
+      <td>1171</td>
+      <td>115</td>
+      <td>120</td>
     </tr>
     <tr>
       <td></td>
@@ -55060,8 +66930,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -55090,12 +66959,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>118</td>
-      <td>2059</td>
+      <td>2798</td>
+      <td>2798</td>
+      <td>314</td>
+      <td>314</td>
+      <td>2452</td>
+      <td>2452</td>
+      <td>508</td>
+      <td>508</td>
+      <td>914</td>
+      <td>914</td>
+      <td>89</td>
+      <td>89</td>
+      <td>6164</td>
+      <td>6164</td>
+      <td>911</td>
+      <td>911</td>
     </tr>
     <tr>
       <td></td>
@@ -55158,8 +67042,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>10</td>
-      <td>29</td>
+      <td>35</td>
+      <td>35</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>35</td>
+      <td>35</td>
+      <td>13</td>
+      <td>13</td>
     </tr>
     <tr>
       <td></td>
@@ -55188,8 +67086,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -55218,12 +67115,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>768</td>
-      <td>99863</td>
+      <td>117975</td>
+      <td>117975</td>
+      <td>1693</td>
+      <td>1693</td>
+      <td>55063</td>
+      <td>55063</td>
+      <td>796</td>
+      <td>796</td>
+      <td>9325</td>
+      <td>9325</td>
+      <td>639</td>
+      <td>639</td>
+      <td>182363</td>
+      <td>182363</td>
+      <td>3128</td>
+      <td>3128</td>
     </tr>
     <tr>
       <td></td>
@@ -55252,8 +67164,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -55282,12 +67193,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>548</td>
-      <td>9530</td>
+      <td>12692</td>
+      <td>13292</td>
+      <td>1349</td>
+      <td>1400</td>
+      <td>16645</td>
+      <td>16645</td>
+      <td>2140</td>
+      <td>2140</td>
+      <td>6214</td>
+      <td>6214</td>
+      <td>431</td>
+      <td>431</td>
+      <td>35551</td>
+      <td>36151</td>
+      <td>3920</td>
+      <td>3971</td>
     </tr>
     <tr>
       <td></td>
@@ -55316,8 +67242,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -55347,11 +67272,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>54</td>
-      <td>475</td>
+      <td>513</td>
+      <td>557</td>
+      <td>152</td>
+      <td>155</td>
+      <td>74</td>
+      <td>74</td>
+      <td>35</td>
+      <td>35</td>
+      <td>10</td>
+      <td>10</td>
+      <td>4</td>
+      <td>4</td>
+      <td>597</td>
+      <td>641</td>
+      <td>191</td>
+      <td>194</td>
     </tr>
     <tr>
       <td></td>
@@ -55414,8 +67354,22 @@
       <td>7</td>
       <td>0</td>
       <td>0</td>
-      <td>261</td>
-      <td>3610</td>
+      <td>4130</td>
+      <td>4130</td>
+      <td>447</td>
+      <td>447</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>4130</td>
+      <td>4130</td>
+      <td>447</td>
+      <td>447</td>
     </tr>
     <tr>
       <td></td>
@@ -55423,7 +67377,7 @@
       <td>meme_dreme, meme_fimo, meme_meme, meme_psp_gen</td>
       <td>The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.</td>
       <td>meme_meme</td>
-      <td>meme_meme, meme_fimo</td>
+      <td>meme_fimo, meme_meme</td>
       <td></td>
       <td>meme_meme</td>
       <td>An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.</td>
@@ -55458,7 +67412,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>2</td>
       <td>0</td>
@@ -55474,12 +67427,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
-      <td>235</td>
-      <td>22352</td>
+      <td>20990</td>
+      <td>22979</td>
+      <td>762</td>
+      <td>892</td>
+      <td>10975</td>
+      <td>25929</td>
+      <td>1551</td>
+      <td>3249</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31965</td>
+      <td>48908</td>
+      <td>2313</td>
+      <td>4141</td>
     </tr>
     <tr>
       <td></td>
@@ -55522,7 +67490,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -55538,12 +67505,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>287</td>
-      <td>6584</td>
+      <td>6413</td>
+      <td>7000</td>
+      <td>705</td>
+      <td>743</td>
+      <td>7260</td>
+      <td>7260</td>
+      <td>1171</td>
+      <td>1171</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13673</td>
+      <td>14260</td>
+      <td>1876</td>
+      <td>1914</td>
     </tr>
     <tr>
       <td></td>
@@ -55608,6 +67590,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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+      <td>0</td>
+      <td>0</td>
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     <tr>
       <td></td>
@@ -55672,6 +67668,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -55700,11 +67710,11 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
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-      <td>2</td>
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       <td>0</td>
       <td>0</td>
@@ -55734,8 +67744,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>244</td>
-      <td>2483</td>
+      <td>3150</td>
+      <td>3150</td>
+      <td>477</td>
+      <td>477</td>
+      <td>730</td>
+      <td>730</td>
+      <td>196</td>
+      <td>196</td>
+      <td>1183</td>
+      <td>1183</td>
+      <td>151</td>
+      <td>151</td>
+      <td>5063</td>
+      <td>5063</td>
+      <td>824</td>
+      <td>824</td>
     </tr>
     <tr>
       <td></td>
@@ -55800,6 +67824,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -55828,11 +67866,10 @@
       <td>2</td>
       <td>1</td>
       <td>2</td>
-      <td>2</td>
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       <td>1</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -55859,11 +67896,26 @@
       <td>0</td>
       <td>1</td>
       <td>0</td>
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       <td>0</td>
       <td>0</td>
-      <td>192</td>
-      <td>4329</td>
+      <td>6135</td>
+      <td>6135</td>
+      <td>382</td>
+      <td>382</td>
+      <td>881</td>
+      <td>881</td>
+      <td>151</td>
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+      <td>1094</td>
+      <td>1094</td>
+      <td>104</td>
+      <td>104</td>
+      <td>8110</td>
+      <td>8110</td>
+      <td>637</td>
+      <td>637</td>
     </tr>
     <tr>
       <td></td>
@@ -55928,6 +67980,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -55948,7 +68014,7 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk</td>
-      <td>5.34c21f2</td>
+      <td>7.bba0d80</td>
       <td>metaeuk</td>
       <td>6.a5d39d9</td>
       <td>Homology-based gene prediction</td>
@@ -55990,8 +68056,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>16</td>
-      <td>184</td>
+      <td>312</td>
+      <td>312</td>
+      <td>40</td>
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+      <td>40</td>
+      <td>40</td>
     </tr>
     <tr>
       <td></td>
@@ -56020,10 +68100,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
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       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -56050,12 +68129,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>6</td>
-      <td>753</td>
+      <td>556</td>
+      <td>756</td>
+      <td>17</td>
+      <td>21</td>
+      <td>310</td>
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+      <td>866</td>
+      <td>1270</td>
+      <td>52</td>
+      <td>76</td>
     </tr>
     <tr>
       <td></td>
@@ -56084,11 +68178,10 @@
       <td>1</td>
       <td>2</td>
       <td>4</td>
-      <td>4</td>
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       <td>1</td>
       <td>2</td>
       <td>4</td>
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       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -56115,11 +68208,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>4</td>
       <td>0</td>
-      <td>499</td>
-      <td>11069</td>
+      <td>16629</td>
+      <td>16648</td>
+      <td>1183</td>
+      <td>1187</td>
+      <td>3983</td>
+      <td>3983</td>
+      <td>572</td>
+      <td>572</td>
+      <td>4747</td>
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+      <td>278</td>
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+      <td>25359</td>
+      <td>25378</td>
+      <td>2033</td>
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     </tr>
     <tr>
       <td></td>
@@ -56182,8 +68290,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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+      <td>142</td>
+      <td>32</td>
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       <td>0</td>
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+      <td>379</td>
+      <td>379</td>
+      <td>47</td>
+      <td>47</td>
+      <td>521</td>
+      <td>521</td>
+      <td>79</td>
+      <td>79</td>
     </tr>
     <tr>
       <td></td>
@@ -56246,8 +68368,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -56310,8 +68446,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>0</td>
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     <tr>
       <td></td>
@@ -56356,7 +68506,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -56370,12 +68519,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>7</td>
-      <td>1226</td>
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+      <td>1229</td>
+      <td>25</td>
+      <td>33</td>
+      <td>1153</td>
+      <td>1376</td>
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     </tr>
     <tr>
       <td></td>
@@ -56420,7 +68584,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -56434,12 +68597,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>109</td>
-      <td>2206</td>
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     </tr>
     <tr>
       <td></td>
@@ -56468,8 +68646,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
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       <td>1</td>
       <td>1</td>
@@ -56498,12 +68675,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>178</td>
-      <td>11938</td>
+      <td>13357</td>
+      <td>13479</td>
+      <td>554</td>
+      <td>562</td>
+      <td>8416</td>
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+      <td>898</td>
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+      <td>85</td>
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+      <td>22671</td>
+      <td>22793</td>
+      <td>1087</td>
+      <td>1095</td>
     </tr>
     <tr>
       <td></td>
@@ -56532,8 +68724,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
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-      <td>1</td>
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@@ -56562,12 +68753,27 @@
       <td>0</td>
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-      <td>1588</td>
-      <td>260442</td>
+      <td>346530</td>
+      <td>349075</td>
+      <td>4323</td>
+      <td>4419</td>
+      <td>108535</td>
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+      <td>4075</td>
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+      <td>22331</td>
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+      <td>1166</td>
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@@ -56596,10 +68802,9 @@
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       <td>0</td>
       <td>2</td>
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-      <td>2</td>
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@@ -56627,11 +68832,26 @@
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-      <td>842</td>
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@@ -56694,8 +68914,22 @@
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -56758,8 +68992,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
-      <td>10</td>
+      <td>18</td>
+      <td>18</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>9</td>
+      <td>9</td>
     </tr>
     <tr>
       <td></td>
@@ -56804,7 +69052,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -56819,11 +69066,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>66</td>
-      <td>881</td>
+      <td>1117</td>
+      <td>1117</td>
+      <td>116</td>
+      <td>116</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>295</td>
+      <td>295</td>
+      <td>25</td>
+      <td>25</td>
+      <td>1412</td>
+      <td>1412</td>
+      <td>141</td>
+      <td>141</td>
     </tr>
     <tr>
       <td></td>
@@ -56868,7 +69130,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -56882,12 +69143,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>1</td>
       <td>0</td>
-      <td>236</td>
-      <td>100920</td>
+      <td>191295</td>
+      <td>191295</td>
+      <td>1111</td>
+      <td>1111</td>
+      <td>42265</td>
+      <td>42265</td>
+      <td>320</td>
+      <td>320</td>
+      <td>10904</td>
+      <td>10904</td>
+      <td>83</td>
+      <td>83</td>
+      <td>244464</td>
+      <td>244464</td>
+      <td>1514</td>
+      <td>1514</td>
     </tr>
     <tr>
       <td></td>
@@ -56916,8 +69192,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -56946,12 +69221,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>635</td>
-      <td>9304</td>
+      <td>13300</td>
+      <td>13471</td>
+      <td>1480</td>
+      <td>1501</td>
+      <td>6532</td>
+      <td>6532</td>
+      <td>1167</td>
+      <td>1167</td>
+      <td>10334</td>
+      <td>11841</td>
+      <td>1083</td>
+      <td>1300</td>
+      <td>30166</td>
+      <td>31844</td>
+      <td>3730</td>
+      <td>3968</td>
     </tr>
     <tr>
       <td></td>
@@ -57014,8 +69304,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>19</td>
-      <td>317</td>
+      <td>339</td>
+      <td>339</td>
+      <td>56</td>
+      <td>56</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>339</td>
+      <td>339</td>
+      <td>56</td>
+      <td>56</td>
     </tr>
     <tr>
       <td></td>
@@ -57060,7 +69364,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -57075,11 +69378,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>21</td>
-      <td>262</td>
+      <td>1278</td>
+      <td>1278</td>
+      <td>87</td>
+      <td>87</td>
+      <td>168</td>
+      <td>168</td>
+      <td>24</td>
+      <td>24</td>
+      <td>102</td>
+      <td>102</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1548</td>
+      <td>1548</td>
+      <td>116</td>
+      <td>116</td>
     </tr>
     <tr>
       <td></td>
@@ -57108,8 +69426,7 @@
       <td>129</td>
       <td>129</td>
       <td>129</td>
-      <td>129</td>
-      <td>129</td>
+      <td>0</td>
       <td>129</td>
       <td>129</td>
       <td>129</td>
@@ -57138,12 +69455,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>126</td>
       <td>129</td>
       <td>129</td>
       <td>0</td>
-      <td>14353</td>
-      <td>302916</td>
+      <td>297546</td>
+      <td>326056</td>
+      <td>37506</td>
+      <td>41763</td>
+      <td>565218</td>
+      <td>682083</td>
+      <td>72163</td>
+      <td>89926</td>
+      <td>167400</td>
+      <td>182490</td>
+      <td>26963</td>
+      <td>28404</td>
+      <td>1030164</td>
+      <td>1190629</td>
+      <td>136632</td>
+      <td>160093</td>
     </tr>
     <tr>
       <td></td>
@@ -57206,8 +69538,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>34</td>
-      <td>803</td>
+      <td>864</td>
+      <td>929</td>
+      <td>91</td>
+      <td>101</td>
+      <td>1100</td>
+      <td>1100</td>
+      <td>175</td>
+      <td>175</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1964</td>
+      <td>2029</td>
+      <td>266</td>
+      <td>276</td>
     </tr>
     <tr>
       <td></td>
@@ -57272,6 +69618,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>485</td>
+      <td>871</td>
+      <td>159</td>
+      <td>298</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>485</td>
+      <td>871</td>
+      <td>159</td>
+      <td>298</td>
     </tr>
     <tr>
       <td></td>
@@ -57334,8 +69694,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>53</td>
+      <td>106</td>
+      <td>106</td>
+      <td>25</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>106</td>
+      <td>106</td>
+      <td>25</td>
+      <td>25</td>
     </tr>
     <tr>
       <td></td>
@@ -57364,8 +69738,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -57397,9 +69770,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>8320</td>
-      <td>162790</td>
+      <td>182221</td>
+      <td>192389</td>
+      <td>19343</td>
+      <td>20494</td>
+      <td>163961</td>
+      <td>182413</td>
+      <td>26449</td>
+      <td>29758</td>
+      <td>40663</td>
+      <td>41855</td>
+      <td>5974</td>
+      <td>6157</td>
+      <td>386845</td>
+      <td>416657</td>
+      <td>51766</td>
+      <td>56409</td>
     </tr>
     <tr>
       <td></td>
@@ -57428,8 +69816,7 @@
       <td>6</td>
       <td>6</td>
       <td>6</td>
-      <td>6</td>
-      <td>6</td>
+      <td>0</td>
       <td>6</td>
       <td>6</td>
       <td>6</td>
@@ -57458,12 +69845,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>6</td>
       <td>6</td>
       <td>6</td>
       <td>0</td>
-      <td>669</td>
-      <td>18347</td>
+      <td>21587</td>
+      <td>22119</td>
+      <td>1940</td>
+      <td>2033</td>
+      <td>29284</td>
+      <td>29284</td>
+      <td>3626</td>
+      <td>3626</td>
+      <td>8194</td>
+      <td>8194</td>
+      <td>545</td>
+      <td>545</td>
+      <td>59065</td>
+      <td>59597</td>
+      <td>6111</td>
+      <td>6204</td>
     </tr>
     <tr>
       <td></td>
@@ -57528,6 +69930,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -57590,8 +70006,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
       <td>0</td>
-      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -57656,6 +70086,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>204</td>
+      <td>204</td>
+      <td>75</td>
+      <td>75</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>204</td>
+      <td>204</td>
+      <td>75</td>
+      <td>75</td>
     </tr>
     <tr>
       <td></td>
@@ -57700,7 +70144,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -57714,12 +70157,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>3</td>
-      <td>836</td>
+      <td>839</td>
+      <td>839</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>269</td>
+      <td>269</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1108</td>
+      <td>1108</td>
+      <td>17</td>
+      <td>17</td>
     </tr>
     <tr>
       <td></td>
@@ -57748,8 +70206,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -57778,12 +70235,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2195</td>
-      <td>63235</td>
+      <td>99052</td>
+      <td>100009</td>
+      <td>5671</td>
+      <td>5755</td>
+      <td>40386</td>
+      <td>40386</td>
+      <td>3371</td>
+      <td>3371</td>
+      <td>17919</td>
+      <td>17919</td>
+      <td>2188</td>
+      <td>2188</td>
+      <td>157357</td>
+      <td>158314</td>
+      <td>11230</td>
+      <td>11314</td>
     </tr>
     <tr>
       <td></td>
@@ -57812,11 +70284,11 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -57846,8 +70318,22 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>15</td>
-      <td>1074</td>
+      <td>1091</td>
+      <td>1091</td>
+      <td>44</td>
+      <td>44</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1091</td>
+      <td>1091</td>
+      <td>44</td>
+      <td>44</td>
     </tr>
     <tr>
       <td></td>
@@ -57876,8 +70362,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -57906,12 +70391,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>688</td>
-      <td>5487</td>
+      <td>6873</td>
+      <td>6873</td>
+      <td>1664</td>
+      <td>1664</td>
+      <td>17651</td>
+      <td>17651</td>
+      <td>4513</td>
+      <td>4513</td>
+      <td>6228</td>
+      <td>6228</td>
+      <td>972</td>
+      <td>972</td>
+      <td>30752</td>
+      <td>30752</td>
+      <td>7149</td>
+      <td>7149</td>
     </tr>
     <tr>
       <td></td>
@@ -57940,10 +70440,9 @@
       <td>2</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -57970,12 +70469,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>667</td>
-      <td>3177</td>
+      <td>4417</td>
+      <td>4417</td>
+      <td>1024</td>
+      <td>1024</td>
+      <td>6940</td>
+      <td>6940</td>
+      <td>2275</td>
+      <td>2275</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>11358</td>
+      <td>11358</td>
+      <td>3300</td>
+      <td>3300</td>
     </tr>
     <tr>
       <td></td>
@@ -58020,7 +70534,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -58040,11 +70553,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
       <td>ncbi_entrez_eutils</td>
-      <td>ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_egquery, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary</td>
+      <td>ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary</td>
       <td>NCBI Entrez E-Utilties allow fetching data from NCBI Databases</td>
       <td></td>
       <td></td>
@@ -58067,12 +70595,11 @@
       <td></td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
-      <td>0</td>
+      <td>7</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
       <td>0</td>
+      <td>7</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -58099,11 +70626,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
-      <td>8</td>
       <td>0</td>
-      <td>169</td>
-      <td>3193</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>2794</td>
+      <td>3191</td>
+      <td>533</td>
+      <td>664</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2794</td>
+      <td>3191</td>
+      <td>533</td>
+      <td>664</td>
     </tr>
     <tr>
       <td></td>
@@ -58148,7 +70690,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -58167,7 +70708,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>125</td>
+      <td>125</td>
+      <td>26</td>
+      <td>26</td>
+      <td>2489</td>
+      <td>2489</td>
+      <td>139</td>
+      <td>139</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2614</td>
+      <td>2614</td>
+      <td>165</td>
+      <td>165</td>
     </tr>
     <tr>
       <td></td>
@@ -58230,8 +70786,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>95</td>
-      <td>667</td>
+      <td>790</td>
+      <td>790</td>
+      <td>160</td>
+      <td>160</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>790</td>
+      <td>790</td>
+      <td>160</td>
+      <td>160</td>
     </tr>
     <tr>
       <td></td>
@@ -58260,8 +70830,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -58290,12 +70859,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>448</td>
-      <td>25505</td>
+      <td>33637</td>
+      <td>34195</td>
+      <td>1113</td>
+      <td>1172</td>
+      <td>16257</td>
+      <td>16257</td>
+      <td>1816</td>
+      <td>1816</td>
+      <td>7582</td>
+      <td>7582</td>
+      <td>899</td>
+      <td>899</td>
+      <td>57476</td>
+      <td>58034</td>
+      <td>3828</td>
+      <td>3887</td>
     </tr>
     <tr>
       <td></td>
@@ -58324,11 +70908,10 @@
       <td>1</td>
       <td>1</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -58355,11 +70938,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>210</td>
-      <td>4080</td>
+      <td>4411</td>
+      <td>4411</td>
+      <td>396</td>
+      <td>396</td>
+      <td>9708</td>
+      <td>9708</td>
+      <td>279</td>
+      <td>279</td>
+      <td>2099</td>
+      <td>2099</td>
+      <td>212</td>
+      <td>212</td>
+      <td>16218</td>
+      <td>16218</td>
+      <td>887</td>
+      <td>887</td>
     </tr>
     <tr>
       <td></td>
@@ -58422,8 +71020,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>21</td>
-      <td>1266</td>
+      <td>1403</td>
+      <td>1403</td>
+      <td>49</td>
+      <td>49</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1403</td>
+      <td>1403</td>
+      <td>49</td>
+      <td>49</td>
     </tr>
     <tr>
       <td></td>
@@ -58452,8 +71064,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -58482,12 +71093,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>224</td>
-      <td>24740</td>
+      <td>24611</td>
+      <td>29662</td>
+      <td>633</td>
+      <td>716</td>
+      <td>15523</td>
+      <td>21395</td>
+      <td>740</td>
+      <td>1128</td>
+      <td>7751</td>
+      <td>8972</td>
+      <td>125</td>
+      <td>145</td>
+      <td>47885</td>
+      <td>60029</td>
+      <td>1498</td>
+      <td>1989</td>
     </tr>
     <tr>
       <td></td>
@@ -58516,10 +71142,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -58546,12 +71171,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5</td>
-      <td>142</td>
+      <td>107</td>
+      <td>143</td>
+      <td>13</td>
+      <td>15</td>
+      <td>148</td>
+      <td>148</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>255</td>
+      <td>291</td>
+      <td>33</td>
+      <td>35</td>
     </tr>
     <tr>
       <td></td>
@@ -58580,9 +71220,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -58610,12 +71249,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>162</td>
-      <td>6384</td>
+      <td>7780</td>
+      <td>7780</td>
+      <td>337</td>
+      <td>337</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2323</td>
+      <td>2323</td>
+      <td>99</td>
+      <td>99</td>
+      <td>10104</td>
+      <td>10104</td>
+      <td>437</td>
+      <td>437</td>
     </tr>
     <tr>
       <td></td>
@@ -58680,6 +71334,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -58708,9 +71376,8 @@
       <td>0</td>
       <td>10</td>
       <td>10</td>
-      <td>10</td>
       <td>0</td>
-      <td>10</td>
+      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
@@ -58739,11 +71406,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
-      <td>503</td>
-      <td>26251</td>
+      <td>37598</td>
+      <td>37598</td>
+      <td>1277</td>
+      <td>1277</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3862</td>
+      <td>3862</td>
+      <td>280</td>
+      <td>280</td>
+      <td>41460</td>
+      <td>41460</td>
+      <td>1557</td>
+      <td>1557</td>
     </tr>
     <tr>
       <td></td>
@@ -58788,7 +71470,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -58802,12 +71483,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>32</td>
-      <td>1877</td>
+      <td>1850</td>
+      <td>1963</td>
+      <td>79</td>
+      <td>93</td>
+      <td>1370</td>
+      <td>1370</td>
+      <td>194</td>
+      <td>194</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3220</td>
+      <td>3333</td>
+      <td>273</td>
+      <td>287</td>
     </tr>
     <tr>
       <td></td>
@@ -58836,11 +71532,11 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -58870,8 +71566,22 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>2</td>
-      <td>25</td>
+      <td>26</td>
+      <td>26</td>
+      <td>6</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>6</td>
+      <td>6</td>
     </tr>
     <tr>
       <td></td>
@@ -58900,11 +71610,10 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -58935,7 +71644,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>12</td>
+      <td>12</td>
     </tr>
     <tr>
       <td></td>
@@ -58980,7 +71704,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -58994,12 +71717,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
-      <td>39</td>
-      <td>2654</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>87</td>
+      <td>87</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>87</td>
+      <td>87</td>
     </tr>
     <tr>
       <td></td>
@@ -59062,8 +71800,22 @@
       <td>17</td>
       <td>17</td>
       <td>0</td>
-      <td>22</td>
-      <td>655</td>
+      <td>582</td>
+      <td>663</td>
+      <td>68</td>
+      <td>69</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>582</td>
+      <td>663</td>
+      <td>68</td>
+      <td>69</td>
     </tr>
     <tr>
       <td></td>
@@ -59128,6 +71880,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -59190,8 +71956,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>24</td>
-      <td>321</td>
+      <td>500</td>
+      <td>500</td>
+      <td>45</td>
+      <td>45</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>500</td>
+      <td>500</td>
+      <td>45</td>
+      <td>45</td>
     </tr>
     <tr>
       <td></td>
@@ -59254,8 +72034,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>53</td>
-      <td>774</td>
+      <td>897</td>
+      <td>897</td>
+      <td>99</td>
+      <td>99</td>
+      <td>1792</td>
+      <td>1792</td>
+      <td>239</td>
+      <td>239</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2689</td>
+      <td>2689</td>
+      <td>338</td>
+      <td>338</td>
     </tr>
     <tr>
       <td></td>
@@ -59269,7 +72063,7 @@
       <td>OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.</td>
       <td>Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment</td>
       <td>Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/davidemms/OrthoFinder</td>
       <td>Phylogenetics, Sequence Analysis</td>
       <td>orthofinder</td>
@@ -59278,17 +72072,17 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder</td>
       <td>2.5.5</td>
       <td>orthofinder</td>
-      <td>2.5.5</td>
+      <td>3.0.1b1</td>
       <td>Genome comparison, Genome alignment</td>
       <td>Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -59318,8 +72112,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>239</td>
-      <td>1333</td>
+      <td>2018</td>
+      <td>2018</td>
+      <td>419</td>
+      <td>419</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>438</td>
+      <td>438</td>
+      <td>58</td>
+      <td>58</td>
+      <td>2456</td>
+      <td>2456</td>
+      <td>477</td>
+      <td>477</td>
     </tr>
     <tr>
       <td></td>
@@ -59384,6 +72192,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -59448,6 +72270,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -59510,8 +72346,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>196</td>
+      <td>196</td>
+      <td>16</td>
+      <td>16</td>
+      <td>19</td>
+      <td>19</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>215</td>
+      <td>215</td>
+      <td>30</td>
+      <td>30</td>
     </tr>
     <tr>
       <td></td>
@@ -59540,8 +72390,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -59570,12 +72419,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>7457</td>
+      <td>7457</td>
+      <td>508</td>
+      <td>508</td>
+      <td>8518</td>
+      <td>8518</td>
+      <td>377</td>
+      <td>377</td>
+      <td>2760</td>
+      <td>2760</td>
       <td>259</td>
-      <td>7276</td>
+      <td>259</td>
+      <td>18735</td>
+      <td>18735</td>
+      <td>1144</td>
+      <td>1144</td>
     </tr>
     <tr>
       <td></td>
@@ -59638,8 +72502,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>31</td>
-      <td>90</td>
+      <td>203</td>
+      <td>203</td>
+      <td>65</td>
+      <td>65</td>
+      <td>288</td>
+      <td>288</td>
+      <td>62</td>
+      <td>62</td>
+      <td>110</td>
+      <td>110</td>
+      <td>20</td>
+      <td>20</td>
+      <td>601</td>
+      <td>601</td>
+      <td>147</td>
+      <td>147</td>
     </tr>
     <tr>
       <td></td>
@@ -59668,8 +72546,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -59698,12 +72575,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>565</td>
-      <td>5260</td>
+      <td>6204</td>
+      <td>6211</td>
+      <td>1261</td>
+      <td>1261</td>
+      <td>6667</td>
+      <td>6667</td>
+      <td>1143</td>
+      <td>1143</td>
+      <td>1160</td>
+      <td>1160</td>
+      <td>189</td>
+      <td>189</td>
+      <td>14031</td>
+      <td>14038</td>
+      <td>2593</td>
+      <td>2593</td>
     </tr>
     <tr>
       <td></td>
@@ -59768,6 +72660,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -59830,8 +72736,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>17</td>
+      <td>17</td>
     </tr>
     <tr>
       <td></td>
@@ -59894,8 +72814,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>22</td>
+      <td>22</td>
+      <td>109</td>
+      <td>109</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>167</td>
+      <td>167</td>
+      <td>41</td>
+      <td>41</td>
     </tr>
     <tr>
       <td></td>
@@ -59916,7 +72850,7 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram</td>
-      <td>1.0.1</td>
+      <td>1.0.2</td>
       <td>openjdk</td>
       <td></td>
       <td></td>
@@ -59924,8 +72858,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -59954,12 +72887,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>312</td>
-      <td>4180</td>
+      <td>5505</td>
+      <td>5505</td>
+      <td>510</td>
+      <td>510</td>
+      <td>7932</td>
+      <td>8582</td>
+      <td>811</td>
+      <td>909</td>
+      <td>736</td>
+      <td>736</td>
+      <td>119</td>
+      <td>119</td>
+      <td>14173</td>
+      <td>14823</td>
+      <td>1440</td>
+      <td>1538</td>
     </tr>
     <tr>
       <td></td>
@@ -60022,8 +72970,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>9</td>
+      <td>9</td>
     </tr>
     <tr>
       <td></td>
@@ -60067,7 +73029,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -60082,12 +73043,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>150</td>
-      <td>4305</td>
+      <td>6269</td>
+      <td>6866</td>
+      <td>260</td>
+      <td>292</td>
+      <td>5530</td>
+      <td>20068</td>
+      <td>467</td>
+      <td>1664</td>
+      <td>5647</td>
+      <td>8471</td>
+      <td>198</td>
+      <td>300</td>
+      <td>17446</td>
+      <td>35405</td>
+      <td>925</td>
+      <td>2256</td>
     </tr>
     <tr>
       <td></td>
@@ -60132,7 +73108,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -60147,11 +73122,26 @@
       <td>0</td>
       <td>1</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>74</td>
-      <td>2565</td>
+      <td>5462</td>
+      <td>5462</td>
+      <td>334</td>
+      <td>334</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>309</td>
+      <td>309</td>
+      <td>52</td>
+      <td>52</td>
+      <td>5771</td>
+      <td>5771</td>
+      <td>386</td>
+      <td>386</td>
     </tr>
     <tr>
       <td></td>
@@ -60180,11 +73170,10 @@
       <td>0</td>
       <td>1</td>
       <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>4</td>
-      <td>4</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -60211,11 +73200,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>82</td>
-      <td>812</td>
+      <td>1199</td>
+      <td>1199</td>
+      <td>193</td>
+      <td>193</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1205</td>
+      <td>1205</td>
+      <td>194</td>
+      <td>194</td>
     </tr>
     <tr>
       <td></td>
@@ -60244,9 +73248,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -60274,12 +73277,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>104</td>
-      <td>1770</td>
+      <td>1975</td>
+      <td>2034</td>
+      <td>246</td>
+      <td>258</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>553</td>
+      <td>564</td>
+      <td>140</td>
+      <td>144</td>
+      <td>2528</td>
+      <td>2598</td>
+      <td>386</td>
+      <td>402</td>
     </tr>
     <tr>
       <td></td>
@@ -60287,7 +73305,7 @@
       <td>picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile</td>
       <td>Picard SAM/BAM manipulation tools.</td>
       <td>picard_samtofastq</td>
-      <td>picard_reordersam, picard_samtofastq, picard_fastqtosam, picard_replacesamheader</td>
+      <td>picard_samtofastq, picard_replacesamheader, picard_fastqtosam, picard_reordersam</td>
       <td></td>
       <td>picard_samtofastq</td>
       <td>Create a FASTQ file.</td>
@@ -60308,8 +73326,7 @@
       <td>31</td>
       <td>31</td>
       <td>31</td>
-      <td>31</td>
-      <td>31</td>
+      <td>0</td>
       <td>31</td>
       <td>31</td>
       <td>31</td>
@@ -60338,12 +73355,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>31</td>
       <td>31</td>
       <td>31</td>
       <td>0</td>
-      <td>3735</td>
-      <td>374458</td>
+      <td>386934</td>
+      <td>399039</td>
+      <td>11024</td>
+      <td>11956</td>
+      <td>366646</td>
+      <td>589980</td>
+      <td>32000</td>
+      <td>57111</td>
+      <td>56622</td>
+      <td>62258</td>
+      <td>2845</td>
+      <td>3398</td>
+      <td>810202</td>
+      <td>1051277</td>
+      <td>45869</td>
+      <td>72465</td>
     </tr>
     <tr>
       <td></td>
@@ -60406,8 +73438,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>116</td>
+      <td>1607</td>
+      <td>1607</td>
+      <td>41</td>
+      <td>41</td>
+      <td>490</td>
+      <td>490</td>
+      <td>53</td>
+      <td>53</td>
+      <td>127</td>
+      <td>127</td>
+      <td>4</td>
+      <td>4</td>
+      <td>2224</td>
+      <td>2224</td>
+      <td>98</td>
+      <td>98</td>
     </tr>
     <tr>
       <td></td>
@@ -60436,11 +73482,10 @@
       <td>0</td>
       <td>6</td>
       <td>5</td>
-      <td>6</td>
+      <td>0</td>
       <td>0</td>
       <td>6</td>
       <td>5</td>
-      <td>6</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -60467,11 +73512,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>45</td>
-      <td>1095</td>
+      <td>867</td>
+      <td>1128</td>
+      <td>144</td>
+      <td>165</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2106</td>
+      <td>2106</td>
+      <td>121</td>
+      <td>121</td>
+      <td>2973</td>
+      <td>3234</td>
+      <td>265</td>
+      <td>286</td>
     </tr>
     <tr>
       <td></td>
@@ -60534,8 +73594,22 @@
       <td>7</td>
       <td>0</td>
       <td>0</td>
-      <td>88</td>
-      <td>1000</td>
+      <td>2532</td>
+      <td>2532</td>
+      <td>382</td>
+      <td>382</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1311</td>
+      <td>1311</td>
+      <td>83</td>
+      <td>83</td>
+      <td>3844</td>
+      <td>3844</td>
+      <td>466</td>
+      <td>466</td>
     </tr>
     <tr>
       <td></td>
@@ -60564,8 +73638,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -60594,12 +73667,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>467</td>
-      <td>7942</td>
+      <td>9045</td>
+      <td>9458</td>
+      <td>1115</td>
+      <td>1144</td>
+      <td>7989</td>
+      <td>7989</td>
+      <td>1070</td>
+      <td>1070</td>
+      <td>3945</td>
+      <td>4137</td>
+      <td>726</td>
+      <td>741</td>
+      <td>20979</td>
+      <td>21584</td>
+      <td>2911</td>
+      <td>2955</td>
     </tr>
     <tr>
       <td></td>
@@ -60644,7 +73732,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -60658,12 +73745,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>83</td>
-      <td>983</td>
+      <td>1245</td>
+      <td>1245</td>
+      <td>231</td>
+      <td>231</td>
+      <td>9046</td>
+      <td>9046</td>
+      <td>630</td>
+      <td>630</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10291</td>
+      <td>10291</td>
+      <td>861</td>
+      <td>861</td>
     </tr>
     <tr>
       <td></td>
@@ -60726,8 +73828,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>16</td>
-      <td>208</td>
+      <td>201</td>
+      <td>210</td>
+      <td>23</td>
+      <td>24</td>
+      <td>998</td>
+      <td>998</td>
+      <td>76</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1199</td>
+      <td>1208</td>
+      <td>99</td>
+      <td>100</td>
     </tr>
     <tr>
       <td></td>
@@ -60770,7 +73886,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -60786,12 +73901,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>278</td>
-      <td>22589</td>
+      <td>37086</td>
+      <td>37272</td>
+      <td>711</td>
+      <td>734</td>
+      <td>6346</td>
+      <td>6346</td>
+      <td>583</td>
+      <td>583</td>
+      <td>3065</td>
+      <td>3065</td>
+      <td>61</td>
+      <td>61</td>
+      <td>46497</td>
+      <td>46683</td>
+      <td>1355</td>
+      <td>1378</td>
     </tr>
     <tr>
       <td></td>
@@ -60820,8 +73950,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -60851,11 +73980,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
-      <td>22</td>
+      <td>14652</td>
+      <td>14652</td>
+      <td>251</td>
+      <td>251</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>101</td>
+      <td>101</td>
+      <td>18</td>
+      <td>18</td>
+      <td>14753</td>
+      <td>14753</td>
+      <td>269</td>
+      <td>269</td>
     </tr>
     <tr>
       <td></td>
@@ -60884,10 +74028,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -60914,12 +74057,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>46</td>
-      <td>669</td>
+      <td>851</td>
+      <td>851</td>
+      <td>127</td>
+      <td>127</td>
+      <td>249</td>
+      <td>249</td>
+      <td>43</td>
+      <td>43</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1100</td>
+      <td>1100</td>
+      <td>170</td>
+      <td>170</td>
     </tr>
     <tr>
       <td></td>
@@ -60948,9 +74106,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -60979,11 +74136,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>24</td>
-      <td>239</td>
+      <td>731</td>
+      <td>731</td>
+      <td>86</td>
+      <td>86</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>4</td>
+      <td>4</td>
+      <td>773</td>
+      <td>773</td>
+      <td>90</td>
+      <td>90</td>
     </tr>
     <tr>
       <td></td>
@@ -61027,7 +74199,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -61042,12 +74213,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1046</td>
-      <td>185468</td>
+      <td>262015</td>
+      <td>262852</td>
+      <td>2627</td>
+      <td>2711</td>
+      <td>83623</td>
+      <td>83623</td>
+      <td>1918</td>
+      <td>1918</td>
+      <td>52558</td>
+      <td>52558</td>
+      <td>1037</td>
+      <td>1037</td>
+      <td>398196</td>
+      <td>399033</td>
+      <td>5582</td>
+      <td>5666</td>
     </tr>
     <tr>
       <td></td>
@@ -61092,7 +74278,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>13</td>
       <td>0</td>
       <td>0</td>
@@ -61107,11 +74292,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>6</td>
       <td>13</td>
       <td>0</td>
-      <td>409</td>
-      <td>18773</td>
+      <td>19942</td>
+      <td>20587</td>
+      <td>1055</td>
+      <td>1245</td>
+      <td>33619</td>
+      <td>40808</td>
+      <td>2183</td>
+      <td>2594</td>
+      <td>9261</td>
+      <td>9261</td>
+      <td>365</td>
+      <td>365</td>
+      <td>62822</td>
+      <td>70656</td>
+      <td>3603</td>
+      <td>4204</td>
     </tr>
     <tr>
       <td></td>
@@ -61176,6 +74376,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>63244</td>
+      <td>65177</td>
+      <td>1392</td>
+      <td>1599</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>63244</td>
+      <td>65177</td>
+      <td>1392</td>
+      <td>1599</td>
     </tr>
     <tr>
       <td></td>
@@ -61238,8 +74452,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>254</td>
-      <td>2350</td>
+      <td>3463</td>
+      <td>3463</td>
+      <td>538</td>
+      <td>538</td>
+      <td>1853</td>
+      <td>1853</td>
+      <td>256</td>
+      <td>256</td>
+      <td>1097</td>
+      <td>1097</td>
+      <td>70</td>
+      <td>70</td>
+      <td>6413</td>
+      <td>6413</td>
+      <td>864</td>
+      <td>864</td>
     </tr>
     <tr>
       <td></td>
@@ -61268,10 +74496,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -61298,12 +74525,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>70</td>
-      <td>7881</td>
+      <td>10152</td>
+      <td>10626</td>
+      <td>253</td>
+      <td>281</td>
+      <td>10581</td>
+      <td>10581</td>
+      <td>1240</td>
+      <td>1240</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20733</td>
+      <td>21207</td>
+      <td>1493</td>
+      <td>1521</td>
     </tr>
     <tr>
       <td></td>
@@ -61332,9 +74574,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -61345,7 +74586,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -61367,7 +74608,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1902</td>
+      <td>1902</td>
+      <td>167</td>
+      <td>167</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1902</td>
+      <td>1902</td>
+      <td>167</td>
+      <td>167</td>
     </tr>
     <tr>
       <td></td>
@@ -61412,7 +74668,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -61427,11 +74682,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>286</td>
-      <td>1734</td>
+      <td>2064</td>
+      <td>2173</td>
+      <td>678</td>
+      <td>695</td>
+      <td>2900</td>
+      <td>2900</td>
+      <td>1034</td>
+      <td>1034</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4964</td>
+      <td>5073</td>
+      <td>1712</td>
+      <td>1729</td>
     </tr>
     <tr>
       <td></td>
@@ -61460,8 +74730,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -61490,12 +74759,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3233</td>
-      <td>371445</td>
+      <td>464359</td>
+      <td>476554</td>
+      <td>7475</td>
+      <td>7721</td>
+      <td>313285</td>
+      <td>331256</td>
+      <td>11243</td>
+      <td>12384</td>
+      <td>131211</td>
+      <td>141875</td>
+      <td>4358</td>
+      <td>4947</td>
+      <td>908855</td>
+      <td>949685</td>
+      <td>23076</td>
+      <td>25052</td>
     </tr>
     <tr>
       <td></td>
@@ -61558,8 +74842,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
-      <td>5</td>
+      <td>10</td>
+      <td>10</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>7</td>
+      <td>7</td>
     </tr>
     <tr>
       <td></td>
@@ -61604,7 +74902,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -61618,12 +74915,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>200</td>
-      <td>3320</td>
+      <td>3962</td>
+      <td>3962</td>
+      <td>501</td>
+      <td>501</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3962</td>
+      <td>3962</td>
+      <td>501</td>
+      <td>501</td>
     </tr>
     <tr>
       <td></td>
@@ -61686,8 +74998,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>15</td>
+      <td>24</td>
+      <td>24</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>24</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -61750,8 +75076,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>36</td>
-      <td>1423</td>
+      <td>1319</td>
+      <td>1507</td>
+      <td>81</td>
+      <td>92</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1319</td>
+      <td>1507</td>
+      <td>81</td>
+      <td>92</td>
     </tr>
     <tr>
       <td></td>
@@ -61814,8 +75154,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>167</td>
-      <td>16800</td>
+      <td>17782</td>
+      <td>17782</td>
+      <td>287</td>
+      <td>287</td>
+      <td>853</td>
+      <td>853</td>
+      <td>65</td>
+      <td>65</td>
+      <td>2224</td>
+      <td>2224</td>
+      <td>65</td>
+      <td>65</td>
+      <td>20859</td>
+      <td>20859</td>
+      <td>417</td>
+      <td>417</td>
     </tr>
     <tr>
       <td></td>
@@ -61844,8 +75198,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -61875,11 +75228,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>350</td>
-      <td>21123</td>
+      <td>22742</td>
+      <td>22742</td>
+      <td>557</td>
+      <td>557</td>
+      <td>2159</td>
+      <td>2159</td>
+      <td>716</td>
+      <td>716</td>
+      <td>776</td>
+      <td>776</td>
+      <td>448</td>
+      <td>448</td>
+      <td>25677</td>
+      <td>25677</td>
+      <td>1721</td>
+      <td>1721</td>
     </tr>
     <tr>
       <td></td>
@@ -61942,8 +75310,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>38</td>
-      <td>2424</td>
+      <td>2716</td>
+      <td>2716</td>
+      <td>104</td>
+      <td>104</td>
+      <td>134</td>
+      <td>134</td>
+      <td>43</td>
+      <td>43</td>
+      <td>40</td>
+      <td>40</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2890</td>
+      <td>2890</td>
+      <td>148</td>
+      <td>148</td>
     </tr>
     <tr>
       <td></td>
@@ -61972,8 +75354,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -62002,12 +75383,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>377</td>
-      <td>11332</td>
+      <td>12858</td>
+      <td>13232</td>
+      <td>986</td>
+      <td>996</td>
+      <td>8092</td>
+      <td>8092</td>
+      <td>943</td>
+      <td>943</td>
+      <td>3238</td>
+      <td>3238</td>
+      <td>124</td>
+      <td>124</td>
+      <td>24188</td>
+      <td>24562</td>
+      <td>2053</td>
+      <td>2063</td>
     </tr>
     <tr>
       <td></td>
@@ -62030,7 +75426,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb</td>
       <td>1.4.2</td>
       <td>pysradb</td>
-      <td>2.2.1</td>
+      <td>2.2.2</td>
       <td>Deposition, Data retrieval</td>
       <td>Sequencing, Gene transcripts, Bioinformatics</td>
       <td>0</td>
@@ -62052,7 +75448,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -62067,11 +75462,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>26</td>
-      <td>144</td>
+      <td>163</td>
+      <td>163</td>
+      <td>35</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>163</td>
+      <td>163</td>
+      <td>35</td>
+      <td>35</td>
     </tr>
     <tr>
       <td></td>
@@ -62136,6 +75546,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -62164,10 +75588,9 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -62195,11 +75618,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>68</td>
-      <td>1909</td>
+      <td>2092</td>
+      <td>2342</td>
+      <td>209</td>
+      <td>238</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2094</td>
+      <td>2344</td>
+      <td>210</td>
+      <td>239</td>
     </tr>
     <tr>
       <td></td>
@@ -62228,10 +75666,9 @@
       <td>0</td>
       <td>0</td>
       <td>32</td>
-      <td>32</td>
       <td>0</td>
       <td>0</td>
-      <td>32</td>
+      <td>0</td>
       <td>32</td>
       <td>0</td>
       <td>0</td>
@@ -62259,11 +75696,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>31</td>
       <td>31</td>
       <td>0</td>
-      <td>1155</td>
-      <td>28681</td>
+      <td>31825</td>
+      <td>34677</td>
+      <td>3375</td>
+      <td>3785</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>14</td>
+      <td>14</td>
+      <td>4</td>
+      <td>4</td>
+      <td>31840</td>
+      <td>34692</td>
+      <td>3380</td>
+      <td>3790</td>
     </tr>
     <tr>
       <td></td>
@@ -62326,8 +75778,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>8</td>
+      <td>8</td>
     </tr>
     <tr>
       <td></td>
@@ -62392,6 +75858,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -62420,11 +75900,10 @@
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>1</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -62450,12 +75929,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
-      <td>1328</td>
-      <td>664470</td>
+      <td>684820</td>
+      <td>684820</td>
+      <td>3239</td>
+      <td>3239</td>
+      <td>90503</td>
+      <td>90503</td>
+      <td>3881</td>
+      <td>3881</td>
+      <td>29018</td>
+      <td>29018</td>
+      <td>826</td>
+      <td>826</td>
+      <td>804341</td>
+      <td>804341</td>
+      <td>7946</td>
+      <td>7946</td>
     </tr>
     <tr>
       <td></td>
@@ -62484,8 +75978,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -62514,12 +76007,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3567</td>
-      <td>51567</td>
+      <td>67737</td>
+      <td>69738</td>
+      <td>7787</td>
+      <td>7971</td>
+      <td>51925</td>
+      <td>56602</td>
+      <td>9692</td>
+      <td>10646</td>
+      <td>32003</td>
+      <td>34145</td>
+      <td>3890</td>
+      <td>4127</td>
+      <td>151665</td>
+      <td>160485</td>
+      <td>21369</td>
+      <td>22744</td>
     </tr>
     <tr>
       <td></td>
@@ -62582,8 +76090,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -62612,11 +76134,10 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>1</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -62642,12 +76163,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>561</td>
-      <td>124536</td>
+      <td>130124</td>
+      <td>135361</td>
+      <td>1265</td>
+      <td>1305</td>
+      <td>11135</td>
+      <td>11135</td>
+      <td>922</td>
+      <td>922</td>
+      <td>5939</td>
+      <td>5939</td>
+      <td>153</td>
+      <td>153</td>
+      <td>147198</td>
+      <td>152435</td>
+      <td>2340</td>
+      <td>2380</td>
     </tr>
     <tr>
       <td></td>
@@ -62665,7 +76201,7 @@
       <td>https://github.com/mahulchak/quickmerge</td>
       <td>Assembly</td>
       <td>quickmerge</td>
-      <td>galaxy-australia</td>
+      <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge</td>
       <td>0.3</td>
@@ -62712,6 +76248,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -62740,11 +76290,11 @@
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>1</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -62774,8 +76324,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>82</td>
-      <td>4569</td>
+      <td>3077</td>
+      <td>4581</td>
+      <td>395</td>
+      <td>518</td>
+      <td>2856</td>
+      <td>2856</td>
+      <td>1093</td>
+      <td>1093</td>
+      <td>1977</td>
+      <td>1977</td>
+      <td>19</td>
+      <td>19</td>
+      <td>7910</td>
+      <td>9414</td>
+      <td>1507</td>
+      <td>1630</td>
     </tr>
     <tr>
       <td></td>
@@ -62804,9 +76368,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -62835,11 +76398,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>237</td>
-      <td>2833</td>
+      <td>4844</td>
+      <td>4844</td>
+      <td>480</td>
+      <td>480</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>3</td>
+      <td>3</td>
+      <td>4851</td>
+      <td>4851</td>
+      <td>483</td>
+      <td>483</td>
     </tr>
     <tr>
       <td></td>
@@ -62868,8 +76446,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -62899,11 +76476,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>14</td>
-      <td>176</td>
+      <td>339</td>
+      <td>339</td>
+      <td>30</td>
+      <td>30</td>
+      <td>1737</td>
+      <td>1737</td>
+      <td>256</td>
+      <td>256</td>
+      <td>6</td>
+      <td>6</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2082</td>
+      <td>2082</td>
+      <td>287</td>
+      <td>287</td>
     </tr>
     <tr>
       <td></td>
@@ -62966,8 +76558,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>9</td>
+      <td>9</td>
     </tr>
     <tr>
       <td></td>
@@ -62996,9 +76602,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -63027,11 +76632,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>262</td>
-      <td>6902</td>
+      <td>9477</td>
+      <td>9477</td>
+      <td>438</td>
+      <td>438</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10585</td>
+      <td>10585</td>
+      <td>182</td>
+      <td>182</td>
+      <td>20062</td>
+      <td>20062</td>
+      <td>620</td>
+      <td>620</td>
     </tr>
     <tr>
       <td></td>
@@ -63060,8 +76680,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -63090,12 +76709,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>383</td>
-      <td>6808</td>
+      <td>10905</td>
+      <td>10905</td>
+      <td>966</td>
+      <td>966</td>
+      <td>5100</td>
+      <td>5114</td>
+      <td>587</td>
+      <td>587</td>
+      <td>4955</td>
+      <td>6094</td>
+      <td>765</td>
+      <td>892</td>
+      <td>20960</td>
+      <td>22113</td>
+      <td>2318</td>
+      <td>2445</td>
     </tr>
     <tr>
       <td></td>
@@ -63158,8 +76792,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>30</td>
-      <td>569</td>
+      <td>655</td>
+      <td>655</td>
+      <td>57</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>655</td>
+      <td>655</td>
+      <td>57</td>
+      <td>57</td>
     </tr>
     <tr>
       <td></td>
@@ -63204,7 +76852,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -63219,11 +76866,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>71</td>
-      <td>3370</td>
+      <td>3710</td>
+      <td>3710</td>
+      <td>80</td>
+      <td>80</td>
+      <td>7</td>
+      <td>7</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3717</td>
+      <td>3717</td>
+      <td>86</td>
+      <td>86</td>
     </tr>
     <tr>
       <td></td>
@@ -63252,8 +76914,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -63283,11 +76944,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>48</td>
-      <td>331</td>
+      <td>472</td>
+      <td>472</td>
+      <td>92</td>
+      <td>92</td>
+      <td>32</td>
+      <td>32</td>
+      <td>13</td>
+      <td>13</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td>510</td>
+      <td>510</td>
+      <td>109</td>
+      <td>109</td>
     </tr>
     <tr>
       <td></td>
@@ -63316,8 +76992,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -63347,11 +77022,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>88</td>
-      <td>578</td>
+      <td>859</td>
+      <td>859</td>
+      <td>203</td>
+      <td>203</td>
+      <td>305</td>
+      <td>305</td>
+      <td>142</td>
+      <td>142</td>
+      <td>227</td>
+      <td>227</td>
+      <td>58</td>
+      <td>58</td>
+      <td>1391</td>
+      <td>1391</td>
+      <td>403</td>
+      <td>403</td>
     </tr>
     <tr>
       <td></td>
@@ -63380,11 +77070,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -63414,8 +77104,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>248</td>
-      <td>3750</td>
+      <td>5998</td>
+      <td>5998</td>
+      <td>810</td>
+      <td>810</td>
+      <td>7618</td>
+      <td>7618</td>
+      <td>803</td>
+      <td>803</td>
+      <td>3135</td>
+      <td>3135</td>
+      <td>292</td>
+      <td>292</td>
+      <td>16751</td>
+      <td>16751</td>
+      <td>1905</td>
+      <td>1905</td>
     </tr>
     <tr>
       <td></td>
@@ -63444,8 +77148,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -63475,11 +77178,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>217</td>
-      <td>1177</td>
+      <td>7963</td>
+      <td>7963</td>
+      <td>413</td>
+      <td>413</td>
+      <td>1485</td>
+      <td>1485</td>
+      <td>220</td>
+      <td>220</td>
+      <td>8402</td>
+      <td>8402</td>
+      <td>168</td>
+      <td>168</td>
+      <td>17850</td>
+      <td>17850</td>
+      <td>801</td>
+      <td>801</td>
     </tr>
     <tr>
       <td></td>
@@ -63544,6 +77262,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>415</td>
+      <td>721</td>
+      <td>128</td>
+      <td>219</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>415</td>
+      <td>721</td>
+      <td>128</td>
+      <td>219</td>
     </tr>
     <tr>
       <td></td>
@@ -63572,10 +77304,9 @@
       <td>2</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -63602,12 +77333,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>33</td>
-      <td>3456</td>
+      <td>3543</td>
+      <td>3619</td>
+      <td>108</td>
+      <td>111</td>
+      <td>536</td>
+      <td>536</td>
+      <td>157</td>
+      <td>157</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4079</td>
+      <td>4155</td>
+      <td>265</td>
+      <td>268</td>
     </tr>
     <tr>
       <td></td>
@@ -63670,8 +77416,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5</td>
-      <td>85</td>
+      <td>75</td>
+      <td>86</td>
+      <td>8</td>
+      <td>9</td>
+      <td>138</td>
+      <td>216</td>
+      <td>30</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>213</td>
+      <td>302</td>
+      <td>38</td>
+      <td>66</td>
     </tr>
     <tr>
       <td></td>
@@ -63734,8 +77494,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>2444</td>
+      <td>2444</td>
+      <td>52</td>
+      <td>52</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2444</td>
+      <td>2444</td>
+      <td>52</td>
+      <td>52</td>
     </tr>
     <tr>
       <td></td>
@@ -63798,8 +77572,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
       <td>44</td>
+      <td>44</td>
+      <td>6</td>
+      <td>6</td>
+      <td>77</td>
+      <td>77</td>
+      <td>35</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>41</td>
+      <td>41</td>
     </tr>
     <tr>
       <td></td>
@@ -63828,8 +77616,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -63858,12 +77645,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>4015</td>
-      <td>425658</td>
+      <td>438078</td>
+      <td>473957</td>
+      <td>10142</td>
+      <td>10900</td>
+      <td>325474</td>
+      <td>403925</td>
+      <td>15284</td>
+      <td>18791</td>
+      <td>49662</td>
+      <td>53138</td>
+      <td>1359</td>
+      <td>1449</td>
+      <td>813214</td>
+      <td>931020</td>
+      <td>26785</td>
+      <td>31140</td>
     </tr>
     <tr>
       <td></td>
@@ -63926,8 +77728,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>14</td>
-      <td>161</td>
+      <td>171</td>
+      <td>171</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>171</td>
+      <td>171</td>
+      <td>20</td>
+      <td>20</td>
     </tr>
     <tr>
       <td></td>
@@ -63956,11 +77772,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -63990,8 +77806,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>109</td>
-      <td>1110</td>
+      <td>1522</td>
+      <td>1522</td>
+      <td>254</td>
+      <td>254</td>
+      <td>372</td>
+      <td>372</td>
+      <td>75</td>
+      <td>75</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1899</td>
+      <td>1899</td>
+      <td>330</td>
+      <td>330</td>
     </tr>
     <tr>
       <td></td>
@@ -64020,8 +77850,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -64050,12 +77879,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>656</td>
-      <td>12225</td>
+      <td>15196</td>
+      <td>15685</td>
+      <td>1459</td>
+      <td>1501</td>
+      <td>12188</td>
+      <td>12188</td>
+      <td>1768</td>
+      <td>1768</td>
+      <td>4881</td>
+      <td>5539</td>
+      <td>518</td>
+      <td>555</td>
+      <td>32265</td>
+      <td>33412</td>
+      <td>3745</td>
+      <td>3824</td>
     </tr>
     <tr>
       <td></td>
@@ -64120,6 +77964,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -64184,6 +78042,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -64248,6 +78120,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -64312,6 +78198,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -64376,6 +78276,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -64440,6 +78354,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -64468,8 +78396,7 @@
       <td>22</td>
       <td>22</td>
       <td>22</td>
-      <td>22</td>
-      <td>22</td>
+      <td>0</td>
       <td>22</td>
       <td>22</td>
       <td>22</td>
@@ -64498,12 +78425,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>22</td>
       <td>22</td>
       <td>22</td>
       <td>0</td>
-      <td>3206</td>
-      <td>133498</td>
+      <td>136315</td>
+      <td>147595</td>
+      <td>8341</td>
+      <td>9385</td>
+      <td>138707</td>
+      <td>161046</td>
+      <td>10696</td>
+      <td>12789</td>
+      <td>22718</td>
+      <td>23767</td>
+      <td>1593</td>
+      <td>1695</td>
+      <td>297740</td>
+      <td>332408</td>
+      <td>20630</td>
+      <td>23869</td>
     </tr>
     <tr>
       <td></td>
@@ -64555,19 +78497,33 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>76</td>
-      <td>1236</td>
+      <td>1286</td>
+      <td>1364</td>
+      <td>178</td>
+      <td>193</td>
+      <td>2220</td>
+      <td>2220</td>
+      <td>299</td>
+      <td>299</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3506</td>
+      <td>3584</td>
+      <td>477</td>
+      <td>492</td>
     </tr>
     <tr>
       <td></td>
@@ -64612,7 +78568,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -64626,12 +78581,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>84</td>
-      <td>454</td>
+      <td>463</td>
+      <td>463</td>
+      <td>119</td>
+      <td>119</td>
+      <td>1038</td>
+      <td>1038</td>
+      <td>87</td>
+      <td>87</td>
+      <td>410</td>
+      <td>410</td>
+      <td>24</td>
+      <td>24</td>
+      <td>1911</td>
+      <td>1911</td>
+      <td>230</td>
+      <td>230</td>
     </tr>
     <tr>
       <td></td>
@@ -64645,14 +78615,14 @@
       <td>A tool to mark duplicates and extract discordant and split reads from SAM files.</td>
       <td>Split read mapping</td>
       <td>DNA, Sequencing, Mapping</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/GregoryFaust/samblaster</td>
       <td>SAM, Fastq Manipulation, Variant Analysis</td>
       <td>samblaster</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster</td>
-      <td>0.1.24</td>
+      <td>0.1.26</td>
       <td>samblaster</td>
       <td>0.1.26</td>
       <td>Split read mapping</td>
@@ -64696,6 +78666,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -64760,6 +78744,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -64822,8 +78820,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>18</td>
-      <td>123</td>
+      <td>138</td>
+      <td>138</td>
+      <td>36</td>
+      <td>36</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>138</td>
+      <td>138</td>
+      <td>36</td>
+      <td>36</td>
     </tr>
     <tr>
       <td></td>
@@ -64886,8 +78898,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>7</td>
-      <td>173</td>
+      <td>174</td>
+      <td>174</td>
+      <td>16</td>
+      <td>16</td>
+      <td>399</td>
+      <td>399</td>
+      <td>29</td>
+      <td>29</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>573</td>
+      <td>573</td>
+      <td>45</td>
+      <td>45</td>
     </tr>
     <tr>
       <td></td>
@@ -64950,8 +78976,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>140</td>
+      <td>140</td>
+      <td>5</td>
+      <td>5</td>
+      <td>253</td>
+      <td>253</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>393</td>
+      <td>393</td>
+      <td>11</td>
+      <td>11</td>
     </tr>
     <tr>
       <td></td>
@@ -65016,6 +79056,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -65078,8 +79132,22 @@
       <td>6</td>
       <td>6</td>
       <td>0</td>
-      <td>766</td>
-      <td>51978</td>
+      <td>63789</td>
+      <td>64034</td>
+      <td>2543</td>
+      <td>2547</td>
+      <td>29962</td>
+      <td>29962</td>
+      <td>1185</td>
+      <td>1185</td>
+      <td>18028</td>
+      <td>18028</td>
+      <td>379</td>
+      <td>379</td>
+      <td>111779</td>
+      <td>112024</td>
+      <td>4107</td>
+      <td>4111</td>
     </tr>
     <tr>
       <td></td>
@@ -65142,8 +79210,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>77</td>
-      <td>1365</td>
+      <td>1345</td>
+      <td>1371</td>
+      <td>350</td>
+      <td>351</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>903</td>
+      <td>903</td>
+      <td>29</td>
+      <td>29</td>
+      <td>2248</td>
+      <td>2274</td>
+      <td>379</td>
+      <td>380</td>
     </tr>
     <tr>
       <td></td>
@@ -65195,7 +79277,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -65206,8 +79287,23 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>90</td>
-      <td>721</td>
+      <td>0</td>
+      <td>1059</td>
+      <td>1059</td>
+      <td>222</td>
+      <td>222</td>
+      <td>426</td>
+      <td>426</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1486</td>
+      <td>1486</td>
+      <td>294</td>
+      <td>294</td>
     </tr>
     <tr>
       <td></td>
@@ -65270,8 +79366,22 @@
       <td>16</td>
       <td>16</td>
       <td>0</td>
-      <td>23</td>
-      <td>779</td>
+      <td>809</td>
+      <td>809</td>
+      <td>78</td>
+      <td>78</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>105</td>
+      <td>105</td>
+      <td>16</td>
+      <td>16</td>
+      <td>917</td>
+      <td>917</td>
+      <td>96</td>
+      <td>96</td>
     </tr>
     <tr>
       <td></td>
@@ -65334,8 +79444,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1503</td>
+      <td>1955</td>
+      <td>283</td>
+      <td>402</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1504</td>
+      <td>1956</td>
+      <td>284</td>
+      <td>403</td>
     </tr>
     <tr>
       <td></td>
@@ -65380,7 +79504,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -65395,11 +79518,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>61</td>
-      <td>676</td>
+      <td>901</td>
+      <td>901</td>
+      <td>90</td>
+      <td>90</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>901</td>
+      <td>901</td>
+      <td>90</td>
+      <td>90</td>
     </tr>
     <tr>
       <td></td>
@@ -65462,8 +79600,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>11</td>
-      <td>628</td>
+      <td>284</td>
+      <td>632</td>
+      <td>34</td>
+      <td>38</td>
+      <td>786</td>
+      <td>786</td>
+      <td>61</td>
+      <td>61</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1071</td>
+      <td>1419</td>
+      <td>96</td>
+      <td>100</td>
     </tr>
     <tr>
       <td></td>
@@ -65526,8 +79678,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>50</td>
-      <td>3647</td>
+      <td>5106</td>
+      <td>5106</td>
+      <td>116</td>
+      <td>116</td>
+      <td>6419</td>
+      <td>6419</td>
+      <td>241</td>
+      <td>241</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11525</td>
+      <td>11525</td>
+      <td>357</td>
+      <td>357</td>
     </tr>
     <tr>
       <td></td>
@@ -65592,6 +79758,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -65620,11 +79800,11 @@
       <td>0</td>
       <td>0</td>
       <td>6</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>6</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -65654,8 +79834,22 @@
       <td>6</td>
       <td>0</td>
       <td>0</td>
-      <td>39</td>
-      <td>542</td>
+      <td>931</td>
+      <td>931</td>
+      <td>93</td>
+      <td>93</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>931</td>
+      <td>931</td>
+      <td>93</td>
+      <td>93</td>
     </tr>
     <tr>
       <td></td>
@@ -65718,8 +79912,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>16</td>
-      <td>288</td>
+      <td>342</td>
+      <td>342</td>
+      <td>40</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>342</td>
+      <td>342</td>
+      <td>40</td>
+      <td>40</td>
     </tr>
     <tr>
       <td></td>
@@ -65767,7 +79975,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -65779,11 +79986,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>16</td>
-      <td>68</td>
+      <td>70</td>
+      <td>70</td>
+      <td>19</td>
+      <td>19</td>
+      <td>109</td>
+      <td>109</td>
+      <td>47</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>179</td>
+      <td>179</td>
+      <td>66</td>
+      <td>66</td>
     </tr>
     <tr>
       <td></td>
@@ -65812,11 +80034,10 @@
       <td>0</td>
       <td>2</td>
       <td>5</td>
-      <td>3</td>
+      <td>0</td>
       <td>0</td>
       <td>2</td>
       <td>5</td>
-      <td>3</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -65843,11 +80064,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>129</td>
-      <td>1964</td>
+      <td>3364</td>
+      <td>3364</td>
+      <td>247</td>
+      <td>247</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>244</td>
+      <td>244</td>
+      <td>33</td>
+      <td>33</td>
+      <td>3608</td>
+      <td>3608</td>
+      <td>280</td>
+      <td>280</td>
     </tr>
     <tr>
       <td></td>
@@ -65910,8 +80146,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>2424</td>
+      <td>2424</td>
+      <td>102</td>
+      <td>102</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2424</td>
+      <td>2424</td>
+      <td>102</td>
+      <td>102</td>
     </tr>
     <tr>
       <td></td>
@@ -65974,8 +80224,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>4182</td>
+      <td>4182</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
-      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4182</td>
+      <td>4182</td>
+      <td>42</td>
+      <td>42</td>
     </tr>
     <tr>
       <td></td>
@@ -66004,8 +80268,7 @@
       <td>15</td>
       <td>15</td>
       <td>15</td>
-      <td>15</td>
-      <td>15</td>
+      <td>0</td>
       <td>15</td>
       <td>15</td>
       <td>15</td>
@@ -66034,12 +80297,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>14</td>
       <td>14</td>
       <td>14</td>
       <td>14</td>
-      <td>753</td>
-      <td>59668</td>
+      <td>72816</td>
+      <td>73514</td>
+      <td>2210</td>
+      <td>2300</td>
+      <td>102777</td>
+      <td>107831</td>
+      <td>2313</td>
+      <td>2669</td>
+      <td>154613</td>
+      <td>154613</td>
+      <td>682</td>
+      <td>682</td>
+      <td>330206</td>
+      <td>335958</td>
+      <td>5205</td>
+      <td>5651</td>
     </tr>
     <tr>
       <td></td>
@@ -66102,8 +80380,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>271</td>
+      <td>271</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>271</td>
+      <td>271</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -66132,11 +80424,10 @@
       <td>1</td>
       <td>1</td>
       <td>7</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>7</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -66167,7 +80458,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>11</td>
+      <td>11</td>
+      <td>32</td>
+      <td>32</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>153</td>
+      <td>153</td>
+      <td>16</td>
+      <td>16</td>
     </tr>
     <tr>
       <td></td>
@@ -66212,7 +80518,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66226,12 +80531,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>154</td>
-      <td>763</td>
+      <td>913</td>
+      <td>913</td>
+      <td>308</td>
+      <td>308</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>568</td>
+      <td>568</td>
+      <td>73</td>
+      <td>73</td>
+      <td>1481</td>
+      <td>1481</td>
+      <td>381</td>
+      <td>381</td>
     </tr>
     <tr>
       <td></td>
@@ -66276,7 +80596,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66296,6 +80615,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -66324,8 +80658,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -66354,12 +80687,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1008</td>
-      <td>41600</td>
+      <td>46125</td>
+      <td>47376</td>
+      <td>2273</td>
+      <td>2356</td>
+      <td>40577</td>
+      <td>40577</td>
+      <td>3971</td>
+      <td>3971</td>
+      <td>19960</td>
+      <td>21130</td>
+      <td>1085</td>
+      <td>1199</td>
+      <td>106662</td>
+      <td>109083</td>
+      <td>7329</td>
+      <td>7526</td>
     </tr>
     <tr>
       <td></td>
@@ -66388,10 +80736,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66421,9 +80768,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>269</td>
-      <td>14982</td>
+      <td>18184</td>
+      <td>18937</td>
+      <td>555</td>
+      <td>608</td>
+      <td>10514</td>
+      <td>10514</td>
+      <td>1063</td>
+      <td>1063</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>28698</td>
+      <td>29451</td>
+      <td>1618</td>
+      <td>1671</td>
     </tr>
     <tr>
       <td></td>
@@ -66486,8 +80848,22 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>34</td>
-      <td>142</td>
+      <td>220</td>
+      <td>220</td>
+      <td>68</td>
+      <td>68</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>416</td>
+      <td>416</td>
+      <td>10</td>
+      <td>10</td>
+      <td>636</td>
+      <td>636</td>
+      <td>78</td>
+      <td>78</td>
     </tr>
     <tr>
       <td></td>
@@ -66532,7 +80908,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -66546,12 +80921,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>42</td>
-      <td>1128</td>
+      <td>1369</td>
+      <td>1369</td>
+      <td>125</td>
+      <td>125</td>
+      <td>2398</td>
+      <td>2398</td>
+      <td>420</td>
+      <td>420</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3767</td>
+      <td>3767</td>
+      <td>545</td>
+      <td>545</td>
     </tr>
     <tr>
       <td></td>
@@ -66611,75 +81001,103 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>17</td>
-      <td>91</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>slamdunk</td>
-      <td>alleyoop, slamdunk</td>
-      <td>Slamdunk maps and quantifies SLAMseq reads</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>http://t-neumann.github.io/slamdunk</td>
-      <td>RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers</td>
-      <td>slamdunk</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk</td>
-      <td>0.4.3</td>
-      <td>slamdunk</td>
-      <td>0.4.3</td>
-      <td></td>
-      <td></td>
-      <td>2</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>2</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
+      <td>284</td>
+      <td>284</td>
+      <td>70</td>
+      <td>70</td>
+      <td>165</td>
+      <td>165</td>
+      <td>38</td>
+      <td>38</td>
+      <td>14</td>
+      <td>14</td>
+      <td>2</td>
+      <td>2</td>
+      <td>463</td>
+      <td>463</td>
+      <td>110</td>
+      <td>110</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>slamdunk</td>
+      <td>alleyoop, slamdunk</td>
+      <td>Slamdunk maps and quantifies SLAMseq reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://t-neumann.github.io/slamdunk</td>
+      <td>RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers</td>
+      <td>slamdunk</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk</td>
+      <td>0.4.3</td>
+      <td>slamdunk</td>
+      <td>0.4.3</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
       <td>0</td>
       <td>2</td>
+      <td>0</td>
       <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>2</td>
-      <td>361</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>346</td>
+      <td>362</td>
+      <td>16</td>
+      <td>16</td>
+      <td>872</td>
+      <td>872</td>
+      <td>67</td>
+      <td>67</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1218</td>
+      <td>1234</td>
+      <td>83</td>
+      <td>83</td>
     </tr>
     <tr>
       <td></td>
@@ -66742,8 +81160,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
-      <td>64</td>
+      <td>141</td>
+      <td>141</td>
+      <td>26</td>
+      <td>26</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>141</td>
+      <td>141</td>
+      <td>26</td>
+      <td>26</td>
     </tr>
     <tr>
       <td></td>
@@ -66806,8 +81238,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>6</td>
-      <td>121</td>
+      <td>158</td>
+      <td>158</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>8</td>
+      <td>8</td>
     </tr>
     <tr>
       <td></td>
@@ -66870,8 +81316,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>22</td>
-      <td>203</td>
+      <td>325</td>
+      <td>325</td>
+      <td>61</td>
+      <td>61</td>
+      <td>137</td>
+      <td>137</td>
+      <td>54</td>
+      <td>54</td>
+      <td>843</td>
+      <td>843</td>
+      <td>63</td>
+      <td>63</td>
+      <td>1305</td>
+      <td>1305</td>
+      <td>178</td>
+      <td>178</td>
     </tr>
     <tr>
       <td></td>
@@ -66934,8 +81394,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>133</td>
-      <td>1349</td>
+      <td>1499</td>
+      <td>1638</td>
+      <td>331</td>
+      <td>358</td>
+      <td>779</td>
+      <td>779</td>
+      <td>244</td>
+      <td>244</td>
+      <td>467</td>
+      <td>467</td>
+      <td>83</td>
+      <td>83</td>
+      <td>2745</td>
+      <td>2884</td>
+      <td>658</td>
+      <td>685</td>
     </tr>
     <tr>
       <td></td>
@@ -66998,8 +81472,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1817</td>
+      <td>1817</td>
+      <td>14</td>
+      <td>14</td>
+      <td>4</td>
+      <td>4</td>
+      <td>2</td>
+      <td>2</td>
+      <td>136</td>
+      <td>136</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1957</td>
+      <td>1957</td>
+      <td>20</td>
+      <td>20</td>
     </tr>
     <tr>
       <td></td>
@@ -67028,8 +81516,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -67058,12 +81545,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>58</td>
-      <td>919</td>
+      <td>1141</td>
+      <td>1141</td>
+      <td>134</td>
+      <td>134</td>
+      <td>606</td>
+      <td>606</td>
+      <td>156</td>
+      <td>156</td>
+      <td>2267</td>
+      <td>2267</td>
+      <td>80</td>
+      <td>80</td>
+      <td>4014</td>
+      <td>4014</td>
+      <td>370</td>
+      <td>370</td>
     </tr>
     <tr>
       <td></td>
@@ -67108,7 +81610,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -67123,11 +81624,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>22</td>
-      <td>669</td>
+      <td>905</td>
+      <td>905</td>
+      <td>44</td>
+      <td>44</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>905</td>
+      <td>905</td>
+      <td>44</td>
+      <td>44</td>
     </tr>
     <tr>
       <td></td>
@@ -67156,8 +81672,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -67186,12 +81701,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>2</td>
       <td>0</td>
-      <td>1372</td>
-      <td>105708</td>
+      <td>121363</td>
+      <td>124773</td>
+      <td>3448</td>
+      <td>3602</td>
+      <td>92504</td>
+      <td>92504</td>
+      <td>3945</td>
+      <td>3945</td>
+      <td>48068</td>
+      <td>52034</td>
+      <td>2705</td>
+      <td>3073</td>
+      <td>261935</td>
+      <td>269311</td>
+      <td>10098</td>
+      <td>10620</td>
     </tr>
     <tr>
       <td></td>
@@ -67236,7 +81766,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -67250,12 +81779,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>367</td>
-      <td>4558</td>
+      <td>6555</td>
+      <td>6555</td>
+      <td>807</td>
+      <td>807</td>
+      <td>5336</td>
+      <td>5336</td>
+      <td>171</td>
+      <td>171</td>
+      <td>1143</td>
+      <td>1143</td>
+      <td>182</td>
+      <td>182</td>
+      <td>13034</td>
+      <td>13034</td>
+      <td>1160</td>
+      <td>1160</td>
     </tr>
     <tr>
       <td></td>
@@ -67300,7 +81844,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -67314,12 +81857,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>284</td>
-      <td>5107</td>
+      <td>6597</td>
+      <td>6597</td>
+      <td>663</td>
+      <td>663</td>
+      <td>1467</td>
+      <td>1467</td>
+      <td>256</td>
+      <td>256</td>
+      <td>1279</td>
+      <td>1279</td>
+      <td>114</td>
+      <td>114</td>
+      <td>9343</td>
+      <td>9343</td>
+      <td>1033</td>
+      <td>1033</td>
     </tr>
     <tr>
       <td></td>
@@ -67348,8 +81906,7 @@
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
@@ -67359,8 +81916,8 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -67378,12 +81935,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>2676</td>
-      <td>95592</td>
+      <td>103826</td>
+      <td>108296</td>
+      <td>7181</td>
+      <td>7908</td>
+      <td>115727</td>
+      <td>178110</td>
+      <td>15871</td>
+      <td>22769</td>
+      <td>11817</td>
+      <td>13155</td>
+      <td>2148</td>
+      <td>2321</td>
+      <td>231370</td>
+      <td>299561</td>
+      <td>25200</td>
+      <td>32998</td>
     </tr>
     <tr>
       <td></td>
@@ -67412,8 +81984,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -67442,12 +82013,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>533</td>
-      <td>760352</td>
+      <td>764895</td>
+      <td>764895</td>
+      <td>1276</td>
+      <td>1276</td>
+      <td>94572</td>
+      <td>94572</td>
+      <td>1636</td>
+      <td>1636</td>
+      <td>26990</td>
+      <td>26990</td>
+      <td>561</td>
+      <td>561</td>
+      <td>886457</td>
+      <td>886457</td>
+      <td>3473</td>
+      <td>3473</td>
     </tr>
     <tr>
       <td></td>
@@ -67476,8 +82062,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -67507,11 +82092,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>156</td>
-      <td>3530</td>
+      <td>3683</td>
+      <td>3683</td>
+      <td>338</td>
+      <td>338</td>
+      <td>1401</td>
+      <td>1401</td>
+      <td>433</td>
+      <td>433</td>
+      <td>1029</td>
+      <td>1029</td>
+      <td>95</td>
+      <td>95</td>
+      <td>6113</td>
+      <td>6113</td>
+      <td>866</td>
+      <td>866</td>
     </tr>
     <tr>
       <td></td>
@@ -67540,8 +82140,7 @@
       <td>8</td>
       <td>8</td>
       <td>8</td>
-      <td>8</td>
-      <td>8</td>
+      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>8</td>
@@ -67551,8 +82150,8 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
       <td>0</td>
+      <td>8</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -67570,12 +82169,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
-      <td>1352</td>
-      <td>5114712</td>
+      <td>5142904</td>
+      <td>5146618</td>
+      <td>3602</td>
+      <td>4283</td>
+      <td>382391</td>
+      <td>421190</td>
+      <td>7013</td>
+      <td>9678</td>
+      <td>104030</td>
+      <td>105024</td>
+      <td>960</td>
+      <td>1184</td>
+      <td>5629325</td>
+      <td>5672832</td>
+      <td>11575</td>
+      <td>15145</td>
     </tr>
     <tr>
       <td></td>
@@ -67638,8 +82252,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>11</td>
-      <td>46</td>
+      <td>52</td>
+      <td>55</td>
+      <td>23</td>
+      <td>24</td>
+      <td>421</td>
+      <td>421</td>
+      <td>75</td>
+      <td>75</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>476</td>
+      <td>98</td>
+      <td>99</td>
     </tr>
     <tr>
       <td></td>
@@ -67702,8 +82330,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>31</td>
-      <td>528</td>
+      <td>509</td>
+      <td>554</td>
+      <td>107</td>
+      <td>128</td>
+      <td>474</td>
+      <td>474</td>
+      <td>190</td>
+      <td>190</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>983</td>
+      <td>1028</td>
+      <td>297</td>
+      <td>318</td>
     </tr>
     <tr>
       <td></td>
@@ -67748,7 +82390,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -67762,12 +82403,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>13</td>
-      <td>621</td>
+      <td>659</td>
+      <td>659</td>
+      <td>42</td>
+      <td>42</td>
+      <td>296</td>
+      <td>296</td>
+      <td>92</td>
+      <td>92</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>955</td>
+      <td>955</td>
+      <td>134</td>
+      <td>134</td>
     </tr>
     <tr>
       <td></td>
@@ -67812,7 +82468,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -67827,11 +82482,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -67839,7 +82509,7 @@
       <td>spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades</td>
       <td>SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.</td>
       <td>spades</td>
-      <td>spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades</td>
+      <td>spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades</td>
       <td></td>
       <td>SPAdes</td>
       <td>St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.</td>
@@ -67860,8 +82530,7 @@
       <td>9</td>
       <td>9</td>
       <td>9</td>
-      <td>9</td>
-      <td>9</td>
+      <td>0</td>
       <td>9</td>
       <td>9</td>
       <td>9</td>
@@ -67890,12 +82559,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>9</td>
       <td>3</td>
       <td>0</td>
-      <td>3547</td>
-      <td>72953</td>
+      <td>82716</td>
+      <td>87113</td>
+      <td>8209</td>
+      <td>8526</td>
+      <td>120471</td>
+      <td>120475</td>
+      <td>14787</td>
+      <td>14790</td>
+      <td>54067</td>
+      <td>61541</td>
+      <td>5817</td>
+      <td>6653</td>
+      <td>257254</td>
+      <td>269129</td>
+      <td>28813</td>
+      <td>29969</td>
     </tr>
     <tr>
       <td></td>
@@ -67940,7 +82624,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -67954,12 +82637,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>34</td>
-      <td>446</td>
+      <td>450</td>
+      <td>491</td>
+      <td>91</td>
+      <td>100</td>
+      <td>4270</td>
+      <td>4270</td>
+      <td>288</td>
+      <td>288</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4720</td>
+      <td>4761</td>
+      <td>379</td>
+      <td>388</td>
     </tr>
     <tr>
       <td></td>
@@ -68024,6 +82722,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -68086,8 +82798,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>12</td>
-      <td>1278</td>
+      <td>1436</td>
+      <td>1436</td>
+      <td>23</td>
+      <td>23</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1436</td>
+      <td>1436</td>
+      <td>23</td>
+      <td>23</td>
     </tr>
     <tr>
       <td></td>
@@ -68150,8 +82876,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>67</td>
+      <td>142</td>
+      <td>142</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>142</td>
+      <td>142</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -68180,8 +82920,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -68210,12 +82949,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>6247</td>
-      <td>350032</td>
+      <td>364871</td>
+      <td>376580</td>
+      <td>16710</td>
+      <td>17342</td>
+      <td>583675</td>
+      <td>678448</td>
+      <td>53271</td>
+      <td>59638</td>
+      <td>48131</td>
+      <td>50455</td>
+      <td>5910</td>
+      <td>6181</td>
+      <td>996677</td>
+      <td>1105483</td>
+      <td>75891</td>
+      <td>83161</td>
     </tr>
     <tr>
       <td></td>
@@ -68260,7 +83014,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -68275,11 +83028,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>22</td>
-      <td>205</td>
+      <td>297</td>
+      <td>297</td>
+      <td>40</td>
+      <td>40</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>368</td>
+      <td>368</td>
+      <td>41</td>
+      <td>41</td>
     </tr>
     <tr>
       <td></td>
@@ -68308,11 +83076,11 @@
       <td>0</td>
       <td>13</td>
       <td>13</td>
-      <td>12</td>
+      <td>0</td>
       <td>0</td>
       <td>13</td>
       <td>13</td>
-      <td>12</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -68342,8 +83110,22 @@
       <td>13</td>
       <td>13</td>
       <td>0</td>
-      <td>152</td>
-      <td>11635</td>
+      <td>6440</td>
+      <td>11998</td>
+      <td>465</td>
+      <td>593</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4070</td>
+      <td>4070</td>
+      <td>76</td>
+      <td>76</td>
+      <td>10510</td>
+      <td>16068</td>
+      <td>541</td>
+      <td>669</td>
     </tr>
     <tr>
       <td></td>
@@ -68372,9 +83154,8 @@
       <td>0</td>
       <td>12</td>
       <td>12</td>
-      <td>12</td>
       <td>0</td>
-      <td>12</td>
+      <td>0</td>
       <td>12</td>
       <td>12</td>
       <td>0</td>
@@ -68403,11 +83184,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>12</td>
       <td>12</td>
       <td>0</td>
-      <td>238</td>
-      <td>7292</td>
+      <td>8437</td>
+      <td>8592</td>
+      <td>626</td>
+      <td>646</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18016</td>
+      <td>18016</td>
+      <td>270</td>
+      <td>270</td>
+      <td>26453</td>
+      <td>26608</td>
+      <td>896</td>
+      <td>916</td>
     </tr>
     <tr>
       <td></td>
@@ -68450,7 +83246,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -68466,12 +83261,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>35</td>
-      <td>1212</td>
+      <td>1312</td>
+      <td>1383</td>
+      <td>82</td>
+      <td>95</td>
+      <td>2198</td>
+      <td>3076</td>
+      <td>234</td>
+      <td>303</td>
+      <td>173</td>
+      <td>173</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3683</td>
+      <td>4632</td>
+      <td>319</td>
+      <td>401</td>
     </tr>
     <tr>
       <td></td>
@@ -68536,6 +83346,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -68580,7 +83404,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -68594,12 +83417,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>53</td>
-      <td>549</td>
+      <td>669</td>
+      <td>669</td>
+      <td>112</td>
+      <td>112</td>
+      <td>1261</td>
+      <td>1261</td>
+      <td>417</td>
+      <td>417</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1930</td>
+      <td>1930</td>
+      <td>529</td>
+      <td>529</td>
     </tr>
     <tr>
       <td></td>
@@ -68628,8 +83466,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -68661,9 +83498,24 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
+      <td>2</td>
       <td>0</td>
-      <td>2165</td>
-      <td>167659</td>
+      <td>178677</td>
+      <td>187728</td>
+      <td>4972</td>
+      <td>5347</td>
+      <td>320780</td>
+      <td>407379</td>
+      <td>10825</td>
+      <td>15171</td>
+      <td>26375</td>
+      <td>28921</td>
+      <td>1032</td>
+      <td>1167</td>
+      <td>525832</td>
+      <td>624028</td>
+      <td>16829</td>
+      <td>21685</td>
     </tr>
     <tr>
       <td></td>
@@ -68692,10 +83544,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -68722,12 +83573,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>59</td>
-      <td>2623</td>
+      <td>2858</td>
+      <td>3001</td>
+      <td>118</td>
+      <td>123</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2858</td>
+      <td>3001</td>
+      <td>118</td>
+      <td>123</td>
     </tr>
     <tr>
       <td></td>
@@ -68792,46 +83658,74 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>swift</td>
-      <td>swiftlink</td>
-      <td>Parallel MCMC Linkage Analysis</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>https://github.com/ajm/swiftlink</td>
-      <td>Variant Analysis</td>
-      <td>swiftlink</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift</td>
-      <td>1.0</td>
-      <td>swiftlink</td>
-      <td>1.0</td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>swift</td>
+      <td>swiftlink</td>
+      <td>Parallel MCMC Linkage Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/ajm/swiftlink</td>
+      <td>Variant Analysis</td>
+      <td>swiftlink</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift</td>
+      <td>1.0</td>
+      <td>swiftlink</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -68918,8 +83812,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>30</td>
+      <td>30</td>
+      <td>2</td>
       <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>30</td>
+      <td>30</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -68948,8 +83856,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -68978,12 +83885,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>741</td>
-      <td>208652</td>
+      <td>216072</td>
+      <td>216115</td>
+      <td>1811</td>
+      <td>1814</td>
+      <td>12326</td>
+      <td>12326</td>
+      <td>1558</td>
+      <td>1558</td>
+      <td>16136</td>
+      <td>16136</td>
+      <td>256</td>
+      <td>256</td>
+      <td>244534</td>
+      <td>244577</td>
+      <td>3625</td>
+      <td>3628</td>
     </tr>
     <tr>
       <td></td>
@@ -68997,7 +83919,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>tabular_to_fastq</td>
@@ -69006,17 +83928,17 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -69046,8 +83968,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>200</td>
-      <td>7388</td>
+      <td>7011</td>
+      <td>8135</td>
+      <td>449</td>
+      <td>482</td>
+      <td>9473</td>
+      <td>28494</td>
+      <td>626</td>
+      <td>2183</td>
+      <td>850</td>
+      <td>1090</td>
+      <td>80</td>
+      <td>104</td>
+      <td>17334</td>
+      <td>37719</td>
+      <td>1155</td>
+      <td>2769</td>
     </tr>
     <tr>
       <td></td>
@@ -69092,7 +84028,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -69106,12 +84041,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>7</td>
+      <td>158</td>
       <td>164</td>
+      <td>15</td>
+      <td>16</td>
+      <td>722</td>
+      <td>865</td>
+      <td>40</td>
+      <td>73</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>880</td>
+      <td>1029</td>
+      <td>55</td>
+      <td>89</td>
     </tr>
     <tr>
       <td></td>
@@ -69174,8 +84124,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>61</td>
+      <td>61</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>11</td>
+      <td>11</td>
     </tr>
     <tr>
       <td></td>
@@ -69240,6 +84204,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -69284,7 +84262,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -69304,6 +84281,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -69332,8 +84324,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -69362,12 +84353,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1801</td>
-      <td>27426</td>
+      <td>36069</td>
+      <td>36922</td>
+      <td>5257</td>
+      <td>5431</td>
+      <td>25255</td>
+      <td>30822</td>
+      <td>5066</td>
+      <td>5826</td>
+      <td>7949</td>
+      <td>7949</td>
+      <td>1584</td>
+      <td>1584</td>
+      <td>69273</td>
+      <td>75693</td>
+      <td>11907</td>
+      <td>12841</td>
     </tr>
     <tr>
       <td></td>
@@ -69396,11 +84402,10 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -69431,7 +84436,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>34</td>
+      <td>34</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>34</td>
+      <td>34</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -69494,8 +84514,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>198</td>
-      <td>5161</td>
+      <td>6372</td>
+      <td>6395</td>
+      <td>372</td>
+      <td>379</td>
+      <td>7339</td>
+      <td>7339</td>
+      <td>378</td>
+      <td>378</td>
+      <td>6966</td>
+      <td>6966</td>
+      <td>154</td>
+      <td>154</td>
+      <td>20677</td>
+      <td>20700</td>
+      <td>904</td>
+      <td>911</td>
     </tr>
     <tr>
       <td></td>
@@ -69558,8 +84592,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>209</td>
-      <td>19252</td>
+      <td>22977</td>
+      <td>22977</td>
+      <td>461</td>
+      <td>461</td>
+      <td>3888</td>
+      <td>3888</td>
+      <td>274</td>
+      <td>274</td>
+      <td>3611</td>
+      <td>3611</td>
+      <td>80</td>
+      <td>80</td>
+      <td>30476</td>
+      <td>30476</td>
+      <td>815</td>
+      <td>815</td>
     </tr>
     <tr>
       <td></td>
@@ -69588,8 +84636,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -69619,11 +84666,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>229</td>
-      <td>1584</td>
+      <td>1941</td>
+      <td>1941</td>
+      <td>466</td>
+      <td>466</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>463</td>
+      <td>463</td>
+      <td>112</td>
+      <td>112</td>
+      <td>2404</td>
+      <td>2404</td>
+      <td>578</td>
+      <td>578</td>
     </tr>
     <tr>
       <td></td>
@@ -69686,8 +84748,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>167</td>
-      <td>2290</td>
+      <td>2955</td>
+      <td>2955</td>
+      <td>335</td>
+      <td>335</td>
+      <td>6090</td>
+      <td>6090</td>
+      <td>348</td>
+      <td>348</td>
+      <td>2347</td>
+      <td>2347</td>
+      <td>72</td>
+      <td>72</td>
+      <td>11392</td>
+      <td>11392</td>
+      <td>755</td>
+      <td>755</td>
     </tr>
     <tr>
       <td></td>
@@ -69750,8 +84826,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>7</td>
-      <td>81</td>
+      <td>203</td>
+      <td>203</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>203</td>
+      <td>203</td>
+      <td>20</td>
+      <td>20</td>
     </tr>
     <tr>
       <td></td>
@@ -69816,6 +84906,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -69878,8 +84982,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>33</td>
-      <td>871</td>
+      <td>1013</td>
+      <td>1013</td>
+      <td>74</td>
+      <td>74</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1083</td>
+      <td>1083</td>
+      <td>78</td>
+      <td>78</td>
     </tr>
     <tr>
       <td></td>
@@ -69924,7 +85042,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -69938,12 +85055,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>8</td>
-      <td>69</td>
+      <td>106</td>
+      <td>106</td>
+      <td>16</td>
+      <td>16</td>
+      <td>155</td>
+      <td>155</td>
+      <td>47</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>261</td>
+      <td>261</td>
+      <td>63</td>
+      <td>63</td>
     </tr>
     <tr>
       <td></td>
@@ -69991,7 +85123,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -70003,11 +85134,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>17</td>
-      <td>1881</td>
+      <td>1915</td>
+      <td>1915</td>
+      <td>42</td>
+      <td>42</td>
+      <td>1972</td>
+      <td>1972</td>
+      <td>225</td>
+      <td>225</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3887</td>
+      <td>3887</td>
+      <td>267</td>
+      <td>267</td>
     </tr>
     <tr>
       <td></td>
@@ -70036,10 +85182,9 @@
       <td>2</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -70071,7 +85216,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>9</td>
+      <td>9</td>
+      <td>6</td>
+      <td>6</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>71</td>
+      <td>71</td>
+      <td>14</td>
+      <td>14</td>
     </tr>
     <tr>
       <td></td>
@@ -70100,10 +85260,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70135,7 +85294,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -70198,8 +85372,22 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>58</td>
-      <td>2439</td>
+      <td>3314</td>
+      <td>3314</td>
+      <td>124</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3314</td>
+      <td>3314</td>
+      <td>124</td>
+      <td>124</td>
     </tr>
     <tr>
       <td></td>
@@ -70228,8 +85416,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -70241,7 +85428,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -70258,12 +85445,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>348</td>
-      <td>5468</td>
+      <td>5964</td>
+      <td>6418</td>
+      <td>944</td>
+      <td>970</td>
+      <td>5450</td>
+      <td>5450</td>
+      <td>1066</td>
+      <td>1066</td>
+      <td>2610</td>
+      <td>2796</td>
+      <td>317</td>
+      <td>344</td>
+      <td>14024</td>
+      <td>14664</td>
+      <td>2327</td>
+      <td>2380</td>
     </tr>
     <tr>
       <td></td>
@@ -70326,8 +85528,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>84</td>
-      <td>907</td>
+      <td>1039</td>
+      <td>1039</td>
+      <td>189</td>
+      <td>189</td>
+      <td>2672</td>
+      <td>3349</td>
+      <td>467</td>
+      <td>485</td>
+      <td>358</td>
+      <td>358</td>
+      <td>47</td>
+      <td>47</td>
+      <td>4069</td>
+      <td>4746</td>
+      <td>703</td>
+      <td>721</td>
     </tr>
     <tr>
       <td></td>
@@ -70390,8 +85606,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5</td>
-      <td>229</td>
+      <td>250</td>
+      <td>254</td>
+      <td>31</td>
+      <td>31</td>
+      <td>174</td>
+      <td>174</td>
+      <td>45</td>
+      <td>45</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>424</td>
+      <td>428</td>
+      <td>76</td>
+      <td>76</td>
     </tr>
     <tr>
       <td></td>
@@ -70420,8 +85650,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -70450,12 +85679,27 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5862</td>
-      <td>305866</td>
+      <td>352353</td>
+      <td>383014</td>
+      <td>14547</td>
+      <td>15408</td>
+      <td>632385</td>
+      <td>839058</td>
+      <td>39323</td>
+      <td>49850</td>
+      <td>125340</td>
+      <td>139097</td>
+      <td>5268</td>
+      <td>5975</td>
+      <td>1110078</td>
+      <td>1361169</td>
+      <td>59138</td>
+      <td>71233</td>
     </tr>
     <tr>
       <td></td>
@@ -70484,11 +85728,10 @@
       <td>9</td>
       <td>13</td>
       <td>13</td>
-      <td>13</td>
+      <td>0</td>
       <td>9</td>
       <td>13</td>
       <td>13</td>
-      <td>13</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -70514,12 +85757,27 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>11</td>
       <td>13</td>
       <td>12</td>
       <td>0</td>
-      <td>1762</td>
-      <td>31951</td>
+      <td>35698</td>
+      <td>39132</td>
+      <td>4376</td>
+      <td>4632</td>
+      <td>44509</td>
+      <td>44509</td>
+      <td>6714</td>
+      <td>6714</td>
+      <td>21883</td>
+      <td>23889</td>
+      <td>1924</td>
+      <td>2070</td>
+      <td>102090</td>
+      <td>107530</td>
+      <td>13014</td>
+      <td>13416</td>
     </tr>
     <tr>
       <td></td>
@@ -70564,7 +85822,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70578,12 +85835,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>151</td>
-      <td>1796</td>
+      <td>1968</td>
+      <td>2080</td>
+      <td>374</td>
+      <td>390</td>
+      <td>1825</td>
+      <td>1825</td>
+      <td>527</td>
+      <td>527</td>
+      <td>862</td>
+      <td>1060</td>
+      <td>161</td>
+      <td>195</td>
+      <td>4655</td>
+      <td>4965</td>
+      <td>1062</td>
+      <td>1112</td>
     </tr>
     <tr>
       <td></td>
@@ -70612,9 +85884,8 @@
       <td>0</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
       <td>0</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -70643,11 +85914,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
+      <td>14681</td>
+      <td>14681</td>
+      <td>265</td>
+      <td>265</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4488</td>
+      <td>4488</td>
+      <td>147</td>
       <td>147</td>
-      <td>8942</td>
+      <td>19169</td>
+      <td>19169</td>
+      <td>412</td>
+      <td>412</td>
     </tr>
     <tr>
       <td></td>
@@ -70676,10 +85962,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70711,7 +85996,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
+      <td>17</td>
+      <td>17</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>7</td>
+      <td>7</td>
     </tr>
     <tr>
       <td></td>
@@ -70740,10 +86040,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -70770,12 +86069,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>10</td>
-      <td>368</td>
+      <td>255</td>
+      <td>379</td>
+      <td>31</td>
+      <td>37</td>
+      <td>281</td>
+      <td>281</td>
+      <td>64</td>
+      <td>64</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>536</td>
+      <td>660</td>
+      <td>95</td>
+      <td>101</td>
     </tr>
     <tr>
       <td></td>
@@ -70827,19 +86141,33 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>48</td>
-      <td>502</td>
+      <td>413</td>
+      <td>511</td>
+      <td>84</td>
+      <td>118</td>
+      <td>441</td>
+      <td>441</td>
+      <td>123</td>
+      <td>123</td>
+      <td>21</td>
+      <td>21</td>
+      <td>2</td>
+      <td>2</td>
+      <td>875</td>
+      <td>973</td>
+      <td>209</td>
+      <td>243</td>
     </tr>
     <tr>
       <td></td>
@@ -70902,8 +86230,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>88</td>
-      <td>1408</td>
+      <td>1802</td>
+      <td>1802</td>
+      <td>225</td>
+      <td>225</td>
+      <td>6963</td>
+      <td>6963</td>
+      <td>904</td>
+      <td>904</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8765</td>
+      <td>8765</td>
+      <td>1129</td>
+      <td>1129</td>
     </tr>
     <tr>
       <td></td>
@@ -70968,6 +86310,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -71032,6 +86388,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -71083,7 +86453,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -71096,6 +86465,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -71160,6 +86544,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -71224,6 +86622,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -71288,6 +86700,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -71352,6 +86778,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -71416,6 +86856,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -71480,6 +86934,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -71508,8 +86976,7 @@
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
@@ -71538,12 +87005,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>379</td>
-      <td>61618</td>
+      <td>55050</td>
+      <td>68123</td>
+      <td>1090</td>
+      <td>1223</td>
+      <td>9001</td>
+      <td>9001</td>
+      <td>906</td>
+      <td>906</td>
+      <td>12444</td>
+      <td>12444</td>
+      <td>187</td>
+      <td>187</td>
+      <td>76495</td>
+      <td>89568</td>
+      <td>2183</td>
+      <td>2316</td>
     </tr>
     <tr>
       <td></td>
@@ -71572,8 +87054,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -71602,12 +87083,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1558</td>
-      <td>65732</td>
+      <td>74120</td>
+      <td>77648</td>
+      <td>3798</td>
+      <td>3963</td>
+      <td>64946</td>
+      <td>90075</td>
+      <td>5451</td>
+      <td>7380</td>
+      <td>19516</td>
+      <td>20422</td>
+      <td>2010</td>
+      <td>2080</td>
+      <td>158582</td>
+      <td>188145</td>
+      <td>11259</td>
+      <td>13423</td>
     </tr>
     <tr>
       <td></td>
@@ -71670,8 +87166,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
+      <td>1060</td>
+      <td>1060</td>
+      <td>5</td>
       <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>1060</td>
+      <td>1060</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -71700,10 +87210,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -71730,12 +87239,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>20</td>
-      <td>637</td>
+      <td>518</td>
+      <td>677</td>
+      <td>75</td>
+      <td>87</td>
+      <td>234</td>
+      <td>234</td>
+      <td>65</td>
+      <td>65</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>752</td>
+      <td>911</td>
+      <td>140</td>
+      <td>152</td>
     </tr>
     <tr>
       <td></td>
@@ -71783,7 +87307,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -71795,11 +87318,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>94</td>
-      <td>3164</td>
+      <td>5936</td>
+      <td>5936</td>
+      <td>147</td>
+      <td>147</td>
+      <td>523</td>
+      <td>523</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6459</td>
+      <td>6459</td>
+      <td>162</td>
+      <td>162</td>
     </tr>
     <tr>
       <td></td>
@@ -71862,8 +87400,22 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>16</td>
-      <td>273</td>
+      <td>381</td>
+      <td>381</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>381</td>
+      <td>381</td>
+      <td>37</td>
+      <td>37</td>
     </tr>
     <tr>
       <td></td>
@@ -71926,8 +87478,22 @@
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>3</td>
-      <td>88</td>
+      <td>95</td>
+      <td>95</td>
+      <td>14</td>
+      <td>14</td>
+      <td>516</td>
+      <td>516</td>
+      <td>67</td>
+      <td>67</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>611</td>
+      <td>611</td>
+      <td>81</td>
+      <td>81</td>
     </tr>
     <tr>
       <td></td>
@@ -71956,8 +87522,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -71986,12 +87551,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>492</td>
-      <td>9779</td>
+      <td>10711</td>
+      <td>11502</td>
+      <td>1442</td>
+      <td>1560</td>
+      <td>16705</td>
+      <td>16705</td>
+      <td>3135</td>
+      <td>3135</td>
+      <td>1036</td>
+      <td>1036</td>
+      <td>100</td>
+      <td>100</td>
+      <td>28452</td>
+      <td>29243</td>
+      <td>4677</td>
+      <td>4795</td>
     </tr>
     <tr>
       <td></td>
@@ -72054,8 +87634,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>273</td>
+      <td>273</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>273</td>
+      <td>273</td>
+      <td>12</td>
+      <td>12</td>
     </tr>
     <tr>
       <td></td>
@@ -72099,7 +87693,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -72115,11 +87708,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>29</td>
-      <td>751</td>
+      <td>1097</td>
+      <td>1097</td>
+      <td>46</td>
+      <td>46</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1162</td>
+      <td>1162</td>
+      <td>51</td>
+      <td>51</td>
     </tr>
     <tr>
       <td></td>
@@ -72148,8 +87756,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -72178,12 +87785,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>352</td>
-      <td>167913</td>
+      <td>169090</td>
+      <td>169679</td>
+      <td>823</td>
+      <td>874</td>
+      <td>16304</td>
+      <td>42215</td>
+      <td>1141</td>
+      <td>2594</td>
+      <td>2485</td>
+      <td>2511</td>
+      <td>169</td>
+      <td>172</td>
+      <td>187879</td>
+      <td>214405</td>
+      <td>2133</td>
+      <td>3640</td>
     </tr>
     <tr>
       <td></td>
@@ -72212,8 +87834,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -72242,12 +87863,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>8</td>
-      <td>357</td>
+      <td>882</td>
+      <td>888</td>
+      <td>30</td>
+      <td>32</td>
+      <td>6118</td>
+      <td>8261</td>
+      <td>36</td>
+      <td>114</td>
+      <td>175</td>
+      <td>184</td>
+      <td>6</td>
+      <td>6</td>
+      <td>7175</td>
+      <td>9333</td>
+      <td>72</td>
+      <td>152</td>
     </tr>
     <tr>
       <td></td>
@@ -72276,8 +87912,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -72306,12 +87941,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>286</td>
-      <td>15803</td>
+      <td>6879</td>
+      <td>17157</td>
+      <td>897</td>
+      <td>1219</td>
+      <td>7585</td>
+      <td>14509</td>
+      <td>1245</td>
+      <td>1925</td>
+      <td>1648</td>
+      <td>1681</td>
+      <td>225</td>
+      <td>229</td>
+      <td>16112</td>
+      <td>33347</td>
+      <td>2367</td>
+      <td>3373</td>
     </tr>
     <tr>
       <td></td>
@@ -72374,8 +88024,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>87</td>
-      <td>872</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>174</td>
+      <td>174</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>174</td>
+      <td>174</td>
     </tr>
     <tr>
       <td></td>
@@ -72404,8 +88068,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -72434,12 +88097,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>77</td>
-      <td>2181</td>
+      <td>2797</td>
+      <td>2850</td>
+      <td>157</td>
+      <td>181</td>
+      <td>3668</td>
+      <td>14532</td>
+      <td>652</td>
+      <td>1392</td>
+      <td>494</td>
+      <td>507</td>
+      <td>61</td>
+      <td>63</td>
+      <td>6959</td>
+      <td>17889</td>
+      <td>870</td>
+      <td>1636</td>
     </tr>
     <tr>
       <td></td>
@@ -72468,8 +88146,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -72498,12 +88175,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>28</td>
-      <td>192</td>
+      <td>189</td>
+      <td>203</td>
+      <td>62</td>
+      <td>66</td>
+      <td>497</td>
+      <td>1828</td>
+      <td>155</td>
+      <td>387</td>
+      <td>184</td>
+      <td>197</td>
+      <td>11</td>
+      <td>11</td>
+      <td>870</td>
+      <td>2228</td>
+      <td>228</td>
+      <td>464</td>
     </tr>
     <tr>
       <td></td>
@@ -72532,8 +88224,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -72562,12 +88253,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>80</td>
-      <td>3217</td>
+      <td>3017</td>
+      <td>4049</td>
+      <td>185</td>
+      <td>210</td>
+      <td>4709</td>
+      <td>20250</td>
+      <td>406</td>
+      <td>1147</td>
+      <td>507</td>
+      <td>527</td>
+      <td>40</td>
+      <td>42</td>
+      <td>8233</td>
+      <td>24826</td>
+      <td>631</td>
+      <td>1399</td>
     </tr>
     <tr>
       <td></td>
@@ -72596,8 +88302,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -72626,12 +88331,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>13</td>
-      <td>471</td>
+      <td>416</td>
+      <td>478</td>
+      <td>35</td>
+      <td>40</td>
+      <td>3969</td>
+      <td>10457</td>
+      <td>82</td>
+      <td>309</td>
+      <td>362</td>
+      <td>378</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4747</td>
+      <td>11313</td>
+      <td>125</td>
+      <td>357</td>
     </tr>
     <tr>
       <td></td>
@@ -72660,8 +88380,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -72690,12 +88409,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>39</td>
-      <td>675</td>
+      <td>745</td>
+      <td>767</td>
+      <td>96</td>
+      <td>106</td>
+      <td>803</td>
+      <td>1895</td>
+      <td>222</td>
+      <td>627</td>
+      <td>241</td>
+      <td>256</td>
+      <td>16</td>
+      <td>17</td>
+      <td>1789</td>
+      <td>2918</td>
+      <td>334</td>
+      <td>750</td>
     </tr>
     <tr>
       <td></td>
@@ -72724,8 +88458,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -72754,12 +88487,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>99</td>
-      <td>1695</td>
+      <td>1422</td>
+      <td>2020</td>
+      <td>284</td>
+      <td>505</td>
+      <td>4951</td>
+      <td>19530</td>
+      <td>1021</td>
+      <td>2669</td>
+      <td>493</td>
+      <td>516</td>
+      <td>60</td>
+      <td>62</td>
+      <td>6866</td>
+      <td>22066</td>
+      <td>1365</td>
+      <td>3236</td>
     </tr>
     <tr>
       <td></td>
@@ -72788,8 +88536,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -72818,12 +88565,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>14</td>
-      <td>244</td>
+      <td>233</td>
+      <td>253</td>
+      <td>37</td>
+      <td>42</td>
+      <td>234</td>
+      <td>1839</td>
+      <td>79</td>
+      <td>287</td>
+      <td>199</td>
+      <td>214</td>
+      <td>11</td>
+      <td>12</td>
+      <td>666</td>
+      <td>2306</td>
+      <td>127</td>
+      <td>341</td>
     </tr>
     <tr>
       <td></td>
@@ -72852,8 +88614,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -72882,12 +88643,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>40</td>
-      <td>564</td>
+      <td>572</td>
+      <td>585</td>
+      <td>90</td>
+      <td>92</td>
+      <td>2063</td>
+      <td>2427</td>
+      <td>139</td>
+      <td>296</td>
+      <td>272</td>
+      <td>290</td>
+      <td>19</td>
+      <td>22</td>
+      <td>2907</td>
+      <td>3302</td>
+      <td>248</td>
+      <td>410</td>
     </tr>
     <tr>
       <td></td>
@@ -72916,8 +88692,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -72946,12 +88721,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>882</td>
-      <td>44437</td>
+      <td>37489</td>
+      <td>47142</td>
+      <td>2113</td>
+      <td>2218</td>
+      <td>75128</td>
+      <td>162296</td>
+      <td>5730</td>
+      <td>10533</td>
+      <td>2626</td>
+      <td>2736</td>
+      <td>320</td>
+      <td>331</td>
+      <td>115243</td>
+      <td>212174</td>
+      <td>8163</td>
+      <td>13082</td>
     </tr>
     <tr>
       <td></td>
@@ -72980,8 +88770,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -73010,12 +88799,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>71</td>
-      <td>917</td>
+      <td>926</td>
+      <td>957</td>
+      <td>155</td>
+      <td>173</td>
+      <td>2291</td>
+      <td>5323</td>
+      <td>313</td>
+      <td>985</td>
+      <td>251</td>
+      <td>265</td>
+      <td>28</td>
+      <td>31</td>
+      <td>3468</td>
+      <td>6545</td>
+      <td>496</td>
+      <td>1189</td>
     </tr>
     <tr>
       <td></td>
@@ -73044,8 +88848,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -73074,12 +88877,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>6</td>
-      <td>177</td>
+      <td>172</td>
+      <td>183</td>
+      <td>21</td>
+      <td>25</td>
+      <td>351</td>
+      <td>879</td>
+      <td>67</td>
+      <td>201</td>
+      <td>312</td>
+      <td>342</td>
+      <td>15</td>
+      <td>16</td>
+      <td>835</td>
+      <td>1404</td>
+      <td>103</td>
+      <td>242</td>
     </tr>
     <tr>
       <td></td>
@@ -73108,8 +88926,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -73138,12 +88955,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>36</td>
-      <td>718</td>
+      <td>778</td>
+      <td>794</td>
+      <td>107</td>
+      <td>112</td>
+      <td>2414</td>
+      <td>3721</td>
+      <td>179</td>
+      <td>508</td>
+      <td>209</td>
+      <td>225</td>
+      <td>20</td>
+      <td>21</td>
+      <td>3401</td>
+      <td>4740</td>
+      <td>306</td>
+      <td>641</td>
     </tr>
     <tr>
       <td></td>
@@ -73172,8 +89004,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -73202,12 +89033,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>48</td>
-      <td>451</td>
+      <td>502</td>
+      <td>555</td>
+      <td>134</td>
+      <td>143</td>
+      <td>3428</td>
+      <td>6338</td>
+      <td>266</td>
+      <td>858</td>
+      <td>220</td>
+      <td>235</td>
+      <td>23</td>
+      <td>24</td>
+      <td>4150</td>
+      <td>7128</td>
+      <td>423</td>
+      <td>1025</td>
     </tr>
     <tr>
       <td></td>
@@ -73236,8 +89082,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -73266,12 +89111,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>90</td>
-      <td>1370</td>
+      <td>1964</td>
+      <td>1991</td>
+      <td>182</td>
+      <td>186</td>
+      <td>1937</td>
+      <td>3846</td>
+      <td>188</td>
+      <td>644</td>
+      <td>567</td>
+      <td>601</td>
+      <td>26</td>
+      <td>27</td>
+      <td>4468</td>
+      <td>6438</td>
+      <td>396</td>
+      <td>857</td>
     </tr>
     <tr>
       <td></td>
@@ -73300,8 +89160,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -73330,12 +89189,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>10</td>
-      <td>279</td>
+      <td>269</td>
+      <td>310</td>
+      <td>38</td>
+      <td>42</td>
+      <td>358</td>
+      <td>1071</td>
+      <td>89</td>
+      <td>287</td>
+      <td>179</td>
+      <td>213</td>
+      <td>12</td>
+      <td>14</td>
+      <td>806</td>
+      <td>1594</td>
+      <td>139</td>
+      <td>343</td>
     </tr>
     <tr>
       <td></td>
@@ -73364,8 +89238,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -73394,12 +89267,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>590</td>
+      <td>711</td>
+      <td>28</td>
+      <td>33</td>
+      <td>403</td>
+      <td>831</td>
+      <td>75</td>
+      <td>200</td>
+      <td>190</td>
+      <td>214</td>
+      <td>10</td>
       <td>12</td>
-      <td>708</td>
+      <td>1183</td>
+      <td>1756</td>
+      <td>113</td>
+      <td>245</td>
     </tr>
     <tr>
       <td></td>
@@ -73428,8 +89316,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -73458,12 +89345,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5</td>
-      <td>159</td>
+      <td>161</td>
+      <td>168</td>
+      <td>13</td>
+      <td>15</td>
+      <td>153</td>
+      <td>350</td>
+      <td>27</td>
+      <td>75</td>
+      <td>184</td>
+      <td>192</td>
+      <td>6</td>
+      <td>6</td>
+      <td>498</td>
+      <td>710</td>
+      <td>46</td>
+      <td>96</td>
     </tr>
     <tr>
       <td></td>
@@ -73492,8 +89394,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -73522,12 +89423,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>29</td>
-      <td>854</td>
+      <td>830</td>
+      <td>900</td>
+      <td>69</td>
+      <td>88</td>
+      <td>1315</td>
+      <td>6257</td>
+      <td>237</td>
+      <td>959</td>
+      <td>344</td>
+      <td>363</td>
+      <td>20</td>
+      <td>21</td>
+      <td>2489</td>
+      <td>7520</td>
+      <td>326</td>
+      <td>1068</td>
     </tr>
     <tr>
       <td></td>
@@ -73556,8 +89472,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -73586,12 +89501,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>63</td>
-      <td>1852</td>
+      <td>1868</td>
+      <td>1904</td>
+      <td>174</td>
+      <td>185</td>
+      <td>18378</td>
+      <td>24175</td>
+      <td>422</td>
+      <td>1279</td>
+      <td>537</td>
+      <td>674</td>
+      <td>70</td>
+      <td>73</td>
+      <td>20783</td>
+      <td>26753</td>
+      <td>666</td>
+      <td>1537</td>
     </tr>
     <tr>
       <td></td>
@@ -73620,8 +89550,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -73650,12 +89579,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>265</td>
-      <td>972774</td>
+      <td>976544</td>
+      <td>977015</td>
+      <td>703</td>
+      <td>748</td>
+      <td>64155</td>
+      <td>81830</td>
+      <td>981</td>
+      <td>2103</td>
+      <td>11044</td>
+      <td>11069</td>
+      <td>225</td>
+      <td>229</td>
+      <td>1051743</td>
+      <td>1069914</td>
+      <td>1909</td>
+      <td>3080</td>
     </tr>
     <tr>
       <td></td>
@@ -73700,7 +89644,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -73714,12 +89657,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>74</td>
-      <td>2020</td>
+      <td>2157</td>
+      <td>2287</td>
+      <td>198</td>
+      <td>209</td>
+      <td>3930</td>
+      <td>5591</td>
+      <td>446</td>
+      <td>744</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6087</td>
+      <td>7878</td>
+      <td>644</td>
+      <td>953</td>
     </tr>
     <tr>
       <td></td>
@@ -73782,8 +89740,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>2</td>
+      <td>7</td>
+      <td>7</td>
+      <td>4</td>
+      <td>4</td>
+      <td>22</td>
+      <td>22</td>
+      <td>6</td>
+      <td>6</td>
+      <td>16</td>
+      <td>16</td>
+      <td>1</td>
+      <td>1</td>
+      <td>45</td>
+      <td>45</td>
+      <td>11</td>
+      <td>11</td>
     </tr>
     <tr>
       <td></td>
@@ -73812,8 +89784,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -73842,12 +89813,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2083</td>
-      <td>25420</td>
+      <td>25171</td>
+      <td>27943</td>
+      <td>3899</td>
+      <td>4270</td>
+      <td>51187</td>
+      <td>51187</td>
+      <td>7557</td>
+      <td>7557</td>
+      <td>28546</td>
+      <td>28619</td>
+      <td>3585</td>
+      <td>3613</td>
+      <td>104904</td>
+      <td>107749</td>
+      <td>15041</td>
+      <td>15440</td>
     </tr>
     <tr>
       <td></td>
@@ -73890,7 +89876,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -73906,12 +89891,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>255</td>
-      <td>4741</td>
+      <td>4715</td>
+      <td>5343</td>
+      <td>888</td>
+      <td>965</td>
+      <td>9575</td>
+      <td>9576</td>
+      <td>2117</td>
+      <td>2117</td>
+      <td>3271</td>
+      <td>5524</td>
+      <td>1050</td>
+      <td>1397</td>
+      <td>17561</td>
+      <td>20443</td>
+      <td>4055</td>
+      <td>4479</td>
     </tr>
     <tr>
       <td></td>
@@ -73934,7 +89934,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko</td>
       <td>1.3.1</td>
       <td>verkko</td>
-      <td>2.2</td>
+      <td>2.2.1</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -73974,8 +89974,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
-      <td>22</td>
+      <td>48</td>
+      <td>48</td>
+      <td>25</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>25</td>
+      <td>25</td>
     </tr>
     <tr>
       <td></td>
@@ -74004,10 +90018,9 @@
       <td>0</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -74034,12 +90047,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>3</td>
-      <td>477</td>
+      <td>478</td>
+      <td>478</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>478</td>
+      <td>478</td>
+      <td>17</td>
+      <td>17</td>
     </tr>
     <tr>
       <td></td>
@@ -74068,11 +90096,10 @@
       <td>0</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -74103,7 +90130,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>94</td>
+      <td>94</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>94</td>
+      <td>94</td>
+      <td>16</td>
+      <td>16</td>
     </tr>
     <tr>
       <td></td>
@@ -74166,8 +90208,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -74230,8 +90286,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>40</td>
-      <td>234</td>
+      <td>574</td>
+      <td>574</td>
+      <td>76</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>574</td>
+      <td>574</td>
+      <td>76</td>
+      <td>76</td>
     </tr>
     <tr>
       <td></td>
@@ -74260,8 +90330,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -74290,12 +90359,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1749</td>
-      <td>30946</td>
+      <td>34917</td>
+      <td>36852</td>
+      <td>3670</td>
+      <td>3786</td>
+      <td>54931</td>
+      <td>54931</td>
+      <td>5597</td>
+      <td>5597</td>
+      <td>7183</td>
+      <td>7183</td>
+      <td>905</td>
+      <td>905</td>
+      <td>97031</td>
+      <td>98966</td>
+      <td>10172</td>
+      <td>10288</td>
     </tr>
     <tr>
       <td></td>
@@ -74324,8 +90408,7 @@
       <td>8</td>
       <td>8</td>
       <td>8</td>
-      <td>8</td>
-      <td>8</td>
+      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>8</td>
@@ -74354,12 +90437,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
-      <td>182</td>
-      <td>8507</td>
+      <td>9694</td>
+      <td>10338</td>
+      <td>559</td>
+      <td>628</td>
+      <td>12282</td>
+      <td>53546</td>
+      <td>1031</td>
+      <td>2007</td>
+      <td>5334</td>
+      <td>5672</td>
+      <td>246</td>
+      <td>277</td>
+      <td>27310</td>
+      <td>69556</td>
+      <td>1836</td>
+      <td>2912</td>
     </tr>
     <tr>
       <td></td>
@@ -74424,6 +90522,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -74488,6 +90600,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -74516,8 +90642,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -74546,12 +90671,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>74</td>
-      <td>2379</td>
+      <td>2720</td>
+      <td>2818</td>
+      <td>206</td>
+      <td>228</td>
+      <td>10299</td>
+      <td>30578</td>
+      <td>1354</td>
+      <td>3657</td>
+      <td>1226</td>
+      <td>1285</td>
+      <td>50</td>
+      <td>59</td>
+      <td>14245</td>
+      <td>34681</td>
+      <td>1610</td>
+      <td>3944</td>
     </tr>
     <tr>
       <td></td>
@@ -74614,8 +90754,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1601</td>
+      <td>1601</td>
+      <td>106</td>
+      <td>106</td>
+      <td>1108</td>
+      <td>1108</td>
+      <td>172</td>
+      <td>172</td>
+      <td>200</td>
+      <td>200</td>
+      <td>15</td>
+      <td>15</td>
+      <td>2909</td>
+      <td>2909</td>
+      <td>293</td>
+      <td>293</td>
     </tr>
     <tr>
       <td></td>
@@ -74678,8 +90832,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>85</td>
+      <td>537</td>
+      <td>537</td>
+      <td>19</td>
+      <td>19</td>
+      <td>12</td>
+      <td>12</td>
+      <td>7</td>
+      <td>7</td>
+      <td>297</td>
+      <td>297</td>
+      <td>2</td>
+      <td>2</td>
+      <td>846</td>
+      <td>846</td>
+      <td>28</td>
+      <td>28</td>
     </tr>
     <tr>
       <td></td>
@@ -74742,8 +90910,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>27</td>
-      <td>248</td>
+      <td>279</td>
+      <td>279</td>
+      <td>46</td>
+      <td>46</td>
+      <td>12</td>
+      <td>12</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>291</td>
+      <td>291</td>
+      <td>50</td>
+      <td>50</td>
     </tr>
     <tr>
       <td></td>
@@ -74806,8 +90988,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3</td>
-      <td>234</td>
+      <td>128</td>
+      <td>235</td>
+      <td>7</td>
+      <td>8</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>128</td>
+      <td>236</td>
+      <td>7</td>
+      <td>9</td>
     </tr>
     <tr>
       <td></td>
@@ -74867,44 +91063,91 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>618</td>
+      <td>618</td>
+      <td>176</td>
+      <td>176</td>
+      <td>336</td>
+      <td>336</td>
+      <td>62</td>
+      <td>62</td>
+      <td>588</td>
+      <td>588</td>
+      <td>25</td>
+      <td>25</td>
+      <td>1542</td>
+      <td>1542</td>
+      <td>263</td>
+      <td>263</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>zerone</td>
+      <td>zerone</td>
+      <td>ChIP-seq discretization and quality control</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/nanakiksc/zerone</td>
+      <td>ChIP-seq</td>
+      <td>zerone</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone</td>
+      <td>1.0</td>
+      <td>zerone</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>64</td>
-      <td>344</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>zerone</td>
-      <td>zerone</td>
-      <td>ChIP-seq discretization and quality control</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>Up-to-date</td>
-      <td>https://github.com/nanakiksc/zerone</td>
-      <td>ChIP-seq</td>
-      <td>zerone</td>
-      <td>iuc</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone</td>
-      <td>1.0</td>
-      <td>zerone</td>
-      <td>1.0</td>
-      <td></td>
-      <td></td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>83</td>
+      <td>96</td>
+      <td>9</td>
+      <td>12</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -74913,29 +91156,10 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
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-      <td>0</td>
-      <td>0</td>
-      <td>1</td>
-      <td>1</td>
-      <td>1</td>
-      <td>0</td>
-      <td>2</td>
-      <td>90</td>
+      <td>83</td>
+      <td>96</td>
+      <td>9</td>
+      <td>12</td>
     </tr>
     <tr>
       <td></td>
@@ -74964,11 +91188,11 @@
       <td>0</td>
       <td>0</td>
       <td>11</td>
-      <td>9</td>
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       <td>0</td>
       <td>0</td>
       <td>11</td>
-      <td>9</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -74998,8 +91222,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
-      <td>102</td>
+      <td>516</td>
+      <td>516</td>
+      <td>128</td>
+      <td>128</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>516</td>
+      <td>516</td>
+      <td>128</td>
+      <td>128</td>
     </tr>
     <tr>
       <td></td>
@@ -75028,11 +91266,11 @@
       <td>0</td>
       <td>0</td>
       <td>6</td>
-      <td>5</td>
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       <td>0</td>
       <td>0</td>
       <td>6</td>
-      <td>5</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -75062,8 +91300,22 @@
       <td>5</td>
       <td>0</td>
       <td>0</td>
+      <td>352</td>
+      <td>352</td>
+      <td>36</td>
+      <td>36</td>
+      <td>0</td>
       <td>0</td>
-      <td>82</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>352</td>
+      <td>352</td>
+      <td>36</td>
+      <td>36</td>
     </tr>
     <tr>
       <td></td>
@@ -75092,11 +91344,10 @@
       <td>0</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
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       <td>0</td>
       <td>3</td>
-      <td>3</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -75127,7 +91378,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>53</td>
+      <td>53</td>
+      <td>18</td>
+      <td>18</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>53</td>
+      <td>53</td>
+      <td>18</td>
+      <td>18</td>
     </tr>
     <tr>
       <td></td>
@@ -75156,9 +91422,8 @@
       <td>0</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
       <td>0</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -75187,11 +91452,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>4</td>
       <td>0</td>
-      <td>73</td>
-      <td>1004</td>
+      <td>1038</td>
+      <td>1038</td>
+      <td>146</td>
+      <td>146</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>849</td>
+      <td>849</td>
+      <td>38</td>
+      <td>38</td>
+      <td>1887</td>
+      <td>1887</td>
+      <td>184</td>
+      <td>184</td>
     </tr>
     <tr>
       <td></td>
@@ -75254,8 +91534,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>34</td>
-      <td>2689</td>
+      <td>2467</td>
+      <td>2959</td>
+      <td>88</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1097</td>
+      <td>1097</td>
+      <td>18</td>
+      <td>18</td>
+      <td>3564</td>
+      <td>4056</td>
+      <td>106</td>
+      <td>142</td>
     </tr>
     <tr>
       <td></td>
@@ -75284,11 +91578,11 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -75318,8 +91612,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>175</td>
-      <td>40271</td>
+      <td>49465</td>
+      <td>49465</td>
+      <td>281</td>
+      <td>281</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>49465</td>
+      <td>49465</td>
+      <td>281</td>
+      <td>281</td>
     </tr>
     <tr>
       <td></td>
@@ -75362,7 +91670,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -75378,12 +91685,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>7</td>
       <td>5</td>
       <td>0</td>
-      <td>243</td>
-      <td>40666</td>
+      <td>41793</td>
+      <td>41881</td>
+      <td>510</td>
+      <td>511</td>
+      <td>1126</td>
+      <td>1126</td>
+      <td>159</td>
+      <td>159</td>
+      <td>1552</td>
+      <td>1552</td>
+      <td>85</td>
+      <td>85</td>
+      <td>44471</td>
+      <td>44559</td>
+      <td>754</td>
+      <td>755</td>
     </tr>
     <tr>
       <td></td>
@@ -75448,6 +91770,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -75510,8 +91846,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>75</td>
+      <td>75</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>75</td>
+      <td>75</td>
+      <td>9</td>
+      <td>9</td>
     </tr>
     <tr>
       <td></td>
@@ -75563,7 +91913,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75576,6 +91925,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -75638,8 +92002,22 @@
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
-      <td>11</td>
+      <td>13</td>
+      <td>13</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -75691,7 +92069,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75704,6 +92081,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -75768,6 +92160,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -75830,8 +92236,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>49</td>
-      <td>385</td>
+      <td>410</td>
+      <td>419</td>
+      <td>134</td>
+      <td>137</td>
+      <td>363</td>
+      <td>363</td>
+      <td>99</td>
+      <td>99</td>
+      <td>158</td>
+      <td>158</td>
+      <td>13</td>
+      <td>13</td>
+      <td>931</td>
+      <td>940</td>
+      <td>246</td>
+      <td>249</td>
     </tr>
     <tr>
       <td></td>
@@ -75875,7 +92295,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75891,11 +92310,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>200</td>
-      <td>5749</td>
+      <td>5769</td>
+      <td>6802</td>
+      <td>567</td>
+      <td>650</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1</td>
+      <td>5769</td>
+      <td>6805</td>
+      <td>567</td>
+      <td>651</td>
     </tr>
     <tr>
       <td></td>
@@ -75947,7 +92381,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -75960,6 +92393,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -76002,7 +92450,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -76018,12 +92465,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>510</td>
-      <td>8913</td>
+      <td>10600</td>
+      <td>10729</td>
+      <td>1150</td>
+      <td>1159</td>
+      <td>1042</td>
+      <td>1042</td>
+      <td>255</td>
+      <td>255</td>
+      <td>2756</td>
+      <td>2756</td>
+      <td>215</td>
+      <td>215</td>
+      <td>14398</td>
+      <td>14527</td>
+      <td>1620</td>
+      <td>1629</td>
     </tr>
     <tr>
       <td></td>
@@ -76086,8 +92548,22 @@
       <td>4</td>
       <td>3</td>
       <td>0</td>
-      <td>53</td>
-      <td>459</td>
+      <td>493</td>
+      <td>493</td>
+      <td>119</td>
+      <td>119</td>
+      <td>441</td>
+      <td>441</td>
+      <td>148</td>
+      <td>148</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>934</td>
+      <td>934</td>
+      <td>267</td>
+      <td>267</td>
     </tr>
     <tr>
       <td></td>
@@ -76116,9 +92592,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76147,11 +92622,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -76214,8 +92704,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>101</td>
-      <td>1232</td>
+      <td>1063</td>
+      <td>1237</td>
+      <td>257</td>
+      <td>300</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1063</td>
+      <td>1237</td>
+      <td>257</td>
+      <td>300</td>
     </tr>
     <tr>
       <td></td>
@@ -76260,7 +92764,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76280,6 +92783,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -76324,7 +92842,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76339,11 +92856,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>121</td>
-      <td>22499</td>
+      <td>24916</td>
+      <td>27120</td>
+      <td>283</td>
+      <td>347</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24916</td>
+      <td>27120</td>
+      <td>283</td>
+      <td>347</td>
     </tr>
     <tr>
       <td></td>
@@ -76387,7 +92919,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76408,6 +92939,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
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+      <td>1</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -76452,7 +92998,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76472,6 +93017,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -76515,7 +93075,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76536,6 +93095,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
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+      <td>1</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -76580,7 +93154,6 @@
       <td>0</td>
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       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76600,6 +93173,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -76643,7 +93231,6 @@
       <td>0</td>
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       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -76659,11 +93246,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>159</td>
-      <td>264558</td>
+      <td>264392</td>
+      <td>265217</td>
+      <td>483</td>
+      <td>552</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>264392</td>
+      <td>265217</td>
+      <td>483</td>
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     </tr>
     <tr>
       <td></td>
@@ -76726,8 +93328,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>3</td>
-      <td>1348</td>
+      <td>1186</td>
+      <td>1356</td>
+      <td>21</td>
+      <td>32</td>
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+      <td>1186</td>
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+      <td>21</td>
+      <td>32</td>
     </tr>
     <tr>
       <td></td>
@@ -76790,8 +93406,22 @@
       <td>1</td>
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       <td>0</td>
-      <td>5</td>
-      <td>198</td>
+      <td>234</td>
+      <td>234</td>
+      <td>11</td>
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+      <td>4</td>
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+      <td>4</td>
+      <td>4</td>
+      <td>92</td>
+      <td>92</td>
+      <td>3</td>
+      <td>3</td>
+      <td>330</td>
+      <td>330</td>
+      <td>18</td>
+      <td>18</td>
     </tr>
     <tr>
       <td></td>
@@ -76854,8 +93484,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>52</td>
+      <td>52</td>
       <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>52</td>
       <td>52</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -76918,8 +93562,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -76963,7 +93621,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -76979,11 +93636,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>101</td>
-      <td>7766</td>
+      <td>9869</td>
+      <td>9869</td>
+      <td>158</td>
+      <td>158</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6886</td>
+      <td>6886</td>
+      <td>146</td>
+      <td>146</td>
+      <td>16755</td>
+      <td>16755</td>
+      <td>304</td>
+      <td>304</td>
     </tr>
     <tr>
       <td></td>
@@ -77012,11 +93684,10 @@
       <td>0</td>
       <td>9</td>
       <td>11</td>
-      <td>11</td>
+      <td>0</td>
       <td>0</td>
       <td>9</td>
       <td>11</td>
-      <td>11</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -77042,12 +93713,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>9</td>
       <td>11</td>
       <td>9</td>
       <td>0</td>
-      <td>277</td>
-      <td>48705</td>
+      <td>41875</td>
+      <td>50702</td>
+      <td>663</td>
+      <td>713</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1</td>
+      <td>1</td>
+      <td>7512</td>
+      <td>7512</td>
+      <td>231</td>
+      <td>231</td>
+      <td>49399</td>
+      <td>58226</td>
+      <td>895</td>
+      <td>945</td>
     </tr>
     <tr>
       <td></td>
@@ -77110,8 +93796,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>16</td>
-      <td>217</td>
+      <td>218</td>
+      <td>218</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>17</td>
+      <td>17</td>
     </tr>
     <tr>
       <td></td>
@@ -77174,8 +93874,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>6</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -77238,8 +93952,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>13</td>
+      <td>14</td>
+      <td>14</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -77268,11 +93996,11 @@
       <td>0</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -77302,8 +94030,22 @@
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>19</td>
-      <td>174</td>
+      <td>183</td>
+      <td>183</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>183</td>
+      <td>183</td>
+      <td>20</td>
+      <td>20</td>
     </tr>
     <tr>
       <td></td>
@@ -77368,6 +94110,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -77411,7 +94167,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -77432,6 +94187,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -77494,8 +94264,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>23</td>
-      <td>237</td>
+      <td>239</td>
+      <td>239</td>
+      <td>35</td>
+      <td>35</td>
+      <td>16</td>
+      <td>16</td>
+      <td>2</td>
+      <td>2</td>
+      <td>182</td>
+      <td>182</td>
+      <td>3</td>
+      <td>3</td>
+      <td>437</td>
+      <td>437</td>
+      <td>40</td>
+      <td>40</td>
     </tr>
     <tr>
       <td></td>
@@ -77540,7 +94324,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -77555,11 +94338,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>352</td>
-      <td>3612</td>
+      <td>4822</td>
+      <td>4824</td>
+      <td>613</td>
+      <td>614</td>
+      <td>1317</td>
+      <td>1317</td>
+      <td>204</td>
+      <td>204</td>
+      <td>3088</td>
+      <td>3795</td>
+      <td>252</td>
+      <td>289</td>
+      <td>9227</td>
+      <td>9936</td>
+      <td>1069</td>
+      <td>1107</td>
     </tr>
     <tr>
       <td></td>
@@ -77588,10 +94386,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -77619,11 +94416,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>55</td>
-      <td>585</td>
+      <td>1184</td>
+      <td>1184</td>
+      <td>154</td>
+      <td>154</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1184</td>
+      <td>1184</td>
+      <td>154</td>
+      <td>154</td>
     </tr>
     <tr>
       <td></td>
@@ -77688,6 +94500,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -77750,8 +94576,22 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>11</td>
-      <td>81</td>
+      <td>170</td>
+      <td>170</td>
+      <td>26</td>
+      <td>26</td>
+      <td>195</td>
+      <td>195</td>
+      <td>39</td>
+      <td>39</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>365</td>
+      <td>365</td>
+      <td>65</td>
+      <td>65</td>
     </tr>
     <tr>
       <td></td>
@@ -77796,7 +94636,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -77816,6 +94655,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -77880,6 +94734,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -77908,8 +94776,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -77938,12 +94805,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>57</td>
-      <td>1652</td>
+      <td>1729</td>
+      <td>1744</td>
+      <td>144</td>
+      <td>146</td>
+      <td>450</td>
+      <td>450</td>
+      <td>72</td>
+      <td>72</td>
+      <td>361</td>
+      <td>361</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2540</td>
+      <td>2555</td>
+      <td>228</td>
+      <td>230</td>
     </tr>
     <tr>
       <td></td>
@@ -78008,6 +94890,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -78070,8 +94966,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>34</td>
-      <td>439</td>
+      <td>441</td>
+      <td>451</td>
+      <td>83</td>
+      <td>87</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>444</td>
+      <td>454</td>
+      <td>85</td>
+      <td>89</td>
     </tr>
     <tr>
       <td></td>
@@ -78100,8 +95010,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -78131,11 +95040,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>99</td>
-      <td>799</td>
+      <td>867</td>
+      <td>877</td>
+      <td>213</td>
+      <td>216</td>
+      <td>339</td>
+      <td>339</td>
+      <td>94</td>
+      <td>94</td>
+      <td>64</td>
+      <td>64</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1270</td>
+      <td>1280</td>
+      <td>312</td>
+      <td>315</td>
     </tr>
     <tr>
       <td></td>
@@ -78164,11 +95088,11 @@
       <td>0</td>
       <td>0</td>
       <td>6</td>
-      <td>6</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>6</td>
-      <td>6</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -78198,8 +95122,22 @@
       <td>6</td>
       <td>0</td>
       <td>0</td>
-      <td>146</td>
-      <td>658</td>
+      <td>967</td>
+      <td>967</td>
+      <td>308</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>967</td>
+      <td>967</td>
+      <td>308</td>
+      <td>308</td>
     </tr>
     <tr>
       <td></td>
@@ -78264,6 +95202,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -78328,6 +95280,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -78356,11 +95322,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
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       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -78390,8 +95356,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>161</td>
-      <td>4758</td>
+      <td>4813</td>
+      <td>5555</td>
+      <td>687</td>
+      <td>805</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>961</td>
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+      <td>87</td>
+      <td>87</td>
+      <td>5774</td>
+      <td>6516</td>
+      <td>774</td>
+      <td>892</td>
     </tr>
     <tr>
       <td></td>
@@ -78454,7 +95434,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
       <td>6</td>
     </tr>
     <tr>
@@ -78520,6 +95514,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -78567,7 +95575,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -78584,6 +95591,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -78646,8 +95668,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
+      <td>28</td>
       <td>33</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>134</td>
+      <td>134</td>
+      <td>4</td>
+      <td>4</td>
+      <td>162</td>
+      <td>167</td>
+      <td>8</td>
+      <td>8</td>
     </tr>
     <tr>
       <td></td>
@@ -78710,8 +95746,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -78774,8 +95824,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
-      <td>15</td>
+      <td>72</td>
+      <td>72</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>171</td>
+      <td>171</td>
+      <td>14</td>
+      <td>14</td>
+      <td>243</td>
+      <td>243</td>
+      <td>28</td>
+      <td>28</td>
     </tr>
     <tr>
       <td></td>
@@ -78838,8 +95902,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>11</td>
-      <td>245</td>
+      <td>262</td>
+      <td>262</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>256</td>
+      <td>256</td>
+      <td>6</td>
+      <td>6</td>
+      <td>518</td>
+      <td>518</td>
+      <td>44</td>
+      <td>44</td>
     </tr>
     <tr>
       <td></td>
@@ -78902,7 +95980,21 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
+      <td>11</td>
+      <td>11</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>7</td>
       <td>7</td>
     </tr>
     <tr>
@@ -78968,6 +96060,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -79032,6 +96138,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -79096,6 +96216,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -79158,8 +96292,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>95</td>
-      <td>973</td>
+      <td>1151</td>
+      <td>1151</td>
+      <td>184</td>
+      <td>184</td>
+      <td>356</td>
+      <td>356</td>
+      <td>77</td>
+      <td>77</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1510</td>
+      <td>1510</td>
+      <td>262</td>
+      <td>262</td>
     </tr>
     <tr>
       <td></td>
@@ -79219,11 +96367,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1900</td>
+      <td>1901</td>
+      <td>412</td>
+      <td>413</td>
+      <td>609</td>
+      <td>609</td>
+      <td>131</td>
+      <td>131</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>201</td>
-      <td>1599</td>
+      <td>2509</td>
+      <td>2510</td>
+      <td>543</td>
+      <td>544</td>
     </tr>
     <tr>
       <td></td>
@@ -79252,8 +96414,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -79282,12 +96443,27 @@
       <td>0</td>
       <td>0</td>
       <td>3</td>
+      <td>0</td>
       <td>1</td>
       <td>3</td>
       <td>1</td>
       <td>0</td>
-      <td>510</td>
-      <td>30565</td>
+      <td>34432</td>
+      <td>34437</td>
+      <td>1149</td>
+      <td>1152</td>
+      <td>42</td>
+      <td>42</td>
+      <td>2</td>
+      <td>2</td>
+      <td>21027</td>
+      <td>21027</td>
+      <td>413</td>
+      <td>413</td>
+      <td>55501</td>
+      <td>55506</td>
+      <td>1564</td>
+      <td>1567</td>
     </tr>
     <tr>
       <td></td>
@@ -79352,6 +96528,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -79414,8 +96604,22 @@
       <td>7</td>
       <td>0</td>
       <td>0</td>
-      <td>48</td>
-      <td>706</td>
+      <td>738</td>
+      <td>738</td>
+      <td>98</td>
+      <td>98</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>42</td>
+      <td>42</td>
+      <td>4</td>
+      <td>4</td>
+      <td>781</td>
+      <td>781</td>
+      <td>103</td>
+      <td>103</td>
     </tr>
     <tr>
       <td></td>
@@ -79478,8 +96682,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>45</td>
+      <td>45</td>
+      <td>4</td>
       <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>45</td>
+      <td>45</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -79542,8 +96760,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>15</td>
-      <td>331</td>
+      <td>232</td>
+      <td>336</td>
+      <td>39</td>
+      <td>40</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>232</td>
+      <td>336</td>
+      <td>39</td>
+      <td>40</td>
     </tr>
     <tr>
       <td></td>
@@ -79595,7 +96827,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -79608,6 +96839,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -79636,8 +96882,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -79666,12 +96911,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>461</td>
-      <td>29886</td>
+      <td>30917</td>
+      <td>32191</td>
+      <td>1142</td>
+      <td>1257</td>
+      <td>36869</td>
+      <td>36869</td>
+      <td>1346</td>
+      <td>1346</td>
+      <td>5236</td>
+      <td>5236</td>
+      <td>230</td>
+      <td>230</td>
+      <td>73022</td>
+      <td>74296</td>
+      <td>2718</td>
+      <td>2833</td>
     </tr>
     <tr>
       <td></td>
@@ -79734,8 +96994,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>28</td>
+      <td>29</td>
+      <td>29</td>
+      <td>8</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>8</td>
+      <td>8</td>
     </tr>
     <tr>
       <td></td>
@@ -79800,6 +97074,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -79864,6 +97152,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -79928,6 +97230,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -79992,6 +97308,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -80054,8 +97384,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>12</td>
-      <td>261</td>
+      <td>264</td>
+      <td>264</td>
+      <td>69</td>
+      <td>69</td>
+      <td>34</td>
+      <td>34</td>
+      <td>11</td>
+      <td>11</td>
+      <td>103</td>
+      <td>103</td>
+      <td>1</td>
+      <td>1</td>
+      <td>401</td>
+      <td>401</td>
+      <td>81</td>
+      <td>81</td>
     </tr>
     <tr>
       <td></td>
@@ -80118,8 +97462,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1</td>
       <td>1</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
       <td>18</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -80163,7 +97521,6 @@
       <td>0</td>
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-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -80184,6 +97541,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -80212,8 +97584,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -80243,11 +97614,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>426</td>
-      <td>26274</td>
+      <td>26717</td>
+      <td>29932</td>
+      <td>1026</td>
+      <td>1072</td>
+      <td>42990</td>
+      <td>42990</td>
+      <td>1176</td>
+      <td>1176</td>
+      <td>9619</td>
+      <td>9619</td>
+      <td>230</td>
+      <td>230</td>
+      <td>79326</td>
+      <td>82541</td>
+      <td>2432</td>
+      <td>2478</td>
     </tr>
     <tr>
       <td></td>
@@ -80312,6 +97698,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -80376,6 +97776,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -80440,6 +97854,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -80504,6 +97932,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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       <td></td>
@@ -80568,6 +98010,20 @@
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@@ -80632,6 +98088,20 @@
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@@ -80694,8 +98164,22 @@
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-      <td>645</td>
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     </tr>
     <tr>
       <td></td>
@@ -80758,8 +98242,22 @@
       <td>0</td>
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     <tr>
       <td></td>
@@ -80824,6 +98322,20 @@
       <td>0</td>
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     <tr>
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@@ -80852,11 +98364,10 @@
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-      <td>28</td>
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@@ -80888,6 +98399,21 @@
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@@ -80952,6 +98478,20 @@
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@@ -81016,6 +98556,20 @@
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       <td></td>
@@ -81144,6 +98712,20 @@
       <td>0</td>
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@@ -81208,6 +98790,20 @@
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@@ -81236,11 +98832,11 @@
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@@ -81270,8 +98866,22 @@
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       <td>8</td>
       <td>0</td>
-      <td>10</td>
-      <td>1475</td>
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     </tr>
     <tr>
       <td></td>
@@ -81285,7 +98895,7 @@
       <td>geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.</td>
       <td>Sequence annotation, Taxonomic classification</td>
       <td>Sequence analysis</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/apcamargo/genomad/</td>
       <td>Metagenomics</td>
       <td>genomad</td>
@@ -81294,7 +98904,7 @@
       <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad</td>
       <td>1.8.0</td>
       <td>genomad</td>
-      <td>1.8.0</td>
+      <td>1.8.1</td>
       <td>Sequence annotation, Taxonomic classification</td>
       <td>Sequence analysis</td>
       <td>0</td>
@@ -81336,6 +98946,20 @@
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@@ -81400,6 +99024,20 @@
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@@ -81464,6 +99101,21 @@
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@@ -81526,8 +99178,22 @@
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@@ -81570,7 +99236,6 @@
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@@ -81586,12 +99251,27 @@
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@@ -81656,6 +99336,20 @@
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@@ -81784,6 +99492,20 @@
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@@ -81848,6 +99570,20 @@
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@@ -81976,6 +99726,20 @@
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       <td>0</td>
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-      <td>78</td>
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@@ -82104,6 +99882,20 @@
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-      <td>1678</td>
+      <td>1982</td>
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@@ -82232,6 +100037,21 @@
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@@ -82294,8 +100114,22 @@
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@@ -82358,8 +100192,22 @@
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@@ -82424,6 +100271,21 @@
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@@ -82486,8 +100348,22 @@
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     <tr>
       <td></td>
@@ -82552,6 +100428,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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@@ -82614,8 +100504,22 @@
       <td>1</td>
       <td>1</td>
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-      <td>4</td>
-      <td>275</td>
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       <td></td>
@@ -82680,6 +100584,20 @@
       <td>0</td>
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       <td></td>
@@ -82742,8 +100660,22 @@
       <td>0</td>
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       <td>0</td>
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     <tr>
       <td></td>
@@ -82808,6 +100740,20 @@
       <td>0</td>
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@@ -82859,7 +100805,6 @@
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@@ -82872,6 +100817,21 @@
       <td>0</td>
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       <td></td>
@@ -82916,7 +100876,6 @@
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@@ -82936,6 +100895,21 @@
       <td>0</td>
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       <td>0</td>
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       <td></td>
@@ -82998,8 +100972,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3</td>
-      <td>111</td>
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     <tr>
       <td></td>
@@ -83064,6 +101052,20 @@
       <td>0</td>
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     <tr>
       <td></td>
@@ -83128,6 +101130,20 @@
       <td>0</td>
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       <td>0</td>
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       <td></td>
@@ -83179,7 +101195,6 @@
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       <td>2</td>
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@@ -83192,6 +101207,21 @@
       <td>0</td>
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       <td></td>
@@ -83235,7 +101265,6 @@
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@@ -83256,6 +101285,21 @@
       <td>0</td>
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       <td>0</td>
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     <tr>
       <td></td>
@@ -83320,6 +101364,20 @@
       <td>0</td>
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     <tr>
       <td></td>
@@ -83348,9 +101406,8 @@
       <td>0</td>
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-      <td>2</td>
       <td>0</td>
-      <td>2</td>
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@@ -83378,12 +101435,27 @@
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -83435,7 +101507,6 @@
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@@ -83443,11 +101514,26 @@
       <td>0</td>
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     <tr>
       <td></td>
@@ -83510,8 +101596,22 @@
       <td>1</td>
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       <td>0</td>
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-      <td>41</td>
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     <tr>
       <td></td>
@@ -83576,6 +101676,20 @@
       <td>0</td>
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     <tr>
       <td></td>
@@ -83638,8 +101752,22 @@
       <td>0</td>
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     <tr>
       <td></td>
@@ -83668,11 +101796,11 @@
       <td>2</td>
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       <td>14</td>
-      <td>11</td>
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@@ -83702,8 +101830,22 @@
       <td>9</td>
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     <tr>
       <td></td>
@@ -83747,7 +101889,6 @@
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@@ -83762,12 +101903,27 @@
       <td>0</td>
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+      <td>12850</td>
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     <tr>
       <td></td>
@@ -83810,7 +101966,6 @@
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@@ -83826,12 +101981,27 @@
       <td>0</td>
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       <td></td>
@@ -83894,8 +102064,22 @@
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@@ -83938,7 +102122,6 @@
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@@ -83955,11 +102138,26 @@
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@@ -84022,8 +102220,22 @@
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@@ -84060,7 +102272,7 @@
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@@ -84086,8 +102298,22 @@
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@@ -84152,6 +102378,20 @@
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@@ -84214,8 +102454,22 @@
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@@ -84260,7 +102514,6 @@
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@@ -84275,11 +102528,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>10</td>
-      <td>123</td>
+      <td>126</td>
+      <td>126</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>126</td>
+      <td>126</td>
+      <td>20</td>
+      <td>20</td>
     </tr>
     <tr>
       <td></td>
@@ -84322,7 +102590,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -84339,11 +102606,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>115</td>
-      <td>636</td>
+      <td>980</td>
+      <td>980</td>
+      <td>323</td>
+      <td>323</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>980</td>
+      <td>980</td>
+      <td>323</td>
+      <td>323</td>
     </tr>
     <tr>
       <td></td>
@@ -84406,8 +102688,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>15</td>
-      <td>4181</td>
+      <td>4471</td>
+      <td>4471</td>
+      <td>29</td>
+      <td>29</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4471</td>
+      <td>4471</td>
+      <td>29</td>
+      <td>29</td>
     </tr>
     <tr>
       <td></td>
@@ -84470,8 +102766,22 @@
       <td>6</td>
       <td>6</td>
       <td>0</td>
-      <td>104</td>
-      <td>2522</td>
+      <td>2730</td>
+      <td>2831</td>
+      <td>260</td>
+      <td>262</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1540</td>
+      <td>1540</td>
+      <td>71</td>
+      <td>71</td>
+      <td>4270</td>
+      <td>4371</td>
+      <td>331</td>
+      <td>333</td>
     </tr>
     <tr>
       <td></td>
@@ -84534,8 +102844,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>8</td>
+      <td>8</td>
     </tr>
     <tr>
       <td></td>
@@ -84600,6 +102924,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -84651,7 +102989,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -84664,6 +103001,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1458</td>
+      <td>1458</td>
+      <td>36</td>
+      <td>36</td>
+      <td>1458</td>
+      <td>1458</td>
+      <td>36</td>
+      <td>36</td>
     </tr>
     <tr>
       <td></td>
@@ -84726,8 +103078,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>2</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -84790,8 +103156,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3</td>
-      <td>759</td>
+      <td>331</td>
+      <td>762</td>
+      <td>20</td>
+      <td>34</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>137</td>
+      <td>137</td>
+      <td>4</td>
+      <td>4</td>
+      <td>468</td>
+      <td>899</td>
+      <td>24</td>
+      <td>38</td>
     </tr>
     <tr>
       <td></td>
@@ -84854,8 +103234,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>264</td>
-      <td>3266</td>
+      <td>3610</td>
+      <td>3610</td>
+      <td>559</td>
+      <td>559</td>
+      <td>1728</td>
+      <td>1728</td>
+      <td>434</td>
+      <td>434</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5338</td>
+      <td>5338</td>
+      <td>993</td>
+      <td>993</td>
     </tr>
     <tr>
       <td></td>
@@ -84918,8 +103312,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>4</td>
-      <td>140</td>
+      <td>105</td>
+      <td>153</td>
+      <td>12</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>833</td>
+      <td>833</td>
+      <td>93</td>
+      <td>93</td>
+      <td>938</td>
+      <td>986</td>
+      <td>105</td>
+      <td>112</td>
     </tr>
     <tr>
       <td></td>
@@ -84982,8 +103390,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>3</td>
+      <td>3</td>
       <td>0</td>
-      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>3</td>
+      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -84997,7 +103419,7 @@
       <td>MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.</td>
       <td>Spectrum calculation, Spectral library search, Network analysis</td>
       <td>Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/matchms/ms2deepscore</td>
       <td>Metabolomics</td>
       <td>ms2deepscore</td>
@@ -85006,7 +103428,7 @@
       <td>https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore</td>
       <td>2.0.0</td>
       <td>ms2deepscore</td>
-      <td>2.0.0</td>
+      <td>2.1.0</td>
       <td>Spectrum calculation, Spectral library search, Network analysis</td>
       <td>Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening</td>
       <td>0</td>
@@ -85048,6 +103470,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85076,11 +103512,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -85110,8 +103546,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>189</td>
-      <td>19958</td>
+      <td>20749</td>
+      <td>22184</td>
+      <td>455</td>
+      <td>469</td>
+      <td>1239</td>
+      <td>1239</td>
+      <td>71</td>
+      <td>71</td>
+      <td>2666</td>
+      <td>2666</td>
+      <td>53</td>
+      <td>53</td>
+      <td>24654</td>
+      <td>26089</td>
+      <td>579</td>
+      <td>593</td>
     </tr>
     <tr>
       <td></td>
@@ -85174,8 +103624,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5</td>
-      <td>507</td>
+      <td>473</td>
+      <td>529</td>
+      <td>33</td>
+      <td>43</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>529</td>
+      <td>33</td>
+      <td>43</td>
     </tr>
     <tr>
       <td></td>
@@ -85204,9 +103668,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -85235,11 +103698,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>203</td>
+      <td>203</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
       <td>1</td>
-      <td>103</td>
+      <td>1</td>
+      <td>251</td>
+      <td>251</td>
+      <td>11</td>
+      <td>11</td>
     </tr>
     <tr>
       <td></td>
@@ -85268,10 +103746,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -85299,11 +103776,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>110</td>
+      <td>110</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>110</td>
+      <td>110</td>
+      <td>11</td>
+      <td>11</td>
     </tr>
     <tr>
       <td></td>
@@ -85368,6 +103860,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85410,7 +103916,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -85426,12 +103931,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>144</td>
-      <td>2036</td>
+      <td>2353</td>
+      <td>2353</td>
+      <td>559</td>
+      <td>559</td>
+      <td>1122</td>
+      <td>1122</td>
+      <td>211</td>
+      <td>211</td>
+      <td>1091</td>
+      <td>1091</td>
+      <td>35</td>
+      <td>35</td>
+      <td>4566</td>
+      <td>4566</td>
+      <td>805</td>
+      <td>805</td>
     </tr>
     <tr>
       <td></td>
@@ -85494,8 +104014,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>71</td>
-      <td>726</td>
+      <td>795</td>
+      <td>795</td>
+      <td>104</td>
+      <td>104</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>461</td>
+      <td>461</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1256</td>
+      <td>1256</td>
+      <td>116</td>
+      <td>116</td>
     </tr>
     <tr>
       <td></td>
@@ -85558,8 +104092,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>19</td>
-      <td>270</td>
+      <td>275</td>
+      <td>275</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>275</td>
+      <td>275</td>
+      <td>38</td>
+      <td>38</td>
     </tr>
     <tr>
       <td></td>
@@ -85624,6 +104172,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85686,8 +104248,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>33</td>
-      <td>844</td>
+      <td>854</td>
+      <td>860</td>
+      <td>110</td>
+      <td>111</td>
+      <td>79</td>
+      <td>79</td>
+      <td>15</td>
+      <td>15</td>
+      <td>274</td>
+      <td>274</td>
+      <td>13</td>
+      <td>13</td>
+      <td>1207</td>
+      <td>1213</td>
+      <td>138</td>
+      <td>139</td>
     </tr>
     <tr>
       <td></td>
@@ -85752,6 +104328,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85780,8 +104370,7 @@
       <td>16</td>
       <td>16</td>
       <td>16</td>
-      <td>16</td>
-      <td>16</td>
+      <td>0</td>
       <td>16</td>
       <td>16</td>
       <td>16</td>
@@ -85810,12 +104399,27 @@
       <td>0</td>
       <td>0</td>
       <td>16</td>
+      <td>15</td>
       <td>16</td>
       <td>16</td>
       <td>15</td>
       <td>0</td>
-      <td>4066</td>
-      <td>365597</td>
+      <td>391141</td>
+      <td>443752</td>
+      <td>9760</td>
+      <td>10546</td>
+      <td>306361</td>
+      <td>350178</td>
+      <td>11767</td>
+      <td>13684</td>
+      <td>227235</td>
+      <td>244814</td>
+      <td>3192</td>
+      <td>3617</td>
+      <td>924737</td>
+      <td>1038744</td>
+      <td>24719</td>
+      <td>27847</td>
     </tr>
     <tr>
       <td></td>
@@ -85859,7 +104463,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -85880,6 +104483,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -85908,11 +104526,11 @@
       <td>1</td>
       <td>0</td>
       <td>2</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>2</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -85942,8 +104560,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
-      <td>45</td>
+      <td>352</td>
+      <td>352</td>
+      <td>42</td>
+      <td>42</td>
+      <td>8</td>
+      <td>8</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>360</td>
+      <td>360</td>
+      <td>48</td>
+      <td>48</td>
     </tr>
     <tr>
       <td></td>
@@ -86006,7 +104638,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
+      <td>6</td>
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       <td>0</td>
+      <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
       <td>6</td>
     </tr>
     <tr>
@@ -86070,8 +104716,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>98</td>
+      <td>98</td>
+      <td>6</td>
+      <td>6</td>
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       <td>0</td>
+      <td>98</td>
+      <td>98</td>
+      <td>6</td>
+      <td>6</td>
     </tr>
     <tr>
       <td></td>
@@ -86134,8 +104794,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>4</td>
+      <td>4</td>
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+      <td>0</td>
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       <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -86200,6 +104874,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -86264,6 +104952,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -86328,6 +105030,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -86392,6 +105108,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -86456,6 +105186,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -86520,6 +105264,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -86582,8 +105340,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>25</td>
-      <td>347</td>
+      <td>491</td>
+      <td>491</td>
+      <td>52</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>491</td>
+      <td>491</td>
+      <td>52</td>
+      <td>52</td>
     </tr>
     <tr>
       <td></td>
@@ -86646,8 +105418,22 @@
       <td>141</td>
       <td>124</td>
       <td>0</td>
-      <td>886</td>
-      <td>105432</td>
+      <td>32169</td>
+      <td>108654</td>
+      <td>3316</td>
+      <td>4889</td>
+      <td>50</td>
+      <td>50</td>
+      <td>15</td>
+      <td>15</td>
+      <td>940</td>
+      <td>940</td>
+      <td>245</td>
+      <td>245</td>
+      <td>33159</td>
+      <td>109644</td>
+      <td>3576</td>
+      <td>5149</td>
     </tr>
     <tr>
       <td></td>
@@ -86710,8 +105496,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>15</td>
-      <td>288</td>
+      <td>282</td>
+      <td>295</td>
+      <td>32</td>
+      <td>33</td>
+      <td>420</td>
+      <td>420</td>
+      <td>8</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>702</td>
+      <td>715</td>
+      <td>40</td>
+      <td>41</td>
     </tr>
     <tr>
       <td></td>
@@ -86774,8 +105574,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>245</td>
+      <td>245</td>
+      <td>10</td>
+      <td>10</td>
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+      <td>245</td>
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+      <td>10</td>
       <td>10</td>
-      <td>228</td>
     </tr>
     <tr>
       <td></td>
@@ -86838,8 +105652,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>20</td>
-      <td>238</td>
+      <td>174</td>
+      <td>244</td>
+      <td>65</td>
+      <td>76</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>174</td>
+      <td>244</td>
+      <td>65</td>
+      <td>76</td>
     </tr>
     <tr>
       <td></td>
@@ -86902,8 +105730,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>9</td>
-      <td>498</td>
+      <td>506</td>
+      <td>511</td>
+      <td>54</td>
+      <td>55</td>
+      <td>21</td>
+      <td>21</td>
+      <td>12</td>
+      <td>12</td>
+      <td>163</td>
+      <td>163</td>
+      <td>8</td>
+      <td>8</td>
+      <td>690</td>
+      <td>695</td>
+      <td>74</td>
+      <td>75</td>
     </tr>
     <tr>
       <td></td>
@@ -86966,8 +105808,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>23</td>
-      <td>4862</td>
+      <td>7047</td>
+      <td>7047</td>
+      <td>76</td>
+      <td>76</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>7047</td>
+      <td>7047</td>
+      <td>76</td>
+      <td>76</td>
     </tr>
     <tr>
       <td></td>
@@ -87030,8 +105886,22 @@
       <td>3</td>
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       <td>0</td>
-      <td>13</td>
-      <td>717</td>
+      <td>1222</td>
+      <td>1222</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>1222</td>
+      <td>1222</td>
+      <td>28</td>
+      <td>28</td>
     </tr>
     <tr>
       <td></td>
@@ -87094,8 +105964,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>9</td>
-      <td>468</td>
+      <td>472</td>
+      <td>472</td>
+      <td>56</td>
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+      <td>16</td>
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+      <td>10</td>
+      <td>10</td>
+      <td>149</td>
+      <td>149</td>
+      <td>5</td>
+      <td>5</td>
+      <td>637</td>
+      <td>637</td>
+      <td>71</td>
+      <td>71</td>
     </tr>
     <tr>
       <td></td>
@@ -87124,8 +106008,7 @@
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
@@ -87154,12 +106037,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>4</td>
       <td>2</td>
       <td>0</td>
-      <td>485</td>
-      <td>17477</td>
+      <td>11986</td>
+      <td>17898</td>
+      <td>1046</td>
+      <td>1153</td>
+      <td>1314</td>
+      <td>1314</td>
+      <td>389</td>
+      <td>389</td>
+      <td>3034</td>
+      <td>3034</td>
+      <td>118</td>
+      <td>118</td>
+      <td>16334</td>
+      <td>22246</td>
+      <td>1553</td>
+      <td>1660</td>
     </tr>
     <tr>
       <td></td>
@@ -87224,6 +106122,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -87286,8 +106198,22 @@
       <td>4</td>
       <td>4</td>
       <td>0</td>
-      <td>5</td>
-      <td>368</td>
+      <td>338</td>
+      <td>378</td>
+      <td>15</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1059</td>
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+      <td>13</td>
+      <td>13</td>
+      <td>1397</td>
+      <td>1437</td>
+      <td>28</td>
+      <td>29</td>
     </tr>
     <tr>
       <td></td>
@@ -87352,6 +106278,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -87395,7 +106335,6 @@
       <td>0</td>
       <td>0</td>
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-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -87416,6 +106355,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -87480,6 +106434,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -87544,6 +106512,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -87608,6 +106590,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -87659,7 +106655,6 @@
       <td>0</td>
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-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -87672,6 +106667,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -87736,6 +106746,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -87798,8 +106822,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>366</td>
+      <td>366</td>
       <td>4</td>
+      <td>4</td>
+      <td>0</td>
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+      <td>366</td>
       <td>366</td>
+      <td>4</td>
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     </tr>
     <tr>
       <td></td>
@@ -87862,8 +106900,22 @@
       <td>1</td>
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       <td>0</td>
-      <td>5</td>
-      <td>14</td>
+      <td>16</td>
+      <td>16</td>
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       <td></td>
@@ -87926,8 +106978,22 @@
       <td>1</td>
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       <td>0</td>
-      <td>3</td>
       <td>6</td>
+      <td>6</td>
+      <td>4</td>
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     </tr>
     <tr>
       <td></td>
@@ -87990,8 +107056,22 @@
       <td>1</td>
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       <td>0</td>
-      <td>5</td>
       <td>721</td>
+      <td>721</td>
+      <td>8</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>721</td>
+      <td>721</td>
+      <td>8</td>
+      <td>8</td>
     </tr>
     <tr>
       <td></td>
@@ -88054,8 +107134,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>6</td>
       <td>96</td>
+      <td>96</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>96</td>
+      <td>96</td>
+      <td>12</td>
+      <td>12</td>
     </tr>
     <tr>
       <td></td>
@@ -88118,8 +107212,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
       <td>686</td>
+      <td>686</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>686</td>
+      <td>686</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -88182,8 +107290,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
       <td>89</td>
+      <td>89</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>89</td>
+      <td>89</td>
+      <td>6</td>
+      <td>6</td>
     </tr>
     <tr>
       <td></td>
@@ -88246,8 +107368,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>604</td>
+      <td>604</td>
       <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>604</td>
       <td>604</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -88310,8 +107446,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
       <td>694</td>
+      <td>694</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>694</td>
+      <td>694</td>
+      <td>6</td>
+      <td>6</td>
     </tr>
     <tr>
       <td></td>
@@ -88374,8 +107524,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>15</td>
+      <td>15</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -88440,6 +107604,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -88468,11 +107646,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -88568,6 +107760,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -88627,11 +107833,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>20</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>20</td>
+      <td>20</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -88694,8 +107914,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>46</td>
-      <td>469</td>
+      <td>333</td>
+      <td>502</td>
+      <td>62</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>333</td>
+      <td>502</td>
+      <td>62</td>
+      <td>62</td>
     </tr>
     <tr>
       <td></td>
@@ -88758,8 +107992,22 @@
       <td>6</td>
       <td>6</td>
       <td>0</td>
-      <td>33</td>
-      <td>2509</td>
+      <td>2626</td>
+      <td>2626</td>
+      <td>150</td>
+      <td>150</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>609</td>
+      <td>609</td>
+      <td>9</td>
+      <td>9</td>
+      <td>3235</td>
+      <td>3235</td>
+      <td>159</td>
+      <td>159</td>
     </tr>
     <tr>
       <td></td>
@@ -88824,6 +108072,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -88886,8 +108148,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>81</td>
+      <td>92</td>
+      <td>92</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>92</td>
+      <td>92</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -88950,8 +108226,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
-      <td>36</td>
+      <td>53</td>
+      <td>53</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>53</td>
+      <td>53</td>
+      <td>6</td>
+      <td>6</td>
     </tr>
     <tr>
       <td></td>
@@ -89014,8 +108304,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>11246</td>
+      <td>11246</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>11246</td>
+      <td>11246</td>
+      <td>13</td>
+      <td>13</td>
     </tr>
     <tr>
       <td></td>
@@ -89044,10 +108348,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -89075,11 +108378,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>6</td>
-      <td>230</td>
+      <td>197</td>
+      <td>241</td>
+      <td>17</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>197</td>
+      <td>241</td>
+      <td>17</td>
+      <td>22</td>
     </tr>
     <tr>
       <td></td>
@@ -89142,8 +108460,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>32</td>
+      <td>32</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>32</td>
+      <td>32</td>
+      <td>3</td>
+      <td>3</td>
     </tr>
     <tr>
       <td></td>
@@ -89208,6 +108540,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -89270,8 +108616,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
-      <td>59</td>
+      <td>172</td>
+      <td>172</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>172</td>
+      <td>172</td>
+      <td>9</td>
+      <td>9</td>
     </tr>
     <tr>
       <td></td>
@@ -89300,8 +108660,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -89331,11 +108690,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>16</td>
+      <td>58</td>
+      <td>58</td>
+      <td>22</td>
+      <td>22</td>
+      <td>29</td>
+      <td>29</td>
+      <td>14</td>
+      <td>14</td>
+      <td>344</td>
+      <td>344</td>
+      <td>4</td>
+      <td>4</td>
+      <td>431</td>
+      <td>431</td>
+      <td>40</td>
+      <td>40</td>
     </tr>
     <tr>
       <td></td>
@@ -89398,8 +108772,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>14</td>
-      <td>175</td>
+      <td>166</td>
+      <td>179</td>
+      <td>32</td>
+      <td>33</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>414</td>
+      <td>414</td>
+      <td>13</td>
+      <td>13</td>
+      <td>580</td>
+      <td>593</td>
+      <td>45</td>
+      <td>46</td>
     </tr>
     <tr>
       <td></td>
@@ -89464,6 +108852,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -89492,9 +108894,8 @@
       <td>0</td>
       <td>8</td>
       <td>8</td>
-      <td>8</td>
       <td>0</td>
-      <td>8</td>
+      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
@@ -89523,11 +108924,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>8</td>
       <td>0</td>
       <td>0</td>
-      <td>7</td>
-      <td>296</td>
+      <td>862</td>
+      <td>862</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td>910</td>
+      <td>910</td>
+      <td>13</td>
+      <td>13</td>
     </tr>
     <tr>
       <td></td>
@@ -89556,9 +108972,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -89591,7 +109006,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>47</td>
+      <td>47</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>47</td>
+      <td>47</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -89620,11 +109050,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
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       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
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       <td>0</td>
       <td>0</td>
@@ -89656,6 +109086,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>2</td>
+      <td>2</td>
+      <td>93</td>
+      <td>93</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -89684,8 +109128,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -89714,12 +109157,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>495</td>
-      <td>60307</td>
+      <td>78648</td>
+      <td>78834</td>
+      <td>1144</td>
+      <td>1156</td>
+      <td>18063</td>
+      <td>18063</td>
+      <td>870</td>
+      <td>870</td>
+      <td>4455</td>
+      <td>6051</td>
+      <td>194</td>
+      <td>289</td>
+      <td>101166</td>
+      <td>102948</td>
+      <td>2208</td>
+      <td>2315</td>
     </tr>
     <tr>
       <td></td>
@@ -89748,11 +109206,11 @@
       <td>0</td>
       <td>0</td>
       <td>7</td>
-      <td>7</td>
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       <td>7</td>
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       <td>0</td>
@@ -89782,8 +109240,22 @@
       <td>7</td>
       <td>7</td>
       <td>0</td>
-      <td>22</td>
-      <td>526</td>
+      <td>438</td>
+      <td>542</td>
+      <td>128</td>
+      <td>157</td>
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+      <td>0</td>
+      <td>438</td>
+      <td>542</td>
+      <td>128</td>
+      <td>157</td>
     </tr>
     <tr>
       <td></td>
@@ -89846,8 +109318,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -89912,6 +109398,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -89963,7 +109463,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -89976,6 +109475,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1725</td>
+      <td>1790</td>
+      <td>56</td>
+      <td>57</td>
+      <td>1725</td>
+      <td>1790</td>
+      <td>56</td>
+      <td>57</td>
     </tr>
     <tr>
       <td></td>
@@ -90040,6 +109554,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -90104,6 +109632,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -90166,8 +109708,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -90232,6 +109788,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -90294,8 +109864,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
-      <td>39</td>
+      <td>40</td>
+      <td>40</td>
+      <td>11</td>
+      <td>11</td>
+      <td>520</td>
+      <td>520</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>560</td>
+      <td>560</td>
+      <td>42</td>
+      <td>42</td>
     </tr>
     <tr>
       <td></td>
@@ -90324,11 +109908,11 @@
       <td>1</td>
       <td>2</td>
       <td>2</td>
-      <td>1</td>
+      <td>0</td>
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       <td>2</td>
       <td>2</td>
-      <td>1</td>
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       <td>0</td>
       <td>0</td>
@@ -90358,8 +109942,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
+      <td>46</td>
+      <td>46</td>
+      <td>19</td>
+      <td>19</td>
+      <td>15</td>
       <td>15</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>62</td>
+      <td>62</td>
+      <td>24</td>
+      <td>24</td>
     </tr>
     <tr>
       <td></td>
@@ -90388,11 +109986,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
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       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -90424,6 +110022,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -90475,7 +110087,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -90483,11 +110094,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>363</td>
+      <td>430</td>
+      <td>158</td>
+      <td>183</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>67</td>
-      <td>377</td>
+      <td>146</td>
+      <td>13</td>
+      <td>39</td>
+      <td>430</td>
+      <td>576</td>
+      <td>171</td>
+      <td>222</td>
     </tr>
     <tr>
       <td></td>
@@ -90550,8 +110176,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>86</td>
-      <td>561</td>
+      <td>682</td>
+      <td>682</td>
+      <td>172</td>
+      <td>172</td>
+      <td>322</td>
+      <td>322</td>
+      <td>74</td>
+      <td>74</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1007</td>
+      <td>1007</td>
+      <td>249</td>
+      <td>249</td>
     </tr>
     <tr>
       <td></td>
@@ -90603,7 +110243,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -90616,6 +110255,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>684</td>
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+      <td>17</td>
+      <td>17</td>
+      <td>684</td>
+      <td>684</td>
+      <td>17</td>
+      <td>17</td>
     </tr>
     <tr>
       <td></td>
@@ -90660,7 +110314,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -90680,6 +110333,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -90742,8 +110410,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>9</td>
+      <td>13</td>
+      <td>13</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>10</td>
+      <td>10</td>
     </tr>
     <tr>
       <td></td>
@@ -90808,6 +110490,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -90870,8 +110566,22 @@
       <td>14</td>
       <td>13</td>
       <td>0</td>
-      <td>2185</td>
-      <td>39356</td>
+      <td>45501</td>
+      <td>45666</td>
+      <td>4832</td>
+      <td>4868</td>
+      <td>7304</td>
+      <td>7304</td>
+      <td>1846</td>
+      <td>1846</td>
+      <td>3106</td>
+      <td>3106</td>
+      <td>457</td>
+      <td>457</td>
+      <td>55911</td>
+      <td>56076</td>
+      <td>7135</td>
+      <td>7171</td>
     </tr>
     <tr>
       <td></td>
@@ -90934,8 +110644,22 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>16</td>
-      <td>387</td>
+      <td>381</td>
+      <td>388</td>
+      <td>99</td>
+      <td>100</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>297</td>
+      <td>297</td>
+      <td>9</td>
+      <td>9</td>
+      <td>678</td>
+      <td>685</td>
+      <td>108</td>
+      <td>109</td>
     </tr>
     <tr>
       <td></td>
@@ -90998,8 +110722,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
       <td>110</td>
+      <td>110</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>110</td>
+      <td>110</td>
+      <td>19</td>
+      <td>19</td>
     </tr>
     <tr>
       <td></td>
@@ -91051,7 +110789,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -91062,8 +110799,23 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>90</td>
-      <td>721</td>
+      <td>0</td>
+      <td>1059</td>
+      <td>1059</td>
+      <td>222</td>
+      <td>222</td>
+      <td>426</td>
+      <td>426</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1486</td>
+      <td>1486</td>
+      <td>294</td>
+      <td>294</td>
     </tr>
     <tr>
       <td></td>
@@ -91126,8 +110878,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>13</td>
-      <td>83</td>
+      <td>97</td>
+      <td>97</td>
+      <td>41</td>
+      <td>41</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>97</td>
+      <td>97</td>
+      <td>41</td>
+      <td>41</td>
     </tr>
     <tr>
       <td></td>
@@ -91190,8 +110956,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
       <td>25</td>
+      <td>25</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>25</td>
+      <td>25</td>
+      <td>5</td>
+      <td>5</td>
     </tr>
     <tr>
       <td></td>
@@ -91256,6 +111036,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -91318,8 +111112,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -91364,7 +111172,6 @@
       <td>0</td>
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-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -91384,6 +111191,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -91412,11 +111234,10 @@
       <td>14</td>
       <td>14</td>
       <td>14</td>
-      <td>11</td>
+      <td>0</td>
       <td>14</td>
       <td>14</td>
       <td>14</td>
-      <td>11</td>
       <td>0</td>
       <td>0</td>
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@@ -91446,8 +111267,23 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>181</td>
-      <td>1966</td>
+      <td>0</td>
+      <td>2296</td>
+      <td>2328</td>
+      <td>673</td>
+      <td>676</td>
+      <td>141</td>
+      <td>141</td>
+      <td>39</td>
+      <td>39</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2437</td>
+      <td>2469</td>
+      <td>712</td>
+      <td>715</td>
     </tr>
     <tr>
       <td></td>
@@ -91510,8 +111346,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>2</td>
+      <td>2</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>2</td>
+      <td>2</td>
     </tr>
     <tr>
       <td></td>
@@ -91574,8 +111424,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
-      <td>63</td>
+      <td>54</td>
+      <td>64</td>
+      <td>4</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>54</td>
+      <td>64</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -91620,7 +111484,6 @@
       <td>0</td>
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       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -91635,11 +111498,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
-      <td>24</td>
-      <td>293</td>
+      <td>312</td>
+      <td>312</td>
+      <td>71</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>312</td>
+      <td>312</td>
+      <td>71</td>
+      <td>71</td>
     </tr>
     <tr>
       <td></td>
@@ -91691,7 +111569,6 @@
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-      <td>0</td>
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       <td>0</td>
@@ -91704,6 +111581,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     </tr>
     <tr>
       <td></td>
@@ -91747,7 +111639,6 @@
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       <td>1</td>
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       <td>0</td>
@@ -91768,6 +111659,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -91811,7 +111717,6 @@
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-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -91832,6 +111737,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -91896,6 +111816,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -91960,6 +111894,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -92004,7 +111952,6 @@
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-      <td>0</td>
       <td>2</td>
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       <td>0</td>
@@ -92024,6 +111971,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -92086,8 +112048,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
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     </tr>
     <tr>
       <td></td>
@@ -92152,6 +112128,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -92216,6 +112206,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -92244,10 +112248,9 @@
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       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
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@@ -92274,12 +112277,27 @@
       <td>0</td>
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       <td>0</td>
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       <td>0</td>
-      <td>56</td>
-      <td>769</td>
+      <td>789</td>
+      <td>840</td>
+      <td>130</td>
+      <td>134</td>
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     </tr>
     <tr>
       <td></td>
@@ -92323,7 +112341,6 @@
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-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -92344,6 +112361,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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+      <td>80</td>
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     </tr>
     <tr>
       <td></td>
@@ -92387,7 +112419,6 @@
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-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -92408,6 +112439,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -92436,11 +112482,11 @@
       <td>4</td>
       <td>0</td>
       <td>7</td>
-      <td>7</td>
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@@ -92470,8 +112516,22 @@
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       <td>0</td>
-      <td>21</td>
-      <td>225</td>
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+      <td>44</td>
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+      <td>283</td>
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+      <td>47</td>
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     </tr>
     <tr>
       <td></td>
@@ -92500,10 +112560,9 @@
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       <td>5</td>
-      <td>5</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
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@@ -92531,11 +112590,26 @@
       <td>0</td>
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       <td>0</td>
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       <td>0</td>
-      <td>10</td>
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+      <td>38</td>
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+      <td>328</td>
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     </tr>
     <tr>
       <td></td>
@@ -92600,6 +112674,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
       <td></td>
@@ -92664,6 +112752,20 @@
       <td>0</td>
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     <tr>
       <td></td>
@@ -92706,7 +112808,6 @@
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@@ -92723,11 +112824,26 @@
       <td>0</td>
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+      <td>57</td>
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+      <td>10</td>
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+      <td>20</td>
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       <td>8</td>
-      <td>50</td>
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     </tr>
     <tr>
       <td></td>
@@ -92790,8 +112906,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>49</td>
-      <td>643</td>
+      <td>649</td>
+      <td>685</td>
+      <td>138</td>
+      <td>142</td>
+      <td>473</td>
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+      <td>105</td>
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+      <td>761</td>
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+      <td>18</td>
+      <td>18</td>
+      <td>1883</td>
+      <td>1919</td>
+      <td>261</td>
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     </tr>
     <tr>
       <td></td>
@@ -92854,8 +112984,22 @@
       <td>1</td>
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       <td>0</td>
-      <td>6</td>
       <td>57</td>
+      <td>69</td>
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     </tr>
     <tr>
       <td></td>
@@ -92918,8 +113062,22 @@
       <td>1</td>
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       <td>0</td>
-      <td>78</td>
-      <td>941</td>
+      <td>965</td>
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     </tr>
     <tr>
       <td></td>
@@ -92962,7 +113120,6 @@
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@@ -92978,12 +113135,27 @@
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-      <td>115</td>
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+      <td>29</td>
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+      <td>6220</td>
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     </tr>
     <tr>
       <td></td>
@@ -93046,8 +113218,22 @@
       <td>1</td>
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-      <td>79</td>
-      <td>1360</td>
+      <td>1488</td>
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     </tr>
     <tr>
       <td></td>
@@ -93112,6 +113298,20 @@
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@@ -93174,8 +113374,22 @@
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-      <td>25</td>
-      <td>86</td>
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       <td></td>
@@ -93240,6 +113454,20 @@
       <td>0</td>
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       <td></td>
@@ -93304,6 +113532,20 @@
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       <td></td>
@@ -93368,6 +113610,20 @@
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       <td></td>
@@ -93432,6 +113688,20 @@
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@@ -93460,11 +113730,11 @@
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       <td>0</td>
       <td>0</td>
@@ -93494,8 +113764,22 @@
       <td>4</td>
       <td>4</td>
       <td>0</td>
-      <td>351</td>
-      <td>12203</td>
+      <td>14412</td>
+      <td>14590</td>
+      <td>722</td>
+      <td>732</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14412</td>
+      <td>14590</td>
+      <td>722</td>
+      <td>732</td>
     </tr>
     <tr>
       <td></td>
@@ -93560,6 +113844,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -93624,6 +113922,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -93652,8 +113964,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -93683,11 +113994,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>39</td>
+      <td>39</td>
+      <td>6</td>
       <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>9</td>
+      <td>9</td>
     </tr>
     <tr>
       <td></td>
@@ -93716,11 +114042,11 @@
       <td>5</td>
       <td>2</td>
       <td>6</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>2</td>
       <td>6</td>
-      <td>5</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -93750,8 +114076,22 @@
       <td>6</td>
       <td>2</td>
       <td>0</td>
-      <td>175</td>
-      <td>5876</td>
+      <td>5995</td>
+      <td>5995</td>
+      <td>275</td>
+      <td>275</td>
+      <td>66</td>
+      <td>66</td>
+      <td>23</td>
+      <td>23</td>
+      <td>295</td>
+      <td>295</td>
+      <td>3</td>
+      <td>3</td>
+      <td>6356</td>
+      <td>6356</td>
+      <td>301</td>
+      <td>301</td>
     </tr>
     <tr>
       <td></td>
@@ -93780,10 +114120,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -93811,11 +114150,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
-      <td>14</td>
+      <td>59</td>
+      <td>59</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59</td>
+      <td>59</td>
+      <td>17</td>
+      <td>17</td>
     </tr>
     <tr>
       <td></td>
@@ -93880,6 +114234,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -93908,11 +114276,10 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -93943,7 +114310,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>143</td>
+      <td>143</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>143</td>
+      <td>143</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
     <tr>
       <td></td>
@@ -93987,7 +114369,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -94008,6 +114389,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
     </tr>
     <tr>
       <td></td>
@@ -94070,8 +114466,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
     </tr>
     <tr>
       <td></td>
@@ -94134,8 +114544,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>4</td>
+      <td>4</td>
     </tr>
   </tbody>
 </table>
diff --git a/communities/all/resources/tools.json b/communities/all/resources/tools.json
index c1da03fe..4620380b 100644
--- a/communities/all/resources/tools.json
+++ b/communities/all/resources/tools.json
@@ -42,7 +42,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -59,12 +58,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
+    "No. of tool users (5 years) (usegalaxy.eu)": 0,
+    "No. of tool users (all time) (usegalaxy.eu)": 0,
+    "Tool usage (5 years) (usegalaxy.eu)": 0,
+    "Tool usage (all time) (usegalaxy.eu)": 0,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 0,
+    "No. of tool users (all time) - all main servers": 0,
+    "Tool usage (5 years) - all main servers": 0,
+    "Tool usage (all time) - all main servers": 0
   },
   {
     "Galaxy wrapper id": "baric_archive",
@@ -97,11 +111,11 @@
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 0,
     "Available on UseGalaxy.eu": 0,
-    "Available on UseGalaxy.fr": 2,
+    "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 0,
     "Tools available on UseGalaxy.eu": 0,
-    "Tools available on UseGalaxy.fr": 2,
+    "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
     "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
@@ -110,7 +124,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -127,12 +140,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
+    "No. of tool users (5 years) (usegalaxy.eu)": 0,
+    "No. of tool users (all time) (usegalaxy.eu)": 0,
+    "Tool usage (5 years) (usegalaxy.eu)": 0,
+    "Tool usage (all time) (usegalaxy.eu)": 0,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 0,
+    "No. of tool users (all time) - all main servers": 0,
+    "Tool usage (5 years) - all main servers": 0,
+    "Tool usage (all time) - all main servers": 0
   },
   {
     "Galaxy wrapper id": "braker",
@@ -177,7 +205,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -194,12 +221,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 1,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 17,
-    "Total tool usage (usegalaxy.eu)": 109
+    "No. of tool users (5 years) (usegalaxy.eu)": 165,
+    "No. of tool users (all time) (usegalaxy.eu)": 165,
+    "Tool usage (5 years) (usegalaxy.eu)": 48,
+    "Tool usage (all time) (usegalaxy.eu)": 48,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 165,
+    "No. of tool users (all time) - all main servers": 165,
+    "Tool usage (5 years) - all main servers": 48,
+    "Tool usage (all time) - all main servers": 48
   },
   {
     "Galaxy wrapper id": "braker3",
@@ -249,11 +291,11 @@
     "Available on UseGalaxy.org (Main)": 0,
     "Available on UseGalaxy.org.au": 1,
     "Available on UseGalaxy.eu": 1,
-    "Available on UseGalaxy.fr": 1,
+    "Available on UseGalaxy.fr": 0,
     "Tools available on UseGalaxy.org (Main)": 0,
     "Tools available on UseGalaxy.org.au": 1,
     "Tools available on UseGalaxy.eu": 1,
-    "Tools available on UseGalaxy.fr": 1,
+    "Tools available on UseGalaxy.fr": 0,
     "Tools available on APOSTL": 0,
     "Tools available on ARGs-OAP": 0,
     "Tools available on CIRM-CFBP": 0,
@@ -262,7 +304,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -279,12 +320,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 10,
-    "Total tool usage (usegalaxy.eu)": 567
+    "No. of tool users (5 years) (usegalaxy.eu)": 1938,
+    "No. of tool users (all time) (usegalaxy.eu)": 1938,
+    "Tool usage (5 years) (usegalaxy.eu)": 294,
+    "Tool usage (all time) (usegalaxy.eu)": 294,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 412,
+    "No. of tool users (all time) (usegalaxy.org.au)": 412,
+    "Tool usage (5 years) (usegalaxy.org.au)": 71,
+    "Tool usage (all time) (usegalaxy.org.au)": 71,
+    "No. of tool users (5 years) - all main servers": 2350,
+    "No. of tool users (all time) - all main servers": 2350,
+    "Tool usage (5 years) - all main servers": 365,
+    "Tool usage (all time) - all main servers": 365
   },
   {
     "Galaxy wrapper id": "feelnc2asko",
@@ -329,7 +385,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -346,12 +401,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
+    "No. of tool users (5 years) (usegalaxy.eu)": 0,
+    "No. of tool users (all time) (usegalaxy.eu)": 0,
+    "Tool usage (5 years) (usegalaxy.eu)": 0,
+    "Tool usage (all time) (usegalaxy.eu)": 0,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 0,
+    "No. of tool users (all time) - all main servers": 0,
+    "Tool usage (5 years) - all main servers": 0,
+    "Tool usage (all time) - all main servers": 0
   },
   {
     "Galaxy wrapper id": "gcms2isocor",
@@ -396,7 +466,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -413,12 +482,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
+    "No. of tool users (5 years) (usegalaxy.eu)": 0,
+    "No. of tool users (all time) (usegalaxy.eu)": 0,
+    "Tool usage (5 years) (usegalaxy.eu)": 0,
+    "Tool usage (all time) (usegalaxy.eu)": 0,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 0,
+    "No. of tool users (all time) - all main servers": 0,
+    "Tool usage (5 years) - all main servers": 0,
+    "Tool usage (all time) - all main servers": 0
   },
   {
     "Galaxy wrapper id": "get_pairs",
@@ -463,7 +547,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -480,12 +563,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
+    "No. of tool users (5 years) (usegalaxy.eu)": 0,
+    "No. of tool users (all time) (usegalaxy.eu)": 0,
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-      "meme_fimo"
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       "picard_samtofastq",
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+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 0,
+    "No. of tool users (all time) - all main servers": 0,
+    "Tool usage (5 years) - all main servers": 0,
+    "Tool usage (all time) - all main servers": 0
   },
   {
     "Galaxy wrapper id": "scripting",
@@ -106943,7 +127193,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -106960,12 +127209,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
+    "No. of tool users (5 years) (usegalaxy.eu)": 0,
+    "No. of tool users (all time) (usegalaxy.eu)": 0,
+    "Tool usage (5 years) (usegalaxy.eu)": 0,
+    "Tool usage (all time) (usegalaxy.eu)": 0,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 0,
+    "No. of tool users (all time) - all main servers": 0,
+    "Tool usage (5 years) - all main servers": 0,
+    "Tool usage (all time) - all main servers": 0
   },
   {
     "Galaxy wrapper id": "baseline_calculator",
@@ -107011,7 +127275,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -107028,12 +127291,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
+    "No. of tool users (5 years) (usegalaxy.eu)": 0,
+    "No. of tool users (all time) (usegalaxy.eu)": 0,
+    "Tool usage (5 years) (usegalaxy.eu)": 0,
+    "Tool usage (all time) (usegalaxy.eu)": 0,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 0,
+    "No. of tool users (all time) - all main servers": 0,
+    "Tool usage (5 years) - all main servers": 0,
+    "Tool usage (all time) - all main servers": 0
   },
   {
     "Galaxy wrapper id": "dose_responses",
@@ -107078,7 +127356,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -107095,12 +127372,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
+    "No. of tool users (5 years) (usegalaxy.eu)": 0,
+    "No. of tool users (all time) (usegalaxy.eu)": 0,
+    "Tool usage (5 years) (usegalaxy.eu)": 0,
+    "Tool usage (all time) (usegalaxy.eu)": 0,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 0,
+    "No. of tool users (all time) - all main servers": 0,
+    "Tool usage (5 years) - all main servers": 0,
+    "Tool usage (all time) - all main servers": 0
   },
   {
     "Galaxy wrapper id": "vibrant",
@@ -107167,7 +127459,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -107184,12 +127475,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
+    "No. of tool users (5 years) (usegalaxy.eu)": 0,
+    "No. of tool users (all time) (usegalaxy.eu)": 0,
+    "Tool usage (5 years) (usegalaxy.eu)": 0,
+    "Tool usage (all time) (usegalaxy.eu)": 0,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 0,
+    "No. of tool users (all time) - all main servers": 0,
+    "Tool usage (5 years) - all main servers": 0,
+    "Tool usage (all time) - all main servers": 0
   },
   {
     "Galaxy wrapper id": "virsorter",
@@ -107244,7 +127550,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -107261,12 +127566,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
+    "No. of tool users (5 years) (usegalaxy.eu)": 0,
+    "No. of tool users (all time) (usegalaxy.eu)": 0,
+    "Tool usage (5 years) (usegalaxy.eu)": 0,
+    "Tool usage (all time) (usegalaxy.eu)": 0,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 0,
+    "No. of tool users (all time) - all main servers": 0,
+    "Tool usage (5 years) - all main servers": 0,
+    "Tool usage (all time) - all main servers": 0
   },
   {
     "Galaxy wrapper id": "pyvo_integration",
@@ -107311,7 +127631,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -107328,12 +127647,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 1,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 4,
-    "Total tool usage (usegalaxy.eu)": 36
+    "No. of tool users (5 years) (usegalaxy.eu)": 53,
+    "No. of tool users (all time) (usegalaxy.eu)": 53,
+    "Tool usage (5 years) (usegalaxy.eu)": 6,
+    "Tool usage (all time) (usegalaxy.eu)": 6,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 53,
+    "No. of tool users (all time) - all main servers": 53,
+    "Tool usage (5 years) - all main servers": 6,
+    "Tool usage (all time) - all main servers": 6
   },
   {
     "Galaxy wrapper id": "astropytools",
@@ -107380,7 +127714,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -107397,12 +127730,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 3,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 3,
-    "Total tool usage (usegalaxy.eu)": 11
+    "No. of tool users (5 years) (usegalaxy.eu)": 13,
+    "No. of tool users (all time) (usegalaxy.eu)": 13,
+    "Tool usage (5 years) (usegalaxy.eu)": 5,
+    "Tool usage (all time) (usegalaxy.eu)": 5,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 13,
+    "No. of tool users (all time) - all main servers": 13,
+    "Tool usage (5 years) - all main servers": 5,
+    "Tool usage (all time) - all main servers": 5
   },
   {
     "Galaxy wrapper id": "cta",
@@ -107447,7 +127795,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -107464,12 +127811,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
+    "No. of tool users (5 years) (usegalaxy.eu)": 0,
+    "No. of tool users (all time) (usegalaxy.eu)": 0,
+    "Tool usage (5 years) (usegalaxy.eu)": 0,
+    "Tool usage (all time) (usegalaxy.eu)": 0,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 0,
+    "No. of tool users (all time) - all main servers": 0,
+    "Tool usage (5 years) - all main servers": 0,
+    "Tool usage (all time) - all main servers": 0
   },
   {
     "Galaxy wrapper id": "hess",
@@ -107514,7 +127876,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -107531,12 +127892,27 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
+    "No. of tool users (5 years) (usegalaxy.eu)": 1,
+    "No. of tool users (all time) (usegalaxy.eu)": 1,
+    "Tool usage (5 years) (usegalaxy.eu)": 1,
+    "Tool usage (all time) (usegalaxy.eu)": 1,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 1,
+    "No. of tool users (all time) - all main servers": 1,
+    "Tool usage (5 years) - all main servers": 1,
+    "Tool usage (all time) - all main servers": 1
   },
   {
     "Galaxy wrapper id": "sgwb",
@@ -107581,7 +127957,6 @@
     "Tools available on CoralSNP": 0,
     "Tools available on CropGalaxy": 0,
     "Tools available on Dintor": 0,
-    "Tools available on FreeBioinfo": 0,
     "Tools available on GASLINI": 0,
     "Tools available on Galaxy@AuBi": 0,
     "Tools available on Galaxy@Pasteur": 0,
@@ -107598,11 +127973,26 @@
     "Tools available on Oqtans": 0,
     "Tools available on Palfinder": 0,
     "Tools available on PepSimili": 0,
+    "Tools available on PhagePromotor": 0,
     "Tools available on UseGalaxy.be": 0,
     "Tools available on UseGalaxy.cz": 0,
     "Tools available on UseGalaxy.no": 0,
     "Tools available on Viral Variant Visualizer (VVV)": 0,
-    "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
-    "Total tool usage (usegalaxy.eu)": 0
+    "No. of tool users (5 years) (usegalaxy.eu)": 5,
+    "No. of tool users (all time) (usegalaxy.eu)": 5,
+    "Tool usage (5 years) (usegalaxy.eu)": 2,
+    "Tool usage (all time) (usegalaxy.eu)": 2,
+    "No. of tool users (5 years) (usegalaxy.org)": 0,
+    "No. of tool users (all time) (usegalaxy.org)": 0,
+    "Tool usage (5 years) (usegalaxy.org)": 0,
+    "Tool usage (all time) (usegalaxy.org)": 0,
+    "No. of tool users (5 years) (usegalaxy.org.au)": 0,
+    "No. of tool users (all time) (usegalaxy.org.au)": 0,
+    "Tool usage (5 years) (usegalaxy.org.au)": 0,
+    "Tool usage (all time) (usegalaxy.org.au)": 0,
+    "No. of tool users (5 years) - all main servers": 5,
+    "No. of tool users (all time) - all main servers": 5,
+    "Tool usage (5 years) - all main servers": 2,
+    "Tool usage (all time) - all main servers": 2
   }
 ]
diff --git a/communities/all/resources/tools.tsv b/communities/all/resources/tools.tsv
index 219dbb46..c778899f 100644
--- a/communities/all/resources/tools.tsv
+++ b/communities/all/resources/tools.tsv
@@ -1,1472 +1,1470 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)
-2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	6541
-2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	13760
-2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	6834
-2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	656
-2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	6156
-3d_tensor_feature_dimension_reduction	ip_3d_tensor_feature_dimension_reduction	Dimensionality reduction for features (channels) of 3D tensor data using UMAP								To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	3d_tensor_feature_dimension_reduction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction	0.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-Ensembl-REST	get_feature_info, get_genetree, get_sequences	A suite of Galaxy tools designed to work with Ensembl REST API.								To update	https://rest.ensembl.org	Data Source		earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	0.1.2	requests				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	47	2889
-GAFA	gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	45
-TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	984
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40
-apoc	apoc	Large-scale structural comparison of protein pockets								To update	http://cssb.biology.gatech.edu/APoc	Computational chemistry	apoc	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc	1.0+galaxy1	apoc	1b16			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	3
-apollo	create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism	Access an Apollo instance from Galaxy								To update	https://github.com/galaxy-genome-annotation/python-apollo	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo		apollo	4.2.13			0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	0	301	1896
-askomics	askomics_integrate	Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/								To update	https://github.com/askomics/	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics		askocli	0.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-askor	askor_de	AskoR links EdgeR and AskOmics								To update	https://github.com/askomics/askoR	Transcriptomics	askor_de	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	0.2	bioconductor-limma	3.58.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bamclipper	bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-baric_archive	baric_archive_rennes, baric_archive_toulouse	A data source tool to fetch data from a BARIC Archive server.								To update	https://www.cesgo.org/catibaric/	Data Source		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	1.1.0					0	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-batched_lastz	batched_lastz	Galaxy wrapper for the batching Lastz runs								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	batched_lastz	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	1.04.22	lastz	1.04.22			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	38	1523
-binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	1273
-binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	29
-bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9
-biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-biohansel_bionumeric_converter	bionumeric_convert	Convert BioHansel output data to a Bionumerics friendly form								To update	https://github.com/phac-nml/galaxy_tools	Text Manipulation	biohansel_bionumeric_converter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter	0.2.0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-blast_parser	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	296
-braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	17	109
-braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	567
-bundle_collections	bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.58			0	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-camera	abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos									To update		Metabolomics	camera	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera	1.48.0	r-snow	0.4_1			1	2	2	2	1	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	2	0	30	623
-cfm	cfmid	Competitive Fragmentation Modeling (CFM)								Up-to-date	https://sourceforge.net/p/cfm-id/	Metabolomics	cfmid	computational-metabolomics	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	33	cfm	33			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chado	analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree	Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado								To update	https://github.com/galaxy-genome-annotation/python-chado	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado		python-chado	2.3.9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-collapse_collection	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1583	33934
-color-deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	16
-colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-combineJSON	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-combine_tabular_collection	combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	78
-concat_paired	concat_fastqs	Concatenate paired datasets								To update	https://github.com/phac-nml/concat	Text Manipulation	concat_paired	nml	https://github.com/phac-nml/concat	https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	16546
-correlation_analysis	correlation_analysis	[Metabolomics][W4M] Metabolites Correlation Analysis								To update	http://workflow4metabolomics.org	Metabolomics	correlation_analysis	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis	1.0.1+galaxy0	r-batch	1.1_4			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	25	272
-cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	8518
-csvtk	csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq	Rapid data investigation and manipulation of csv/tsv files								To update	https://bioinf.shenwei.me/csvtk/	Text Manipulation	csvtk	nml	https://github.com/shenwei356/csvtk	https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk	0.20.0	csvtk	0.30.0			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	20	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-curl_post	curl_post	Send file via cURL POST								To update	https://github.com/bmcv	Data Export, Web Services	curl_post	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curl_post	0.0.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	440
-curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	12
-detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	46
-ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	9907
-ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	45	899
-export_to_cluster	export_to_cluster	Export datasets to cluster								To update	https://github.com/TGAC/earlham-galaxytools/	Data Export	export_to_cluster	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster	0.0.2	EXPORT_DIR_PREFIX				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fasta2bed	fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fasta_extract	fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	10
-fastqc_stats	FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-feelnc2asko	feelnc2asko	Convert FeelNC GTF to GFF3								To update	https://github.com/tderrien/FEELnc	Convert Formats	feelnc2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-feht	feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gblocks	gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b			0	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
-gcms2isocor	gcms2isocor	Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs								To update	https://github.com/p2m2/p2m2tools	Metabolomics	gcms2isocor	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor	0.2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gcms2isocor	gcms2isocor	Conversion from GCMS PostRun Analysis to Isocor								To update		Metabolomics	gcms2isocor	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-genenotebook	genenotebook_build	Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io								Up-to-date	https://genenotebook.github.io	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	0.4.16	genoboo	0.4.16			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-genform	genform	genform: generation of molecular formulas by high-resolution MS and MS/MS data								To update	https://sourceforge.net/projects/genform/	Metabolomics	genform	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform		genform	r8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	68
-get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gnali	gnali	A tool to find nonessential, loss-of-function gene variants								Up-to-date	https://github.com/phac-nml/gnali/	Variant Analysis	gnali	nml	https://github.com/phac-nml/gnali/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali	1.1.0	gnali	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gstf_preparation	gstf_preparation	GeneSeqToFamily preparation converts data for the workflow								To update	https://github.com/TGAC/earlham-galaxytools/	Convert Formats	gstf_preparation	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	0.4.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	397
-hcluster_sg	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	238
-hcluster_sg_parser	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	290
-helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	93
-hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	41	621
-image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	12
-imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	21825
-influx_data_manager	influx_data_manager	Handling influx_si data inputs in Galaxy workflows								To update	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/	Metabolomics	influx_si_data_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager	1.0.2	influx-si-data-manager	1.0.3			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-influx_si	influx_si	metabolic flux estimation based on [in]stationary labeling								To update	https://github.com/sgsokol/influx	Metabolomics	influx_si	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si	7.0.1	influx_si	7.0.4			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ipo	ipo4retgroup, ipo4xcmsSet	[W4M][LC-MS] IPO								To update	https://github.com/rietho/IPO	Metabolomics	ipo	lecorguille	https://github.com/rietho/IPO	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo	1.10.0	bioconductor-ipo	1.28.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-isoplot	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	2
-jbrowse	jbrowse_to_container	A tool allowing to export a JBrowse dataset into a JBrowse docker container								To update	https://jbrowse.org	Web Services	jbrowse_to_container	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse		python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kaptive	kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kat_sect	kat_@EXECUTABLE@	SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.								To update			kat_sect	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kegalign	kegalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	kegalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	0.1.2.7	kegalign-full	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kmd_hmdb_data_plot	kmd_hmdb_data_plot	retrieves data from KMD HMDB API and produce plot and csv file								To update	https://github.com/workflow4metabolomics/tools-metabolomics	Metabolomics	kmd_hmdb_data_plot	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	36
-landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	857
-logol	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	114	936
-mahotas-features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	37
-mauve_contig_mover	mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-meneco	meneco	Meneco computes minimal completions to your draft network with reactions from a repair network								Up-to-date	http://bioasp.github.io/meneco/	Systems Biology	meneco	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	1.5.2	meneco	1.5.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25
-metfrag	metfrag	[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity)								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag	2.4.5+galaxy3	metfrag	2.4.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	153
-metfrag-vis	metfrag_vis	[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis	2.4.5+galaxy0	metfrag	2.4.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	12
-miranda	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	41	6076
-miranda2asko	miranda2asko	Converts miRanda output into AskOmics format								To update		Convert Formats	miranda2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	0.2	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mixmodel4repeated_measures	mixmodel4repeated_measures	[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model								To update	http://workflow4metabolomics.org	Metabolomics	mixmodel4repeated_measures	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures	3.1.0	r-lme4				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	322	89021
-morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
-ms2snoop	ms2snoop	[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.								To update	http://workflow4metabolomics.org	Metabolomics	ms2snoop	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop	2.2.1	r-base				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-msPurity	mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								Up-to-date	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity	1.28.0	bioconductor-mspurity	1.28.0			0	0	10	11	0	0	10	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	40	709
-msp_split	msp_split	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								To update	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		tomnl	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split	0.0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ncbi_fcs_adaptor	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-nmr_annotation	NmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation								To update	http://workflow4metabolomics.org	Metabolomics	nmr_annotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_annotation	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation	3.0.0	r-batch	1.1_4			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	47
-nmr_annotation2d	2DNmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra								To update	http://workflow4metabolomics.org	Metabolomics	2dnmrannotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d	2.0.0	r-batch	1.1_4			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-nmr_preprocessing	NMR_Preprocessing, NMR_Read	[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction								To update	http://workflow4metabolomics.org	Metabolomics	nmr_preprocessing	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_preprocessing	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing		r-batch	1.1_4			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	4	140
-normalization	normalization	[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data								To update	http://workflow4metabolomics.org	Metabolomics	normalization	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/normalization	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization	1.0.7	r-batch	1.1_4			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	133
-openlabcds2csv	openlabcds2csv	"Creates a summary of several ""Internal Standard Report"" OpenLabCDS results."								To update		Metabolomics	openlabcds2csv	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	60
-pangolin	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	0	0	259	7276
-patrist	patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-peptimapper	peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.1					0	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42
-physiofit	physiofit	PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit	workflow4metabolomics	https://github.com/MetaSys-LISBP/PhysioFit	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit	3.4.0	physiofit	3.4.0			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-physiofit_manager	physiofit_data_manager	Handling of physiofit input files								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager	1.0.1	physiofit_data_manager	1.0.1			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-plasmid_profiler	plasmid_profiler	Explores plasmid content in WGS data								To update			plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler	0.1.6	r				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-plasmid_profiler_suite		Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-plotheatmap	plotheatmap	This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output.								To update		Computational chemistry	plotheatmap	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	1.0	bioconductor-preprocesscore	1.64.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-pneumocat	pneumocat	Pneumococcal Capsular Typing of illumina fastq reads								Up-to-date	https://github.com/phe-bioinformatics/PneumoCaT	Variant Analysis	pneumocat	nml	https://github.com/phe-bioinformatics/PneumoCaT	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat	1.2.1	pneumocat	1.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-points2binaryimage	ip_points_to_binaryimage	Points to Binary Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2binaryimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage	0.3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	41
-points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	31
-points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	29
-projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	85
-projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	21343
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pseudogenome	pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-quasitools	aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0			0	12	0	12	0	12	0	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rdock	rdock	Docking ligands to proteins and nucleic acids								To update	http://rdock.sourceforge.net/	Computational chemistry	rdock	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock	1.0	rDock	2013.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-refseq_masher	refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2			2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16
-replace_chromosome_names	replace_chromosome_names	Replace chromosome names								To update		Text Manipulation	replace_chromosome_names	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names	0.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	537
-rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7
-rsat_filter_snps	rsat_filter_snps	Filter SNPs in RSAT Matrix Scan output								To update	https://github.com/TGAC/earlham-galaxytools/	ChIP-seq, Systems Biology	rsat_filter_snps	earlham	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	512
-segalign	segalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/gsneha26/SegAlign	Next Gen Mappers	segalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	0.1.2.7	segalign-galaxy	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	3
-seqtk_nml	seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	133	2489
-skyline2isocor	skyline2isocor	Converting skyline output to IsoCor input								Up-to-date	https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor	Metabolomics	skyline2isocor	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor	1.0.0	skyline2isocor	1.0.0			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	102
-smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-smart_domains	smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-smina	smina	smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization								To update	https://sourceforge.net/projects/smina/	Computational chemistry	smina	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina	1.0	smina	2017.11.9			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	493
-spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spatyper	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42
-spolpred	spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.1	giatools	0.3.1	Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	16
-srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205
-staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	889	12673
-stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	13
-suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	2	4	4	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	2	5
-suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	5	67
-suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	31	202
-suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	9	73
-suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	26	114
-suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	22	21	21	21	22	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	43	168
-suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	4	4
-suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2	6
-suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	48	263
-suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	17	17	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	59	213
-suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	20
-suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	6	14
-suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	40	232
-suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	12	37
-suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0
-suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	13
-suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	1	1
-suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	22	172
-suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	7	8	8	8	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	8	16
-suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	124	7087
-superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	16
-t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	70	8690
-tree_relabeler	tree_relabel	Relabels the tips of a newick formatted tree.								To update		Text Manipulation	tree_relabeler	nml	https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler	https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tripal	analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync	Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal								To update	https://github.com/galaxy-genome-annotation/python-tripal	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal		python-tripal	3.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-unzip	unzip	Unzip file								To update	https://github.com/bmcv	Convert Formats	unzip	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip	6.0	unzip				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	508	5370
-visceral-evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25
-voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-w4mclassfilter	w4mclassfilter	Filter W4M data by values or metadata								To update	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper	Metabolomics	w4mclassfilter	eschen42	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter	0.98.19	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	2834
-w4mconcatenate	W4Mconcatenate	[W4M][Utils] concatenate two Metadata tables								To update	http://workflow4metabolomics.org	Metabolomics	w4mconcatenate	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate	1.0.0+galaxy0	r-base				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-w4mcorcov	w4mcorcov	OPLS-DA Contrasts of Univariate Results								To update	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper	Metabolomics	w4mcorcov	eschen42	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov	0.98.18	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	368
-w4mjoinpn	w4mjoinpn	Join positive- and negative-mode W4M datasets								To update	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper	Metabolomics	w4mjoinpn	eschen42	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn	0.98.2	coreutils	8.25			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	171
-wade	wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	38
-xcms	abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw		XCMS	XCMS		xcms	Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data.  The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling.	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Biological imaging, Data visualisation, Metabolomics	Up-to-date	https://github.com/sneumann/xcms	Metabolomics	xcms	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms	4.0.0	bioconductor-xcms	4.0.0	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Data visualisation, Metabolomics	9	11	12	12	9	11	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	10	9	0	356	29809
-10x_bamtofastq	10x_bamtofastq	Converts 10x Genomics BAM to FASTQ								Up-to-date	https://github.com/10XGenomics/bamtofastq	Convert Formats	10x_bamtofastq	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	1.4.1	10x_bamtofastq	1.4.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	46	228
-AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	116
-AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	10	3060
-CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	45191
-CollectResults	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	1961
-CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	108
-GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	133
-LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	45325
-NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	28	62388
-Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	68
-PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	1932
-Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	1758
-Structure_GSPAN	structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	2925
-add_line_to_file	add_line_to_file	Adds a text line to the beginning or end of a file.								To update		Text Manipulation	add_line_to_file	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	0.1.0	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	193	14480
-add_value	addValue	Add a value as a new column.								To update		Text Manipulation	add_value	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value	https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value	1.0.1	perl				1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	591	367167
-agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	42	481
-align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	329
-antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	52
-antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	279	14596
-aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	65
-atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	26	257
-augustus	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	516	8864
-bamhash	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	169
-barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-basecoverage	gops_basecoverage_1	Base Coverage of all intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	basecoverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	2	308
-best_regression_subsets	BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	3
-bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2
-bigwig_to_bedgraph	bigwig_to_bedgraph	Convert from bigWig to bedGraph format								To update		Convert Formats	bigwig_to_bedgraph	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	0.1.0	ucsc_tools				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	5749
-bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13
-bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531
-bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	4	4	4	0	332	12876
-blat_coverage_report	generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-blat_mapping	blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685
-blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	34	3009
-blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	15	1478
-bowtie_wrappers	bowtie_wrapper	Galaxy wrappers for the Bowtie short read mapping tools.								To update	http://bowtie-bio.sourceforge.net/	Next Gen Mappers	bowtie_wrappers	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers	https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers	1.2.0	bowtie	1.3.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	506	22988
-canonical_correlation_analysis	cca1	Canonical Correlation Analysis								To update		Statistics	canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis	1.0.0	R				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10	74
-canu	canu	Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).	canu	canu		CANU	De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.	De-novo assembly	Genomics	Up-to-date	https://github.com/marbl/canu		canu	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/canu	https://github.com/bgruening/galaxytools/tree/master/tools/canu	2.2	canu	2.2	De-novo assembly	Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	533	13021
-categorize_elements_satisfying_criteria	categorize_elements_satisfying_criteria	Categorize Elements satisfying criteria.								To update		Statistics	categorize_elements_satisfying_criteria	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria	https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	40
-ccat	peakcalling_ccat	Control-based ChIP-seq Analysis Tool								To update		ChIP-seq	ccat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat	0.0.2	ccat	3.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	173
-cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	0	178	4614
-cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	43
-change_case	ChangeCase	Convert column case.								To update		Text Manipulation	change_case	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case	https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case	1.0.1	perl				1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	1	1	1	1	931	10965
-chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	418	15690
-chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-circexplorer	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	251
-clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cluster	gops_cluster_1	Cluster the intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	cluster	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1	801
-cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	102
-cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	1	108
-cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	342
-column_arrange_by_header	bg_column_arrange_by_header	Column arrange by header name								To update		Text Manipulation	column_arrange_by_header	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	179	3781
-combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	147
-compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	220
-compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	332
-complement	gops_complement_1	Complement intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	complement	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1	233
-compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	94
-compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	65
-compute_q_values	compute_q_values	Compute q-values based on multiple simultaneous tests p-values								To update		Statistics	compute_q_values	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values	1.0.1	R				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	35
-concat	gops_concat_1	Concatenate two bed files								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	concat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat	1.0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	309	564900
-condense_characters	Condense characters1	Condense consecutive characters.								To update		Text Manipulation	condense_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters	1.0.0					1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-convert_characters	Convert characters1	Convert delimiters to tab.								To update		Text Manipulation	convert_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters	1.0.1	python				1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	475	23829
-convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-correlation	cor2	Correlation for numeric columns								To update		Statistics	correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation	1.0.0	rpy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	47	837
-count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	49	271
-count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-coverage	gops_coverage_1	Coverage of a set of intervals on second set of intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	coverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	17	1502
-coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cpat	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.								Up-to-date	https://github.com/liguowang/cpat	Transcriptomics	cpat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	3.0.5	cpat	3.0.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	134
-crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	74	3389
-ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	203
-cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	1782
-cummerbund_to_tabular	cummerbund_to_cuffdiff	Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.								To update		Convert Formats, Next Gen Mappers	cummerbund_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular	1.0.1					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	1204
-cut_columns	Cut1	Select columns from a dataset.								To update		Text Manipulation	cut_columns	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns	1.0.2					1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	1	1	1	1	5064	1957541
-delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	39
-dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	72
-dgidb_annotator	dgidb_annotate	Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)								To update		Systems Biology, Variant Analysis	dgidb_annotator	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator	0.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	65
-diff	diff	GNU diff tool that calculates the differences between two files.								To update	http://www.gnu.org/software/diffutils/	Text Manipulation	diff	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diff	https://github.com/bgruening/galaxytools/tree/master/tools/diff	3.7	diffutils				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	30	235
-diffbind		Diffbind provides functions for  processing  ChIP-Seq  data.								To update	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	32
-dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1576
-dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	83
-draw_stacked_barplots	draw_stacked_barplots	Draw Stacked Bar Plots for different categories and different criteria								To update		Graphics, Statistics	draw_stacked_barplots	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots	https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots	1.0.0	R				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	173
-dwt_cor_ava_perclass	compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Feature Occurrences								To update		Statistics	dwt_cor_ava_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dwt_cor_avb_all	compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features								To update		Statistics	dwt_cor_avb_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dwt_ivc_all	compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Second Moments for Feature Occurrences								To update		Statistics	dwt_ivc_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dwt_var_perclass	compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom	Compute P-values and Max Variances for Feature Occurrences								To update		Statistics	dwt_var_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dwt_var_perfeature	dwt_var1	Wavelet variance using Discrete Wavelet Transfoms								To update		Statistics	dwt_var_perfeature	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature	1.0.2	r-bitops				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	36
-ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-edta	edta	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. 	edta	edta		The Extensive de novo TE Annotator (EDTA)	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	To update	https://github.com/oushujun/EDTA	Variant Analysis	edta	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta	https://github.com/bgruening/galaxytools/tree/master/tools/edta		edta	2.2.0	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	58	484
-effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-epicseg	epicseg_segment	EpiCSeg is a tool for conducting chromatin segmentation.								To update	https://github.com/lamortenera/epicseg	Epigenetics	epicseg	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	@VERSION_STRING@	epicseg	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	245
-exparna	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-express	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	325
-fasta_compute_length	fasta_compute_length	Compute sequence length								To update		Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	380	7758
-fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	35793
-fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	350	48649
-fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	622	105935
-fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	679	5765
-fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								Up-to-date		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	459	5676
-fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	22385
-file_manipulation	bg_uniq	This tool returns all unique lines from a tab-separated file.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	Text Manipulation	unique	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	0.4	python				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	176	8496
-filter_transcripts_via_tracking	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	20
-find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	69
-find_subsequences	bg_find_subsequences									To update			find_subsequences	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences	0.3	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	763
-flanking_features	flanking_features_1	Fetch closest non-overlapping feature for every interval								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	flanking_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features	4.0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	20	671
-flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904
-footprint	footprint	Find transcription factor footprints								To update	https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/	Epigenetics	footprint	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	1.0.0	footprint	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	57
-format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	166
-format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	166	5588
-generate_pc_lda_matrix	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	119
-get_flanks	get_flanks1	Get flanks returns flanking region/s for every gene								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	get_flanks	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	555	324598
-get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	0	15	186
-getindelrates_3way	indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-getindels_2way	getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	To update	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.7	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	418	8159
-gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	27	660
-glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4	11
-gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	71
-graph_converter	graph_converter	Convert between different graph formats								To update		Convert Formats	graph_converter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-graphclust	graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6
-graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	43	2605
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651
-graphprot	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy2	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	474
-hclust2	hclust2	Plots heatmaps								To update	https://bitbucket.org/nsegata/hclust2/	Data Visualization	hclust2	rnateam	https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2	https://github.com/bgruening/galaxytools/tree/master/tools/hclust2	0.99	hclust2	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hgv_fundo	hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0
-hgv_hilbertvis	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0
-hictk	hictk	Convert cooler to juicebox_hic								Up-to-date	https://github.com/paulsengroup/hictk	Convert Formats, Epigenetics	hictk	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	1.0.0	hictk	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hicup	hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater	The HiCUP-Pipeline from the Bioinformatics Babraham Institute.								To update	https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html	Epigenetics	hicup	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	0.9.2					7	0	7	0	7	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	6	0	76	921
-hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228
-histogram	histogram_rpy	Histogram of a numeric column								To update		Graphics, Statistics	histogram	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram	https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram	1.0.4	rpy2	2.7.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	242	4350
-homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-htseq-clip	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	77
-illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20240614			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	26	1537
-improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	22
-infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	67	100294
-inforna		INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139
-intarna	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.1	intarna	3.4.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	7569
-intersect	gops_intersect_1	Intersect the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1003	348449
-iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	868
-jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse_2	jbrowse_2		JBrowse 2	Modular genome browser with views of synteny and structural variation.	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.15.4	jbrowse2	2.15.4	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-join	gops_join_1	Join the intervals of two datasets side-by-side								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	join	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	284	329556
-join_files_on_column_fuzzy	join_files_on_column_fuzzy	Join two files on a common column, allowing a certain difference.								To update		Text Manipulation	join_files_on_column_fuzzy	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	1.0.1	python				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	117	2448
-jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	30
-kernel_canonical_correlation_analysis	kcca1	Kernel Canonical Correlation Analysis								To update		Statistics	kernel_canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis	1.0.0	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	69
-kernel_principal_component_analysis	kpca1	Kernel Principal Component Analysis								To update		Statistics	kernel_principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis	1.0.0	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	156
-kinwalker		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	481	14683
-labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-lastz_paired_reads	lastz_paired_reads_wrapper	Galaxy wrapper for the Lastz alignment tool on paired reads								To update		Next Gen Mappers	lastz_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads	1.1.1	lastz	1.04.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	9
-lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	137
-lda_analysis	lda_analy1	Perform Linear Discriminant Analysis								To update		Graphics, Statistics	lda_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis	1.0.1	R				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	148
-lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152
-linear_regression	LinearRegression1	Perform Linear Regression								To update		Statistics	linear_regression	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression	https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression	1.0.1	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								Up-to-date	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	2.0.1	locarna	2.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	339
-logistic_regression_vif	LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-maf_cpg_filter	cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	2	2	2	0	817	143045
-mapping_to_ucsc	mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mavedb	mavedb_importer	data source for MaveDB								To update		Data Source	mavedb_importer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb	0.9					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	85
-megablast_xml_parser	megablast_xml_parser	Parse blast XML output								To update		Next Gen Mappers, Convert Formats	megablast_xml_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	36	338
-merge	gops_merge_1	Merge the overlapping intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	193	563676
-merge_cols	mergeCols1	Merge columns together.								To update		Text Manipulation	merge_cols	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols	https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols	1.0.3	python				1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	542	28593
-methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5461
-methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	200	16573
-methylkit	methylkit	A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.								To update	http://bioconductor.org/packages/release/bioc/html/methylKit.html	Epigenetics	methylkit	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	0.99.2	bioconductor-methylkit	1.28.0			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	103	3966
-mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-microsatellite_birthdeath	microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-microsats_alignment_level	microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-microsats_mutability	microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	53	895
-mine	maximal_information_based_nonparametric_exploration	Maximal Information-based Nonparametric Exploration								To update		Variant Analysis	mine	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine	0.0.1	MINE				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	11
-minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	185
-mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613
-molecule2gspan	bg_mol2gspan	converter								To update	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	Convert Formats	molecule_to_gspan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	0.2	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-motus	mereg_mOTUs_tables, motus_profiler	Tool for profiling the abundance of microbial taxa.	mOTUs	mOTUs		Metagenomic operational taxonomic units (mOTUs)	Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/motu-tool/mOTUs	Metagenomics	motus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs	https://github.com/bgruening/galaxytools/tree/master/tools/motus	3.1.0	motus	3.1.0	Taxonomic classification	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	76
-multispecies_orthologous_microsats	multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mummer	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	83	652
-music_deconvolution	music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)								Up-to-date	https://github.com/xuranw/MuSiC	Transcriptomics	music	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/	https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution	0.1.1	music-deconvolution	0.1.1			5	5	4	0	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	240	1872
-mutate_snp_codon	mutate_snp_codon_1	Mutate Codons with SNPs								To update		Variant Analysis	mutate_snp_codon	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	47
-nanopolish	nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants	Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.								Up-to-date	https://github.com/jts/nanopolish		nanopolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	0.14.0	nanopolish	0.14.0			0	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	78	8366
-nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40
-netboxr	netboxr	netboxr enables automated discovery of biological process modules by network analysis								To update		Systems Biology	netboxr	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/netboxr	1.6.0	bioconductor-netboxr	1.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	11
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268
-nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	861
-numeric_clustering	numeric_clustering	Clustering tool for numberic values								To update	http://scikit-learn.org/stable/index.html	Statistics	numeric_clustering	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	0.9	anaconda				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	486
-openms	AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.2.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	135	134	0	916	105743
-pandas_rolling_window	pandas_rolling_window	Rolling window calculations								To update	https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html	Statistics	pandas_rolling_window	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	0.1	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	269
-paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	299
-partialr_square	partialRsq	Compute partial R square								To update		Statistics	partialr_square	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square	https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	78	3109
-pearson_correlation	Pearson_and_apos_Correlation1	Pearson and apos Correlation between any two numeric columns								To update		Statistics	pearson_correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-perf	stats_perf_tool	suitable for boolean classification problems								To update	http://osmot.cs.cornell.edu/kddcup/software.html		stats_perf_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/perf	https://github.com/bgruening/galaxytools/tree/master/tools/perf	5.11.0	perf				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	19	165
-pg_tools	pg_dump, pg_import, pg_query	tool suite for dealing with Postgresql databases from Galaxy's history								To update	https://www.postgresql.org	Data Export, Data Source	pgtools	bgruening	https://github.com/bgruening/galaxytools/tools/pgtools	https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools		postgresql				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pgsnp2gd_snp	pgSnp2gd_snp	Convert from pgSnp to gd_snp								To update		Variant Analysis	pgsnp2gd_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pharmcat	pharmcat	Pharmacogenomics Clinical Annotation Tool								To update	https://pharmcat.org/	Variant Analysis	pharmcat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat						1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	82
-pileup_interval	pileup_interval	Pileup-to-Interval condenses pileup format into ranges of bases								To update		SAM	pileup_interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval	1.0.3	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	15	632
-pileup_parser	pileup_parser	Filter pileup on coverage and SNPs								To update	https://github.com/galaxyproject/tools-devteam/	SAM	pileup_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser	1.0.2	perl				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	169	3158
-pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21	275
-piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	1809
-platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-plot_from_lda	plot_for_lda_output1	"Draw ROC plot on ""Perform LDA"" output"								To update		Graphics, Statistics	plot_from_lda	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda	https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda	1.0.1	R				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	73
-plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.4	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	71	1323
-plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	652
-plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	79	843
-poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	116
-predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-principal_component_analysis	pca1	Principal Component Analysis								To update		Statistics	principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis	1.0.2	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	9989
-protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	154
-protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	451	6428
-protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	604
-quality_filter	qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.13.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	309	21353
-rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	1.0		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	36
-rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	38	1226
-rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-remove_beginning	Remove beginning1	Remove lines from the beginning of a file.								To update		Text Manipulation	remove_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning	1.0.0					1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	1409	137310
-remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	42
-repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.0.9_p2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	248	3750
-replaceColumn	replace_column_with_key_value_file	A tool to replace all column entries of a file given by values of a key-value file.								To update		Text Manipulation	replace_column_by_key_value_file	bgruening	https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn	https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn	0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	189	576111
-rest_tool	pubchem_rest_tool	This tool fetches data from pubchem via the PubChem REST API.								To update	https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html	Data Source	pubchem_rest_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	44	628
-rmap	rmap_wrapper	RMAP for Solexa Short Reads Alignment								To update		Next Gen Mappers	rmap	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rmapq	rmapq_wrapper	RMAPQ for Solexa Short Reads Alignment with Quality Scores								To update		Next Gen Mappers	rmapq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	129
-rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	164
-rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	1358
-rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	1074
-rnaformer	infer_rnaformer	RNAformer: RNA secondary structure prediction								To update	https://github.com/automl/RNAformer	RNA	rnaformer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	1.0.0	rnaformer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	33
-rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	86
-rnaz	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	28	43279
-sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	55	4024
-salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	1	2	2	3	1	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	3	3	3	0	969	61937
-sam2interval	sam2interval	Convert SAM to interval.								To update		SAM	sam2interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval	1.0.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20	1189
-sam_bitwise_flag_filter	sam_bw_filter	Filter SAM on bitwise flag values								To update		SAM	sam_bitwise_flag_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter	1.0.1	python				1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	278
-sambamba	sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort	Sambamba: process your BAM data faster!								Up-to-date	https://github.com/biod/sambamba	SAM	sambamba	bgruening	https://github.com/biod/sambamba	https://github.com/bgruening/galaxytools/tree/master/tools/sambamba	1.0.1	sambamba	1.0.1			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765
-samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	296	4948
-samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1450	48426
-scatterplot	scatterplot_rpy	Scatterplot of two numeric columns								To update		Graphics, Statistics	scatterplot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot	1.0.3	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	61	1677
-sed	sed_stream_editor	Manipulate your data with the sed command line tool.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/sed	Text Manipulation	sed_wrapper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sed	https://github.com/bgruening/galaxytools/tree/master/tools/sed	0.0.1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2276
-segemehl	segemehl	segemehl - short read mapping with gaps								To update	http://www.bioinf.uni-leipzig.de/Software/segemehl/	Next Gen Mappers	segemehl	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	0.2.0.4	segemehl	0.3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	1276
-selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	457
-seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	874
-seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	25302
-seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784
-seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
-seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-short_reads_figure_score	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	163
-short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	21	220
-show_beginning	Show beginning1	Select lines from the beginning of a file.								To update		Text Manipulation	show_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning	1.0.0					1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	704	32112
-show_tail	Show tail1	Select lines from the end of a file.								To update		Text Manipulation	show_tail	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail	1.0.0					1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	128	2513
-sicer	peakcalling_sicer	Statistical approach for the Identification of ChIP-Enriched Regions								Up-to-date	https://home.gwu.edu/~wpeng/Software.htm	ChIP-seq	sicer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer	1.1	SICER	1.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	5	374
-sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	16	30	14	31	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	0	958	113932
-snpfreq	hgv_snpFreq	snpFreq significant SNPs in case-control data								To update		Variant Analysis, Statistics	snpfreq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	37
-sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	376	18183
-split_file_on_column	tp_split_on_column	Split a file on a specific column.								To update		Text Manipulation	split_file_on_column	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	0.6	gawk				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	159	5507
-split_file_to_collection	split_file_to_collection	Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	Text Manipulation	split_file_to_collection	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	0.5.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	412	15358
-split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-splitfasta	rbc_splitfasta	Split a multi-sequence fasta file into files containing single sequences								To update		Text Manipulation	splitfasta	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	0.4.0	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	96	1295
-sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	223
-statistics	bg_statistical_hypothesis_testing	Tool for computing statistical tests.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	Statistics	bg_statistical_hypothesis_testing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	0.3	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	304
-stress_ng	stress_ng	stress test a computer system in various selectable ways								To update		Web Services	stress_ng	bgruening-util	https://github.com/ColinIanKing/stress-ng	https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng	0.12.04	stress-ng				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47
-substitution_rates	subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-substitutions	substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-subtract	gops_subtract_1	Subtract the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract	1.0.0	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	182	564229
-subtract_query	subtract_query1	Subtract Whole Dataset from another dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract_query	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query	0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	55	1019
-t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	457
-t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26	947
-t_test_two_samples	t_test_two_samples	T Test for Two Samples								To update		Statistics	t_test_two_samples	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples	https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples	1.0.1	R				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	210
-table_annovar	table_annovar	Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered								To update		Variant Analysis	table_annovar	devteam	Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar	https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar	0.2	annovar				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tables_arithmetic_operations	tables_arithmetic_operations	Arithmetic Operations on tables								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	tables_arithmetic_operations	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations	1.0.0	perl				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	14	2207
-tabular_to_fasta	tab2fasta	Tabular-to-FASTA								To update		Convert Formats	tabular_to_fasta	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta	1.1.1	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	601	319334
-tapscan	tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	713
-text_processing	tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq	High performance text processing tools using the GNU coreutils, sed, awk and friends.								To update	https://www.gnu.org/software/	Text Manipulation	text_processing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	9.3	coreutils	8.25			20	20	20	20	20	20	20	20	0	0	0	0	0	0	0	0	0	0	19	1	19	0	0	19	0	0	0	20	0	0	0	0	0	19	19	19	0	15048	3864895
-tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460
-tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	445
-tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1
-tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	0	312	24167
-tophat_fusion_post	tophat_fusion_post	Wrapper for Tophat-Fusion post step								To update		Transcriptomics	tophat_fusion_post	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post	0.1	blast+				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	216
-trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	2334	238699
-trimmer	trimmer	Trim leading or trailing characters.								To update		Text Manipulation	trimmer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer	0.0.1					1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	1	1	1	188	6058
-trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	0	236	2935
-ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	45	394
-uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.6	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	132	2406
-varscan_version_2	varscan	VarScan wrapper								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan_version_2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2	2.4.2	varscan	2.4.6			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	246	5191
-vcf2pgsnp	vcf2pgSnp	VCF to pgSnp								To update		Variant Analysis	vcf2pgsnp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	206
-vcf_annotate	vcf_annotate	Annotate a VCF file (dbSNP, hapmap)								To update		Variant Analysis	vcf_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
-vcf_extract	vcf_extract	Extract reads from a specified region								To update		Variant Analysis	vcf_extract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vcf_filter	vcf_filter	Filter a VCF file								To update		Variant Analysis	vcf_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	63	388
-vcf_intersect	vcf_intersect	Generate the intersection of two VCF files								To update		Variant Analysis	vcf_intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19
-vcftools_annotate	vcftools_annotate	Annotate VCF using custom/user-defined annotations								To update	https://vcftools.github.io/	Variant Analysis	vcftools_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate	0.1	echo				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	24	171
-vcftools_compare	vcftools_compare	Compare VCF files to get overlap and uniqueness statistics								To update	https://vcftools.github.io/	Variant Analysis	vcftools_compare	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	531
-vcftools_consensus	vcftools_consensus	Apply VCF variants to a fasta file to create consensus sequence								To update	https://vcftools.github.io/	Variant Analysis	vcftools_consensus	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus	0.1.11	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vcftools_isec	vcftools_isec	Intersect multiple VCF datasets								To update	https://vcftools.github.io/	Variant Analysis	vcftools_isec	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec	0.1.1	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	498
-vcftools_merge	vcftools_merge	Merge multiple VCF datasets into a single dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge	0.1.11	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	68	953
-vcftools_slice	vcftools_slice	Subset VCF dataset by genomic regions								To update	https://vcftools.github.io/	Variant Analysis	vcftools_slice	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice	0.1	echo				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	24	411
-vcftools_subset	vcftools_subset	Select samples from a VCF dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_subset	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	17	137
-venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.1.5			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	248	5067
-vienna_rna	viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	0	123	7864
-vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-weightedaverage	wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11
-woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660
-xy_plot	XY_Plot_1	Plotting tool for multiple series and graph types								To update		Graphics, Statistics	xy_plot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot	1.0.2	r-base				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	344	5892
-TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42
-abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	1764	496717
-abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278
-adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	37	217
-add_input_name_as_column	addName	Add input name as column on an existing tabular file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	Text Manipulation	add_input_name_as_column	mvdbeek	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	91	83150
-aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	4	1	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	47	168
-aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	129
-allegro	allegro	Linkage and haplotype analysis from deCODE	allegro	allegro		Allegro	It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	To update	http://www.decode.com/software/	Variant Analysis	allegro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro	@VER@.0	allegro	3	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	53
-ampvis2	ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.9			Analysis, Visualisation	Biodiversity	0	0	19	0	0	0	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	42	267
-amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	591
-ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	7
-anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	625	35620
-annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1175	25975
-argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	38	3528
-art	art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/	Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	Conversion	Bioinformatics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	123	8175
-assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-astral	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees								Up-to-date	https://github.com/smirarab/ASTRAL	Phylogenetics	astral	iuc	https://github.com/usegalaxy-be/galaxytools/tree/main/astral	https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral	5.7.8	astral-tree	5.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
-augustus	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	685	11245
-b2btools	b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.7	Protein disorder prediction, Protein secondary structure prediction		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	12	345
-bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	151	2982
-bam_to_scidx	bam_to_scidx	Contains a tool that converts a BAM file to an ScIdx file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx	Convert Formats	bam_to_scidx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4	128
-bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	208	14021
-bamtools_filter	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1195	114863
-bamtools_split	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	197	4328
-bamutil	bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	39
-bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	2016	44390
-barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	71
-barrnap	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update	https://github.com/tseemann/barrnap	Sequence Analysis	barrnap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	Gene prediction	Genomics, Model organisms, Model organisms	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	160	3938
-basil	basil	Breakpoint detection, including large insertions								Up-to-date	https://github.com/seqan/anise_basil	Variant Analysis	basil	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil	1.2.0	anise_basil	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	266
-bax2bam	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	200
-bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	64
-bbgbigwig	bbgtobigwig	Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://www.encodeproject.org/software/bedgraphtobigwig/	Convert Formats	bbgbigwig	iuc	https://www.encodeproject.org/software/bedgraphtobigwig/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig	0.1	ucsc-bedgraphtobigwig	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.09	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	4	0	0	420	6381
-bcftools	bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@	BCFtools toolkit wrappers	bcftools	bcftools		BCFtools	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.	Data handling, Variant calling	Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment	To update	https://samtools.github.io/bcftools/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools	1.15.1	bcftools	1.21	Data handling, Variant calling	DNA polymorphism, GWAS study, Genotyping experiment	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	7	0	87	2895
-beacon2	beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff	beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://github.com/EGA-archive/beacon2-ri-tools/tree/main	Variant Analysis	beacon2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2	2.0.0	beacon2-ri-tools	2.0.0	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	28
-beacon2-import	beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence	Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants.	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://pypi.org/project/beacon2-import/	Variant Analysis	Beacon2_Import	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import	2.2.4	beacon2-import	2.2.4	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-beagle	beagle	Beagle is a program for phasing and imputing missing genotypes.								To update	https://faculty.washington.edu/browning/beagle/beagle.html	Variant Analysis	beagle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle	5.2_21Apr21.304	beagle	5.4_22Jul22.46e			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	54
-bedops	bedops-sort-bed	BEDOPS: high-performance genomic feature operations								Up-to-date	https://bedops.readthedocs.io/en/latest/	Genomic Interval Operations	bedops_sortbed	iuc	https://bedops.readthedocs.io/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops	2.4.41	bedops	2.4.41			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	28
-bedtools	bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed	bedtools is a powerful toolset for genome arithmetic	bedtools	bedtools		BEDTools	BEDTools is an extensive suite of utilities for comparing genomic features in BED format.	Mapping	Genomics	Up-to-date	https://github.com/arq5x/bedtools2	Genomic Interval Operations, Text Manipulation	bedtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools	2.31.1	bedtools	2.31.1	Mapping	Genomics	37	37	37	37	37	37	37	37	0	0	0	0	0	0	0	0	0	0	37	6	37	0	0	37	0	0	0	37	0	0	0	0	0	37	37	37	0	5844	901750
-bellerophon	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	123	1194
-berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bigwig_outlier_bed	bigwig_outlier_bed	pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files	bigtools	bigtools		bigtools	Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.			To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	Sequence Analysis	bigwig_outlier_bed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed	0.2.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	81
-bioext	bioext_bam2msa, bioext_bealign	A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!								Up-to-date	https://pypi.python.org/pypi/biopython-extensions/	Next Gen Mappers		iuc	https://github.com/davebx/bioext-gx/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext	0.21.9	python-bioext	0.21.9			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	2	0	0	363	15228
-bioinformatics_cafe	fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	978
-biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	98	3906
-bioperl	bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	Data handling, Service invocation	Genomics, Software engineering	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	240	6736
-biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3
-blast	magicblast	Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome								Up-to-date	https://ncbi.github.io/magicblast/	Next Gen Mappers	magicblast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast	1.7.0	magicblast	1.7.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	78	511
-blastxml_to_gapped_gff3	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	185
-bowtie2	bowtie2	Bowtie2: Fast and sensitive read alignment	bowtie2	bowtie2		Bowtie 2	Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.	Read mapping	Mapping, Genomics, Mapping	To update	http://bowtie-bio.sourceforge.net/bowtie2	Next Gen Mappers	bowtie2	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2	2.5.3	bowtie2	2.5.4	Read mapping	Mapping, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	1	0	0	1	1	1	0	5136	380252
-bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	326	18351
-breseq	breseq	Predicts mutations in microbial genomes	breseq	breseq		breseq	Runs Breseq software on a set of fastq files.	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	To update	https://github.com/barricklab/breseq	Variant Analysis	breseq	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq	0.35.5	breseq	0.39.0	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	50	1871
-brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template	brew3r.r	brew3r.r		BREW3R.r	This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.	Genome annotation	Transcriptomics, Genomics	To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2			Genome annotation	Transcriptomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1804	86180
-bwa	bwa_mem, bwa	Wrapper for bwa mem, aln, sampe, and samse	bwa	bwa		BWA	Fast, accurate, memory-efficient aligner for short and long sequencing reads	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	Up-to-date	http://bio-bwa.sourceforge.net/	Next Gen Mappers	bwa	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa	0.7.18	bwa	0.7.18	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	2	0	0	0	2	0	0	0	0	0	2	2	2	2	5295	981251
-bwa_mem2	bwa_mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.	bwa-mem2	bwa-mem2		Bwa-mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,  dataset and the running machine.	Sequence alignment	Mapping	Up-to-date	https://github.com/bwa-mem2/bwa-mem2	Next Gen Mappers	bwa_mem2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2	2.2.1	bwa-mem2	2.2.1	Sequence alignment	Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	0	0	1220	44386
-bwameth	bwameth	Fast and accurate alignment of BS-seq reads								Up-to-date	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.7	bwameth	0.2.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	201	10619
-cactus	cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			Multiple sequence alignment, Genome alignment	Genomics, Sequence assembly, Mapping, Phylogenetics	0	2	2	1	0	2	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	26	234
-calculate_contrast_threshold	calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-calculate_numeric_param	calculate_numeric_param	Calculate a numeric parameter value using integer and float values.								To update		Text Manipulation	calculate_numeric_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param	0.1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	1393
-cami_amber	biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert	Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments								Up-to-date	https://github.com/CAMI-challenge/AMBER	Metagenomics	cami_amber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber	2.0.7	cami-amber	2.0.7			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	268	2878
-cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474
-cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	98
-charts	charts	Enables advanced visualization options in Galaxy Charts								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	287	3589
-checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	390	5165
-cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	207
-chewbbaca	chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema	BSR-Based Allele Calling Algorithm								To update	https://github.com/B-UMMI/chewBBACA/tree/master	Variant Analysis	chewbbaca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca		chewbbaca	3.3.10			0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	97	6418
-chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chromeister	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	182	2130
-circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269
-circos	circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile	Build Circos Plots in Galaxy	galactic_circos	galactic_circos		Galactic Circos	Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.	Sequence visualisation		To update	http://circos.ca/	Graphics	circos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos	0.69.8	circos	0.69.9	Sequence visualisation		11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	0	11	11	0	0	0	0	0	0	11	0	0	0	0	0	11	11	11	0	1018	21305
-cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18
-clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	68	1856
-clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	651	46793
-clustering_from_distmat	clustering_from_distmat	Distance matrix-based hierarchical clustering using SciPy								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	Statistics	clustering_from_distmat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat	1.1.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cnv-phenopacket	cnv_phenopacket	cnv-phenopacket Converts TSV metadata file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv_phenopacket	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket	1.0.2	cnv-phenopacket				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cnv-vcf2json	cnv_vcf2json	cnv-vcf2json Converts structural variants VCF file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv-vcf2json	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json	1.1.0	cnv-vcf2json				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cnvkit	cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target	detecting copy number variants and alterations genome-wide from high-throughput sequencing	cnvkit	cnvkit		CNVkit	CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.	Variant calling	DNA structural variation	Up-to-date	https://github.com/etal/cnvkit	Variant Analysis	cnvkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit	0.9.11	cnvkit	0.9.11	Variant calling		0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	45	370
-codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	29	60901
-cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	2757
-colabfold	colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-colibread	commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								To update	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14+galaxy0	commet	24.7.14			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	251
-collection_column_join	collection_column_join	Column Join on Collections								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	Text Manipulation	collection_column_join	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join	0.0.3	coreutils	8.25			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1483	20857
-collection_element_identifiers	collection_element_identifiers	Extract element identifiers of a collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	Text Manipulation	collection_element_identifiers	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers	0.0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	912	5059
-column_maker	Add_a_column1	Compute an expression on every row								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	Text Manipulation	column_maker	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker	2.1	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	2379	3883271
-column_order_header_sort	column_order_header_sort	Sort Column Order by heading								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	Text Manipulation	column_order_header_sort	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort	0.0.1	python				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	80	3258
-column_remove_by_header	column_remove_by_header	Remove columns by header								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	Text Manipulation	column_remove_by_header	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header	1.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	199	8424
-compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-compose_text_param	compose_text_param	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	compose_text_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param	0.1.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	0	0	0	375	35084
-compress_file	compress_file	Compress files.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	Text Manipulation	compress_file	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file	0.1.0	gzip				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	164	3674
-concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	92	786
-cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-coverage_report	CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	72	529
-crispr_studio	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	Visualisation	Sequence analysis, Genomics, Data visualisation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	30	636
-crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	17	347
-crossmap	crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig	CrossMap converts genome coordinates or annotation files between genome assemblies								Up-to-date	http://crossmap.sourceforge.net/	Convert Formats, Genomic Interval Operations	crossmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap	0.7.0	crossmap	0.7.0			5	0	6	0	5	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	5	6	5	0	116	1968
-cuffcompare	cuffcompare	Galaxy wrappers for the Cuffcompare tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffcompare	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	1	1	1	0	65	1130
-cuffdiff	cuffdiff	Galaxy wrappers for the Cuffdiff tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffdiff	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff	2.2.1	cufflinks	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	0	228	5831
-cufflinks	cufflinks	Galaxy wrappers for the Cufflinks tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cufflinks	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	1	0	0	1	1	1	0	319	32218
-cuffmerge	cuffmerge	Galaxy wrappers for the Cuffmerge tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffmerge	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge	2.2.1	cufflinks	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	1	1	1	0	122	3292
-cuffnorm	cuffnorm	The Cuffnorm tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffnorm	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	27	660
-cuffquant	cuffquant	The Cuffquant tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffquant	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	18	688
-cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	5090	232004
-cutesv	cutesv	Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.	cuteSV	cuteSV		cuteSV	Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis	Split read mapping, Genotyping, Structural variation detection	DNA structural variation, Sequencing, Computer science	To update	https://github.com/tjiangHIT/cuteSV	Variant Analysis	cutesv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv	1.0.8	cutesv	2.1.1	Split read mapping, Genotyping, Structural variation detection	Sequencing, Computer science	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	17	235
-cwpair2	cwpair2	Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.								To update		ChIP-seq	cwpair2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2	1.1.1	matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	10	10	10	0	1263	66609
-das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	24	706
-data_source_iris_tcga	data_source_iris_tcga	IRIS-TCGA Data source tool								To update		Data Source	data_source_iris_tcga	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga	https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-datamash	datamash_ops, datamash_reverse, datamash_transpose	GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.								To update	https://www.gnu.org/software/datamash/	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash	1.8	datamash	1.1.0			3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	1	3	3	0	0	1	0	0	0	1	0	0	0	0	0	3	3	3	0	3066	739298
-decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	99
-deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	501
-deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5
-deepvariant	deepvariant	DeepVariant is a deep learning-based variant caller								To update	https://github.com/google/deepvariant	Variant Analysis	deepvariant	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant	1.5.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	182	1889
-deg_annotate	deg_annotate	Annotate DESeq2/DEXSeq output tables								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	Transcriptomics	deg_annotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate	1.1.0	bedtools	2.31.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1774	19910
-delly	delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge	Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.	delly2	delly2		Delly2	Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.	Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis	DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases	To update	https://github.com/dellytools/delly	Variant Analysis	delly	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly	https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly	0.9.1	delly	1.2.9	Indel detection, Structural variation detection, Genotyping	Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	6	0	0	0	0	0	6	6	0	0	124	1135
-deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	4990	95752
-dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	218	16064
-diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	3	3	0	963	49711
-diffbind	diffbind	Diffbind provides functions for  processing  ChIP-Seq  data.	diffbind	diffbind		DiffBind	Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.	Differential binding analysis	ChIP-seq	Up-to-date	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind	3.12.0	bioconductor-diffbind	3.12.0	Differential binding analysis	ChIP-seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	250	6264
-dimet	dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@	DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.								Up-to-date	https://github.com/cbib/DIMet	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet	0.2.4	dimet	0.2.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369
-dnabot	dnabot	DNA assembly using BASIC on OpenTrons								To update	https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT	Synthetic Biology	dnabot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot	3.1.0	dnabot				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dnaweaver	dnaweaver	Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.								Up-to-date	https://github.com/Edinburgh-Genome-Foundry/DnaWeaver	Synthetic Biology	dnaweaver	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver	1.0.2	dnaweaver_synbiocad	1.0.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	39	6886
-drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	46	646
-dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	126	3934
-ebi_tools	ebi_search_rest_results	Tools to query and download data from several EMBL-EBI databases								To update	http://www.ebi.ac.uk/services/all	Web Services, Data Source	ebi_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools	0.1.1	six				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	52	382
-edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	945	18117
-egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	177	2524
-emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	107	107	107	0	1816	89530
-ena_upload	ena_upload	Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 								To update	https://github.com/usegalaxy-eu/ena-upload-cli	Data Export	ena_upload	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload	0.7.3	ena-upload-cli	0.7.4			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	0	14	208
-enasearch	enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data	A Python library for interacting with ENA's API								To update	https://github.com/bebatut/enasearch	Data Source	enasearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch		enasearch	0.2.2			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	126	2257
-ensembl_vep	ensembl_vep	Ensembl VEP: Annotate VCFs with variant effect predictions								Up-to-date	https://github.com/Ensembl/ensembl-vep	Variant Analysis	ensembl_vep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep	112.0	ensembl-vep	112.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	119	2653
-episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	736
-evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-exomedepth	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	29	410
-exonerate	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	988
-export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	200	5265
-extract_genomic_dna	Extract genomic DNA 1	Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.								To update		Genomic Interval Operations	extract_genomic_dna	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna	https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna	3.0.3+galaxy2	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	1	1	1	1	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	285	11846
-falco	falco	A high throughput sequence QC analysis tool	falco	falco		Falco	A high-speed FastQC emulation for quality control of sequencing data.	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	Up-to-date	https://github.com/smithlabcode/falco/	Sequence Analysis	falco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco	https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco	1.2.4	falco	1.2.4	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	52	459
-fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	469	ucsc-fasplit	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	242	2644
-fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	68	2912
-fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	29	774
-fasta_nucleotide_color_plot	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	160
-fasta_stats	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1080	35336
-fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	250	3498
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	2803	1055760
-fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	66	8676
-fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	266	14222
-fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1028	94802
-fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	69	2503
-fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	170
-fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	122	8410
-fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1087	17024
-fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	245	16635
-fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	196	3092
-fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	51	1178
-fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	11	220
-fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1509	15172
-fastq_stats	fastq_stats	FASTQ Summary Statistics by column								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	221	4246
-fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	419	13599
-fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	93	12593
-fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	210	9757
-fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	0	17447	1556625
-fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1266	4333
-fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1371	178178
-fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	379	55434
-fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	27	1810
-fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	128	16591
-fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	96	3333
-fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	114	61218
-fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	25	249
-fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	63	2176
-fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	68	2280
-fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	156	10832
-fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	205	13149
-fatovcf	fatovcf	Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_fatovcf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	448	ucsc-fatovcf	448		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	285
-featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	4679	696399
-feelnc	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	Annotation, Classification	Functional, regulatory and non-coding RNA	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46	1191
-fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	307	5240
-filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	617	30483
-flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	14	331
-flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	74	13759
-fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	68	1102
-freebayes	freebayes, bamleftalign	Galaxy Freebayes Bayesian genetic variant detector tool	freebayes	freebayes		FreeBayes	Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	To update	https://github.com/ekg/freebayes	Variant Analysis	freebayes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes	1.3.6	freebayes	1.3.8	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	3059	155087
-freec	control_freec	Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.	freec	freec		FREEC	A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.	Copy number estimation, Variant calling, Genome alignment	DNA structural variation, Oncology, Human genetics, Data mining	To update	http://boevalab.inf.ethz.ch/FREEC/	Variant Analysis	control_freec	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec	11.6	gawk		Copy number estimation, Variant calling, Genome alignment	Oncology, Human genetics, Data mining	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	44	665
-freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	55	20021
-fsd	fsd, fsd_beforevsafter, fsd_regions, td	Tool that plots a histogram of sizes of read families								To update		Graphics	duplex_family_size_distribution	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd	1.0.2	matplotlib				4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	900	5906
-gatk4	gatk4_mutect2	A Galaxy wrapper for Mutect2 from GATK								To update	https://software.broadinstitute.org/gatk/gatk4	Variant Analysis	gatk4_mutect2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	181	2483
-gdcwebapp	data_source_gdcwebapp	GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format								To update	http://bioinf.iasi.cnr.it/gdcwebapp/	Data Source, Convert Formats	gdcwebapp	iuc	https://github.com/fabio-cumbo/GDCWebApp4Galaxy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp	1.0.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0
-gecko	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	112	519
-gemini	gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	Sequence analysis, Genetic variation analysis	Sequence analysis	1	2	2	2	1	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	662	4916
-genebed_maf_to_fasta	GeneBed_Maf_Fasta2	Stitch gene blocks given a set of coding exon intervals								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	Genomic Interval Operations	genebed_maf_to_fasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta	1.0.1+galaxy0					1	1	1	1	1	1	1	1	0	1	0	0	0	1	0	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	0	1	4
-genehunter_modscore	genehunter_modscore	Maximised LOD score pedigree analysis utility								To update	https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1	Variant Analysis	genehunter_modscore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore	3.0.0	ghm	3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-geneiobio	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	67
-genetrack	genetrack	"Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand."								To update		ChIP-seq	genetrack	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack		numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-genomescope	genomescope	Analyze unassembled short reads								Up-to-date	https://github.com/tbenavi1/genomescope2.0	Statistics	genomescope	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope	2.0.1	genomescope2	2.0.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	329	2118
-genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	46
-genrich	genrich	Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).								To update	https://github.com/jsh58/Genrich	ChIP-seq	genrich	iuc	https://github.com/jsh58/Genrich	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich	0.5+galaxy2	genrich	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	79	3515
-get_hrun	get_hrun	Annotate indel variants with homopolymer context								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	Variant Analysis	get_hrun	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun	0.5.9.2	pyfaidx	0.8.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	4
-getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495
-gfa_to_fa	gfa_to_fa	gfa_to_fa - Converting GFA format to Fasta format								To update	http://gfa-spec.github.io/GFA-spec/	Convert Formats	gfa_to_fa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa	0.1.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	332	8274
-gff3_rebase	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	135
-gffcompare	gffcompare	Galaxy wrappers for Geo Pertea's GffCompare package.	gffcompare	gffcompare		gffcompare	Program for comparing, annotating, merging and tracking transcripts in GFF files.	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	https://github.com/gpertea/gffcompare/	Transcriptomics	gffcompare	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare	0.12.6	gffcompare	0.12.6	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	381	3477
-gffread	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	680	10995
-ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	5	5	5	0	1388	22148
-ggupset	emc-ggupset	Create Upset Plots with ggupset								To update	https://github.com/const-ae/ggupset	Graphics	ggupset	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset	1.0	r-ggupset				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	0	187	3965
-goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	408	5484
-goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1210	19167
-gprofiler	gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense	functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more								To update	https://biit.cs.ut.ee/gprofiler	Statistics, Web Services	gprofiler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler	@TOOL_VERSION@+galaxy11	r-gprofiler2				5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	196	3443
-graphembed	graphembed	Compute a 2D embedding of a data matrix given supervised class information								Up-to-date	https://github.com/fabriziocosta/GraphEmbed	Statistics, Graphics	graphembed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed	2.4	graph_embed	2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	63
-graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	432	9277
-gtdb_to_taxdump	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	gtdb_to_taxdump	gtdb_to_taxdump		gtdb_to_taxdump	Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.	Data handling, Mapping, Generation	Computational biology	Up-to-date	https://github.com/nick-youngblut/gtdb_to_taxdump	Metagenomics	gtdb_to_taxdump	iuc	https://github.com/nick-youngblut/gtdb_to_taxdump	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	0.1.9	Data handling, Mapping, Generation	Computational biology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	Up-to-date	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.4.0	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gtfToBed12	gtftobed12	Convert GTF files to BED12 format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README	Convert Formats	gtftobed12	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12	357	ucsc-gtftogenepred	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1200	8107
-gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	145	3340
-gvcftools	gvcftools_extract_variants	gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf.								To update	https://github.com/sequencing/gvcftools	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools	0.1	gvcftools	0.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gwastools	gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	Deposition, Analysis, Annotation	GWAS study	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
-hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	117	4459
-hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	339
-hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295
-happy	som.py	A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.	hap.py	hap.py		hap.py	This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	To update	https://github.com/Illumina/hap.py	Variant Analysis	happy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy	0.3.14	hap.py	0.3.15	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-heatmap2	ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1953	44240
-heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	heinz, bionet		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	242	1186
-hgvsparser	hgvsparser	Parsing and building variant descriptor strings compliant with the HGVS standard								To update	https://github.com/VariantEffect/hgvsParseR/tree/master	Variant Analysis	hgvsparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hicexplorer	hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								Up-to-date	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.5	hicexplorer	3.7.5			38	38	38	4	38	38	38	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	33	36	33	0	1085	66003
-hicstuff	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices								To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410
-hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	137
-hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	4183	299104
-hivclustering	hivclustering	Infers transmission networks from pairwise distances inferred by tn93								To update	https://pypi.org/project/hivclustering/	Next Gen Mappers	hivclustering	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering	1.3.1	python-hivclustering	1.8.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	12	12	12	0	439	33702
-homer	homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	Sequence motif discovery		0	0	5	4	0	0	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	5	0	0	394	6937
-htseq_count	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	Nucleic acid sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1419	154533
-humann	humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.9	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	10	10	10	6	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	1037	19490
-hybpiper	hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.3.0	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	2	17	2	17	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	12	17	12	0	161	10370
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354
-icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127
-idr	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	30	2873
-idr_download	idr_download_by_ids	Image Data Resource downloading tool								To update	https://idr.openmicroscopy.org	Data Source	idr_download_by_ids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download	0.45	omero-py	5.11.1			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10	361
-iedb_api	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	1506
-infercnv	infercnv	Infer Copy Number Variation from Single-Cell RNA-Seq Data								Up-to-date	https://github.com/broadinstitute/infercnv	Transcriptomics, Variant Analysis	infercnv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv	1.20.0	bioconductor-infercnv	1.20.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	94
-integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	58	52965
-intermine_galaxy_exchange	galaxy_intermine_exchange	InterMine Exporter								To update	https://github.com/intermine	Convert Formats	intermine_galaxy_exchange	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange	0.0.1	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	44
-interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	677	35243
-interval2maf	Interval2Maf1	Extract MAF blocks given a set of intervals	bx-python	bx-python		bx-python	Tools for manipulating biological data, particularly multiple sequence alignments.		Sequence analysis	To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	interval2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf	1.0.1+galaxy1	bx-python	0.13.0		Sequence analysis	1	1	1	1	1	1	1	1	0	1	0	0	0	0	0	0	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	105
-intervene	intervene_pairwise, intervene_upset	Create pairwise and upset plots	intervene	intervene		Intervene	Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.	Sequence comparison, Sequence visualisation	Computational biology	Up-to-date	https://intervene.readthedocs.io	Statistics	intervene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene	0.6.5	intervene	0.6.5	Sequence comparison, Sequence visualisation	Computational biology	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	1497
-iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	681	21598
-irissv	irissv	Refine insertion sequences								To update	https://github.com/mkirsche/Iris	Variant Analysis	irissv	iuc	https://github.com/galaxyproject/tools-iuc/tools/irissv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv	1.0.5	samtools	1.21			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4	29
-isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	57581
-isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	822
-ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	5	5	5	0	1171	1224275
-iwtomics	iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot	Interval-Wise Testing for Omics Data	iwtomics	iwtomics		IWTomics	"Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset."	Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison	Statistics and probability	To update	https://bioconductor.org/packages/release/bioc/html/IWTomics.html	Statistics	iwtomics	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics	1.0.0	bioconductor-iwtomics	1.26.0	Differential gene expression analysis, Peak calling, Genome annotation, Comparison	Statistics and probability	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3	542
-jasminesv	jasminesv	Merge structural variants across samples								To update	https://github.com/mkirsche/Jasmine/	Variant Analysis	jasminesv	iuc	https://github.com/galaxyproject/tools-iuc/jasminesv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv	1.0.11	jasminesv	1.1.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3	30
-jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	2346	18229
-jcvi_gff_stats	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.16			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	2469
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138
-join_files_by_id	join_files_by_id	This tool will join datasets according to a column with identifier								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	Text Manipulation	join_files_by_id	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id	1.0	r-data.table	1.11.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-jq	jq	JQ is a lightweight and flexible command-line JSON processor								To update	https://stedolan.github.io/jq/	Text Manipulation	jq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq	1.0	jq	1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	21	2312
-jvarkit	jvarkit_wgscoverageplotter	Jvarkit : Java utilities for Bioinformatics								Up-to-date	https://lindenb.github.io/jvarkit/	SAM	jvarkit	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit	20201223	jvarkit-wgscoverageplotter	20201223			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	249	6285
-kallisto	kallisto_pseudo, kallisto_quant	kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.	kallisto	kallisto		kallisto	A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.	Gene expression profiling	Transcriptomics, RNA-seq, Gene expression	To update	https://pachterlab.github.io/kallisto/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto	0.48.0	kallisto	0.51.1	Gene expression profiling	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	299	24155
-kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	363
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022
-king	king	Kinship-based INference for Gwas								Up-to-date	http://people.virginia.edu/~wc9c/KING/	Variant Analysis	king	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/king	2.2.7	king	2.2.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	5
-kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.0.9	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	319
-kma	kma_map	Map with KMA								To update	https://bitbucket.org/genomicepidemiology/kma	Next Gen Mappers	kma	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma	1.4.14	kma	1.4.15			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0
-kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	33	594
-kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	5	0	1209	33778
-kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	2367	185308
-kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	182	1444
-kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	354	2527
-krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	703	16525
-krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-last	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1584	Sequence alignment	Comparative genomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	41	227
-lastz	lastz_wrapper_2, lastz_d_wrapper	Galaxy wrappers for the Lastz and Lastz_d	lastz	lastz		LASTZ	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.	Sequence alignment, Read mapping	Genomics	Up-to-date	https://github.com/lastz/lastz	Next Gen Mappers	lastz	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz	1.04.22	lastz	1.04.22	Sequence alignment, Read mapping	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	2	0	0	0	0	0	0	0	0	0	2	2	2	0	188	83331
-lcrgenie	lcrgenie	Ligase Chain Reaction Genie								To update	https://github.com/neilswainston/LCRGenie	Synthetic Biology	lcrgenie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie	1.0.2	lcr_genie				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	55
-length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	322	4090
-limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1012	20344
-lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	37
-links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405
-lofreq	lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi	LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.								Up-to-date	https://csb5.github.io/lofreq/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq	2.1.5	lofreq	2.1.5			5	5	5	4	5	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	0	0	0	4	0	0	0	0	0	5	5	5	0	1791	4150903
-lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	647
-lumpy_sv	lumpy_prep, lumpy_sv	LUMPY - a general probabilistic framework for structural variant discovery								Up-to-date	http://layerlab.org/software/	Variant Analysis	lumpy_sv	iuc	https://github.com/arq5x/lumpy-sv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv	0.3.1	lumpy-sv	0.3.1			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	105	1164
-m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3
-maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	188
-macs2	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	0	0	9	0	0	0	0	0	9	9	9	0	1969	84521
-maf_stats	maf_stats1	MAF Coverage statistics								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	maf_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats	1.0.2+galaxy0					1	1	1	1	1	1	1	1	0	1	0	0	0	1	0	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	0	3	21
-maftoaxt	maftoaxt	Convert dataset from MAF to axt format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_maftoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	469	ucsc-maftoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mageck	mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test	Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	mageck	mageck		MAGeCK	Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	Genetic variation analysis	Genetics, Genetic variation, Genomics	To update	https://sourceforge.net/projects/mageck/	Genome editing		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck	0.5.9.2	mageck	0.5.9.5	Genetic variation analysis	Genetics, Genetic variation, Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	587	10503
-maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	554	5591
-malt	malt_run	Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.								To update	https://github.com/husonlab/malt	Next Gen Mappers	malt_run	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt	0.5.3	malt	0.62			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	22
-map_param_value	map_param_value	Map a parameter value to another value								To update		Text Manipulation	map_param_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	1528
-mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	167
-mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	27	9763
-mashmap	mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	576
-maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	118	2059
-mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	29
-medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	3	3	3	0	768	99863
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475
-megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	261	3610
-meme	meme_dreme, meme_fimo, meme_meme, meme_psp_gen	The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.	meme_meme	meme_meme, meme_fimo		meme_meme	An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	To update	http://meme-suite.org/	ChIP-seq	meme	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme	5.5.6	meme	5.5.7	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	3	0	4	0	3	0	4	0	0	0	0	0	0	0	0	0	0	0	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	3	4	4	0	235	22352
-meme_chip	meme_chip	Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.								To update	http://meme-suite.org/	ChIP-seq	meme_chip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip	4.11.2	graphicsmagick	1.3.26			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	287	6584
-meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-merlin	merlin	Pedigree Analysis package	merlin	merlin		Merlin	Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation	Haplotype mapping, Genetic mapping	GWAS study, Mapping	Up-to-date	http://csg.sph.umich.edu/abecasis/Merlin/	Variant Analysis	merlin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin	1.1.2	merlin	1.1.2	Haplotype mapping	GWAS study, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	2	2	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	192	4329
-metabuli	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	metabuli	metabuli		metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid	Taxonomic classification	Taxonomy	To update	https://github.com/steineggerlab/Metabuli	Sequence Analysis, Metagenomics	metabuli	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli	1.0.5	metabuli	1.0.8	Taxonomic classification	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	184
-metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	753
-metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	4	1	2	4	4	0	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	499	11069
-metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mg_toolkit	mg_toolkit_bulk_download, mg_toolkit_original_metadata	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	mg-toolkit	mg-toolkit		mg-toolkit	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	Data retrieval	Metagenomics	Up-to-date	https://github.com/EBI-Metagenomics/emg-toolkit	Metagenomics	mg_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	0.10.4	mg-toolkit	0.10.4	Data retrieval	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-microsatbed	microsatbed	Select microsatellites for a bed file								To update	https://github.com/lmdu/pytrf	Sequence Analysis	microsatbed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed	1.3.3	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-migmap	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	Sequence analysis, Read mapping	Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	1226
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938
-minimap2	minimap2	A fast pairwise aligner for genomic and spliced nucleotide sequences	minimap2	minimap2		Minimap2	Pairwise aligner for genomic and spliced nucleotide sequences	Pairwise sequence alignment	Mapping	Up-to-date	https://github.com/lh3/minimap2	Next Gen Mappers	minimap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2	2.28	minimap2	2.28	Pairwise sequence alignment	Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1588	260442
-miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	30	842
-mirmachine	mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mirnature	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	10
-mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881
-mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	0	236	100920
-mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	635	9304
-moabs	moabs	MOABS for differential methylation analysis on Bisulfite sequencing data.								To update	https://github.com/sunnyisgalaxy/moabs	Epigenetics	moabs	iuc	https://github.com/sunnyisgalaxy/moabs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs	1.3.4.6	moabs	1.3.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	317
-mosdepth	mosdepth	fast and flexible BAM/CRAM depth calculation								Up-to-date	https://github.com/brentp/mosdepth	SAM	mosdepth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth	0.3.8	mosdepth	0.3.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	262
-mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	129	129	129	129	129	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	126	129	129	0	14353	302916
-msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	803
-multigps	multigps	Analyzes collections of multi-condition ChIP-seq data.								To update	http://mahonylab.org/software/multigps/	ChIP-seq	multigps	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps	0.74.0	fonts-conda-ecosystem				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	53
-multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	8320	162790
-mummer4	mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1			6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	6	3	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	669	18347
-mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mzmine	mzmine_batch	mass-spectrometry data processing, with the main focus on LC-MS data	mzmine	mzmine		MZmine	Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	Up-to-date	http://mzmine.github.io/	Metabolomics	mzmine_batch	iuc	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine	3.9.0	mzmine	3.9.0	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3
-naltorfs	bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2			3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	3	836
-nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	2195	63235
-nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	15	1074
-ncbi_acc_download	ncbi_acc_download	Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API								Up-to-date	https://github.com/kblin/ncbi-acc-download	Data Source	ncbi_acc_download	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download	0.2.8	ncbi-acc-download	0.2.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	688	5487
-ncbi_datasets	datasets_download_gene, datasets_download_genome	NCBI datasets downloads biological sequence data across all domains of life from NCBI.	ncbi_datasets	ncbi_datasets		NCBI Datasets	NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.	Data handling, Sequence database search, Data retrieval	Biological databases	To update	https://github.com/ncbi/datasets	Data Source	ncbi_datasets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets	16.20.0	ncbi-datasets-cli		Data handling, Sequence database search, Data retrieval	Biological databases	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	1	2	2	0	667	3177
-ncbi_entrez_direct	ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch	NCBI Entrez Direct allow fetching data from NCBI Databases								Up-to-date	http://www.ncbi.nlm.nih.gov/books/NBK179288/	Data Source	ncbi_entrez_direct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct	22.4	entrez-direct	22.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ncbi_entrez_eutils	ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_egquery, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary	NCBI Entrez E-Utilties allow fetching data from NCBI Databases								To update	https://www.ncbi.nlm.nih.gov/books/NBK25501/	Data Source	ncbi_entrez_eutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils	1.70	python				0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	4	0	0	0	2	0	0	0	0	0	0	8	8	0	169	3193
-ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667
-newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	448	25505
-nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	2	1	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	2	0	0	210	4080
-ngmlr	ngmlr	CoNvex Gap-cost alignMents for Long Reads	ngmlr	ngmlr		NGMLR	An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping, DNA structural variation	Up-to-date	https://github.com/philres/ngmlr	Next Gen Mappers	ngmlr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr	0.2.7	ngmlr	0.2.7	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	21	1266
-ngsutils	ngsutils_bam_filter	NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.	ngsutils	ngsutils		NGSUtils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets	Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering	Genomics, Transcriptomics	To update	https://github.com/ngsutils/ngsutils	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils		ngsutils	0.5.9	Read pre-processing, Variant calling, Formatting, Sequence contamination filtering	Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	224	24740
-nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	142
-novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	162	6384
-nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	503	26251
-ococo	ococo	Variant detection of SNVs								To update	https://github.com/karel-brinda/ococo	Variant Analysis	ococo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo	0.1.2.6	ococo	0.1.2.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32	1877
-odgi	odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6			0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	2	25
-omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	39	2654
-onto_toolkit	onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def	ONTO-Toolkit is a collection of tools for managing ontologies.								Up-to-date	http://search.cpan.org/~easr/ONTO-PERL-1.45/	Ontology Manipulation	onto_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit	1.45	perl-onto-perl	1.45			0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	0	22	655
-optdoe	optdoe	Optimal Design Of Experiment								To update	https://github.com/pablocarb/doebase	Synthetic Biology	optdoe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe	v2.0.2	doebase				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-optitype	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	321
-orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	774
-orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	Up-to-date	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	2.5.5	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	239	1333
-packaged_annotation_loader	packaged_annotation_loader	Tool to make cached genome annotation data available as a list of datasets collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	Data Source	packaged_annotation_loader	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pacu	pacu_map, pacu_snp	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.	pacu	pacu		PACU	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).	Clustering	Phylogenetics, Sequence analysis	Up-to-date	https://github.com/BioinformaticsPlatformWIV-ISP/PACU	Sequence Analysis, Phylogenetics	pacu	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu	0.0.5	pacu_snp	0.0.5	Clustering	Phylogenetics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pairtools	pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0			5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pangolin	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	Tree-based sequence alignment, Variant classification	Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	0	0	259	7276
-parse_mito_blast	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	31	90
-pathview	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	565	5260
-pbgcpp	pbgcpp	Compute genomic consensus and call variants using PacBio reads mapped to a reference	genomicconsensus	genomicconsensus		GenomicConsensus	The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.	Variant calling	Mapping	Up-to-date	https://github.com/PacificBiosciences/gcpp	Variant Analysis	pbgcpp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp	2.0.2	pbgcpp	2.0.2	Variant calling	Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pbmm2	pbmm2	A minimap2 SMRT wrapper for PacBio data.	pbmm2	pbmm2		pbmm2	pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.	Pairwise sequence alignment, Sorting	Mapping	Up-to-date	https://github.com/PacificBiosciences/pbmm2	Next Gen Mappers	pbmm2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2	1.14.99	pbmm2	1.14.99	Pairwise sequence alignment, Sorting	Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pe_histogram	pe_histogram	Contains a tool that produces an insert size histogram for a paired-end BAM file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram	Graphics	pe_histogram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram	1.0.1	openjdk				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	0	312	4180
-peakzilla	peakzilla	Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.								To update	https://github.com/steinmann/peakzilla	ChIP-seq	peakzilla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla	1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	150	4305
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers
+2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1434	6746	120	122	0	0	0	0	305	305	11	11	1739	7051	131	133
+2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1156	13842	40	42	0	0	0	0	121	121	4	4	1277	13963	44	46
+2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	591	6863	38	40	0	0	0	0	119	119	3	3	710	6982	41	43
+2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	762	782	100	101	0	0	0	0	230	230	14	14	992	1012	114	115
+2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	948	6261	98	100	0	0	0	0	153	153	13	13	1101	6414	111	113
+Ensembl-REST	get_feature_info, get_genetree, get_sequences	A suite of Galaxy tools designed to work with Ensembl REST API.								To update	https://rest.ensembl.org	Data Source		earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	0.1.2	requests				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	474	2914	132	163	0	0	0	0	0	0	0	0	474	2914	132	163
+GAFA	gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	47	6	6	0	0	0	0	0	0	0	0	40	47	6	6
+TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1003	1022	48	52	0	0	0	0	0	0	0	0	1003	1022	48	52
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	41	2	2	0	0	0	0	0	0	0	0	36	41	2	2
+apoc	apoc	Large-scale structural comparison of protein pockets								To update	http://cssb.biology.gatech.edu/APoc	Computational chemistry	apoc	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc	1.0+galaxy1	apoc	1b16			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	4	4	4	1	1	1	1	0	0	0	0	5	5	5	5
+apollo	create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism	Access an Apollo instance from Galaxy								To update	https://github.com/galaxy-genome-annotation/python-apollo	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo		apollo	4.2.13			0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	0	3600	3760	883	911	6	6	4	4	0	0	0	0	3606	3766	887	915
+askomics	askomics_integrate	Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/								To update	https://github.com/askomics/	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics		askocli	0.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+askor	askor_de	AskoR links EdgeR and AskOmics								To update	https://github.com/askomics/askoR	Transcriptomics	askor_de	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	0.2	bioconductor-limma	3.58.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+bamclipper	bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+baric_archive	baric_archive_rennes, baric_archive_toulouse	A data source tool to fetch data from a BARIC Archive server.								To update	https://www.cesgo.org/catibaric/	Data Source		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	1.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+batched_lastz	batched_lastz	Galaxy wrapper for the batching Lastz runs								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	batched_lastz	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	1.04.22	lastz	1.04.22			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	123	123	5	5	0	0	0	0	123	123	5	5
+bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1635	1671	123	124	0	0	0	0	334	334	21	21	1969	2005	144	145
+binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	401	1385	87	88	0	0	0	0	188	188	9	9	589	1573	96	97
+binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	29	1	1	0	0	0	0	0	0	0	0	24	29	1	1
+bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	61	61	4	4	0	0	0	0	0	0	0	0	61	61	4	4
+biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+biohansel_bionumeric_converter	bionumeric_convert	Convert BioHansel output data to a Bionumerics friendly form								To update	https://github.com/phac-nml/galaxy_tools	Text Manipulation	biohansel_bionumeric_converter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter	0.2.0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+blast_parser	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	417	438	99	104	0	0	0	0	0	0	0	0	417	438	99	104
+braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	165	165	48	48	0	0	0	0	0	0	0	0	165	165	48	48
+braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1938	1938	294	294	0	0	0	0	412	412	71	71	2350	2350	365	365
+bundle_collections	bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.58			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	1	1518	1526	73	76	1520	1528	74	77
+camera	abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos									To update		Metabolomics	camera	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera	1.48.0	r-snow	0.4_1			1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	2	0	677	787	114	120	60	60	30	30	734	746	26	26	1471	1593	170	176
+cfm	cfmid	Competitive Fragmentation Modeling (CFM)								Up-to-date	https://sourceforge.net/p/cfm-id/	Metabolomics	cfmid	computational-metabolomics	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	33	cfm	33			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+chado	analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree	Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado								To update	https://github.com/galaxy-genome-annotation/python-chado	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado		python-chado	2.3.9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+collapse_collection	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	39518	40471	3555	3629	22007	24841	3536	4045	3969	4101	814	835	65494	69413	7905	8509
+color_deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	16	2	3	0	0	0	0	0	0	0	0	15	16	2	3
+colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	40	40	2	2	0	0	0	0	0	0	0	0	40	40	2	2
+combineJSON	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+combine_tabular_collection	combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	76	82	11	12	0	0	0	0	0	0	0	0	76	82	11	12
+concat_paired	concat_fastqs	Concatenate paired datasets								To update	https://github.com/phac-nml/concat	Text Manipulation	concat_paired	nml	https://github.com/phac-nml/concat	https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16077	16547	11	11	0	0	0	0	0	0	0	0	16077	16547	11	11
+correlation_analysis	correlation_analysis	[Metabolomics][W4M] Metabolites Correlation Analysis								To update	http://workflow4metabolomics.org	Metabolomics	correlation_analysis	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis	1.0.1+galaxy0	r-batch	1.1_4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	314	326	73	75	0	0	0	0	129	129	6	6	443	455	79	81
+cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9942	9942	26	26	0	0	0	0	0	0	0	0	9942	9942	26	26
+csvtk	csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq	Rapid data investigation and manipulation of csv/tsv files								To update	https://bioinf.shenwei.me/csvtk/	Text Manipulation	csvtk	nml	https://github.com/shenwei356/csvtk	https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk	0.20.0	csvtk	0.30.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	20	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	12	2	2	0	0	0	0	0	0	0	0	12	12	2	2
+detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	43	48	8	8	0	0	0	0	0	0	0	0	43	48	8	8
+ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12996	12996	137	137	10	10	1	1	0	0	0	0	13006	13006	138	138
+ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	820	966	89	106	0	0	0	0	0	0	0	0	820	966	89	106
+export_to_cluster	export_to_cluster	Export datasets to cluster								To update	https://github.com/TGAC/earlham-galaxytools/	Data Export	export_to_cluster	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster	0.0.2	EXPORT_DIR_PREFIX				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fasta2bed	fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fasta_extract	fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	10	10	1	1	0	0	0	0	1286	1827	144	181	1296	1837	145	182
+fastqc_stats	FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+feelnc2asko	feelnc2asko	Convert FeelNC GTF to GFF3								To update	https://github.com/tderrien/FEELnc	Convert Formats	feelnc2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+feht	feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gblocks	gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	466	466	62	62	466	466	62	62
+gcms2isocor	gcms2isocor	Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs								To update	https://github.com/p2m2/p2m2tools	Metabolomics	gcms2isocor	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor	0.2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gcms2isocor	gcms2isocor	Conversion from GCMS PostRun Analysis to Isocor								To update		Metabolomics	gcms2isocor	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+genenotebook	genenotebook_build	Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io								Up-to-date	https://genenotebook.github.io	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	0.4.16	genoboo	0.4.16			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1
+genform	genform	genform: generation of molecular formulas by high-resolution MS and MS/MS data								To update	https://sourceforge.net/projects/genform/	Metabolomics	genform	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform		genform	r8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	68	68	4	4	0	0	0	0	0	0	0	0	68	68	4	4
+get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gnali	gnali	A tool to find nonessential, loss-of-function gene variants								Up-to-date	https://github.com/phac-nml/gnali/	Variant Analysis	gnali	nml	https://github.com/phac-nml/gnali/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali	1.1.0	gnali	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gstf_preparation	gstf_preparation	GeneSeqToFamily preparation converts data for the workflow								To update	https://github.com/TGAC/earlham-galaxytools/	Convert Formats	gstf_preparation	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	0.4.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	377	400	17	17	0	0	0	0	0	0	0	0	377	400	17	17
+hcluster_sg	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	243	263	54	57	0	0	0	0	0	0	0	0	243	263	54	57
+hcluster_sg_parser	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	266	293	22	25	0	0	0	0	0	0	0	0	266	293	22	25
+helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	267	267	39	39	0	0	0	0	80	80	7	7	347	347	46	46
+hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	273	659	101	102	0	0	0	0	153	153	15	15	426	812	116	117
+image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	2	2	0	0	0	0	0	0	0	0	58	58	2	2
+image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	5	5	0	0	0	0	0	0	0	0	16	16	5	5
+imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21409	21849	10	12	0	0	0	0	0	0	0	0	21409	21849	10	12
+influx_data_manager	influx_data_manager	Handling influx_si data inputs in Galaxy workflows								To update	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/	Metabolomics	influx_si_data_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager	1.0.2	influx-si-data-manager	1.0.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+influx_si	influx_si	metabolic flux estimation based on [in]stationary labeling								To update	https://github.com/sgsokol/influx	Metabolomics	influx_si	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si	7.0.1	influx_si	7.0.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ipo	ipo4retgroup, ipo4xcmsSet	[W4M][LC-MS] IPO								To update	https://github.com/rietho/IPO	Metabolomics	ipo	lecorguille	https://github.com/rietho/IPO	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo	1.10.0	bioconductor-ipo	1.28.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+isoplot	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	4	3	3	0	0	0	0	0	0	0	0	4	4	3	3
+jbrowse	jbrowse_to_container	A tool allowing to export a JBrowse dataset into a JBrowse docker container								To update	https://jbrowse.org	Web Services	jbrowse_to_container	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse		python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+kaptive	kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+kat_sect	kat_@EXECUTABLE@	SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.								To update			kat_sect	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+kegalign	kegalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	kegalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	0.1.2.7	kegalign-full	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	5	5	1	1
+kmd_hmdb_data_plot	kmd_hmdb_data_plot	retrieves data from KMD HMDB API and produce plot and csv file								To update	https://github.com/workflow4metabolomics/tools-metabolomics	Metabolomics	kmd_hmdb_data_plot	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	38	2	2	0	0	0	0	0	0	0	0	34	38	2	2
+landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	887	927	13	15	4	4	3	3	0	0	0	0	891	931	16	18
+logol	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1219	1219	182	182	0	0	0	0	37	37	4	4	1256	1256	186	186
+mahotas_features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	44	6	6	0	0	0	0	0	0	0	0	39	44	6	6
+mauve_contig_mover	mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+meneco	meneco	Meneco computes minimal completions to your draft network with reactions from a repair network								Up-to-date	http://bioasp.github.io/meneco/	Systems Biology	meneco	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	1.5.2	meneco	1.5.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	25	2	3	0	0	0	0	0	0	0	0	18	25	2	3
+metfrag	metfrag	[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity)								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag	2.4.5+galaxy3	metfrag	2.4.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	192	192	20	20	0	0	0	0	0	0	0	0	192	192	20	20
+metfrag-vis	metfrag_vis	[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis	2.4.5+galaxy0	metfrag	2.4.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	50	14	14	0	0	0	0	0	0	0	0	50	50	14	14
+miranda	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6408	6514	94	99	0	0	0	0	0	0	0	0	6408	6514	94	99
+miranda2asko	miranda2asko	Converts miRanda output into AskOmics format								To update		Convert Formats	miranda2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	0.2	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mixmodel4repeated_measures	mixmodel4repeated_measures	[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model								To update	http://workflow4metabolomics.org	Metabolomics	mixmodel4repeated_measures	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures	3.1.0	r-lme4				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	119024	119024	628	628	42	42	2	2	36310	36310	191	191	155376	155376	821	821
+morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ms2snoop	ms2snoop	[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.								To update	http://workflow4metabolomics.org	Metabolomics	ms2snoop	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop	2.2.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+msPurity	mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								Up-to-date	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity	1.28.0	bioconductor-mspurity	1.28.0			0	0	10	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	848	848	91	91	0	0	0	0	0	0	0	0	848	848	91	91
+msp_split	msp_split	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								To update	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		tomnl	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split	0.0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mzxmlshaper	mzxmlshaper	Convert mzML, mzXML or netCDF files to mzML or mzXML								To update	https://rdrr.io/bioc/mzR/	Metabolomics	mzxmlshaper	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper	1.0.0+galaxy0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	6	6	0	0	0	0	15	15	6	6
+ncbi_fcs_adaptor	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	842	842	93	93	0	0	0	0	842	842	93	93
+nmr_annotation	NmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation								To update	http://workflow4metabolomics.org	Metabolomics	nmr_annotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_annotation	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation	3.0.0	r-batch	1.1_4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	49	49	5	5	0	0	0	0	0	0	0	0	49	49	5	5
+nmr_annotation2d	2DNmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra								To update	http://workflow4metabolomics.org	Metabolomics	2dnmrannotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d	2.0.0	r-batch	1.1_4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+nmr_preprocessing	NMR_Preprocessing, NMR_Read	[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction								To update	http://workflow4metabolomics.org	Metabolomics	nmr_preprocessing	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_preprocessing	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing		r-batch	1.1_4			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	142	142	8	8	0	0	0	0	335	341	9	9	477	483	17	17
+normalization	normalization	[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data								To update	http://workflow4metabolomics.org	Metabolomics	normalization	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/normalization	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization	1.0.7	r-batch	1.1_4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	152	162	39	40	0	0	0	0	233	236	12	12	385	398	51	52
+openlabcds2csv	openlabcds2csv	"Creates a summary of several ""Internal Standard Report"" OpenLabCDS results."								To update		Metabolomics	openlabcds2csv	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	149	149	31	31	0	0	0	0	18	18	1	1	167	167	32	32
+pangolin	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	0	0	7457	7457	508	508	8518	8518	377	377	2760	2760	259	259	18735	18735	1144	1144
+patrist	patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+peptimapper	peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	42	1	2	0	0	0	0	0	0	0	0	36	42	1	2
+physiofit	physiofit	PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit	workflow4metabolomics	https://github.com/MetaSys-LISBP/PhysioFit	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit	3.4.0	physiofit	3.4.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+physiofit_manager	physiofit_data_manager	Handling of physiofit input files								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager	1.0.1	physiofit_data_manager	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+plasmid_profiler	plasmid_profiler	Explores plasmid content in WGS data								To update			plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler	0.1.6	r				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+plasmid_profiler_suite		Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+plotheatmap	plotheatmap	This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output.								To update		Computational chemistry	plotheatmap	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	1.0	bioconductor-preprocesscore	1.64.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pneumocat	pneumocat	Pneumococcal Capsular Typing of illumina fastq reads								Up-to-date	https://github.com/phe-bioinformatics/PneumoCaT	Variant Analysis	pneumocat	nml	https://github.com/phe-bioinformatics/PneumoCaT	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat	1.2.1	pneumocat	1.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	33	33	2	2	0	0	0	0	0	0	0	0	33	33	2	2
+points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	4	4	0	0	0	0	0	0	0	0	29	29	4	4
+projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	86	4	6	0	0	0	0	0	0	0	0	40	86	4	6
+projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20858	21444	14	18	0	0	0	0	0	0	0	0	20858	21444	14	18
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pseudogenome	pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+quasitools	aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0			0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13483	13483	434	434	13483	13483	434	434
+rdock	rdock	Docking ligands to proteins and nucleic acids								To update	http://rdock.sourceforge.net/	Computational chemistry	rdock	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock	1.0	rDock	2013.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+refseq_masher	refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	428	428	35	35	141	141	42	42	0	0	0	0	569	569	77	77
+repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	95	38	38	0	0	0	0	0	0	0	0	95	95	38	38
+replace_chromosome_names	replace_chromosome_names	Replace chromosome names								To update		Text Manipulation	replace_chromosome_names	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names	0.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	514	573	69	83	0	0	0	0	0	0	0	0	514	573	69	83
+rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	7	7	0	0	0	0	0	0	0	0	15	15	7	7
+rsat_filter_snps	rsat_filter_snps	Filter SNPs in RSAT Matrix Scan output								To update	https://github.com/TGAC/earlham-galaxytools/	ChIP-seq, Systems Biology	rsat_filter_snps	earlham	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	477	520	13	16	0	0	0	0	0	0	0	0	477	520	13	16
+segalign	segalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/gsneha26/SegAlign	Next Gen Mappers	segalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	0.1.2.7	segalign-galaxy	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	252	252	47	47	0	0	0	0	252	252	47	47
+segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	2	2	0	0	0	0	0	0	0	0	7	7	2	2
+seqtk_nml	seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3457	3457	301	301	0	0	0	0	556	556	65	65	4013	4013	366	366
+skyline2isocor	skyline2isocor	Converting skyline output to IsoCor input								Up-to-date	https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor	Metabolomics	skyline2isocor	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor	1.0.0	skyline2isocor	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	96	103	4	5	0	0	0	0	4	4	1	1	100	107	5	6
+smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+smart_domains	smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+smina	smina	smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization								To update	https://sourceforge.net/projects/smina/	Computational chemistry	smina	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina	1.0	smina	2017.11.9			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	499	499	16	16	44	44	10	10	0	0	0	0	543	543	26	26
+spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+spatyper	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	44	51	2	3	0	0	0	0	0	0	0	0	44	51	2	3
+spolpred	spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.1	giatools	0.3.1	Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	4	4	0	0	0	0	0	0	0	0	16	16	4	4
+srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41
+staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20778	20891	2030	2045	9520	9520	1424	1424	6753	6753	864	864	37051	37164	4318	4333
+stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	249	249	32	32	16	16	10	10	102	102	16	16	367	367	58	58
+suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	117	117	41	41	84	84	24	24	161	161	13	13	362	362	78	78
+suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	217	217	47	47	42	42	20	20	96	96	12	12	355	355	79	79
+suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	721	721	160	160	350	350	91	91	214	214	35	35	1285	1285	286	286
+suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	125	125	30	30	13	13	9	9	83	83	8	8	221	221	47	47
+suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	396	396	134	134	121	121	57	57	144	144	39	39	661	661	230	230
+suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	22	0	21	21	22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	964	964	318	318	249	249	118	118	475	475	108	108	1688	1688	544	544
+suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	8	8	8	8	13	13	11	11	1302	1302	19	19	1323	1323	38	38
+suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	58	58	23	23	24	24	11	11	92	92	11	11	174	174	45	45
+suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	863	863	220	220	237	237	98	98	181	181	41	41	1281	1281	359	359
+suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	0	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	983	983	287	287	375	375	144	144	907	907	106	106	2265	2265	537	537
+suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	46	46	13	13	9	9	5	5	0	0	0	0	55	55	18	18
+suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	0	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	37	37	16	16	22	22	7	7	89	89	14	14	148	148	37	37
+suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	615	615	143	143	246	246	75	75	115	115	27	27	976	976	245	245
+suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	330	330	83	83	64	64	40	40	195	195	49	49	589	589	172	172
+suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	4	4	4	4	5	5	5	5	1	1	1	1	10	10	10	10
+suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	14	14	16	16	6	6	37	37	2	2	82	82	22	22
+suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	0	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	10	10	3	3	14	14	10	10	5	5	5	5	29	29	18	18
+suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	664	664	145	145	113	113	43	43	255	255	50	50	1032	1032	238	238
+suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	84	84	52	52	25	25	16	16	9	9	5	5	118	118	73	73
+suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14941	14941	383	383	25941	25941	255	255	2856	2856	112	112	43738	43738	750	750
+superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	5	5	0	0	0	0	0	0	0	0	26	26	5	5
+t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3783	9125	211	229	1	1	1	1	0	0	0	0	3784	9126	212	230
+tree_relabeler	tree_relabel	Relabels the tips of a newick formatted tree.								To update		Text Manipulation	tree_relabeler	nml	https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler	https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+tripal	analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync	Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal								To update	https://github.com/galaxy-genome-annotation/python-tripal	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal		python-tripal	3.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+unzip	unzip	Unzip file								To update	https://github.com/bmcv	Convert Formats	unzip	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip	6.0	unzip				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6942	7024	1345	1356	1	1	1	1	2461	2461	266	266	9404	9486	1612	1623
+visceral_evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	1	1	0	0	0	0	0	0	0	0	20	25	1	1
+voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	43	43	3	3	0	0	0	0	0	0	0	0	43	43	3	3
+w4mclassfilter	w4mclassfilter	Filter W4M data by values or metadata								To update	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper	Metabolomics	w4mclassfilter	eschen42	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter	0.98.19	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2370	2836	9	10	0	0	0	0	1482	1509	4	4	3852	4345	13	14
+w4mconcatenate	W4Mconcatenate	[W4M][Utils] concatenate two Metadata tables								To update	http://workflow4metabolomics.org	Metabolomics	w4mconcatenate	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate	1.0.0+galaxy0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+w4mcorcov	w4mcorcov	OPLS-DA Contrasts of Univariate Results								To update	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper	Metabolomics	w4mcorcov	eschen42	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov	0.98.18	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	238	375	10	10	0	0	0	0	10	10	2	2	248	385	12	12
+w4mjoinpn	w4mjoinpn	Join positive- and negative-mode W4M datasets								To update	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper	Metabolomics	w4mjoinpn	eschen42	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn	0.98.2	coreutils	8.25			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	150	171	7	7	0	0	0	0	7	7	2	2	157	178	9	9
+wade	wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	38	2	3	0	0	0	0	0	0	0	0	32	38	2	3
+xcms	abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw		XCMS	XCMS		xcms	Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data.  The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling.	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Biological imaging, Data visualisation, Metabolomics	Up-to-date	https://github.com/sneumann/xcms	Metabolomics	xcms	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms	4.0.0	bioconductor-xcms	4.0.0	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Data visualisation, Metabolomics	9	11	12	0	9	11	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	10	9	0	31909	35790	1357	1384	7099	7099	413	413	5333	5357	330	330	44341	48246	2100	2127
+10x_bamtofastq	10x_bamtofastq	Converts 10x Genomics BAM to FASTQ								Up-to-date	https://github.com/10XGenomics/bamtofastq	Convert Formats	10x_bamtofastq	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	1.4.1	10x_bamtofastq	1.4.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	307	307	80	80	8	8	3	3	3	3	1	1	318	318	84	84
+AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	119	14	17	0	0	0	0	0	0	0	0	45	119	14	17
+AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	189	3094	23	25	0	0	0	0	0	0	0	0	189	3094	23	25
+CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25532	50045	45	57	0	0	0	0	0	0	0	0	25532	50045	45	57
+CollectResults	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1119	2115	50	62	0	0	0	0	0	0	0	0	1119	2115	50	62
+CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	108	1	3	0	0	0	0	0	0	0	0	37	108	1	3
+GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	80	150	18	23	0	0	0	0	0	0	0	0	80	150	18	23
+LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25572	50177	45	57	0	0	0	0	0	0	0	0	25572	50177	45	57
+NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	3210	62854	96	124	0	0	0	0	0	0	0	0	3210	62854	96	124
+Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	71	9	10	0	0	0	0	0	0	0	0	45	71	9	10
+PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1202	2121	48	62	0	0	0	0	0	0	0	0	1202	2121	48	62
+Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1116	1897	57	71	0	0	0	0	0	0	0	0	1116	1897	57	71
+Structure_GSPAN	structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	991	3060	50	62	0	0	0	0	0	0	0	0	991	3060	50	62
+add_line_to_file	add_line_to_file	Adds a text line to the beginning or end of a file.								To update		Text Manipulation	add_line_to_file	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	0.1.0	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	15933	15933	378	378	1736	1736	214	214	380	380	28	28	18049	18049	620	620
+add_value	addValue	Add a value as a new column.								To update		Text Manipulation	add_value	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value	https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value	1.0.1	perl				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	37860	374587	1293	1610	17588	293713	1243	6197	3873	4397	202	229	59321	672697	2738	8036
+agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	244	244	0	0	0	0	119	119	10	10	1555	1555	254	254
+align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	511	541	32	35	0	0	0	0	0	0	0	0	511	541	32	35
+antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	292	306	5	7	0	0	0	0	0	0	0	0	292	306	5	7
+antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15949	16490	726	811	5113	5113	649	649	6043	6043	169	169	27105	27646	1544	1629
+aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	59	74	10	12	0	0	0	0	0	0	0	0	59	74	10	12
+atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	232	279	62	72	0	0	0	0	0	0	0	0	232	279	62	72
+augustus	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10109	11052	1378	1509	12573	12573	2206	2206	5274	5274	369	369	27956	28899	3953	4084
+bamhash	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	158	181	40	44	0	0	0	0	0	0	0	0	158	181	40	44
+barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+basecoverage	gops_basecoverage_1	Base Coverage of all intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	basecoverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	226	308	27	35	2615	45557	302	2284	482	522	32	36	3323	46387	361	2355
+best_regression_subsets	BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3	4	3	4	14	253	7	72	0	0	0	0	17	257	10	76
+bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	2	0	0	0	0	0	0	0	0	3	3	2	2
+bigwig_to_bedgraph	bigwig_to_bedgraph	Convert from bigWig to bedGraph format								To update		Convert Formats	bigwig_to_bedgraph	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	0.1.0	ucsc_tools				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5769	6802	567	650	0	0	0	0	0	3	0	1	5769	6805	567	651
+bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	1	0	0	0	0	0	0	0	0	2	2	1	1
+biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	25	11	11	0	0	0	0	0	0	0	0	25	25	11	11
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	151	151	143	143	43	43	596	596	22	22	1286	1286	216	216
+bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	4	4	4	0	13715	14997	992	1099	0	0	0	0	197	197	22	22	13912	15194	1014	1121
+blat_coverage_report	generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+blat_mapping	blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1527	1527	79	79	6	6	1	1	317	317	26	26	1850	1850	106	106
+blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	768	3043	97	119	14	14	11	11	276	276	9	9	1058	3333	117	139
+blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	811	1501	54	79	64	64	29	29	561	561	15	15	1436	2126	98	123
+bowtie_wrappers	bowtie_wrapper	Galaxy wrappers for the Bowtie short read mapping tools.								To update	http://bowtie-bio.sourceforge.net/	Next Gen Mappers	bowtie_wrappers	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers	https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers	1.2.0	bowtie	1.3.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	24164	25149	1320	1480	17537	203397	1330	17491	15654	15992	291	351	57355	244538	2941	19322
+canonical_correlation_analysis	cca1	Canonical Correlation Analysis								To update		Statistics	canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis	1.0.0	R				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	66	75	16	18	141	505	31	147	0	0	0	0	207	580	47	165
+canu	canu	Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).	canu	canu		CANU	De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.	De-novo assembly	Genomics	Up-to-date	https://github.com/marbl/canu		canu	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/canu	https://github.com/bgruening/galaxytools/tree/master/tools/canu	2.2	canu	2.2	De-novo assembly	Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13360	14618	1383	1444	0	0	0	0	3542	3542	385	385	16902	18160	1768	1829
+categorize_elements_satisfying_criteria	categorize_elements_satisfying_criteria	Categorize Elements satisfying criteria.								To update		Statistics	categorize_elements_satisfying_criteria	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria	https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	41	4	5	0	0	0	0	168	186	12	14	205	227	16	19
+ccat	peakcalling_ccat	Control-based ChIP-seq Analysis Tool								To update		ChIP-seq	ccat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat	0.0.2	ccat	3.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	175	28	39	0	0	0	0	0	0	0	0	88	175	28	39
+cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5946	7379	407	628	0	0	0	0	5946	7379	407	628
+cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	4	4	0	0	0	0	0	0	0	0	14	14	4	4
+cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	0	0	23	23	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	0	4773	4773	749	749	0	0	0	0	5688	5688	94	94	10461	10461	843	843
+cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55	55	11	11	0	0	0	0	0	0	0	0	55	55	11	11
+change_case	ChangeCase	Convert column case.								To update		Text Manipulation	change_case	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case	https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case	1.0.1	perl				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	0	1	1	1	1	10606	12531	2204	2547	9044	17167	1748	2394	923	938	240	245	20573	30636	4192	5186
+chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	62	12	12	0	0	0	0	0	0	0	0	62	62	12	12
+chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	16468	18344	956	991	33692	34453	2559	2625	2948	2948	104	104	53108	55745	3619	3720
+chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+circexplorer	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	211	263	32	40	0	0	0	0	209	209	6	6	420	472	38	46
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	548	548	18	18	0	0	0	0	548	548	18	18
+cluster	gops_cluster_1	Cluster the intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	cluster	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	513	813	18	35	2406	30579	156	1547	1353	1393	17	20	4272	32785	191	1602
+cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2609	2609	3	3	0	0	0	0	0	0	0	0	2609	2609	3	3
+cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	90	112	11	14	0	0	0	0	0	0	0	0	90	112	11	14
+cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	316	355	25	29	0	0	0	0	0	0	0	0	316	355	25	29
+column_arrange_by_header	bg_column_arrange_by_header	Column arrange by header name								To update		Text Manipulation	column_arrange_by_header	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5356	5636	446	484	2026	2026	375	375	1400	1531	117	138	8782	9193	938	997
+combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	530	530	65	65	8	8	6	6	0	0	0	0	538	538	71	71
+compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	221	5	28	0	0	0	0	0	0	0	0	39	221	5	28
+compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	332	28	32	0	0	0	0	0	0	0	0	306	332	28	32
+complement	gops_complement_1	Complement intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	complement	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	187	233	15	20	495	4810	165	836	405	451	7	7	1087	5494	187	863
+compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	85	96	9	10	0	0	0	0	316	334	8	8	401	430	17	18
+compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	55	65	2	2	0	0	0	0	317	335	5	5	372	400	7	7
+compute_q_values	compute_q_values	Compute q-values based on multiple simultaneous tests p-values								To update		Statistics	compute_q_values	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values	1.0.1	R				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	35	0	3	0	0	0	0	0	0	0	0	0	35	0	3
+concat	gops_concat_1	Concatenate two bed files								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	concat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat	1.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	575128	575441	694	783	43420	85345	629	3508	19330	19418	104	117	637878	680204	1427	4408
+condense_characters	Condense characters1	Condense consecutive characters.								To update		Text Manipulation	condense_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters	1.0.0					1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47	2173	28	368	195	205	8	8	242	2378	36	376
+convert_characters	Convert characters1	Convert delimiters to tab.								To update		Text Manipulation	convert_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters	1.0.1	python				1	1	1	0	1	1	1	0	1	1	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	23589	28986	1061	1200	23507	160693	2302	8699	5413	6446	251	329	52509	196125	3614	10228
+convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+correlation	cor2	Correlation for numeric columns								To update		Statistics	correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation	1.0.0	rpy				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	398	876	106	134	412	5568	105	755	192	239	21	27	1002	6683	232	916
+count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	280	307	110	124	712	1277	332	628	476	541	55	79	1468	2125	497	831
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+coverage	gops_coverage_1	Coverage of a set of intervals on second set of intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	coverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1560	1725	43	58	4328	44209	193	2113	283	316	16	18	6171	46250	252	2189
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cpat	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.								Up-to-date	https://github.com/liguowang/cpat	Transcriptomics	cpat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	3.0.5	cpat	3.0.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	204	204	47	47	165	165	40	40	125	125	7	7	494	494	94	94
+crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4066	4139	166	180	0	0	0	0	0	0	0	0	4066	4139	166	180
+ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	196	211	41	48	1	447	1	161	0	0	0	0	197	658	42	209
+cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1251	1803	98	166	3461	15159	486	2044	2425	3338	57	159	7137	20300	641	2369
+cummerbund_to_tabular	cummerbund_to_cuffdiff	Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.								To update		Convert Formats, Next Gen Mappers	cummerbund_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular	1.0.1					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	888	1208	43	97	1334	2683	101	479	0	0	0	0	2222	3891	144	576
+cut_columns	Cut1	Select columns from a dataset.								To update		Text Manipulation	cut_columns	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns	1.0.2					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	0	1	1	1	1	1973168	2034965	11939	12833	352364	803522	12967	30199	128777	133584	2341	2572	2454309	2972071	27247	45604
+delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	40	6	7	0	0	0	0	0	0	0	0	33	40	6	7
+dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	18	18	0	0	0	0	0	0	0	0	89	89	18	18
+dgidb_annotator	dgidb_annotate	Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)								To update		Systems Biology, Variant Analysis	dgidb_annotator	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator	0.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	69	26	30	0	304	0	133	0	0	0	0	59	373	26	163
+diff	diff	GNU diff tool that calculates the differences between two files.								To update	http://www.gnu.org/software/diffutils/	Text Manipulation	diff	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diff	https://github.com/bgruening/galaxytools/tree/master/tools/diff	3.7	diffutils				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	362	362	99	99	23	23	17	17	0	0	0	0	385	385	116	116
+diffbind		Diffbind provides functions for  processing  ChIP-Seq  data.								To update	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26	32	8	9	86	172	20	53	0	0	0	0	112	204	28	62
+dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	921	1626	4	31	0	0	0	0	0	0	0	0	921	1626	4	31
+dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	74	88	12	15	0	0	0	0	0	0	0	0	74	88	12	15
+draw_stacked_barplots	draw_stacked_barplots	Draw Stacked Bar Plots for different categories and different criteria								To update		Graphics, Statistics	draw_stacked_barplots	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots	https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots	1.0.0	R				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	216	47	52	0	0	0	0	183	213	22	31	372	429	69	83
+dwt_cor_ava_perclass	compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Feature Occurrences								To update		Statistics	dwt_cor_ava_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	141	8	11	136	141	8	11
+dwt_cor_avb_all	compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features								To update		Statistics	dwt_cor_avb_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	124	124	7	7	124	124	7	7
+dwt_ivc_all	compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Second Moments for Feature Occurrences								To update		Statistics	dwt_ivc_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	121	123	5	7	121	123	5	7
+dwt_var_perclass	compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom	Compute P-values and Max Variances for Feature Occurrences								To update		Statistics	dwt_var_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	131	132	7	8	131	132	7	8
+dwt_var_perfeature	dwt_var1	Wavelet variance using Discrete Wavelet Transfoms								To update		Statistics	dwt_var_perfeature	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature	1.0.2	r-bitops				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	30	36	2	4	11	11	4	4	206	220	6	7	247	267	12	15
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	28	28	2	2	0	0	0	0	0	0	0	0	28	28	2	2
+edta	edta	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. 	edta	edta		The Extensive de novo TE Annotator (EDTA)	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	To update	https://github.com/oushujun/EDTA	Variant Analysis	edta	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta	https://github.com/bgruening/galaxytools/tree/master/tools/edta		edta	2.2.0	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4495	4495	111	111	0	0	0	0	0	0	0	0	4495	4495	111	111
+effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+epicseg	epicseg_segment	EpiCSeg is a tool for conducting chromatin segmentation.								To update	https://github.com/lamortenera/epicseg	Epigenetics	epicseg	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	@VERSION_STRING@	epicseg	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	160	252	17	21	0	0	0	0	0	0	0	0	160	252	17	21
+exparna	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+express	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	278	337	34	45	0	1184	0	117	2402	2844	23	60	2680	4365	57	222
+fasta_compute_length	fasta_compute_length	Compute sequence length								To update	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.4	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	8547	9136	978	1129	17748	51150	1404	5670	4239	4404	162	190	30534	64690	2544	6989
+fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39695	39742	242	255	13660	19007	600	1398	1521	1603	92	112	54876	60352	934	1765
+fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	47494	51924	889	997	50663	101663	1488	3742	3919	5601	241	276	102076	159188	2618	5015
+fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	108876	113638	1572	1793	82527	192112	2209	8565	5711	7649	275	334	197114	313399	4056	10692
+fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7560	7560	1266	1266	6539	6539	1581	1581	0	0	0	0	14099	14099	2847	2847
+fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								To update		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4881	6165	859	967	29458	99179	3455	11369	2171	2678	259	338	36510	108022	4573	12674
+fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	3	0	0	0	0	0	8	0	3
+featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22308	22388	16	19	350	13711	54	349	0	0	0	0	22658	36099	70	368
+file_manipulation	bg_uniq	This tool returns all unique lines from a tab-separated file.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	Text Manipulation	unique	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	0.4	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	6690	8818	554	612	0	0	0	0	0	0	0	0	6690	8818	554	612
+filter_transcripts_via_tracking	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23	24	9	10	62	635	26	241	2	2	2	2	87	661	37	253
+find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	62	70	10	12	3	1787	1	204	0	0	0	0	65	1857	11	216
+find_subsequences	bg_find_subsequences									To update			find_subsequences	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences	0.3	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	554	784	69	79	2820	3047	323	361	20	20	1	1	3394	3851	393	441
+flanking_features	flanking_features_1	Fetch closest non-overlapping feature for every interval								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	flanking_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features	4.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	589	731	51	63	2445	32847	304	2549	1214	1294	15	22	4248	34872	370	2634
+flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	2	2	0	0	0	0	0	0	0	0	9	9	2	2
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32514	32675	3379	3422	19434	19434	2537	2537	9843	9843	1624	1624	61791	61952	7540	7583
+footprint	footprint	Find transcription factor footprints								To update	https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/	Epigenetics	footprint	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	1.0.0	footprint	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	57	5	5	0	0	0	0	0	0	0	0	57	57	5	5
+format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	189	203	57	60	0	0	0	0	0	0	0	0	189	203	57	60
+format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5940	6474	558	608	0	0	0	0	0	0	0	0	5940	6474	558	608
+generate_pc_lda_matrix	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115	124	29	30	518	1029	102	261	184	198	14	17	817	1351	145	308
+get_flanks	get_flanks1	Get flanks returns flanking region/s for every gene								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	get_flanks	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3768	325011	1462	2044	9350	242043	2201	6583	787	1070	119	146	13905	568124	3782	8773
+get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	746	746	136	136	0	0	0	0	1504	1504	244	244	2250	2250	380	380
+getindelrates_3way	indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	290	20	86	0	0	0	0	70	290	20	86
+getindels_2way	getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	74	237	24	61	0	0	0	0	74	237	24	61
+gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	To update	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.7	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11748	11748	767	767	6560	6560	397	397	2556	2556	106	106	20864	20864	1270	1270
+gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	490	682	74	109	127	14058	20	1798	0	0	0	0	617	14740	94	1907
+glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	11	6	6	85	984	29	230	10	11	7	8	106	1006	42	244
+gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	72	5	7	0	0	0	0	0	0	0	0	34	72	5	7
+graph_converter	graph_converter	Convert between different graph formats								To update		Convert Formats	graph_converter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+graphclust	graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	1	0	0	0	0	0	0	0	0	0	6	0	1
+graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1725	2708	97	99	2	2	2	2	0	0	0	0	1727	2710	99	101
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	7012	7344	323	338	0	0	0	0	0	0	0	0	7012	7344	323	338
+graphprot	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy2	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	463	484	18	19	0	0	0	0	0	0	0	0	463	484	18	19
+hclust2	hclust2	Plots heatmaps								To update	https://bitbucket.org/nsegata/hclust2/	Data Visualization	hclust2	rnateam	https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2	https://github.com/bgruening/galaxytools/tree/master/tools/hclust2	0.99	hclust2	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hgv_fundo	hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	145	1794	33	397	0	0	0	0	145	1794	33	397
+hgv_hilbertvis	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	119	265	16	60	0	0	0	0	119	265	16	60
+hictk	hictk	Convert cooler to juicebox_hic								Up-to-date	https://github.com/paulsengroup/hictk	Convert Formats, Epigenetics	hictk	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	1.0.0	hictk	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	9	9	0	0	0	0	0	0	0	0	17	17	9	9
+hicup	hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater	The HiCUP-Pipeline from the Bioinformatics Babraham Institute.								To update	https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html	Epigenetics	hicup	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	0.9.2					7	0	7	0	7	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	6	0	901	1020	160	184	440	440	111	111	0	0	0	0	1341	1460	271	295
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	0	12	0	0	0	0	0	0	0	0	0	228	0	12
+histogram	histogram_rpy	Histogram of a numeric column								To update		Graphics, Statistics	histogram	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram	https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram	1.0.4	rpy2	2.7.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3748	4661	866	1002	5993	48272	1507	7101	549	746	152	253	10290	53679	2525	8356
+homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+htseq-clip	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	98	98	19	19	0	0	0	0	0	0	0	0	98	98	19	19
+illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20240614			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	1731	1731	109	109	0	0	0	0	0	0	0	0	1731	1731	109	109
+improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	22	1	1	44	292	3	21	0	0	0	0	62	314	4	22
+infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	59700	112582	223	282	0	0	0	0	1157	1221	34	35	60857	113803	257	317
+inforna		INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	157	157	14	14	0	0	0	0	0	0	0	0	157	157	14	14
+intarna	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.1	intarna	3.4.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3071	7652	41	47	0	0	0	0	0	0	0	0	3071	7652	41	47
+intersect	gops_intersect_1	Intersect the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	20472	349984	2351	3007	45587	778988	4359	14116	6087	7417	484	561	72146	1136389	7194	17684
+iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1426	1426	71	71	0	0	0	0	0	0	0	0	1426	1426	71	71
+jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse_2	jbrowse_2		JBrowse 2	Modular genome browser with views of synteny and structural variation.	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.15.4	jbrowse2	2.15.4	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1312	1312	219	219	116	116	58	58	37	37	6	6	1465	1465	283	283
+join	gops_join_1	Join the intervals of two datasets side-by-side								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	join	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	15624	330820	1864	2438	52317	513688	10198	39421	1329	1645	213	289	69270	846153	12275	42148
+join_files_on_column_fuzzy	join_files_on_column_fuzzy	Join two files on a common column, allowing a certain difference.								To update		Text Manipulation	join_files_on_column_fuzzy	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	1.0.1	python				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1980	2697	345	410	0	0	0	0	1081	1081	44	44	3061	3778	389	454
+jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	30	30	2	2	0	0	0	0	0	0	0	0	30	30	2	2
+kernel_canonical_correlation_analysis	kcca1	Kernel Canonical Correlation Analysis								To update		Statistics	kernel_canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis	1.0.0	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	62	70	4	4	207	334	27	71	0	0	0	0	269	404	31	75
+kernel_principal_component_analysis	kpca1	Kernel Principal Component Analysis								To update		Statistics	kernel_principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis	1.0.0	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	144	157	26	30	268	707	83	248	0	0	0	0	412	864	109	278
+kinwalker		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23008	23014	1060	1061	16194	24490	1719	2168	14898	14898	436	436	54100	62402	3215	3665
+labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+lastz_paired_reads	lastz_paired_reads_wrapper	Galaxy wrapper for the Lastz alignment tool on paired reads								To update		Next Gen Mappers	lastz_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads	1.1.1	lastz	1.04.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	9	3	4	0	0	0	0	8	10	5	5	15	19	8	9
+lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	89	137	4	20	118	6136	15	1112	0	0	0	0	207	6273	19	1132
+lda_analysis	lda_analy1	Perform Linear Discriminant Analysis								To update		Graphics, Statistics	lda_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis	1.0.1	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	147	159	46	48	793	1538	101	314	0	4	0	3	940	1701	147	365
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	171	27	30	0	0	0	0	0	0	0	0	149	171	27	30
+linear_regression	LinearRegression1	Perform Linear Regression								To update		Statistics	linear_regression	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression	https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression	1.0.1	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	146	1103	31	271	0	0	0	0	146	1103	31	271
+locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								Up-to-date	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	2.0.1	locarna	2.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	314	350	36	46	0	0	0	0	0	0	0	0	314	350	36	46
+logistic_regression_vif	LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	64	173	12	48	0	0	0	0	64	173	12	48
+maf_cpg_filter	cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	85	356	6	28	0	0	0	0	85	356	6	28
+mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	0	2	2	2	0	172433	174456	1865	1951	108640	122790	4266	5521	20027	20027	1172	1172	301100	317273	7303	8644
+mapping_to_ucsc	mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mavedb	mavedb_importer	data source for MaveDB								To update		Data Source	mavedb_importer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb	0.9					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	2	2	0	0	0	0	0	0	0	0	8	8	2	2
+mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	73	86	5	5	0	0	0	0	0	0	0	0	73	86	5	5
+megablast_xml_parser	megablast_xml_parser	Parse blast XML output								To update		Next Gen Mappers, Convert Formats	megablast_xml_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	743	816	103	141	292	2868	82	459	0	0	0	0	1035	3684	185	600
+merge	gops_merge_1	Merge the overlapping intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	565922	566630	418	441	45844	107523	671	4353	19828	19994	100	137	631594	694147	1189	4931
+merge_cols	mergeCols1	Merge columns together.								To update		Text Manipulation	merge_cols	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols	https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols	1.0.3	python				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	20905	31051	1906	2128	21780	132833	885	3172	1524	1925	122	152	44209	165809	2913	5452
+methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	632	5461	155	453	0	0	0	0	0	0	0	0	632	5461	155	453
+methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	14907	18971	638	894	2677	2677	230	230	2313	2313	83	83	19897	23961	951	1207
+methylkit	methylkit	A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.								To update	http://bioconductor.org/packages/release/bioc/html/methylKit.html	Epigenetics	methylkit	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	0.99.2	bioconductor-methylkit	1.28.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3209	4572	312	442	479	479	79	79	315	315	51	51	4003	5366	442	572
+mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	573	573	3	3	0	0	0	0	0	0	0	0	573	573	3	3
+miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+microsatellite_birthdeath	microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+microsats_alignment_level	microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	135	973	50	140	0	0	0	0	135	973	50	140
+microsats_mutability	microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	34	312	22	87	0	0	0	0	34	312	22	87
+minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1213	1309	115	124	0	0	0	0	0	0	0	0	1213	1309	115	124
+mine	maximal_information_based_nonparametric_exploration	Maximal Information-based Nonparametric Exploration								To update		Variant Analysis	mine	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine	0.0.1	MINE				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	11	8	8	17	63	6	19	0	0	0	0	26	74	14	27
+minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	229	229	32	32	0	0	0	0	0	0	0	0	229	229	32	32
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1020	1020	176	176	414	414	73	73	277	277	20	20	1711	1711	269	269
+molecule2gspan	bg_mol2gspan	converter								To update	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	Convert Formats	molecule_to_gspan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	0.2	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+motus	mereg_mOTUs_tables, motus_profiler	Tool for profiling the abundance of microbial taxa.	mOTUs	mOTUs		Metagenomic operational taxonomic units (mOTUs)	Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/motu-tool/mOTUs	Metagenomics	motus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs	https://github.com/bgruening/galaxytools/tree/master/tools/motus	3.1.0	motus	3.1.0	Taxonomic classification	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	76	9	9	0	0	0	0	0	0	0	0	71	76	9	9
+multispecies_orthologous_microsats	multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mummer	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	883	921	199	211	730	730	199	199	136	202	34	49	1749	1853	432	459
+music_deconvolution	music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)								Up-to-date	https://github.com/xuranw/MuSiC	Transcriptomics	music	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/	https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution	0.1.1	music-deconvolution	0.1.1			5	5	4	0	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	2801	2801	289	289	364	364	80	80	1357	1357	21	21	4522	4522	390	390
+mutate_snp_codon	mutate_snp_codon_1	Mutate Codons with SNPs								To update		Variant Analysis	mutate_snp_codon	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	44	49	5	5	81	417	23	118	0	0	0	0	125	466	28	123
+nanopolish	nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants	Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.								Up-to-date	https://github.com/jts/nanopolish		nanopolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	0.14.0	nanopolish	0.14.0			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	9284	9694	215	229	0	0	0	0	2358	2358	49	49	11642	12052	264	278
+nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	40	1	1	0	0	0	0	0	0	0	0	36	40	1	1
+netboxr	netboxr	netboxr enables automated discovery of biological process modules by network analysis								To update		Systems Biology	netboxr	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/netboxr	1.6.0	bioconductor-netboxr	1.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	12	6	6	0	0	0	0	0	0	0	0	12	12	6	6
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	391	391	158	158	0	0	0	0	0	0	0	0	391	391	158	158
+nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	118	863	19	26	0	0	0	0	0	0	0	0	118	863	19	26
+numeric_clustering	numeric_clustering	Clustering tool for numberic values								To update	http://scikit-learn.org/stable/index.html	Statistics	numeric_clustering	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	0.9	anaconda				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	391	486	5	11	0	0	0	0	0	0	0	0	391	486	5	11
+openms	AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.2.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	135	134	0	31121	108907	3369	5029	50	50	15	15	933	933	242	242	32104	109890	3626	5286
+pandas_rolling_window	pandas_rolling_window	Rolling window calculations								To update	https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html	Statistics	pandas_rolling_window	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	0.1	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	261	275	12	12	63	63	22	22	0	0	0	0	324	338	34	34
+paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	322	349	24	29	0	0	0	0	0	0	0	0	322	349	24	29
+partialr_square	partialRsq	Compute partial R square								To update		Statistics	partialr_square	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square	https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	55	142	8	42	0	0	0	0	55	142	8	42
+peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2807	3337	178	196	0	0	0	0	0	0	0	0	2807	3337	178	196
+pearson_correlation	Pearson_and_apos_Correlation1	Pearson and apos Correlation between any two numeric columns								To update		Statistics	pearson_correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	2	0	2
+perf	stats_perf_tool	suitable for boolean classification problems								To update	http://osmot.cs.cornell.edu/kddcup/software.html		stats_perf_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/perf	https://github.com/bgruening/galaxytools/tree/master/tools/perf	5.11.0	perf				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	773	773	60	60	495	495	72	72	246	246	17	17	1514	1514	149	149
+pg_tools	pg_dump, pg_import, pg_query	tool suite for dealing with Postgresql databases from Galaxy's history								To update	https://www.postgresql.org	Data Export, Data Source	pgtools	bgruening	https://github.com/bgruening/galaxytools/tools/pgtools	https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools		postgresql				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pgsnp2gd_snp	pgSnp2gd_snp	Convert from pgSnp to gd_snp								To update		Variant Analysis	pgsnp2gd_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pharmcat	pharmcat	Pharmacogenomics Clinical Annotation Tool								To update	https://pharmcat.org/	Variant Analysis	pharmcat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat						1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	109	109	29	29	250	250	84	84	0	0	0	0	359	359	113	113
+pileup_interval	pileup_interval	Pileup-to-Interval condenses pileup format into ranges of bases								To update		SAM	pileup_interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval	1.0.3	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	613	640	48	54	1381	7804	201	1552	756	815	22	30	2750	9259	271	1636
+pileup_parser	pileup_parser	Filter pileup on coverage and SNPs								To update	https://github.com/galaxyproject/tools-devteam/	SAM	pileup_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser	1.0.2	perl				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3639	3774	414	461	9754	52522	1247	4531	1893	2433	191	318	15286	58729	1852	5310
+pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	238	283	42	45	0	0	0	0	0	0	0	0	238	283	42	45
+piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1408	2068	94	119	0	0	0	0	0	0	0	0	1408	2068	94	119
+platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+plot_from_lda	plot_for_lda_output1	"Draw ROC plot on ""Perform LDA"" output"								To update		Graphics, Statistics	plot_from_lda	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda	https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda	1.0.1	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	65	77	19	25	153	886	38	343	142	155	8	10	360	1118	65	378
+plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.4	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1342	1472	184	197	902	902	156	156	630	630	24	24	2874	3004	364	377
+plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	408	664	91	122	627	627	118	118	605	605	26	26	1640	1896	235	266
+plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	764	879	213	237	304	304	95	95	193	193	26	26	1261	1376	334	358
+poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	112	120	16	16	4	562	1	140	320	347	7	8	436	1029	24	164
+predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+principal_component_analysis	pca1	Principal Component Analysis								To update		Statistics	principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis	1.0.2	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9788	10032	207	244	3072	8054	607	1488	0	0	0	0	12860	18086	814	1732
+protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	129	155	15	21	0	0	0	0	0	0	0	0	129	155	15	21
+protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	11743	12752	1137	1278	2	2	1	1	0	0	0	0	11745	12754	1138	1279
+protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	465	638	81	100	0	0	0	0	0	0	0	0	465	638	81	100
+quality_filter	qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.13.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	724	35	62	0	0	0	0	98	724	35	62
+rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	27113	27315	839	850	9089	9089	475	475	5452	5452	171	171	41654	41856	1485	1496
+rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	1.0		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	90	90	6	6	0	0	0	0	0	0	0	0	90	90	6	6
+rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	860	1257	88	98	0	0	0	0	0	0	0	0	860	1257	88	98
+rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	49	191	5	46	0	0	0	0	49	191	5	46
+reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+remove_beginning	Remove beginning1	Remove lines from the beginning of a file.								To update		Text Manipulation	remove_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	148572	169964	3525	3682	36694	113826	3910	8163	9713	10577	1475	1598	194979	294367	8910	13443
+remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	44	6	7	0	0	0	0	0	0	0	0	39	44	6	7
+repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.0.9_p2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5998	5998	810	810	7618	7618	803	803	3135	3135	292	292	16751	16751	1905	1905
+replaceColumn	replace_column_with_key_value_file	A tool to replace all column entries of a file given by values of a key-value file.								To update		Text Manipulation	replace_column_by_key_value_file	bgruening	https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn	https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn	0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	577184	577312	463	492	43900	44233	283	373	2190	2190	112	112	623274	623735	858	977
+rest_tool	pubchem_rest_tool	This tool fetches data from pubchem via the PubChem REST API.								To update	https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html	Data Source	pubchem_rest_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	661	681	78	78	0	0	0	0	0	0	0	0	661	681	78	78
+rmap	rmap_wrapper	RMAP for Solexa Short Reads Alignment								To update		Next Gen Mappers	rmap	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rmapq	rmapq_wrapper	RMAPQ for Solexa Short Reads Alignment with Quality Scores								To update		Next Gen Mappers	rmapq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	137	173	40	49	0	0	0	0	0	0	0	0	137	173	40	49
+rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	90	196	9	11	0	0	0	0	0	0	0	0	90	196	9	11
+rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	878	1363	29	35	0	0	0	0	0	0	0	0	878	1363	29	35
+rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1024	1077	18	21	0	0	0	0	0	0	0	0	1024	1077	18	21
+rnaformer	infer_rnaformer	RNAformer: RNA secondary structure prediction								To update	https://github.com/automl/RNAformer	RNA	rnaformer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	1.0.0	rnaformer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	6	6	0	0	0	0	0	0	0	0	26	26	6	6
+rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	33	10	14	0	0	0	0	0	0	0	0	23	33	10	14
+rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	65	89	14	18	0	0	0	0	0	0	0	0	65	89	14	18
+rnaz	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	1156	43309	93	121	0	0	0	0	0	0	0	0	1156	43309	93	121
+sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3628	4168	165	199	8399	14473	573	1147	2710	3000	151	175	14737	21641	889	1521
+salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	0	2	2	3	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	0	3	3	3	0	73085	77081	2243	2319	90634	122835	3402	4726	13371	15818	513	586	177090	215734	6158	7631
+sam2interval	sam2interval	Convert SAM to interval.								To update		SAM	sam2interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1155	1251	57	63	2264	18187	189	1748	525	590	10	17	3944	20028	256	1828
+sam_bitwise_flag_filter	sam_bw_filter	Filter SAM on bitwise flag values								To update		SAM	sam_bitwise_flag_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter	1.0.1	python				1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	96	278	12	26	3554	76029	450	6346	229	345	16	29	3879	76652	478	6401
+sambamba	sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort	Sambamba: process your BAM data faster!								Up-to-date	https://github.com/biod/sambamba	SAM	sambamba	bgruening	https://github.com/biod/sambamba	https://github.com/bgruening/galaxytools/tree/master/tools/sambamba	1.0.1	sambamba	1.0.1			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	297	297	51	51	0	0	0	0	0	0	0	0	297	297	51	51
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3421	3859	340	382	883	883	109	109	1138	1138	15	15	5442	5880	464	506
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6485	6549	720	726	10127	10127	1518	1518	238	238	37	37	16850	16914	2275	2281
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	52099	55110	4053	4497	73194	108684	6930	9936	14771	15714	1222	1419	140064	179508	12205	15852
+scatterplot	scatterplot_rpy	Scatterplot of two numeric columns								To update		Graphics, Statistics	scatterplot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot	1.0.3	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1234	1752	179	261	680	9223	231	1927	0	49	0	18	1914	11024	410	2206
+sed	sed_stream_editor	Manipulate your data with the sed command line tool.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/sed	Text Manipulation	sed_wrapper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sed	https://github.com/bgruening/galaxytools/tree/master/tools/sed	0.0.1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	281	2284	10	53	0	0	0	0	0	0	0	0	281	2284	10	53
+segemehl	segemehl	segemehl - short read mapping with gaps								To update	http://www.bioinf.uni-leipzig.de/Software/segemehl/	Next Gen Mappers	segemehl	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	0.2.0.4	segemehl	0.3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1095	1306	98	113	0	0	0	0	0	0	0	0	1095	1306	98	113
+selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	305	463	43	50	0	0	0	0	0	0	0	0	305	463	43	50
+seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1053	1186	137	195	680	680	206	206	0	0	0	0	1733	1866	343	401
+seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30300	32553	732	799	21726	31891	619	621	2886	2886	144	144	54912	67330	1495	1564
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4322	4714	180	205	0	0	0	0	0	0	0	0	4322	4714	180	205
+seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2196	3529	260	289	2196	3529	260	289
+short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+short_reads_figure_score	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	145	163	25	30	196	3360	23	711	0	0	0	0	341	3523	48	741
+short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	175	220	51	60	350	6657	85	1602	0	0	0	0	525	6877	136	1662
+show_beginning	Show beginning1	Select lines from the beginning of a file.								To update		Text Manipulation	show_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	27232	36366	2184	2789	16648	84460	4191	18767	2785	3276	373	452	46665	124102	6748	22008
+show_tail	Show tail1	Select lines from the end of a file.								To update		Text Manipulation	show_tail	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	1620	2660	378	589	10551	24579	682	1851	284	398	67	83	12455	27637	1127	2523
+sicer	peakcalling_sicer	Statistical approach for the Identification of ChIP-Enriched Regions								Up-to-date	https://home.gwu.edu/~wpeng/Software.htm	ChIP-seq	sicer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer	1.1	SICER	1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	276	379	30	42	972	9053	146	1008	644	689	5	7	1892	10121	181	1057
+sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	0	30	14	31	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	0	82169	116810	2402	2666	18101	18101	2375	2375	17549	17549	321	321	117819	152460	5098	5362
+snpfreq	hgv_snpFreq	snpFreq significant SNPs in case-control data								To update		Variant Analysis, Statistics	snpfreq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	44	10	12	307	649	68	181	227	260	16	23	569	953	94	216
+sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19865	21034	1047	1126	3141	3141	328	328	3304	3304	189	189	26310	27479	1564	1643
+split_file_on_column	tp_split_on_column	Split a file on a specific column.								To update		Text Manipulation	split_file_on_column	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	0.6	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5995	6261	408	453	2150	2150	311	311	26	26	2	2	8171	8437	721	766
+split_file_to_collection	split_file_to_collection	Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	Text Manipulation	split_file_to_collection	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	0.5.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	16415	16623	968	984	9133	9133	672	672	4140	4140	148	148	29688	29896	1788	1804
+split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	3	200	384	31	66	200	397	31	69
+splitfasta	rbc_splitfasta	Split a multi-sequence fasta file into files containing single sequences								To update		Text Manipulation	splitfasta	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	0.4.0	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1772	1811	278	294	3012	3012	564	564	0	0	0	0	4784	4823	842	858
+sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	214	225	17	18	0	0	0	0	0	0	0	0	214	225	17	18
+statistics	bg_statistical_hypothesis_testing	Tool for computing statistical tests.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	Statistics	bg_statistical_hypothesis_testing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	0.3	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	169	346	46	61	0	0	0	0	0	0	0	0	169	346	46	61
+stress_ng	stress_ng	stress test a computer system in various selectable ways								To update		Web Services	stress_ng	bgruening-util	https://github.com/ColinIanKing/stress-ng	https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng	0.12.04	stress-ng				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	62	3	3	0	0	0	0	0	0	0	0	62	62	3	3
+substitution_rates	subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	121	3901	34	747	105	114	4	4	226	4015	38	751
+substitutions	substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	93	901	13	84	0	0	0	0	93	901	13	84
+subtract	gops_subtract_1	Subtract the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	566512	567199	410	470	49985	184650	1473	7631	20648	20897	155	188	637145	772746	2038	8289
+subtract_query	subtract_query1	Subtract Whole Dataset from another dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract_query	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query	0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1178	1450	124	141	3169	40539	636	3435	799	950	26	38	5146	42939	786	3614
+t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	411	472	68	90	102	7952	13	1240	0	0	0	0	513	8424	81	1330
+t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	927	959	65	78	130	7194	18	1143	0	0	0	0	1057	8153	83	1221
+t_test_two_samples	t_test_two_samples	T Test for Two Samples								To update		Statistics	t_test_two_samples	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples	https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	141	215	20	31	520	1166	79	274	1025	1118	11	12	1686	2499	110	317
+table_annovar	table_annovar	Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered								To update		Variant Analysis	table_annovar	devteam	Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar	https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar	0.2	annovar				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16526	64515	2803	7456	0	0	0	0	16526	64515	2803	7456
+tables_arithmetic_operations	tables_arithmetic_operations	Arithmetic Operations on tables								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	tables_arithmetic_operations	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations	1.0.0	perl				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2188	2220	33	38	0	0	0	0	0	0	0	0	2188	2220	33	38
+tabular_to_fasta	tab2fasta	Tabular-to-FASTA								To update		Convert Formats	tabular_to_fasta	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta	1.1.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	329032	333057	1489	1702	79033	215770	2441	8587	27876	33727	296	360	435941	582554	4226	10649
+tapscan	tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	19	6	6	0	0	0	0	0	0	0	0	19	19	6	6
+targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	827	838	89	92	114	114	41	41	900	900	29	29	1841	1852	159	162
+text_processing	tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq	High performance text processing tools using the GNU coreutils, sed, awk and friends.								To update	https://www.gnu.org/software/	Text Manipulation	text_processing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	9.3	coreutils	8.25			20	20	20	0	20	20	20	0	0	0	0	0	0	0	0	0	0	19	1	19	0	0	19	0	0	0	20	0	0	0	0	0	0	19	19	19	0	3898014	4015573	37698	42095	648268	915282	47636	69828	103365	105214	7778	7953	4649647	5036069	93112	119876
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	51	51	0	0	0	0	0	0	0	0	547	547	51	51
+tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	8	8	0	0	0	0	0	0	0	0	15	15	8	8
+tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	445	445	25	25	71	71	32	32	0	0	0	0	516	516	57	57
+tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	158	66524	28	7228	0	0	0	0	158	66525	28	7229
+tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	15496	26623	1076	1664	83063	343017	8372	27829	5388	14057	508	1012	103947	383697	9956	30505
+tophat_fusion_post	tophat_fusion_post	Wrapper for Tophat-Fusion post step								To update		Transcriptomics	tophat_fusion_post	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post	0.1	blast+				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	220	242	41	46	6	814	2	191	100	120	8	12	326	1176	51	249
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	229489	275008	5733	6500	228708	324716	11708	16638	22644	23869	1439	1527	480841	623593	18880	24665
+trimmer	trimmer	Trim leading or trailing characters.								To update		Text Manipulation	trimmer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer	0.0.1					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	5304	7438	447	512	15698	108672	658	2946	266	822	53	81	21268	116932	1158	3539
+trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	4361	4601	741	807	0	0	0	0	2469	2469	190	190	6830	7070	931	997
+ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	373	463	134	151	2249	18611	638	4080	0	0	0	0	2622	19074	772	4231
+uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.6	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2117	2725	341	412	3111	5779	594	1011	806	806	50	50	6034	9310	985	1473
+varscan_version_2	varscan	VarScan wrapper								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan_version_2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2	2.4.2	varscan	2.4.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5058	6139	606	699	17232	53268	2965	5686	2298	2656	424	482	24588	62063	3995	6867
+vcf2pgsnp	vcf2pgSnp	VCF to pgSnp								To update		Variant Analysis	vcf2pgsnp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	191	221	57	65	1399	2700	209	584	0	0	0	0	1590	2921	266	649
+vcf_annotate	vcf_annotate	Annotate a VCF file (dbSNP, hapmap)								To update		Variant Analysis	vcf_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	1	0	1	263	340	31	54	263	342	31	56
+vcf_extract	vcf_extract	Extract reads from a specified region								To update		Variant Analysis	vcf_extract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	513	569	6	9	513	569	6	9
+vcf_filter	vcf_filter	Filter a VCF file								To update		Variant Analysis	vcf_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	400	455	129	140	0	0	0	0	238	606	19	56	638	1061	148	196
+vcf_intersect	vcf_intersect	Generate the intersection of two VCF files								To update		Variant Analysis	vcf_intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	3	0	0	0	0	335	463	19	28	335	482	19	31
+vcftools_annotate	vcftools_annotate	Annotate VCF using custom/user-defined annotations								To update	https://vcftools.github.io/	Variant Analysis	vcftools_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate	0.1	echo				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	155	192	81	90	1853	3943	581	1280	144	156	13	16	2152	4291	675	1386
+vcftools_compare	vcftools_compare	Compare VCF files to get overlap and uniqueness statistics								To update	https://vcftools.github.io/	Variant Analysis	vcftools_compare	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	440	594	127	142	0	0	0	0	0	16	0	12	440	610	127	154
+vcftools_consensus	vcftools_consensus	Apply VCF variants to a fasta file to create consensus sequence								To update	https://vcftools.github.io/	Variant Analysis	vcftools_consensus	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus	0.1.11	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vcftools_isec	vcftools_isec	Intersect multiple VCF datasets								To update	https://vcftools.github.io/	Variant Analysis	vcftools_isec	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec	0.1.1	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	379	537	104	118	0	1	0	1	39	496	28	48	418	1034	132	167
+vcftools_merge	vcftools_merge	Merge multiple VCF datasets into a single dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge	0.1.11	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	817	1084	244	273	0	0	0	0	93	448	44	60	910	1532	288	333
+vcftools_slice	vcftools_slice	Subset VCF dataset by genomic regions								To update	https://vcftools.github.io/	Variant Analysis	vcftools_slice	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice	0.1	echo				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	410	423	56	60	6261	8115	133	362	127	157	10	19	6798	8695	199	441
+vcftools_subset	vcftools_subset	Select samples from a VCF dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_subset	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	134	142	46	49	0	0	0	0	120	142	12	19	254	284	58	68
+venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4519	5476	667	730	9858	18420	986	2010	0	0	0	0	14377	23896	1653	2740
+vienna_rna	viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	0	3197	8107	344	415	0	0	0	0	0	0	0	0	3197	8107	344	415
+vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+weightedaverage	wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	227	2307	17	75	0	0	0	0	227	2307	17	75
+whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	96	96	13	13	0	0	0	0	0	0	0	0	96	96	13	13
+windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	2	171	3961	34	328	0	0	0	0	171	3972	34	330
+woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	1	1	0	0	0	0	0	0	0	0	31	31	1	1
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1619	1715	337	376	0	0	0	0	0	0	0	0	1619	1715	337	376
+xy_plot	XY_Plot_1	Plotting tool for multiple series and graph types								To update		Graphics, Statistics	xy_plot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot	1.0.2	r-base				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4490	6169	768	889	6120	15516	1921	3653	2033	2212	556	590	12643	23897	3245	5132
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	43	43	20	20	0	0	0	0	0	0	0	0	43	43	20	20
+abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	619817	622353	4097	4130	320454	320454	2915	2915	496156	503743	2012	2227	1436427	1446550	9024	9272
+abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1139	1139	109	109	0	0	0	0	0	0	0	0	1139	1139	109	109
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5543	5543	1042	1042	1301	1305	413	414	2030	2030	299	299	8874	8878	1754	1755
+adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	348	348	62	62	0	0	0	0	0	0	0	0	348	348	62	62
+add_input_name_as_column	addName	Add input name as column on an existing tabular file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	Text Manipulation	add_input_name_as_column	mvdbeek	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	76834	86002	227	246	20174	20953	312	395	11	11	2	2	97019	106966	541	643
+aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	200	200	77	77	83	83	39	39	1747	1747	44	44	2030	2030	160	160
+aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	262	36	36	0	0	0	0	0	0	0	0	262	262	36	36
+allegro	allegro	Linkage and haplotype analysis from deCODE	allegro	allegro		Allegro	It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	To update	http://www.decode.com/software/	Variant Analysis	allegro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro	@VER@.0	allegro	3	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	81	81	17	17	0	0	0	0	0	0	0	0	81	81	17	17
+ampvis2	ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.9			Analysis, Visualisation	Biodiversity	0	0	19	0	0	0	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	1213	1213	155	155	0	0	0	0	0	0	0	0	1213	1213	155	155
+amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5734	5734	334	334	1035	1035	106	106	0	0	0	0	6769	6769	440	440
+ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	7	7	0	0	0	0	0	0	0	0	26	26	7	7
+anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	43047	43139	1826	1827	17240	17240	878	878	9309	9309	298	298	69596	69688	3002	3003
+annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	29266	30655	2849	2973	59299	66180	5917	6355	5644	5644	1049	1049	94209	102479	9815	10377
+argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3670	3670	71	71	3	3	2	2	234	234	10	10	3907	3907	83	83
+art	art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/	Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	Conversion	Bioinformatics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	140	140	9	9	0	0	0	0	0	0	0	0	140	140	9	9
+artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	9021	9021	238	238	0	0	0	0	0	0	0	0	9021	9021	238	238
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+astral	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees								Up-to-date	https://github.com/smirarab/ASTRAL	Phylogenetics	astral	iuc	https://github.com/usegalaxy-be/galaxytools/tree/main/astral	https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral	5.7.8	astral-tree	5.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	151	151	5	5	151	151	5	5
+augustus	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	12890	13988	1826	1988	14901	14901	2633	2633	6187	6187	511	511	33978	35076	4970	5132
+b2btools	b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.7	Protein disorder prediction, Protein secondary structure prediction		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	369	369	19	19	0	0	0	0	0	0	0	0	369	369	19	19
+bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11117	11117	534	534	19	19	1	1	9601	9601	167	167	20737	20737	702	702
+bam_to_scidx	bam_to_scidx	Contains a tool that converts a BAM file to an ScIdx file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx	Convert Formats	bam_to_scidx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	83	131	15	20	329	785	50	210	0	0	0	0	412	916	65	230
+bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	14693	15620	653	721	61872	101400	1656	5678	39	39	3	3	76604	117059	2312	6402
+bamtools_filter	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115954	124795	2994	3180	95433	142254	6712	10660	5793	5793	497	497	217180	272842	10203	14337
+bamtools_split	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	9073	9073	401	401	2746	2746	224	224	103	103	10	10	11922	11922	635	635
+bamutil	bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	45	45	20	20	69	69	21	21	258	258	1	1	372	372	42	42
+bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	55392	56095	4951	5035	47603	47603	4916	4916	18089	18089	3121	3121	121084	121787	12988	13072
+barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	111	111	8	8	29	29	10	10	21	21	4	4	161	161	22	22
+barrnap	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update	https://github.com/tseemann/barrnap	Sequence Analysis	barrnap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	Gene prediction	Genomics, Model organisms, Model organisms	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6041	6041	316	316	0	0	0	0	6723	7273	240	322	12764	13314	556	638
+basil	basil	Breakpoint detection, including large insertions								Up-to-date	https://github.com/seqan/anise_basil	Variant Analysis	basil	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil	1.2.0	anise_basil	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	306	311	82	83	467	467	99	99	0	0	0	0	773	778	181	182
+bax2bam	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	208	208	26	26	210	210	30	30	0	0	0	0	418	418	56	56
+bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	90	90	28	28	0	0	0	0	0	0	0	0	90	90	28	28
+bbgbigwig	bbgtobigwig	Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://www.encodeproject.org/software/bedgraphtobigwig/	Convert Formats	bbgbigwig	iuc	https://www.encodeproject.org/software/bedgraphtobigwig/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig	0.1	ucsc-bedgraphtobigwig	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	42	42	7	7	175	175	26	26	0	0	0	0	217	217	33	33
+bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.09	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	4	0	0	11989	11989	768	768	4458	4458	652	652	2507	2507	80	80	18954	18954	1500	1500
+bcftools	bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@	BCFtools toolkit wrappers	bcftools	bcftools		BCFtools	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.	Data handling, Variant calling	Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment	To update	https://samtools.github.io/bcftools/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools	1.15.1	bcftools	1.21	Data handling, Variant calling	DNA polymorphism, GWAS study, Genotyping experiment	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	7	0	2352	3092	234	265	0	0	0	0	0	0	0	0	2352	3092	234	265
+beacon2	beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff	beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://github.com/EGA-archive/beacon2-ri-tools/tree/main	Variant Analysis	beacon2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2	2.0.0	beacon2-ri-tools	2.0.0	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	33	33	9	9	0	0	0	0	0	0	0	0	33	33	9	9
+beacon2-import	beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence	Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants.	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://pypi.org/project/beacon2-import/	Variant Analysis	Beacon2_Import	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import	2.2.4	beacon2-import	2.2.4	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22	22	7	7	0	0	0	0	0	0	0	0	22	22	7	7
+beagle	beagle	Beagle is a program for phasing and imputing missing genotypes.								To update	https://faculty.washington.edu/browning/beagle/beagle.html	Variant Analysis	beagle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle	5.2_21Apr21.304	beagle	5.4_22Jul22.46e			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	88	88	28	28	0	0	0	0	0	0	0	0	88	88	28	28
+bedops	bedops-sort-bed	BEDOPS: high-performance genomic feature operations								Up-to-date	https://bedops.readthedocs.io/en/latest/	Genomic Interval Operations	bedops_sortbed	iuc	https://bedops.readthedocs.io/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops	2.4.41	bedops	2.4.41			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	93	93	36	36	181	181	62	62	0	0	0	0	274	274	98	98
+bedtools	bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed	bedtools is a powerful toolset for genome arithmetic	bedtools	bedtools		BEDTools	BEDTools is an extensive suite of utilities for comparing genomic features in BED format.	Mapping	Genomics	Up-to-date	https://github.com/arq5x/bedtools2	Genomic Interval Operations, Text Manipulation	bedtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools	2.31.1	bedtools	2.31.1	Mapping	Genomics	37	37	37	0	37	37	37	0	0	0	0	0	0	0	0	0	0	37	6	37	0	0	37	0	0	0	37	0	0	0	0	0	0	37	37	37	0	916111	962278	13235	14525	407944	647621	25849	41751	84008	89233	2486	2832	1408063	1699132	41570	59108
+bellerophon	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1611	1611	262	262	763	763	67	67	543	543	30	30	2917	2917	359	359
+berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	617	617	63	63	617	617	63	63
+bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	544	544	20	20	0	0	0	0	0	0	0	0	544	544	20	20
+bigwig_outlier_bed	bigwig_outlier_bed	pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files	bigtools	bigtools		bigtools	Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.			To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	Sequence Analysis	bigwig_outlier_bed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed	0.2.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	218	218	5	5	0	0	0	0	0	0	0	0	218	218	5	5
+binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	126	126	42	42	0	0	0	0	0	0	0	0	126	126	42	42
+bioext	bioext_bam2msa, bioext_bealign	A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!								Up-to-date	https://pypi.python.org/pypi/biopython-extensions/	Next Gen Mappers		iuc	https://github.com/davebx/bioext-gx/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext	0.21.9	python-bioext	0.21.9			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	17413	17413	822	822	15349	15349	2020	2020	2	2	1	1	32764	32764	2843	2843
+bioinformatics_cafe	fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1137	1137	97	97	1029	1029	71	71	0	0	0	0	2166	2166	168	168
+biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12725	12725	297	297	2851	5049	450	638	2171	2371	214	239	17747	20145	961	1174
+bioperl	bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	Data handling, Service invocation	Genomics, Software engineering	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7738	7931	478	508	8301	8301	849	849	1369	1369	154	154	17408	17601	1481	1511
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6243	6243	375	375	0	0	0	0	6243	6243	375	375
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	3	1	1	0	0	0	0	0	0	0	0	3	3	1	1
+blast	magicblast	Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome								Up-to-date	https://ncbi.github.io/magicblast/	Next Gen Mappers	magicblast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast	1.7.0	magicblast	1.7.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	738	738	151	151	0	0	0	0	2	2	1	1	740	740	152	152
+blastxml_to_gapped_gff3	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	585	585	102	102	172	172	63	63	135	135	16	16	892	892	181	181
+bowtie2	bowtie2	Bowtie2: Fast and sensitive read alignment	bowtie2	bowtie2		Bowtie 2	Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.	Read mapping	Mapping, Genomics, Mapping	To update	http://bowtie-bio.sourceforge.net/bowtie2	Next Gen Mappers	bowtie2	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2	2.5.3	bowtie2	2.5.4	Read mapping	Mapping, Genomics, Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	1	1	1	0	397893	427447	12133	13176	577209	903193	33086	52020	60105	67495	3779	4271	1035207	1398135	48998	69467
+bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	51378	51378	775	775	3298	3298	160	160	1660	1660	63	63	56336	56336	998	998
+breseq	breseq	Predicts mutations in microbial genomes	breseq	breseq		breseq	Runs Breseq software on a set of fastq files.	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	To update	https://github.com/barricklab/breseq	Variant Analysis	breseq	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq	0.35.5	breseq	0.39.0	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	2976	2976	98	98	0	0	0	0	884	884	70	70	3860	3860	168	168
+brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template	brew3r.r	brew3r.r		BREW3R.r	This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.	Genome annotation	Transcriptomics, Genomics	To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2			Genome annotation	Transcriptomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6	6	2	2	0	0	0	0	7	7	3	3
+busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	102717	103051	3877	3926	34251	34251	3506	3506	33192	34369	2439	2525	170160	171671	9822	9957
+bwa	bwa_mem, bwa	Wrapper for bwa mem, aln, sampe, and samse	bwa	bwa		BWA	Fast, accurate, memory-efficient aligner for short and long sequencing reads	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	Up-to-date	http://bio-bwa.sourceforge.net/	Next Gen Mappers	bwa	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa	0.7.18	bwa	0.7.18	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	2	0	0	0	2	0	0	0	0	0	0	2	2	2	2	976935	1017671	13526	14401	474702	681286	32627	47624	79802	87191	4219	4954	1531439	1786148	50372	66979
+bwa_mem2	bwa_mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.	bwa-mem2	bwa-mem2		Bwa-mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,  dataset and the running machine.	Sequence alignment	Mapping	Up-to-date	https://github.com/bwa-mem2/bwa-mem2	Next Gen Mappers	bwa_mem2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2	2.2.1	bwa-mem2	2.2.1	Sequence alignment	Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	56619	56619	2324	2324	36631	36631	2808	2808	18121	18121	713	713	111371	111371	5845	5845
+bwameth	bwameth	Fast and accurate alignment of BS-seq reads								Up-to-date	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.7	bwameth	0.2.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7970	11724	643	826	5524	5524	611	611	1242	1242	114	114	14736	18490	1368	1551
+cactus	cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			Multiple sequence alignment, Genome alignment	Genomics, Sequence assembly, Mapping, Phylogenetics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	299	299	61	61	0	0	0	0	1339	1339	95	95	1638	1638	156	156
+calculate_contrast_threshold	calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+calculate_numeric_param	calculate_numeric_param	Calculate a numeric parameter value using integer and float values.								To update		Text Manipulation	calculate_numeric_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param	0.1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1393	1393	10	10	0	0	0	0	0	0	0	0	1393	1393	10	10
+cami_amber	biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert	Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments								Up-to-date	https://github.com/CAMI-challenge/AMBER	Metagenomics	cami_amber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber	2.0.7	cami-amber	2.0.7			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	195	195	4	4	0	0	0	0	0	0	0	0	195	195	4	4
+cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3835	3835	597	597	1359	1359	467	467	646	646	98	98	5840	5840	1162	1162
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10414	10414	510	510	2	2	1	1	2	2	1	1	10418	10418	512	512
+cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	225	225	32	32	271	271	61	61	0	0	0	0	496	496	93	93
+charts	charts	Enables advanced visualization options in Galaxy Charts								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3383	4001	1576	1822	7870	13727	3823	6880	249	350	108	145	11502	18078	5507	8847
+checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	7500	7500	930	930	0	0	0	0	0	0	0	0	7500	7500	930	930
+cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	207	207	1	1	0	0	0	0	0	0	0	0	207	207	1	1
+chewbbaca	chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema	BSR-Based Allele Calling Algorithm								To update	https://github.com/B-UMMI/chewBBACA/tree/master	Variant Analysis	chewbbaca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca		chewbbaca	3.3.10			0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	727	727	76	76	0	0	0	0	0	0	0	0	727	727	76	76
+chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	16542	16542	287	287	1061	1061	102	102	27	27	5	5	17630	17630	394	394
+chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	6	6	0	0	0	0	14	14	6	6
+chromeister	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2696	2696	398	398	0	0	0	0	1235	1235	186	186	3931	3931	584	584
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	524	524	32	32	0	0	0	0	0	0	0	0	524	524	32	32
+circos	circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile	Build Circos Plots in Galaxy	galactic_circos	galactic_circos		Galactic Circos	Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.	Sequence visualisation		To update	http://circos.ca/	Graphics	circos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos	0.69.8	circos	0.69.9	Sequence visualisation		11	11	11	0	11	11	11	0	0	0	0	0	0	0	0	0	0	0	11	11	0	0	0	0	0	0	11	0	0	0	0	0	0	11	11	11	0	26265	26265	2483	2483	31332	31332	3535	3535	26359	26359	999	999	83956	83956	7017	7017
+cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	21	4	4	9	9	5	5	18	18	1	1	48	48	10	10
+clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3388	3388	187	187	1	1	1	1	1	1	1	1	3390	3390	189	189
+clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	79867	80817	1675	1785	49493	87884	3703	7380	8797	9713	670	728	138157	178414	6048	9893
+clustering_from_distmat	clustering_from_distmat	Distance matrix-based hierarchical clustering using SciPy								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	Statistics	clustering_from_distmat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat	1.1.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	5	5	0	0	0	0	0	0	0	0	12	12	5	5
+cnv-phenopacket	cnv_phenopacket	cnv-phenopacket Converts TSV metadata file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv_phenopacket	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket	1.0.2	cnv-phenopacket				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2
+cnv-vcf2json	cnv_vcf2json	cnv-vcf2json Converts structural variants VCF file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv-vcf2json	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json	1.1.0	cnv-vcf2json				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5
+cnvkit	cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target	detecting copy number variants and alterations genome-wide from high-throughput sequencing	cnvkit	cnvkit		CNVkit	CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.	Variant calling	DNA structural variation	Up-to-date	https://github.com/etal/cnvkit	Variant Analysis	cnvkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit	0.9.11	cnvkit	0.9.11	Variant calling		0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	618	618	177	177	0	0	0	0	0	0	0	0	618	618	177	177
+codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	61197	61220	64	65	0	0	0	0	0	0	0	0	61197	61220	64	65
+cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2758	2758	22	22	20	20	10	10	0	0	0	0	2778	2778	32	32
+colabfold	colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6771	6771	50	50	0	0	0	0	6771	6771	50	50
+colibread	commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								Up-to-date	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14	commet	24.7.14			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	273	273	40	40	0	0	0	0	0	0	0	0	273	273	40	40
+collection_column_join	collection_column_join	Column Join on Collections								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	Text Manipulation	collection_column_join	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join	0.0.3	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	23979	25337	3827	4011	21671	25163	4645	5045	2939	3036	688	701	48589	53536	9160	9757
+collection_element_identifiers	collection_element_identifiers	Extract element identifiers of a collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	Text Manipulation	collection_element_identifiers	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers	0.0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6905	7102	1620	1630	7761	7761	1897	1897	1157	1157	243	243	15823	16020	3760	3770
+column_maker	Add_a_column1	Compute an expression on every row								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	Text Manipulation	column_maker	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker	2.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2940752	3907183	5422	6121	263254	737503	6095	13728	96478	97667	884	974	3300484	4742353	12401	20823
+column_order_header_sort	column_order_header_sort	Sort Column Order by heading								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	Text Manipulation	column_order_header_sort	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort	0.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3735	3891	268	297	1923	1923	381	381	0	0	0	0	5658	5814	649	678
+column_remove_by_header	column_remove_by_header	Remove columns by header								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	Text Manipulation	column_remove_by_header	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header	1.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8331	8917	613	662	5206	5206	716	716	1976	1976	27	27	15513	16099	1356	1405
+compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	266	266	39	39	28	28	15	15	0	0	0	0	294	294	54	54
+compose_text_param	compose_text_param	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	compose_text_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param	0.1.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	0	0	0	45827	45831	689	691	7721	7721	303	303	1481	1481	121	121	55029	55033	1113	1115
+compress_file	compress_file	Compress files.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	Text Manipulation	compress_file	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file	0.1.0	gzip				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6343	6343	290	290	3674	3674	286	286	11832	11832	59	59	21849	21849	635	635
+concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	2105	2105	155	155	0	0	0	0	0	0	0	0	2105	2105	155	155
+cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+coverage_report	CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1081	1081	151	151	0	0	0	0	0	0	0	0	1081	1081	151	151
+crispr_studio	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	Visualisation	Sequence analysis, Genomics, Data visualisation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1052	1053	75	76	0	0	0	0	0	0	0	0	1052	1053	75	76
+crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	276	390	61	76	131	131	42	42	0	0	0	0	407	521	103	118
+crossmap	crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig	CrossMap converts genome coordinates or annotation files between genome assemblies								Up-to-date	http://crossmap.sourceforge.net/	Convert Formats, Genomic Interval Operations	crossmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap	0.7.0	crossmap	0.7.0			5	0	6	0	5	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	5	6	5	0	2182	2182	331	331	5251	5251	903	903	0	0	0	0	7433	7433	1234	1234
+cuffcompare	cuffcompare	Galaxy wrappers for the Cuffcompare tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffcompare	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1	1	0	768	1199	171	300	2205	24981	754	5750	251	493	46	98	3224	26673	971	6148
+cuffdiff	cuffdiff	Galaxy wrappers for the Cuffdiff tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffdiff	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff	2.2.1	cufflinks	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	4176	6065	564	725	24284	117007	4952	20249	971	4231	193	616	29431	127303	5709	21590
+cufflinks	cufflinks	Galaxy wrappers for the Cufflinks tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cufflinks	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	1	1	1	0	26122	33320	870	1213	70653	349091	6984	27076	3963	10315	440	836	100738	392726	8294	29125
+cuffmerge	cuffmerge	Galaxy wrappers for the Cuffmerge tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffmerge	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1	1	0	2406	3448	351	637	20978	67769	3641	13764	1209	3057	227	573	24593	74274	4219	14974
+cuffnorm	cuffnorm	The Cuffnorm tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffnorm	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	374	701	81	114	1032	13499	273	1166	262	322	53	70	1668	14522	407	1350
+cuffquant	cuffquant	The Cuffquant tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffquant	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	408	732	54	71	1964	15883	267	1310	308	422	26	46	2680	17037	347	1427
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	259754	272370	11716	12601	334550	362356	18618	20162	64377	65986	3507	3627	658681	700712	33841	36390
+cutesv	cutesv	Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.	cuteSV	cuteSV		cuteSV	Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis	Split read mapping, Genotyping, Structural variation detection	DNA structural variation, Sequencing, Computer science	To update	https://github.com/tjiangHIT/cuteSV	Variant Analysis	cutesv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv	1.0.8	cutesv	2.1.1	Split read mapping, Genotyping, Structural variation detection	Sequencing, Computer science	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	260	260	43	43	0	0	0	0	119	119	8	8	379	379	51	51
+cwpair2	cwpair2	Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.								To update		ChIP-seq	cwpair2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2	1.1.1	matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	173	280	41	83	0	0	0	0	173	280	41	83
+dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	0	10	10	10	0	92240	92240	2716	2716	179176	179176	5317	5317	12478	12478	394	394	283894	283894	8427	8427
+das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1323	1323	47	47	0	0	0	0	0	0	0	0	1323	1323	47	47
+data_source_iris_tcga	data_source_iris_tcga	IRIS-TCGA Data source tool								To update		Data Source	data_source_iris_tcga	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga	https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+datamash	datamash_ops, datamash_reverse, datamash_transpose	GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.								To update	https://www.gnu.org/software/datamash/	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash	1.8	datamash	1.1.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	1	3	3	0	0	1	0	0	0	1	0	0	0	0	0	0	3	3	3	0	748586	760943	7066	7307	98089	112831	5306	6131	16235	16317	2161	2171	862910	890091	14533	15609
+decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	121	121	28	28	0	0	0	0	0	0	0	0	121	121	28	28
+deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	558	558	7	7	0	0	0	0	0	0	0	0	558	558	7	7
+deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	37	37	0	0	0	0	0	0	0	0	65	65	37	37
+deepvariant	deepvariant	DeepVariant is a deep learning-based variant caller								To update	https://github.com/google/deepvariant	Variant Analysis	deepvariant	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant	1.5.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2561	2561	325	325	2916	2916	460	460	0	0	0	0	5477	5477	785	785
+deg_annotate	deg_annotate	Annotate DESeq2/DEXSeq output tables								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	Transcriptomics	deg_annotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate	1.1.0	bedtools	2.31.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22774	23146	4084	4155	33972	33972	5372	5372	4236	4236	846	846	60982	61354	10302	10373
+delly	delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge	Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.	delly2	delly2		Delly2	Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.	Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis	DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases	To update	https://github.com/dellytools/delly	Variant Analysis	delly	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly	https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly	0.9.1	delly	1.2.9	Indel detection, Structural variation detection, Genotyping	Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	6	0	0	0	0	0	0	6	6	0	0	1451	1451	288	288	0	0	0	0	0	0	0	0	1451	1451	288	288
+deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	97434	109474	11355	12514	183905	246475	24951	31957	18551	20166	2647	2905	299890	376115	38953	47376
+dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	14874	16927	533	837	18475	28854	1403	2568	3854	4271	141	163	37203	50052	2077	3568
+diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	0	3	3	0	61376	61746	1847	1895	23164	28729	1140	1556	63034	63034	522	522	147574	153509	3509	3973
+diffbind	diffbind	Diffbind provides functions for  processing  ChIP-Seq  data.	diffbind	diffbind		DiffBind	Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.	Differential binding analysis	ChIP-seq	Up-to-date	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind	3.12.0	bioconductor-diffbind	3.12.0	Differential binding analysis	ChIP-seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7092	7663	606	652	14367	18624	1360	1916	1477	1640	69	84	22936	27927	2035	2652
+dimet	dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@	DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.								Up-to-date	https://github.com/cbib/DIMet	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet	0.2.4	dimet	0.2.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	358	406	124	139	1361	1361	384	384	0	0	0	0	1719	1767	508	523
+dnabot	dnabot	DNA assembly using BASIC on OpenTrons								To update	https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT	Synthetic Biology	dnabot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot	3.1.0	dnabot				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dnaweaver	dnaweaver	Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.								Up-to-date	https://github.com/Edinburgh-Genome-Foundry/DnaWeaver	Synthetic Biology	dnaweaver	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver	1.0.2	dnaweaver_synbiocad	1.0.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	7358	7358	88	88	0	0	0	0	0	0	0	0	7358	7358	88	88
+drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	916	916	113	113	0	0	0	0	0	0	0	0	916	916	113	113
+dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4413	4442	430	431	4403	4403	255	255	1816	1816	33	33	10632	10661	718	719
+ebi_tools	ebi_search_rest_results	Tools to query and download data from several EMBL-EBI databases								To update	http://www.ebi.ac.uk/services/all	Web Services, Data Source	ebi_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools	0.1.1	six				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	276	406	133	163	1421	1421	547	547	0	0	0	0	1697	1827	680	710
+edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	19294	20905	2423	2618	48876	58723	6341	7527	8010	8705	846	892	76180	88333	9610	11037
+egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2809	3060	371	402	5179	5179	759	759	1931	1931	226	226	9919	10170	1356	1387
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	0	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	107	107	107	0	143762	148864	4481	5039	151989	296028	13224	31140	24955	27001	2397	2705	320706	471893	20102	38884
+ena_upload	ena_upload	Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 								To update	https://github.com/usegalaxy-eu/ena-upload-cli	Data Export	ena_upload	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload	0.7.3	ena-upload-cli	0.7.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	366	366	41	41	0	0	0	0	1302	1302	14	14	1668	1668	55	55
+enasearch	enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data	A Python library for interacting with ENA's API								To update	https://github.com/bebatut/enasearch	Data Source	enasearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch		enasearch	0.2.2			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	1989	2302	367	453	0	0	0	0	0	0	0	0	1989	2302	367	453
+ensembl_vep	ensembl_vep	Ensembl VEP: Annotate VCFs with variant effect predictions								Up-to-date	https://github.com/Ensembl/ensembl-vep	Variant Analysis	ensembl_vep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep	112.0	ensembl-vep	112.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3051	3051	171	171	0	0	0	0	0	0	0	0	3051	3051	171	171
+episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	880	880	80	80	221	221	37	37	49	49	3	3	1150	1150	120	120
+evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+exomedepth	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	517	517	61	61	2995	2995	184	184	0	0	0	0	3512	3512	245	245
+exonerate	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1030	1072	185	188	1058	1058	189	189	922	922	35	35	3010	3052	409	412
+export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5396	5938	580	607	628	628	168	168	519	519	107	107	6543	7085	855	882
+extract_genomic_dna	Extract genomic DNA 1	Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.								To update		Genomic Interval Operations	extract_genomic_dna	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna	https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna	3.0.3+galaxy2	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	1	0	0	0	1	1	1	1	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	9409	12735	813	923	20180	259099	2072	11791	168	611	20	63	29757	272445	2905	12777
+falco	falco	A high throughput sequence QC analysis tool	falco	falco		Falco	A high-speed FastQC emulation for quality control of sequencing data.	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	Up-to-date	https://github.com/smithlabcode/falco/	Sequence Analysis	falco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco	https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco	1.2.4	falco	1.2.4	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4298	4298	34	34	0	0	0	0	0	0	0	0	4298	4298	34	34
+fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	601	601	128	128	1165	1165	232	232	0	0	0	0	1766	1766	360	360
+fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	469	ucsc-fasplit	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3278	3361	460	478	6144	6144	595	595	1139	1139	183	183	10561	10644	1238	1256
+fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5191	5367	104	130	5191	5367	104	130
+fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	1	5235	5486	237	288	4060	25609	480	2039	816	1093	73	89	10111	32188	790	2416
+fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	497	808	71	108	2249	5479	216	703	415	437	18	20	3161	6724	305	831
+fasta_nucleotide_color_plot	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	164	179	42	47	758	905	128	170	0	0	0	0	922	1084	170	217
+fasta_stats	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	43726	44512	3104	3259	19941	19941	3693	3693	16788	18589	2467	2650	80455	83042	9264	9602
+fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6685	6685	603	603	0	0	0	0	0	0	0	0	6685	6685	603	603
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	136	11	11	0	0	0	0	0	0	0	0	136	136	11	11
+fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	1	1126086	1127111	6847	6909	422259	422259	10722	10722	76462	76462	2242	2242	1624807	1625832	19811	19873
+fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8604	8799	215	240	54200	75329	919	2957	1562	1680	76	85	64366	85808	1210	3282
+fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15582	18350	690	771	40489	121585	2715	9239	4657	5793	214	287	60728	145728	3619	10297
+fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	92594	102535	2576	2995	179461	897457	9437	44701	15434	25533	664	1073	287489	1025525	12677	48769
+fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2488	3132	215	267	6241	14508	834	2121	4121	4592	131	158	12850	22232	1180	2546
+fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	234	249	43	44	2648	8092	288	983	442	466	12	17	3324	8807	343	1044
+fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5873	8936	532	657	14738	20229	1889	2366	2316	2711	225	261	22927	31876	2646	3284
+fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18216	19573	2348	2492	23484	25936	3482	3851	6207	6551	1402	1442	47907	52060	7232	7785
+fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15628	17130	536	679	24157	58368	1954	5716	1941	2266	172	214	41726	77764	2662	6609
+fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3169	3521	459	535	19309	30747	1410	3441	807	1023	219	247	23285	35291	2088	4223
+fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1271	1393	131	176	12763	58819	2073	8850	430	479	32	51	14464	60691	2236	9077
+fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	335	352	44	47	1583	9696	269	2229	1131	1254	15	27	3049	11302	328	2303
+fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	17279	18386	3826	4062	55268	136888	6055	12590	7685	9356	1854	2043	80232	164630	11735	18695
+fastq_stats	fastq_stats	FASTQ Summary Statistics by column								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3858	4595	680	815	15213	81513	3159	14109	3855	4163	184	256	22926	90271	4023	15180
+fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	36069	37805	1151	1234	45213	99852	2691	6370	8457	13335	408	609	89739	150992	4250	8213
+fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	12895	14110	269	297	13315	30673	612	1810	5125	5373	64	87	31335	50156	945	2194
+fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10114	11383	582	665	23906	92351	1986	8818	1588	2607	108	212	35608	106341	2676	9695
+fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	1	0	1784056	1913280	41344	43940	2269843	3195869	90828	140008	410004	445555	14195	16026	4463903	5554704	146367	199974
+fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5162	5162	2350	2350	10176	10176	4714	4714	2610	2610	991	991	17948	17948	8055	8055
+fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	208349	217568	3421	3732	131388	245005	5108	13227	18655	18655	679	679	358392	481228	9208	17638
+fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	65542	65631	1049	1071	25992	25992	2147	2147	6733	7339	649	745	98267	98962	3845	3963
+fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1769	2020	88	101	6948	24960	358	2424	623	998	32	50	9340	27978	478	2575
+fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	16957	18124	225	260	37001	89126	919	2720	863	989	56	68	54821	108239	1200	3048
+fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3140	3520	178	212	13975	117900	1198	6006	409	712	36	55	17524	122132	1412	6273
+fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	64187	67981	326	349	87477	185555	781	3067	16563	17125	58	78	168227	270661	1165	3494
+fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	174	272	61	92	4295	25068	1056	4180	1127	1171	70	89	5596	26511	1187	4361
+fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2218	2344	168	206	20551	60032	3784	9866	2347	2460	234	256	25116	64836	4186	10328
+fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2364	2526	180	214	6572	11745	303	1024	462	696	49	64	9398	14967	532	1302
+fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10707	12597	356	415	21568	67304	574	1527	719	861	61	78	32994	80762	991	2020
+fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	13584	14557	550	641	123676	206733	2034	8390	2819	4757	229	267	140079	226047	2813	9298
+fatovcf	fatovcf	Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_fatovcf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	448	ucsc-fatovcf	448		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	385	385	46	46	587	587	107	107	58	58	5	5	1030	1030	158	158
+featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	740719	770524	11699	12547	643892	784396	23272	27598	66108	68867	2348	2463	1450719	1623787	37319	42608
+feelnc	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	Annotation, Classification	Functional, regulatory and non-coding RNA	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1375	1500	95	99	797	797	116	116	59	59	3	3	2231	2356	214	218
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5618	5820	582	607	21673	21673	938	938	869	869	110	110	28160	28362	1630	1655
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	53310	53944	1499	1575	25043	25043	726	726	10824	10824	593	593	89177	89811	2818	2894
+flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	1985	1985	41	41	0	0	0	0	0	0	0	0	1985	1985	41	41
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22017	22304	239	255	9399	14886	462	709	4	4	1	1	31420	37194	702	965
+fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1257	1450	150	162	0	0	0	0	1052	1052	45	45	2309	2502	195	207
+freebayes	freebayes, bamleftalign	Galaxy Freebayes Bayesian genetic variant detector tool	freebayes	freebayes		FreeBayes	Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	To update	https://github.com/ekg/freebayes	Variant Analysis	freebayes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes	1.3.6	freebayes	1.3.8	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	149715	171093	8158	8794	144708	256315	15996	25107	19156	21936	2251	2571	313579	449344	26405	36472
+freec	control_freec	Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.	freec	freec		FREEC	A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.	Copy number estimation, Variant calling, Genome alignment	DNA structural variation, Oncology, Human genetics, Data mining	To update	http://boevalab.inf.ethz.ch/FREEC/	Variant Analysis	control_freec	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec	11.6	gawk		Copy number estimation, Variant calling, Genome alignment	Oncology, Human genetics, Data mining	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	748	748	91	91	0	0	0	0	12	12	1	1	760	760	92	92
+freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	21757	21757	101	101	217	217	21	21	0	0	0	0	21974	21974	122	122
+fsd	fsd, fsd_beforevsafter, fsd_regions, td	Tool that plots a histogram of sizes of read families								To update		Graphics	duplex_family_size_distribution	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd	1.0.2	matplotlib				4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	578	578	34	34	0	0	0	0	578	578	34	34
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	8648	8648	1408	1408	32	32	6	6	6406	6406	597	597	15086	15086	2011	2011
+gatk4	gatk4_mutect2	A Galaxy wrapper for Mutect2 from GATK								To update	https://software.broadinstitute.org/gatk/gatk4	Variant Analysis	gatk4_mutect2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3463	3463	452	452	9040	9040	1639	1639	0	0	0	0	12503	12503	2091	2091
+gdcwebapp	data_source_gdcwebapp	GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format								To update	http://bioinf.iasi.cnr.it/gdcwebapp/	Data Source, Convert Formats	gdcwebapp	iuc	https://github.com/fabio-cumbo/GDCWebApp4Galaxy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp	1.0.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gecko	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	723	723	235	235	0	0	0	0	786	786	95	95	1509	1509	330	330
+gemini	gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	Sequence analysis, Genetic variation analysis	Sequence analysis	1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	4967	5475	1863	1992	992	1118	279	370	3756	3811	423	425	9715	10404	2565	2787
+genebed_maf_to_fasta	GeneBed_Maf_Fasta2	Stitch gene blocks given a set of coding exon intervals								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	Genomic Interval Operations	genebed_maf_to_fasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta	1.0.1+galaxy0					1	1	1	0	1	1	1	0	0	1	0	0	0	1	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	1	0	4	4	2	2	221	2905	23	279	0	0	0	0	225	2909	25	281
+genehunter_modscore	genehunter_modscore	Maximised LOD score pedigree analysis utility								To update	https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1	Variant Analysis	genehunter_modscore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore	3.0.0	ghm	3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+geneiobio	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	101	101	25	25	0	0	0	0	59	59	6	6	160	160	31	31
+genetrack	genetrack	"Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand."								To update		ChIP-seq	genetrack	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack		numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	445	660	104	197	0	0	0	0	445	660	104	197
+genomescope	genomescope	Analyze unassembled short reads								Up-to-date	https://github.com/tbenavi1/genomescope2.0	Statistics	genomescope	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope	2.0.1	genomescope2	2.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3181	3181	665	665	2112	2112	435	435	1622	1622	148	148	6915	6915	1248	1248
+genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	47	47	13	13	0	0	0	0	0	0	0	0	47	47	13	13
+genrich	genrich	Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).								To update	https://github.com/jsh58/Genrich	ChIP-seq	genrich	iuc	https://github.com/jsh58/Genrich	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich	0.5+galaxy2	genrich	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3534	3577	402	405	2840	2840	419	419	571	571	31	31	6945	6988	852	855
+get_hrun	get_hrun	Annotate indel variants with homopolymer context								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	Variant Analysis	get_hrun	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun	0.5.9.2	pyfaidx	0.8.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1542	1542	159	159	0	0	0	0	587	587	64	64	2129	2129	223	223
+gfa_to_fa	gfa_to_fa	gfa_to_fa - Converting GFA format to Fasta format								To update	http://gfa-spec.github.io/GFA-spec/	Convert Formats	gfa_to_fa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa	0.1.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9664	9775	763	765	5623	5623	493	493	1000	1000	135	135	16287	16398	1391	1393
+gff3_rebase	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	806	812	68	68	197	197	37	37	132	132	12	12	1135	1141	117	117
+gffcompare	gffcompare	Galaxy wrappers for Geo Pertea's GffCompare package.	gffcompare	gffcompare		gffcompare	Program for comparing, annotating, merging and tracking transcripts in GFF files.	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	https://github.com/gpertea/gffcompare/	Transcriptomics	gffcompare	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare	0.12.6	gffcompare	0.12.6	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3560	3980	916	999	5281	8000	1713	2521	1468	1642	208	225	10309	13622	2837	3745
+gffread	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12828	13716	1740	1829	15217	23818	2588	3486	4423	4423	732	732	32468	41957	5060	6047
+ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	0	5	5	5	0	24606	25662	3463	3630	26805	26808	5143	5144	8174	8237	1259	1279	59585	60707	9865	10053
+ggupset	emc-ggupset	Create Upset Plots with ggupset								To update	https://github.com/const-ae/ggupset	Graphics	ggupset	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset	1.0	r-ggupset				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	0	4343	4343	407	407	0	0	0	0	0	0	0	0	4343	4343	407	407
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	5800	6212	826	871	7756	7756	1048	1048	1149	1149	215	215	14705	15117	2089	2134
+goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	20207	21960	2807	3139	24488	26198	3066	3321	4155	4155	545	545	48850	52313	6418	7005
+gprofiler	gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense	functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more								To update	https://biit.cs.ut.ee/gprofiler	Statistics, Web Services	gprofiler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler	@TOOL_VERSION@+galaxy11	r-gprofiler2				5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	4001	4001	614	614	7882	7882	1238	1238	0	0	0	0	11883	11883	1852	1852
+graphembed	graphembed	Compute a 2D embedding of a data matrix given supervised class information								Up-to-date	https://github.com/fabriziocosta/GraphEmbed	Statistics, Graphics	graphembed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed	2.4	graph_embed	2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	78	78	6	6	120	120	43	43	0	0	0	0	198	198	49	49
+graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	9816	10927	1285	1350	1273	1273	368	368	1104	1104	242	242	12193	13304	1895	1960
+gtdb_to_taxdump	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	gtdb_to_taxdump	gtdb_to_taxdump		gtdb_to_taxdump	Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.	Data handling, Mapping, Generation	Computational biology	Up-to-date	https://github.com/nick-youngblut/gtdb_to_taxdump	Metagenomics	gtdb_to_taxdump	iuc	https://github.com/nick-youngblut/gtdb_to_taxdump	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	0.1.9	Data handling, Mapping, Generation	Computational biology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	Up-to-date	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.4.0	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	476	476	87	87	0	0	0	0	588	588	74	74	1064	1064	161	161
+gtfToBed12	gtftobed12	Convert GTF files to BED12 format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README	Convert Formats	gtftobed12	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12	357	ucsc-gtftogenepred	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	8329	9363	3336	3828	8009	8009	3130	3130	1577	1577	344	344	17915	18949	6810	7302
+gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3690	3811	326	336	3323	3323	235	235	1895	2429	234	258	8908	9563	795	829
+gvcftools	gvcftools_extract_variants	gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf.								To update	https://github.com/sequencing/gvcftools	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools	0.1	gvcftools	0.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gwastools	gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	Deposition, Analysis, Annotation	GWAS study	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	7303	7303	222	222	20	20	2	2	0	0	0	0	7323	7323	224	224
+hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	349	359	32	33	364	364	53	53	0	0	0	0	713	723	85	86
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	103	103	4	4	103	103	4	4
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	502	502	66	66	0	0	0	0	0	0	0	0	502	502	66	66
+happy	som.py	A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.	hap.py	hap.py		hap.py	This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	To update	https://github.com/Illumina/hap.py	Variant Analysis	happy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy	0.3.14	hap.py	0.3.15	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+heatmap2	ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	0	46700	50808	4645	5114	64214	70429	5799	6830	7783	7912	704	724	118697	129149	11148	12668
+heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	bionet, heinz		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	1281	1434	367	442	1559	1559	636	636	678	678	52	52	3518	3671	1055	1130
+hgvsparser	hgvsparser	Parsing and building variant descriptor strings compliant with the HGVS standard								To update	https://github.com/VariantEffect/hgvsParseR/tree/master	Variant Analysis	hgvsparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6346	6346	2	2	0	0	0	0	0	0	0	0	6346	6346	2	2
+hicexplorer	hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								Up-to-date	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.5	hicexplorer	3.7.5			38	38	38	0	38	38	38	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	33	36	33	0	44449	68602	3236	4177	46	46	21	21	1328	1328	67	67	45823	69976	3324	4265
+hicstuff	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices								To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1819	1819	539	539	1334	1334	389	389	2472	2472	137	137	5625	5625	1065	1065
+hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	156	156	20	20	0	0	0	0	220	220	11	11	376	376	31	31
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	337151	353499	10046	10719	699868	896164	26656	34018	87016	94859	5302	5695	1124035	1344522	42004	50432
+hivclustering	hivclustering	Infers transmission networks from pairwise distances inferred by tn93								To update	https://pypi.org/project/hivclustering/	Next Gen Mappers	hivclustering	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering	1.3.1	python-hivclustering	1.8.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	0	0	12	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	12	0	35919	36952	1283	1321	0	0	0	0	3023	3023	180	180	38942	39975	1463	1501
+homer	homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	Sequence motif discovery		0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	5	0	0	8531	8531	633	633	0	0	0	0	0	0	0	0	8531	8531	633	633
+htseq_count	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	Nucleic acid sequence analysis	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	144907	168824	3703	4366	213407	346792	10798	16485	27209	33124	2613	2854	385523	548740	17114	23705
+humann	humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.9	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	10	10	0	6	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	26659	26659	2067	2067	865	865	174	174	3238	3238	351	351	30762	30762	2592	2592
+hybpiper	hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.3.0	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1571	1571	3	3	0	0	0	0	144	144	4	4	1715	1715	7	7
+hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	0	17	2	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	12	17	12	0	11429	11429	428	428	7751	7751	676	676	715	715	58	58	19895	19895	1162	1162
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	473	473	93	93	0	0	0	0	0	0	0	0	473	473	93	93
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	1200	1220	187	195	1588	1588	267	267	0	0	0	0	2788	2808	454	462
+idr	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2953	3027	109	114	1710	1710	199	199	0	0	0	0	4663	4737	308	313
+idr_download	idr_download_by_ids	Image Data Resource downloading tool								To update	https://idr.openmicroscopy.org	Data Source	idr_download_by_ids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download	0.45	omero-py	5.11.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	404	404	37	37	0	0	0	0	24	24	1	1	428	428	38	38
+iedb_api	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1539	1539	35	35	0	0	0	0	0	0	0	0	1539	1539	35	35
+infercnv	infercnv	Infer Copy Number Variation from Single-Cell RNA-Seq Data								Up-to-date	https://github.com/broadinstitute/infercnv	Transcriptomics, Variant Analysis	infercnv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv	1.20.0	bioconductor-infercnv	1.20.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	2	2	0	0	0	0	0	0	0	0	10	10	2	2
+instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	102	102	16	16	0	0	0	0	0	0	0	0	102	102	16	16
+integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55149	55149	161	161	0	0	0	0	6085	6085	73	73	61234	61234	234	234
+intermine_galaxy_exchange	galaxy_intermine_exchange	InterMine Exporter								To update	https://github.com/intermine	Convert Formats	intermine_galaxy_exchange	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange	0.0.1	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	46	6	12	72	87	13	15	108	108	1	1	217	241	20	28
+interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34689	55189	1634	1713	65	65	15	15	10897	10897	607	607	45651	66151	2256	2335
+interval2maf	Interval2Maf1	Extract MAF blocks given a set of intervals	bx-python	bx-python		bx-python	Tools for manipulating biological data, particularly multiple sequence alignments.		Sequence analysis	To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	interval2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf	1.0.1+galaxy1	bx-python	0.13.0		Sequence analysis	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	32	107	7	10	758	19538	87	1246	16	24	2	2	806	19669	96	1258
+intervene	intervene_pairwise, intervene_upset	Create pairwise and upset plots	intervene	intervene		Intervene	Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.	Sequence comparison, Sequence visualisation	Computational biology	Up-to-date	https://intervene.readthedocs.io	Statistics	intervene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene	0.6.5	intervene	0.6.5	Sequence comparison, Sequence visualisation	Computational biology	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1557	1607	278	292	4458	4458	458	458	0	0	0	0	6015	6065	736	750
+iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	28279	28481	1623	1646	24662	24662	2093	2093	9780	10086	979	992	62721	63229	4695	4731
+irissv	irissv	Refine insertion sequences								To update	https://github.com/mkirsche/Iris	Variant Analysis	irissv	iuc	https://github.com/galaxyproject/tools-iuc/tools/irissv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv	1.0.5	samtools	1.21			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	29	29	8	8	0	0	0	0	0	0	0	0	29	29	8	8
+isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	59386	59386	151	151	56	56	1	1	4741	4741	59	59	64183	64183	211	211
+isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1301	1301	59	59	1331	1331	60	60	507	507	9	9	3139	3139	128	128
+ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	0	5	5	5	0	1252220	1252220	2366	2366	126027	126027	2496	2496	41901	41901	993	993	1420148	1420148	5855	5855
+iwtomics	iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot	Interval-Wise Testing for Omics Data	iwtomics	iwtomics		IWTomics	"Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset."	Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison	Statistics and probability	To update	https://bioconductor.org/packages/release/bioc/html/IWTomics.html	Statistics	iwtomics	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics	1.0.0	bioconductor-iwtomics	1.26.0	Differential gene expression analysis, Peak calling, Genome annotation, Comparison	Statistics and probability	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	675	690	27	28	159	251	29	49	383	383	12	12	1217	1324	68	89
+jasminesv	jasminesv	Merge structural variants across samples								To update	https://github.com/mkirsche/Jasmine/	Variant Analysis	jasminesv	iuc	https://github.com/galaxyproject/tools-iuc/jasminesv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv	1.0.11	jasminesv	1.1.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32	32	9	9	53	53	19	19	0	0	0	0	85	85	28	28
+jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	21153	22174	5514	5779	17428	17428	6458	6458	15673	17267	3248	3786	54254	56869	15220	16023
+jcvi_gff_stats	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.16			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2747	2926	596	637	2311	2311	741	741	1145	1145	469	469	6203	6382	1806	1847
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1825	1825	237	237	0	0	0	0	971	971	56	56	2796	2796	293	293
+join_files_by_id	join_files_by_id	This tool will join datasets according to a column with identifier								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	Text Manipulation	join_files_by_id	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id	1.0	r-data.table	1.11.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+jq	jq	JQ is a lightweight and flexible command-line JSON processor								To update	https://stedolan.github.io/jq/	Text Manipulation	jq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq	1.0	jq	1.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	660	2374	61	63	336	336	82	82	281	281	11	11	1277	2991	154	156
+jvarkit	jvarkit_wgscoverageplotter	Jvarkit : Java utilities for Bioinformatics								Up-to-date	https://lindenb.github.io/jvarkit/	SAM	jvarkit	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit	20201223	jvarkit-wgscoverageplotter	20201223			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7179	7179	509	509	11138	11138	1145	1145	0	0	0	0	18317	18317	1654	1654
+kallisto	kallisto_pseudo, kallisto_quant	kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.	kallisto	kallisto		kallisto	A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.	Gene expression profiling	Transcriptomics, RNA-seq, Gene expression	To update	https://pachterlab.github.io/kallisto/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto	0.48.0	kallisto	0.51.1	Gene expression profiling	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	28398	29031	932	965	73705	80087	2603	3025	5333	5567	218	230	107436	114685	3753	4220
+kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	379	379	53	53	8259	8259	271	271	0	0	0	0	8638	8638	324	324
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	8	8	8	0	1995	2091	174	193	1430	1430	389	389	1580	1580	56	56	5005	5101	619	638
+king	king	Kinship-based INference for Gwas								Up-to-date	http://people.virginia.edu/~wc9c/KING/	Variant Analysis	king	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/king	2.2.7	king	2.2.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	8	4	4	0	0	0	0	0	0	0	0	8	8	4	4
+kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.1.0	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	503	503	58	58	0	0	0	0	0	0	0	0	503	503	58	58
+kma	kma_map	Map with KMA								To update	https://bitbucket.org/genomicepidemiology/kma	Next Gen Mappers	kma	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma	1.4.14	kma	1.4.15			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1
+kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1342	1342	63	63	0	0	0	0	0	0	0	0	1342	1342	63	63
+kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	5	5	5	0	48136	48164	2754	2760	59952	130398	5869	8654	29008	31148	1936	2200	137096	209710	10559	13614
+kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	271367	271786	6384	6409	101752	101752	4662	4662	53562	53562	1663	1663	426681	427100	12709	12734
+kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3185	3185	495	495	0	0	0	0	385	385	48	48	3570	3570	543	543
+kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3981	3986	769	771	4087	5610	991	1284	88	88	41	41	8156	9684	1801	2096
+krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	48516	48516	2373	2373	8787	8787	943	943	4369	4369	393	393	61672	61672	3709	3709
+krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+last	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1584	Sequence alignment	Comparative genomics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	329	329	94	94	0	0	0	0	0	0	0	0	329	329	94	94
+lastz	lastz_wrapper_2, lastz_d_wrapper	Galaxy wrappers for the Lastz and Lastz_d	lastz	lastz		LASTZ	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.	Sequence alignment, Read mapping	Genomics	Up-to-date	https://github.com/lastz/lastz	Next Gen Mappers	lastz	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz	1.04.22	lastz	1.04.22	Sequence alignment, Read mapping	Genomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	77409	84356	447	475	156658	193590	870	3511	38579	38780	173	203	272646	316726	1490	4189
+lcrgenie	lcrgenie	Ligase Chain Reaction Genie								To update	https://github.com/neilswainston/LCRGenie	Synthetic Biology	lcrgenie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie	1.0.2	lcr_genie				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	92	92	8	8	0	0	0	0	0	0	0	0	92	92	8	8
+length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	4349	4466	666	698	2093	2286	928	998	201	201	77	77	6643	6953	1671	1773
+limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23442	24466	2379	2475	45734	49342	4565	5032	9327	9517	835	842	78503	83325	7779	8349
+lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	39	4	4	0	0	0	0	0	0	0	0	39	39	4	4
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	512	512	126	126	0	0	0	0	480	480	65	65	992	992	191	191
+lofreq	lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi	LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.								Up-to-date	https://csb5.github.io/lofreq/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq	2.1.5	lofreq	2.1.5			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	0	0	0	4	0	0	0	0	0	0	5	5	5	0	4176367	4176367	4301	4301	509615	509615	8213	8213	106342	106342	1815	1815	4792324	4792324	14329	14329
+lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	822	822	14	14	0	0	0	0	0	0	0	0	822	822	14	14
+lumpy_sv	lumpy_prep, lumpy_sv	LUMPY - a general probabilistic framework for structural variant discovery								Up-to-date	http://layerlab.org/software/	Variant Analysis	lumpy_sv	iuc	https://github.com/arq5x/lumpy-sv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv	0.3.1	lumpy-sv	0.3.1			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	1534	1534	199	199	0	0	0	0	0	0	0	0	1534	1534	199	199
+m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	44	44	11	11	0	0	0	0	0	0	0	0	44	44	11	11
+maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2835	2835	59	59	0	0	0	0	0	0	0	0	2835	2835	59	59
+macs2	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	0	0	9	0	0	0	0	0	0	9	9	9	0	87810	96069	4980	5629	153500	227569	12946	18825	10988	12301	692	807	252298	335939	18618	25261
+maf_stats	maf_stats1	MAF Coverage statistics								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	maf_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats	1.0.2+galaxy0					1	1	1	0	1	1	1	0	0	1	0	0	0	1	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	1	0	15	21	7	9	227	2470	52	464	1	1	1	1	243	2492	60	474
+maftoaxt	maftoaxt	Convert dataset from MAF to axt format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_maftoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	469	ucsc-maftoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mageck	mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test	Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	mageck	mageck		MAGeCK	Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	Genetic variation analysis	Genetics, Genetic variation, Genomics	To update	https://sourceforge.net/projects/mageck/	Genome editing		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck	0.5.9.2	mageck	0.5.9.5	Genetic variation analysis	Genetics, Genetic variation, Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	11761	12093	873	889	5762	5762	473	473	5610	5610	343	343	23133	23465	1689	1705
+maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6417	6861	1315	1366	7235	7235	1858	1858	4112	4112	902	902	17764	18208	4075	4126
+malt	malt_run	Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.								To update	https://github.com/husonlab/malt	Next Gen Mappers	malt_run	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt	0.5.3	malt	0.62			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	24	9	9	0	0	0	0	0	0	0	0	24	24	9	9
+map_param_value	map_param_value	Map a parameter value to another value								To update		Text Manipulation	map_param_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3780	3780	67	67	1012	1012	57	57	105	105	3	3	4897	4897	127	127
+mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7871	7871	32	32	0	0	0	0	0	0	0	0	7871	7871	32	32
+mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	10119	10119	61	61	19	19	9	9	647	647	7	7	10785	10785	77	77
+mashmap	mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	894	894	12	12	81	81	5	5	0	0	0	0	975	975	17	17
+masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	471	582	35	40	589	589	80	80	0	0	0	0	1060	1171	115	120
+maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	1	0	2798	2798	314	314	2452	2452	508	508	914	914	89	89	6164	6164	911	911
+mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	35	13	13	0	0	0	0	0	0	0	0	35	35	13	13
+medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	0	3	3	3	0	117975	117975	1693	1693	55063	55063	796	796	9325	9325	639	639	182363	182363	3128	3128
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	12692	13292	1349	1400	16645	16645	2140	2140	6214	6214	431	431	35551	36151	3920	3971
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	513	557	152	155	74	74	35	35	10	10	4	4	597	641	191	194
+megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	4130	4130	447	447	0	0	0	0	0	0	0	0	4130	4130	447	447
+meme	meme_dreme, meme_fimo, meme_meme, meme_psp_gen	The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.	meme_meme	meme_fimo, meme_meme		meme_meme	An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	To update	http://meme-suite.org/	ChIP-seq	meme	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme	5.5.6	meme	5.5.7	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	3	0	4	0	3	0	4	0	0	0	0	0	0	0	0	0	0	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	4	4	0	20990	22979	762	892	10975	25929	1551	3249	0	0	0	0	31965	48908	2313	4141
+meme_chip	meme_chip	Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.								To update	http://meme-suite.org/	ChIP-seq	meme_chip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip	4.11.2	graphicsmagick	1.3.26			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6413	7000	705	743	7260	7260	1171	1171	0	0	0	0	13673	14260	1876	1914
+meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+merlin	merlin	Pedigree Analysis package	merlin	merlin		Merlin	Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation	Haplotype mapping, Genetic mapping	GWAS study, Mapping	Up-to-date	http://csg.sph.umich.edu/abecasis/Merlin/	Variant Analysis	merlin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin	1.1.2	merlin	1.1.2	Haplotype mapping	GWAS study, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3150	3150	477	477	730	730	196	196	1183	1183	151	151	5063	5063	824	824
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	0	2	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	6135	6135	382	382	881	881	151	151	1094	1094	104	104	8110	8110	637	637
+metabuli	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	metabuli	metabuli		metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid	Taxonomic classification	Taxonomy	To update	https://github.com/steineggerlab/Metabuli	Sequence Analysis, Metagenomics	metabuli	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli	1.0.5	metabuli	1.0.8	Taxonomic classification	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	7.bba0d80	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	312	312	40	40	0	0	0	0	0	0	0	0	312	312	40	40
+metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	556	756	17	21	310	514	35	55	0	0	0	0	866	1270	52	76
+metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	0	1	2	4	0	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	16629	16648	1183	1187	3983	3983	572	572	4747	4747	278	278	25359	25378	2033	2037
+metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	142	142	32	32	0	0	0	0	379	379	47	47	521	521	79	79
+mg_toolkit	mg_toolkit_bulk_download, mg_toolkit_original_metadata	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	mg-toolkit	mg-toolkit		mg-toolkit	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	Data retrieval	Metagenomics	Up-to-date	https://github.com/EBI-Metagenomics/emg-toolkit	Metagenomics	mg_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	0.10.4	mg-toolkit	0.10.4	Data retrieval	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1
+microsatbed	microsatbed	Select microsatellites for a bed file								To update	https://github.com/lmdu/pytrf	Sequence Analysis	microsatbed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed	1.3.3	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	228	4	4	18	18	1	1	0	0	0	0	246	246	5	5
+migmap	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	Sequence analysis, Read mapping	Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1082	1229	25	33	1153	1376	70	89	0	0	0	0	2235	2605	95	122
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7116	7116	256	256	0	0	0	0	278	278	60	60	7394	7394	316	316
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13357	13479	554	562	8416	8416	448	448	898	898	85	85	22671	22793	1087	1095
+minimap2	minimap2	A fast pairwise aligner for genomic and spliced nucleotide sequences	minimap2	minimap2		Minimap2	Pairwise aligner for genomic and spliced nucleotide sequences	Pairwise sequence alignment	Mapping	Up-to-date	https://github.com/lh3/minimap2	Next Gen Mappers	minimap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2	2.28	minimap2	2.28	Pairwise sequence alignment	Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	346530	349075	4323	4419	108535	108535	4075	4075	22331	22331	1166	1166	477396	479941	9564	9660
+miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1244	1244	86	86	24	24	15	15	0	0	0	0	1268	1268	101	101
+mirmachine	mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2
+mirnature	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	18	18	9	9	0	0	0	0	0	0	0	0	18	18	9	9
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1117	1117	116	116	0	0	0	0	295	295	25	25	1412	1412	141	141
+mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	0	191295	191295	1111	1111	42265	42265	320	320	10904	10904	83	83	244464	244464	1514	1514
+mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	13300	13471	1480	1501	6532	6532	1167	1167	10334	11841	1083	1300	30166	31844	3730	3968
+moabs	moabs	MOABS for differential methylation analysis on Bisulfite sequencing data.								To update	https://github.com/sunnyisgalaxy/moabs	Epigenetics	moabs	iuc	https://github.com/sunnyisgalaxy/moabs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs	1.3.4.6	moabs	1.3.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	339	339	56	56	0	0	0	0	0	0	0	0	339	339	56	56
+mosdepth	mosdepth	fast and flexible BAM/CRAM depth calculation								Up-to-date	https://github.com/brentp/mosdepth	SAM	mosdepth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth	0.3.8	mosdepth	0.3.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1278	1278	87	87	168	168	24	24	102	102	5	5	1548	1548	116	116
+mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	0	129	129	129	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	126	129	129	0	297546	326056	37506	41763	565218	682083	72163	89926	167400	182490	26963	28404	1030164	1190629	136632	160093
+msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	864	929	91	101	1100	1100	175	175	0	0	0	0	1964	2029	266	276
+multigps	multigps	Analyzes collections of multi-condition ChIP-seq data.								To update	http://mahonylab.org/software/multigps/	ChIP-seq	multigps	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps	0.74.0	fonts-conda-ecosystem				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	485	871	159	298	0	0	0	0	485	871	159	298
+multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	106	106	25	25	0	0	0	0	0	0	0	0	106	106	25	25
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	182221	192389	19343	20494	163961	182413	26449	29758	40663	41855	5974	6157	386845	416657	51766	56409
+mummer4	mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1			6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	6	3	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	21587	22119	1940	2033	29284	29284	3626	3626	8194	8194	545	545	59065	59597	6111	6204
+mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mzmine	mzmine_batch	mass-spectrometry data processing, with the main focus on LC-MS data	mzmine	mzmine		MZmine	Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	Up-to-date	http://mzmine.github.io/	Metabolomics	mzmine_batch	iuc	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine	3.9.0	mzmine	3.9.0	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5
+naltorfs	bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2			3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	204	204	75	75	0	0	0	0	204	204	75	75
+nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	839	839	12	12	0	0	0	0	269	269	5	5	1108	1108	17	17
+nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	99052	100009	5671	5755	40386	40386	3371	3371	17919	17919	2188	2188	157357	158314	11230	11314
+nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1091	1091	44	44	0	0	0	0	0	0	0	0	1091	1091	44	44
+ncbi_acc_download	ncbi_acc_download	Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API								Up-to-date	https://github.com/kblin/ncbi-acc-download	Data Source	ncbi_acc_download	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download	0.2.8	ncbi-acc-download	0.2.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6873	6873	1664	1664	17651	17651	4513	4513	6228	6228	972	972	30752	30752	7149	7149
+ncbi_datasets	datasets_download_gene, datasets_download_genome	NCBI datasets downloads biological sequence data across all domains of life from NCBI.	ncbi_datasets	ncbi_datasets		NCBI Datasets	NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.	Data handling, Sequence database search, Data retrieval	Biological databases	To update	https://github.com/ncbi/datasets	Data Source	ncbi_datasets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets	16.20.0	ncbi-datasets-cli		Data handling, Sequence database search, Data retrieval	Biological databases	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	1	2	2	0	4417	4417	1024	1024	6940	6940	2275	2275	1	1	1	1	11358	11358	3300	3300
+ncbi_entrez_direct	ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch	NCBI Entrez Direct allow fetching data from NCBI Databases								Up-to-date	http://www.ncbi.nlm.nih.gov/books/NBK179288/	Data Source	ncbi_entrez_direct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct	22.4	entrez-direct	22.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	2	0	0	0	0	0	3	0	2
+ncbi_entrez_eutils	ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary	NCBI Entrez E-Utilties allow fetching data from NCBI Databases								To update	https://www.ncbi.nlm.nih.gov/books/NBK25501/	Data Source	ncbi_entrez_eutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils	1.70	python				0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	4	0	0	0	2	0	0	0	0	0	0	0	7	7	0	2794	3191	533	664	0	0	0	0	0	0	0	0	2794	3191	533	664
+ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	125	125	26	26	2489	2489	139	139	0	0	0	0	2614	2614	165	165
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	790	790	160	160	0	0	0	0	0	0	0	0	790	790	160	160
+newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33637	34195	1113	1172	16257	16257	1816	1816	7582	7582	899	899	57476	58034	3828	3887
+nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	0	2	0	0	4411	4411	396	396	9708	9708	279	279	2099	2099	212	212	16218	16218	887	887
+ngmlr	ngmlr	CoNvex Gap-cost alignMents for Long Reads	ngmlr	ngmlr		NGMLR	An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping, DNA structural variation	Up-to-date	https://github.com/philres/ngmlr	Next Gen Mappers	ngmlr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr	0.2.7	ngmlr	0.2.7	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1403	1403	49	49	0	0	0	0	0	0	0	0	1403	1403	49	49
+ngsutils	ngsutils_bam_filter	NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.	ngsutils	ngsutils		NGSUtils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets	Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering	Genomics, Transcriptomics	To update	https://github.com/ngsutils/ngsutils	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils		ngsutils	0.5.9	Read pre-processing, Variant calling, Formatting, Sequence contamination filtering	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	24611	29662	633	716	15523	21395	740	1128	7751	8972	125	145	47885	60029	1498	1989
+nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	107	143	13	15	148	148	20	20	0	0	0	0	255	291	33	35
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	7780	7780	337	337	1	1	1	1	2323	2323	99	99	10104	10104	437	437
+nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	37598	37598	1277	1277	0	0	0	0	3862	3862	280	280	41460	41460	1557	1557
+ococo	ococo	Variant detection of SNVs								To update	https://github.com/karel-brinda/ococo	Variant Analysis	ococo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo	0.1.2.6	ococo	0.1.2.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1850	1963	79	93	1370	1370	194	194	0	0	0	0	3220	3333	273	287
+odgi	odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	26	26	6	6	0	0	0	0	0	0	0	0	26	26	6	6
+omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	158	158	12	12	0	0	0	0	0	0	0	0	158	158	12	12
+ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	3051	3051	87	87	0	0	0	0	0	0	0	0	3051	3051	87	87
+onto_toolkit	onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def	ONTO-Toolkit is a collection of tools for managing ontologies.								Up-to-date	http://search.cpan.org/~easr/ONTO-PERL-1.45/	Ontology Manipulation	onto_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit	1.45	perl-onto-perl	1.45			0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	0	582	663	68	69	0	0	0	0	0	0	0	0	582	663	68	69
+optdoe	optdoe	Optimal Design Of Experiment								To update	https://github.com/pablocarb/doebase	Synthetic Biology	optdoe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe	v2.0.2	doebase				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+optitype	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	500	500	45	45	0	0	0	0	0	0	0	0	500	500	45	45
+orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	897	897	99	99	1792	1792	239	239	0	0	0	0	2689	2689	338	338
+orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	To update	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	3.0.1b1	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2018	2018	419	419	0	0	0	0	438	438	58	58	2456	2456	477	477
+packaged_annotation_loader	packaged_annotation_loader	Tool to make cached genome annotation data available as a list of datasets collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	Data Source	packaged_annotation_loader	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pacu	pacu_map, pacu_snp	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.	pacu	pacu		PACU	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).	Clustering	Phylogenetics, Sequence analysis	Up-to-date	https://github.com/BioinformaticsPlatformWIV-ISP/PACU	Sequence Analysis, Phylogenetics	pacu	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu	0.0.5	pacu_snp	0.0.5	Clustering	Phylogenetics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pairtools	pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0			5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	196	196	16	16	19	19	14	14	0	0	0	0	215	215	30	30
+pangolin	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	Tree-based sequence alignment, Variant classification	Virology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	0	0	7457	7457	508	508	8518	8518	377	377	2760	2760	259	259	18735	18735	1144	1144
+parse_mito_blast	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	65	65	288	288	62	62	110	110	20	20	601	601	147	147
+pathview	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6204	6211	1261	1261	6667	6667	1143	1143	1160	1160	189	189	14031	14038	2593	2593
+pbgcpp	pbgcpp	Compute genomic consensus and call variants using PacBio reads mapped to a reference	genomicconsensus	genomicconsensus		GenomicConsensus	The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.	Variant calling	Mapping	Up-to-date	https://github.com/PacificBiosciences/gcpp	Variant Analysis	pbgcpp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp	2.0.2	pbgcpp	2.0.2	Variant calling	Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pbmm2	pbmm2	A minimap2 SMRT wrapper for PacBio data.	pbmm2	pbmm2		pbmm2	pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.	Pairwise sequence alignment, Sorting	Mapping	Up-to-date	https://github.com/PacificBiosciences/pbmm2	Next Gen Mappers	pbmm2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2	1.14.99	pbmm2	1.14.99	Pairwise sequence alignment, Sorting	Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	70	17	17	0	0	0	0	0	0	0	0	70	70	17	17
+pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	22	22	109	109	19	19	0	0	0	0	167	167	41	41
+pe_histogram	pe_histogram	Contains a tool that produces an insert size histogram for a paired-end BAM file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram	Graphics	pe_histogram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram	1.0.2	openjdk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	5505	5505	510	510	7932	8582	811	909	736	736	119	119	14173	14823	1440	1538
+peakzilla	peakzilla	Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.								To update	https://github.com/steinmann/peakzilla	ChIP-seq	peakzilla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla	1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	9	9	0	0	0	0	0	0	0	0	18	18	9	9
+pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	6269	6866	260	292	5530	20068	467	1664	5647	8471	198	300	17446	35405	925	2256
 pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
                 pharokka
-            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	74	2565
-phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	82	812
-phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	104	1770
-picard	picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile	Picard SAM/BAM manipulation tools.	picard_samtofastq	picard_reordersam, picard_samtofastq, picard_fastqtosam, picard_replacesamheader		picard_samtofastq	Create a FASTQ file.	Formatting	Sequencing	To update	http://broadinstitute.github.io/picard/	SAM	picard	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard	3.1.1	picard	3.2.0	Formatting	Sequencing	31	31	31	31	31	31	31	31	0	0	0	0	0	0	0	0	0	0	31	4	31	0	0	31	0	0	0	31	0	0	0	0	0	31	31	31	0	3735	374458
-pick_value	pick_value	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	pick_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	116
-picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	6	0	6	5	6	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	45	1095
-picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	88	1000
-pilon	pilon	pilon is a tool for assembly improvement and variant analysis in bacteria	pilon	pilon		pilon	Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.	Sequence assembly, Analysis, Read alignment	Assembly	To update	https://github.com/broadinstitute/pilon/wiki	Variant Analysis	pilon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon	1.20.1	pilon	1.24	Sequence assembly, Analysis	Assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	467	7942
-pipelign	pipelign	Multipe sequence alignment								Up-to-date	https://github.com/asmmhossain/pipelign/	Next Gen Mappers	pipelign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign	0.2	pipelign	0.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	83	983
-pizzly	pizzly	Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.								To update	https://github.com/pmelsted/pizzly/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly	0.37.3.1	pizzly	0.37.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	208
-plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	278	22589
-plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	22
-plink	plink	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	plink	plink		PLINK	Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	Genetic variation analysis	GWAS study	Up-to-date	https://www.cog-genomics.org/plink	Genome-Wide Association Study	plink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink	1.90b6.21	plink	1.90b6.21	Genetic variation analysis	GWAS study	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46	669
-polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	239
-porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1046	185468
-poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	6	13	0	409	18773
-presto	presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pretext	pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6			3	2	3	0	3	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	254	2350
-prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	70	7881
-prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-progressivemauve	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update	http://darlinglab.org/mauve/user-guide/progressivemauve.html	Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	286	1734
-prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	3233	371445
-prot-scriber	prot_scriber	Protein annotation of short human readable descriptions								Up-to-date	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.6	prot-scriber	0.1.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	5
-proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	200	3320
-psiclass	psiclass	PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.	psiclass	psiclass		PsiCLASS	Reference-based transcriptome assembler for single or multiple RNA-seq samples	Transcriptome assembly	Sequence assembly	Up-to-date	https://github.com/splicebox/PsiCLASS	Transcriptomics	psiclass	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass	https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass	1.0.3	psiclass	1.0.3	Transcriptome assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	15
-pureclip	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	1423
-purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800
-pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123
-pyega3	pyega3	EGA python client uses the EGA REST API to download authorized datasets and files.								To update	https://github.com/EGA-archive/ega-download-client	Data Source	ega_download_client	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3	5.0.2	pyega3	5.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	38	2424
-pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	377	11332
-pysradb	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.1	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	26	144
-qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	68	1909
-qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	32	0	0	32	32	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	1155	28681
-qiime_extract_viz	qiime_extract_viz	Extract vizualization from QIIME artifacts								To update	http://www.qiime.org	Metagenomics	qiime_extract_viz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz	0.1.0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-qq_tools	qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	1	4	4	4	1	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	4	4	4	0	1328	664470
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567
-query_impc	query_impc	Contains a tool to query the IMPC database.								To update	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	Convert Formats, Web Services	query_impc	iuc	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc	0.9.0	requests				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
-query_tabular	filter_tabular, query_tabular, sqlite_to_tabular	Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular	3.3.1	python				3	3	3	1	3	3	3	1	0	0	0	0	0	0	0	0	0	0	0	3	2	0	0	0	0	0	0	1	0	0	0	0	0	3	3	3	0	561	124536
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
-raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	1	5	5	5	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	82	4569
-ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833
-rapidnj	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2		Phylogeny	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	176
-rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902
-raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	383	6808
-rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	569
-read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	3370
-recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.15.0	recentrifuge	1.15.0	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	331
-red	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	88	578
-repeatmasker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.0.9_p2	Genome annotation	Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	248	3750
-repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	217	1177
-repmatch_gff3	repmatch_gff3	Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.								To update		ChIP-seq	repmatch_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3		matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-reshape2	cast, melt	Flexibly restructure and aggregate data using just the two functions melt and dcast								To update	https://cran.r-project.org/web/packages/reshape2/index.html	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2	1.4.2	r-reshape2				2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	33	3456
-resize_coordinate_window	resize_coordinate_window	Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.								To update		Genomic Interval Operations	resize_coordinate_window	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window	https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window	1.0.2	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	85
-revoluzer	revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	Structural variation detection	Molecular evolution, Phylogeny	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rgcca	rgcca	multi-block analysis								To update	https://github.com/rgcca-factory/RGCCA	Statistics	rgcca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca	3.0.2	rgccacmd	3.0.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	44
-rgrnastar	rna_star, rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	star	star		STAR	Ultrafast universal RNA-seq data aligner	Sequence alignment	RNA-Seq, Transcriptomics	To update	https://github.com/alexdobin/STAR	Next Gen Mappers, Transcriptomics	rgrnastar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar	2.7.11a	star	2.7.11b	Sequence alignment	RNA-Seq, Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	2	0	0	0	2	0	0	0	0	0	2	2	2	0	4015	425658
-ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14	161
-rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	109	1110
-roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	656	12225
-rp2biosensor	rp2biosensor	Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output								To update	https://github.com/brsynth/rp2biosensor	Synthetic Biology	rp2biosensor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor	3.2.1	rp2biosensor				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rp2paths	rp2paths	Enumerate and seperate the different pathways generated by RetroPath2.0								To update	https://github.com/brsynth/rp2paths	Synthetic Biology	rp2paths	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths	1.5.1	rp2paths				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rpbasicdesign	rpbasicdesign	Extracting enzyme IDs from rpSBML files								To update	https://github.com/brsynth/rpbasicdesign	Synthetic Biology	rpbasicdesign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign	1.2.2	rpbasicdesign				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rpfba	rpfba	Perform FBA for the RetroPath2.0 heterologous pathways								To update	https://github.com/brsynth/rptools/releases	Synthetic Biology	rpfba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba	5.12.3	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rptools	rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz	Suite of tools that work on rpSBML format								To update	https://github.com/brsynth/rptools	Synthetic Biology	rptools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools	5.13.1	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rrparser	rrparser	Reaction Rules Parser								To update	https://github.com/brsynth/RRParser	Synthetic Biology	rrparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser	2.5.2	rrparser				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	22	22	22	22	22	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	22	22	22	0	3206	133498
-ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	76	1236
-salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	84	454
-samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	To update	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.24	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-samtools										To update	https://github.com/samtools/samtools	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools	1.20	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sansa	sansa_annotate	Sansa is a tool for structural variant annotation.								To update	https://github.com/dellytools/sansa	Variant Analysis	sansa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa	0.2.1	sansa	0.2.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	18	123
-sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	173
-sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	140
-sbml2sbol	sbml2sbol	Convert SBML to SBOL format								To update	https://github.com/neilswainston/SbmlToSbol	Synthetic Biology	sbml2sbol	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol	0.1.13	sbml2sbol				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	766	51978
-scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	77	1365
-sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	90	721
-schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	23	779
-scikit-bio	scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
-scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	61	676
-scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	628
-seacr	seacr	SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.								Up-to-date	https://github.com/FredHutch/SEACR	Epigenetics, ChIP-seq	seacr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr	1.3	seacr	1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	50	3647
-selenzy_wrapper	selenzy_wrapper	Performs enzyme selection from a reaction query.								Up-to-date	https://github.com/brsynth/selenzy-wrapper	Synthetic Biology	selenzy_wrapper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper	0.3.0	selenzy_wrapper	0.3.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	1	0	0	6	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	39	542
-seq2hla	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	288
-seqcomplexity	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	16	68
-seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	3	0	2	5	3	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	129	1964
-seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12
-seqtk	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	Data handling, Sequence file editing		15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	14	0	14	0	0	14	0	0	0	15	0	0	0	0	0	14	14	14	14	753	59668
-seqwish	seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	271
-seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	1	1	1	7	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0
-shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	154	763
-shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600
-sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	269	14982
-simtext	abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix	A text mining framework for interactive analysis and visualization of similarities among biomedical entities.								To update	https://github.com/dlal-group/simtext	Text Manipulation	simtext	iuc	https://github.com/galaxyproject/tools-iuc/tools/simtext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext	0.0.2	r-argparse	1.0.1			0	2	4	0	0	2	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	34	142
-sina	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	1128
-sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								Up-to-date	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.10.1	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	17	91
-slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	2	361
-sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	64
-smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	121
-smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203
-snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	133	1349
-snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sniffles	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	Up-to-date	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	2.4	sniffles	2.4	Sequence analysis, Structural variation detection	Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	58	919
-snipit	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	Base position variability plotting	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	22	669
-snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	0	1372	105708
-snp-dists	snp_dists	Compute pairwise SNP distance matrix from a FASTA sequence alignment								Up-to-date	https://github.com/tseemann/snp-dists	Variant Analysis	snp_dists	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists	0.8.2	snp-dists	0.8.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	367	4558
-snp-sites	snp_sites	Finds SNP sites from a multi-FASTA alignment file								Up-to-date	https://github.com/sanger-pathogens/snp-sites	Variant Analysis	snp_sites	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites	2.5.1	snp-sites	2.5.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	284	5107
-snpeff	snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names	SnpEff is a genetic variant annotation and effect prediction toolbox								To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff		biopython	1.70			5	5	5	5	5	5	5	5	0	0	0	0	0	0	1	0	0	0	0	5	5	0	0	5	0	0	0	5	0	0	0	0	0	5	5	5	0	2676	95592
-snpeff-covid19	snpeff_sars_cov_2	SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox	snpeff	snpeff		snpEff	Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).	SNP detection	DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs	To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff_sars_cov_2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19				SNP detection	DNA polymorphism, Nucleic acid sites, features and motifs	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	533	760352
-snpfreqplot	snpfreqplot	A plotting app to visualise the SNPs across a region								To update	https://github.com/BrownfieldPlantLab/SNPFreqPlot	Variant Analysis	snpfreqplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot	1.0	r-base				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	0	0	156	3530
-snpsift	snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck	snpEff SnpSift tools from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html	Variant Analysis	snpsift	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift		snpsift	5.2			8	8	8	8	8	8	8	8	0	0	0	0	0	0	8	0	0	0	0	0	8	0	0	8	0	0	0	8	0	0	0	0	0	8	8	8	0	1352	5114712
-snpsift_dbnsfp	snpSift_dbnsfp	snpEff SnpSift dbnsfp tool from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html#dbNSFP	Variant Analysis	snpsift_dbnsfp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	46
-snpsift_genesets	snpSift_geneSets	Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome								To update	http://snpeff.sourceforge.net/SnpSift.html#geneSets	Variant Analysis	snpsift_genesets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	528
-socru	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	621
-sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953
-spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	34	446
-spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	1278
-spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	67
-sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	3	3	3	0	6247	350032
-srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205
-stacks	stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	Data handling	Mapping, Population genetics	0	13	13	12	0	13	13	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	13	0	152	11635
-stacks2	stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65			0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	238	7292
-star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update	https://github.com/STAR-Fusion/STAR-Fusion	Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	1212
-straindesign	straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion	Toolbox to optimize biological model								To update	https://github.com/brsynth/straindesign	Systems Biology, Synthetic Biology	straindesign	iuc	https://github.com/brsynth/straindesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign	3.2.2	straindesign	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-strelka	strelka_germline, strelka_somatic	Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision.								Up-to-date	https://github.com/Illumina/strelka/	Variant Analysis	strelka	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka	2.9.10	strelka	2.9.10			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	53	549
-stringtie	stringtie, stringtie_merge	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	stringtie	stringtie		StringTie	Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.	Transcriptome assembly, RNA-Seq analysis	Transcriptomics, RNA-seq	Up-to-date	http://ccb.jhu.edu/software/stringtie/	Transcriptomics	stringtie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie	2.2.3	stringtie	2.2.3	Transcriptome assembly, RNA-Seq analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	2165	167659
-structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	2623
-structureharvester	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date	http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/	Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-swift	swiftlink	Parallel MCMC Linkage Analysis								Up-to-date	https://github.com/ajm/swiftlink	Variant Analysis	swiftlink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift	1.0	swiftlink	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-syndiva	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	30
-table_compute	table_compute	Perform general-purpose table operations								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	Text Manipulation	table_compute	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute	1.2.4	pandas				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	741	208652
-tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	200	7388
-tag_pileup_frequency	tag_pileup_frequency	Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup	Statistics, SAM, Genomic Interval Operations	tag_pileup_frequency	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency	1.0.2	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	164
-tasmanian_mismatch	tasmanian_mismatch	Analysis of positional mismatches								Up-to-date	https://github.com/nebiolabs/tasmanian-mismatch	Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-taxonkit	name2taxid, profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	taxonkit	taxonkit		TaxonKit	TaxonKit is a practical and efficient NCBI taxonomy toolkit.	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	Up-to-date	https://bioinf.shenwei.me/taxonkit/	Metagenomics	taxonkit	iuc	https://github.com/shenwei356/taxonkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit	0.17.0	taxonkit	0.17.0	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426
-taxpasta	taxpasta	standardise taxonomic profiles	taxpasta	taxpasta		taxpasta	TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	Up-to-date	https://taxpasta.readthedocs.io/en/latest/	Sequence Analysis	taxpasta	iuc	https://github.com/taxprofiler/taxpasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta	0.7.0	taxpasta	0.7.0	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	198	5161
-tb_variant_filter	tb_variant_filter	M. tuberculosis H37Rv VCF filter								Up-to-date	https://github.com/COMBAT-TB/tb_variant_filter	Variant Analysis	tb_variant_filter	iuc	https://github.com/COMBAT-TB/tb_variant_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter	0.4.0	tb_variant_filter	0.4.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	209	19252
-tbl2gff3	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	229	1584
-tbvcfreport	tbvcfreport	Generate HTML report from SnpEff M.tuberculosis VCF(s)								Up-to-date	https://github.com/COMBAT-TB/tbvcfreport	Variant Analysis	tbvcfreport	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport	1.0.1	tbvcfreport	1.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	167	2290
-te_finder	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.21	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	81
-telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tetoolkit	tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	871
-tetyper	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	69
-tn93	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								Up-to-date	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.14	tn93	1.0.14			4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	4	0	0	17	1881
-tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9.1	tooldistillator	0.9.1	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tracegroomer	tracegroomer	TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.								Up-to-date	https://github.com/cbib/TraceGroomer	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer	0.1.4	tracegroomer	0.1.4			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tracy	tracy_align, tracy_assemble, tracy_basecall, tracy_decompose									To update				iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy	0.6.1	tracy	0.7.8			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	58	2439
-transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	348	5468
-transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	84	907
-transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	229
-trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	1	1	1	0	5862	305866
-trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	To update	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.2	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	13	9	13	13	13	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	11	13	12	0	1762	31951
-trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	151	1796
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942
-tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5
-tsne	tsne	T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation								To update	https://cran.r-project.org/web/packages/Rtsne/	Text Manipulation	tsne	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne	0.0.2	r-rtsne	0.13			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10	368
-twobittofa	ucsc-twobittofa	twoBitToFa is a tool to convert all or part of .2bit file to FASTA	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenpath/help/twoBit.html	Convert Formats	ucsc_twobittofa	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	469	ucsc-twobittofa	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	48	502
-tximport	tximport	Wrapper for the Bioconductor package tximport	tximport	tximport		tximport	An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	Up-to-date	http://bioconductor.org/packages/tximport/	Transcriptomics	tximport	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport	1.30.0	bioconductor-tximport	1.30.0	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	1408
-ucsc_axtchain	ucsc_axtchain	Chain together genome alignments	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_axtchain	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain	469	ucsc-axtchain	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ucsc_axttomaf	ucsc_axtomaf	Convert dataset from axt to MAF format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_axttomaf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf	469	ucsc-axttomaf	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ucsc_blat	ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	Up-to-date	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	469	ucsc-blat	469	Sequence alignment	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-ucsc_chainnet	ucsc_chainnet	Make alignment nets out of chains	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainnet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	469	ucsc-chainnet	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ucsc_chainprenet	ucsc_chainprenet	Remove chains that don't have a chance of being netted	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainprenet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet	469	ucsc-chainprenet	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ucsc_chainsort	ucsc_chainsort	Sort chains. By default sorts by score.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainsort	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort	469	ucsc-chainsort	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ucsc_netfilter	ucsc_netfilter	Filter out parts of net	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netfilter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter	469	ucsc-netfilter	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ucsc_netsyntenic	ucsc_netsyntenic	Add synteny info to a net dataset	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netsyntenic	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic	469	ucsc-netsyntenic	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ucsc_nettoaxt	ucsc_nettoaxt	Convert net (and chain) to axt format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_nettoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt	469	ucsc-nettoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	3	5	5	0	379	61618
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732
-usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	1060
-valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20	637
-vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	94	3164
-vardict	vardict_java	VarDict - calls SNVs and indels for tumour-normal pairs								To update	https://github.com/AstraZeneca-NGS/VarDictJava	Variant Analysis	vardict_java	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict	1.8.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	16	273
-variant_analyzer	mut2read, mut2sscs, read2mut	Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data								To update		Variant Analysis	variant_analyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer	2.0.0	matplotlib				3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3	88
-varscan	varscan_copynumber, varscan_mpileup, varscan_somatic	VarScan is a variant caller for high-throughput sequencing data								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/varscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan	2.4.3	varscan	2.4.6			3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	492	9779
-varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vcf2maf	vcf2maf	vcf2maf: Convert VCF into MAF								To update	https://github.com/mskcc/vcf2maf	Convert Formats	vcf2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf	1.6.21	vcf2maf	1.6.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	751
-vcf2tsv	vcf2tsv	Converts VCF files into tab-delimited format								To update	https://github.com/ekg/vcflib	Variant Analysis, Convert Formats	vcf2tsv	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	352	167913
-vcfaddinfo	vcfaddinfo	Adds info fields from the second dataset which are not present in the first dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfaddinfo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	357
-vcfallelicprimitives	vcfallelicprimitives	Splits alleleic primitives (gaps or mismatches) into multiple VCF lines								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfallelicprimitives	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	286	15803
-vcfanno	vcfanno	Annotate VCF files	vcfanno	vcfanno		vcfanno	Fast, flexible annotation of genetic variants.	SNP annotation	Genetic variation, Data submission, annotation and curation	Up-to-date	https://github.com/brentp/vcfanno	Variant Analysis	vcfanno	iuc	https://github.com/galaxyproject/tools-iuc/vcfanno/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno	0.3.5	vcfanno	0.3.5	SNP annotation	Genetic variation, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	87	872
-vcfannotate	vcfannotate	Intersect VCF records with BED annotations								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotate	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	77	2181
-vcfannotategenotypes	vcfannotategenotypes	Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotategenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	28	192
-vcfbedintersect	vcfbedintersect	Intersect VCF and BED datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbedintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	80	3217
-vcfbreakcreatemulti	vcfbreakcreatemulti	Break multiple alleles into multiple records, or combine overallpoing alleles into a single record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbreakcreatemulti	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	471
-vcfcheck	vcfcheck	Verify that the reference allele matches the reference genome								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcheck	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	675
-vcfcombine	vcfcombine	Combine multiple VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcombine	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	99	1695
-vcfcommonsamples	vcfcommonsamples	Output records belonging to samples commong between two datasets.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcommonsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	14	244
-vcfdistance	vcfdistance	Calculate distance to the nearest variant.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfdistance	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	40	564
-vcffilter	vcffilter2	Tool for filtering VCF files								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffilter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	882	44437
-vcffixup	vcffixup	Count the allele frequencies across alleles present in each record in the VCF file.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffixup	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	71	917
-vcfflatten	vcfflatten2	Removes multi-allelic sites by picking the most common alternate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfflatten	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	177
-vcfgeno2haplo	vcfgeno2haplo	Convert genotype-based phased alleles into haplotype alleles								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgeno2haplo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	36	718
-vcfgenotypes	vcfgenotypes	Convert numerical representation of genotypes to allelic.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	48	451
-vcfhethom	vcfhethom	Count the number of heterozygotes and alleles, compute het/hom ratio.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfhethom	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	90	1370
-vcfleftalign	vcfleftalign	Left-align indels and complex variants in VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfleftalign	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10	279
-vcfprimers	vcfprimers	Extract flanking sequences for each VCF record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfprimers	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	708
-vcfrandomsample	vcfrandomsample	Randomly sample sites from VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfrandomsample	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	159
-vcfselectsamples	vcfselectsamples	Select samples from a VCF file								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfselectsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	29	854
-vcfsort	vcfsort	Sort VCF dataset by coordinate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfsort	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	63	1852
-vcfvcfintersect	vcfvcfintersect	Intersect two VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfvcfintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect		vcflib	1.0.10			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	265	972774
-vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	74	2020
-velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741
-verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22
-vg	vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.59.0			0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3	477
-virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-virheat	virheat	generates a heatmap of allele frequencies from vcf files	virheat	virheat		virHEAT	VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.			Up-to-date	https://github.com/jonas-fuchs/virHEAT	Visualization, Variant Analysis	virheat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat	0.7.1	virheat	0.7.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	234
-volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1749	30946
-vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.29.0	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	8	8	8	8	8	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	8	8	8	0	182	8507
-vsnp	vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-weather_app	simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-weblogo3	rgweblogo3	Sequence Logo generator for fasta	weblogo	weblogo		WebLogo	Web-based application designed to make generate sequence logos.	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	To update		Graphics	weblogo3	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3	3.5.0	weblogo	3.7.9	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	74	2379
-wigtobigwig	ucsc_wigtobigwig	converts bedGraph (wig) files into binary bigwig	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenPath/help/bigWig.html	Convert Formats	ucsc_wigtobigwig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig	469	ucsc-wigtobigwig	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-windowmasker	windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.16.0			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	85
-winnowmap	winnowmap	A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.								Up-to-date	https://github.com/marbl/Winnowmap	Next Gen Mappers	winnowmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap	2.03	winnowmap	2.03			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	27	248
-xpath	xpath	XPath XML querying tool								To update	http://search.cpan.org/dist/XML-XPath/	Text Manipulation	xpath	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath	https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath		perl-xml-xpath	1.47			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3	234
-yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344
-zerone	zerone	ChIP-seq discretization and quality control								Up-to-date	https://github.com/nanakiksc/zerone	ChIP-seq	zerone	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone	https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone	1.0	zerone	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	90
-EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	9	0	0	11	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	102
-Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	82
-Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004
-ThermoRawFileParser	thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	2689
-ab1_fastq	ab1_fastq_converter	Tool to convert ab1 files into FASTQ files								To update		Convert Formats	ab1fastq	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq	1.20.0	bioconductor-sangerseqr	1.38.0			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	175	40271
-ambertools	ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap	Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.								To update	http://ambermd.org/AmberTools.php	Molecular Dynamics, Computational chemistry	ambertools	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools	21.10	ambertools				7	2	7	0	7	2	7	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	5	0	243	40666
-appendfdr	append_fdr									To update			appendfdr	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr	0.2.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-artbio_bam_cleaning	artbio_bam_cleaning	filter bam files before somatic-varscan or lumpy-smoove analysis								To update	http://artbio.fr	SAM, Variant Analysis	artbio_bam_cleaning	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	1.10+galaxy0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-astropytools	astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo	AstropyTools library contains Galaxy tools for elementary Astrophysical operations								To update	https://github.com/astropy/astropy	Astronomy	astropytools	volodymyrss	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	0.1.0+galaxy0	astropy				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3	11
-bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bed_to_protein_map	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	49	385
-bigwig_to_bedgraph	bigwig_to_bedgraph	Converts a bigWig file to bedGraph format								To update	http://artbio.fr	Convert Formats	bigwig_to_bedgraph	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	377+galaxy1	ucsc-bigwigtobedgraph	469			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	200	5749
-bigwig_to_wig	bigwig_to_wig	Converts a bigWig file to Wiggle (WIG) format								To update	https://artbio.fr	Convert Formats	bigwig_to_wig	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	3+galaxy0	ucsc-bigwiginfo	469			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-bio3d	bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize	Bio3d is a program that can be used to analyse molecular dynamics trajectories.								To update	http://thegrantlab.org/bio3d/index.php	Computational chemistry	bio3d	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	2.4_1	r-bio3d	2.3_3			5	4	5	0	5	4	5	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	5	5	0	510	8913
-biomoldyn	biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering	Tools for MD analysis								To update	https://github.com/moldyn/	Molecular Dynamics, Computational chemistry	biomoldyn	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn	1.5.2	scipy				4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	3	0	53	459
-biotransformer	biotransformer	BioTransformer is a tool for prediction of small molecule metabolism in mammals.	biotransformer	biotransformer		BioTransformer	BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	Up-to-date	https://bitbucket.org/djoumbou/biotransformerjar/src/master/	Metabolomics	biotransformer	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	3.0.20230403	biotransformer	3.0.20230403	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
-blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	101	1232
-blast_plus_remote_blastp	blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.16.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499
-blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	159	264558
-bumbershoot	idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	3	1348
-c3s	c3s	Copernicus Climate Change Service (C3S)								To update	https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset	Climate Analysis	c3s	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	0.3.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	198
-cads	cads	Copernicus Atmosphere Data Store (ADS)								To update	https://ads.atmosphere.copernicus.eu/#!/home	Climate Analysis	cads	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	52
-calisp	calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
-cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	101	7766
-cardinal	cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								Up-to-date	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	3.4.3	bioconductor-cardinal	3.4.3			0	9	11	11	0	9	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	9	11	9	0	277	48705
-cdo	cdo_info, cdo_operations	CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.								To update	https://code.mpimet.mpg.de/projects/cdo/	Climate Analysis		climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	2.0.0					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	16	217
-cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	6
-cesm	cesm	Community Earth System Model (CESM)								Up-to-date	https://www.cesm.ucar.edu/	Climate Analysis	cesm	climate	https://github.com/ESCOMP/CESM	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm	2.1.3	cesm	2.1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	13
-champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	19	174
-checkv	checkv_end_to_end	Assess quality of single-contig viral genomes	checkv	checkv		CheckV	CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	Up-to-date	https://bitbucket.org/berkeleylab/checkv/	Metagenomics	checkv	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv	1.0.3	checkv	1.0.3	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-climate-stripes	climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	237
-concat_multi_datasets	cat_multi_datasets	Concatenate multiple datasets tail-to-head, including collection datasets.								To update	http://artbio.fr	Text Manipulation	concatenate_multiple_datasets	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	1.4.3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	352	3612
-consensus_from_alignments	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55	585
-consolidate_vcfs	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cooler	cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify	cooler different tools to process Hi-C from mirnylab								To update	https://github.com/open2c/cooler	Epigenetics	cooler	lldelisle	https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler	0.9.3	htslib	1.21			4	0	5	0	4	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	11	81
-cpm_tpm_rpk	cpm_tpm_rpk	Generate CPM,TPM or RPK from raw counts								To update	http://artbio.fr	Transcriptomics	cpm_tpm_rpk	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	0.6.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-cta	cta_astro_tool	Basic simulation of CTA telescope observations using gammapy package								To update		Astronomy	cta_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta	0.0.1+galaxy0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-custom_pro_db	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	57	1652
-custom_pro_db_annotation_data_manager		CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	439
-data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	99	799
-data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	146	658
-data_manager_eggnog_mapper		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-data_manager_eggnog_mapper_abspath		download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dbbuilder	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	161	4758
-decoupler	score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk	decoupler - Ensemble of methods to infer biological activities								To update	https://decoupler-py.readthedocs.io/en/latest/	Transcriptomics	suite_decoupler	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler	1.4.0+galaxy3	decoupler	1.5.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6
-decoyfasta		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-dia_umpire	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	33
-dialignr	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	40
-diann	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	15
-diapysef	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	245
-diffacto	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	7
-digestdb	digestdb									To update			digestdb	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-directag_and_tagrecon										To update			directag_and_tagrecon	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-droplet-barcode-plot	_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	973
-dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	201	1599
-eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	1	3	1	0	510	30565
-embl2fa	embl2fa	Converts EMBL flat format to fasta format								To update	http://artbio.fr	Text Manipulation	embl2fa	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-encyclopedia	encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30			2	4	7	0	2	4	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	48	706
-eodie	eodie	Earth Observation Data Information Extractor								To update	https://eodie.readthedocs.io/	Climate Analysis	eodie	climate	https://gitlab.com/eetun-tiimi/EODIE	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie	1.0.2	eodie				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45
-essential_climate_variables	cds_essential_variability	Get Copernicus Essential Climate Variables for assessing climate variability								To update	https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview	Climate Analysis, Data Source	cds_essential_variability	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	331
-ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	461	29886
-fastg2protlib	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	28
-fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fates-emerald	ctsm_fates	EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model								To update	https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api	Climate Analysis	ctsm_fates	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	2.0	fates-emerald				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	261
-feature_alignment	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18
-fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	426	26274
-filter_compounds	filter_orgmet_anorg	Tool for filtering organometallics/anorganic compounds from a list of compounds.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	filter_compounds	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	3.1.1	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-filter_density	filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-filter_stats	filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-filter_vcf	filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-find_repeats	findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fisher_test	fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	17	645
-fragpipe	fragpipe	Data analysis for mass spectrometry-based proteomics.								Up-to-date	https://fragpipe.nesvilab.org/	Proteomics	fragpipe	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	20.0	fragpipe	20.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-free_energy		Free energy tools of BRIDGE.								To update		Molecular Dynamics, Computational chemistry	freeenergy	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	28	0	0	0	28	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fromHicupToJuicebox	fromHicupToJuicebox	Convert the output of hicup (as sam or bam) to the input of juicebox.								To update		Epigenetics	from_hicup_to_juicebox	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fromgtfTobed12	fromgtfTobed12	Convert GTF files to BED12 format								To update	https://pythonhosted.org/gffutils/contents.html	Convert Formats	fromgtftobed12	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	0.11.1+galaxy1	gffutils	0.13			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	27
-gatk4	filtermutectcalls, mergemutectstats, mutect2	Find somatic variations								To update	http://artbio.fr	Variant Analysis	gatk4	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gc_derivatization	gc_derivatization	In silico derivatization for GC.								Up-to-date	https://github.com/RECETOX/gc-meox-tms	Metabolomics	gc_derivatization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	1.0.1	gc-meox-tms	1.0.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	10	1475
-genomad	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	genomad	genomad		geNomad	geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.	Sequence annotation, Taxonomic classification	Sequence analysis	Up-to-date	https://github.com/apcamargo/genomad/	Metagenomics	genomad	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad	1.8.0	genomad	1.8.0	Sequence annotation, Taxonomic classification	Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-getTn5ExtendedCoverage	getTn5ExtendedCoverage	Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension								To update		Epigenetics	gettn5extendedcoverage	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-gffcompare_to_bed	gffcompare_to_bed	Filter and convert a gffCompare GTF to BED								To update	https://github.com/gpertea/gffcompare/	Convert Formats	gffcompare_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	0.2.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	131	2115
-gromacs	gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj	GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.								To update	https://github.com/gromacs	Molecular Dynamics, Computational chemistry	gromacs	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	2022	gromacs	2021.3			14	8	15	0	14	8	15	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	15	9	0	1442	177844
-gsc_center_scale	center_scale	Center or scale (standardize) data								To update	http://artbio.fr	Statistics	gsc_center_scale	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gsc_filter_cells	filter_cells	Filter single cell RNAseq data on libray depth and number of detected genes								To update	http://artbio.fr	Transcriptomics	gsc_filter_cells	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gsc_filter_genes	filter_genes	Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_filter_genes	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gsc_gene_expression_correlations	single_cell_gene_expression_correlations	Compute single-cell paire-wise gene expressions correlations								To update	http://artbio.fr	Transcriptomics	gsc_gene_expression_correlations	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gsc_mannwhitney_de	mannwhitney_de	Perform a mann-whitney differential testing between two sets of gene expression data								To update	http://artbio.fr	Transcriptomics	gsc_mannwhitney_de	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	4.1.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gsc_scran_normalize	scran_normalize	Normalize raw counts using scran								To update	http://artbio.fr	Transcriptomics	gsc_scran_normalize	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	1.28.1+galaxy0	bioconductor-scran	1.30.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	78
-gsc_signature_score	signature_score	Compute signature scores from single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_signature_score	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	2.3.9+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gtf-2-gene-list	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	155	1678
-guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hardklor	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2	111
-hess	hess_astro_tool	Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope								To update		Astronomy	hess_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess	0.0.2+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-high_dim_heatmap	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-idconvert	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	275
-incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-isolib	isolib	Create an isotopic pattern library for given compounds and adducts.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	isolib	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	1.0.1+galaxy0	bioconductor-metabocoreutils	1.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-justdiff	justdiff	Unix diff								To update	http://artbio.fr	Text Manipulation	justdiff	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	3.10+galaxy0	diffutils				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-justgzip	justgzip	Compress fastq sequence files								To update	http://artbio.fr	Convert Formats	justgzip	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	2.8+galaxy0	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-lfq_protein_quant	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	111
-longorf	longORF	obtain longest ORF in six-frame translations								To update		Sequence Analysis	longorf	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf	0.3.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ltq_iquant_cli										To update			ltq_iquant_cli	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-lumpy_smoove	lumpy_smoove, vcf2hrdetect	Galaxy wrapper of the lumpy-using smoove workflow								To update	http://artbio.fr	Variant Analysis	lumpy_smoove	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	0.2.8+galaxy1	svtyper	0.7.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0
-lumpy_sv	lumpy	Find structural variations								To update	http://artbio.fr	Variant Analysis	lumpy_sv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv	1.3	lumpy-sv	0.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-maldiquant	maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base				0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	2	2	0	25	3797
-manta	manta	Structural variant and indel caller for mapped sequencing data								To update	http://artbio.fr	Variant Analysis	manta	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/manta	https://github.com/ARTbio/tools-artbio/tree/main/tools/manta	1.6	manta	1.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	8	93
-map_peptides_to_bed	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	41
-mapping_quality_stats	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-matchms	matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting	Searching, filtering and converting mass spectral libraries.	matchms	matchms		Matchms	Tool to import, process, clean, and compare mass spectrometry data.	Spectral library search, Format validation, Filtering	Metabolomics	Up-to-date	https://github.com/matchms/matchms	Metabolomics	matchms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	0.27.0	matchms	0.27.0	Spectral library search, Format validation, Filtering	Metabolomics	2	14	14	11	2	14	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	10	187
-maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	415	6078
-mdanalysis	mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf	MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations								To update	https://github.com/MDAnalysis/mdanalysis	Computational chemistry	mdanalysis	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis	1.0.0	mdanalysis				10	5	10	0	10	5	10	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	139	3115
-mdfileconverter	md_converter	A tool for interconverting between different MD structure and trajectory file formats.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter	1.9.7	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	98	26427
-mdslicer	md_slicer	A tool for slicing trajectory files using MDTraj.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer	1.9.9	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	158
-mdtraj	traj_selections_and_merge	MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories								To update	https://github.com/mdtraj/mdtraj	Computational chemistry	mdtraj	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj	1.9.7	mdtraj				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	36
-mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	24
-measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-meta_proteome_analyzer	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	123
-metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	115	636
-metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	4181
-metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	104	2522
-mfassignr	mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot	The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements	mfassignr	mfassignr		MFAssignR	Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements.	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	Up-to-date	https://github.com/RECETOX/MFAssignR	Metabolomics	MFAssignR	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	1.1.1	r-mfassignr	1.1.1	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mgf_formatter	mgf_formatter									Up-to-date			mgf_formatter	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter	1.0.0	mgf-formatter	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-misc	target_screen, use_theoretical_mz_annotations									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	1.0.0	pandas				0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-moFF	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	759
-monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	264	3266
-morpheus	morpheus	Morpheus MS Search Application	morpheus	morpheus		Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.	Peptide database search	Proteomics	To update	https://cwenger.github.io/Morpheus	Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	288	morpheus	290	Peptide database search	Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	140
-mqppep	mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2
-ms2deepscore	ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training	Mass spectra similarity scoring using a trained ms2deepscore model.	ms2deepscore	ms2deepscore		MS2DeepScore	MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	Up-to-date	https://github.com/matchms/ms2deepscore	Metabolomics	ms2deepscore	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	2.0.0	ms2deepscore	2.0.0	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	19958
-msgfplus	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	507
-msmetaenhancer	msmetaenhancer		msmetaenhancer	msmetaenhancer		MSMetaEnhancer	Tool for mass spectra metadata annotation.	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/MSMetaEnhancer	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	0.4.0	msmetaenhancer	0.4.0	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	103
-msms_extractor	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	110
-msp_merge	msp_merge									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	0.1.0	matchms	0.27.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-msstats	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	144	2036
-msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	726
-mt2mq	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	19	270
-mutational_patterns	mutational_patterns	Mutational patterns and signatures in base substitution catalogs								Up-to-date	http://artbio.fr	Variant Analysis	mutational_patterns	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	3.12.0	bioconductor-mutationalpatterns	3.12.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	844
-mzml_validator	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	16	16	16	16	16	0	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	16	16	15	0	4066	365597
-oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45
-ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6
-ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-openmm	pdbfixer	OpenMM is a toolkit for molecular simulation using high performance GPU code.								To update	https://github.com/openmm	Molecular Dynamics, Computational chemistry	openmm	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	1.8.1	pdbfixer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	347
-openms	AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	3.1	openms	3.2.0			8	34	144	0	8	34	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	141	124	0	886	105432
-packmol	packmol	PACKMOL is a package for creating starting structures for Molecular Dynamics simulations								To update	http://m3g.iqm.unicamp.br/packmol/home.shtml	Molecular Dynamics, Computational chemistry	packmol	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol	18.169.1	packmol				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	288
-pathifier	pathifier	pathifier								Up-to-date	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	1.40.0	bioconductor-pathifier	1.40.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	228
-pathwaymatcher	reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	238
-pep_pointer	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	498
-pepquery	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	4862
-pepquery2	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2			0	1	3	0	0	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	13	717
-peptide_genomic_coordinate	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	468
-peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.11			4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	2	0	485	17477
-pepxml_to_xls		Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-percolator	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.7.1			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	5	368
-pi_db_tools	calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pindel	pindel	Pindel detects genome-wide structural variation.								Up-to-date	http://artbio.fr	Variant Analysis	pindel	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel	https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel	0.2.5b9	pindel	0.2.5b9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-pmd_fdr	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-positions2snv_alignment	positions2snv_alignment	Generate alignment of SNVs from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-positions2snv_invariant_alignment	positions2snv_invariant_alignment	Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_invariant_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-probecoverage	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-proteinpilot	convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml									To update			proteinpilot	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-proteomiqon_joinquantpepionswithproteins	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	366
-proteomiqon_labeledproteinquantification	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	14
-proteomiqon_labelfreeproteinquantification	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	6
-proteomiqon_mzmltomzlite	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	721
-proteomiqon_peptidedb	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	96
-proteomiqon_peptidespectrummatching	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	686
-proteomiqon_proteininference	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	89
-proteomiqon_psmbasedquantification	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	604
-proteomiqon_psmstatistics	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	694
-proteore_venn_diagram	proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15
-protxml_to_xls	protxml_to_xls									To update			protxml_to_xls	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-psm2sam	PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-psm_eval	psm_eval									To update			psm_eval	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval	0.1.0	binaries_for_psm_eval				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-psm_validation	psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	20
-psy-maps	psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.3.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	46	469
-pyprophet	pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5			0	5	6	0	0	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	6	6	0	33	2509
-pyscenic	pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/								To update		Transcriptomics, RNA, Sequence Analysis	suite_pyscenic	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic	0.12.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pyteomics	mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.4	Protein identification	Proteomics, Proteomics experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	81
-pyvo_integration	astronomical_archives	Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy								To update		Data Source	astronomicalarchivestool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration	0.10.0	astropy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	36
-qcxms	qcxms_getres, qcxms_neutral_run, qcxms_production_run	QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).								To update	https://github.com/grimme-lab/QCxMS	Computational chemistry, Molecular Dynamics	QCxMS	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	5.2.1					0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-quantp	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	230
-quantwiz_iq	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	32
-query	query	Execute an SQL statement on a set of tables								To update		Text Manipulation	query	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/query	https://github.com/RECETOX/galaxytools/tree/master/tools/query	0.2	click				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	59
-ramclustr	ramclustr, ramclustr_define_experiment		ramclustr	ramclustr		RAMClustR	A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	To update	https://rdrr.io/cran/RAMClustR/	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	1.3.0	r-ramclustr	1.3.1	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2	16
-rawtools	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	175
-rcx-tk	rcx-tk	Tools to process metadata or alkane files.								To update	https://github.com/RECETOX/rcx-tk	Metabolomics	rcx_tk	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk	0.1.0+galaxy0	rcx-tk	0.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-recetox_aplcms	recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise	Peak detection tool for HRMS profile data.	recetox-aplcms	recetox-aplcms		recetox-aplcms	recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	Up-to-date	https://github.com/RECETOX/recetox-aplcms	Metabolomics	recetox-aplcms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	0.13.3	r-recetox-aplcms	0.13.3	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	0	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	7	296
-recetox_msfinder	recetox_msfinder		recetox-msfinder	recetox-msfinder		recetox-msfinder	This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.	Annotation	Metabolomics	To update	https://github.com/RECETOX/recetox-msfinder	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	v3.5.2			Annotation	Metabolomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-recetox_xmsannotator	recetox_xmsannotator_advanced		recetox-xmsannotator	recetox-xmsannotator		recetox-xMSannotator	Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		Up-to-date	https://github.com/RECETOX/recetox-xMSannotator	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator	0.10.0	r-recetox-xmsannotator	0.10.0	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
-regex_find_replace	regex1, regexColumn1	Use python regular expressions to find and replace text								To update		Text Manipulation	regex_find_replace	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	1.0.3	python				2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	495	60307
-regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	22	526
-rem_complex	rem_complex	Removes molecular coordination complexes.								To update	https://github.com/RECETOX/galaxytools	Metabolomics	rem_complex	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rename_annotated_feature	rename_annotated_feature	Update column names in an abundance table using a annotation table with spectral matching results								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	rename_annotated_feature	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-repenrich	edger-repenrich, repenrich	Repeat element profiling								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	Transcriptomics	repenrich	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	2.31.1					0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0
-repenrich2	edger-repenrich2, repenrich2	Repeat element profiling using bowtie2 aligner								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	Transcriptomics	repenrich2	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	2.31.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-retip	retip_apply, retip_descriptors, retip_filter_rt, retip_train		retip	retip		Retip	Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.	Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	To update	https://github.com/PaoloBnn/Retip	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	0.5.4			Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-retrieve_ensembl_bed	retrieve_ensembl_bed	Retrieve cDNA features from Ensembl REST API in BED format								To update	http://rest.ensembl.org/	Data Source	retrieve_ensembl_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-revertR2orientationInBam	revertR2orientationInBam	Revert the mapped orientation of R2 mates in a bam.								To update		SAM	revertr2orientationinbam	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	0.0.2	samtools	1.21			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	39
-riassigner	riassigner, riassigner_from_comment		riassigner	riassigner		RIAssigner	RIAssigner is a python tool for retention index (RI) computation for GC-MS data.	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/RIAssigner	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	0.4.1	riassigner	0.4.1	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	1	2	2	1	1	2	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	15
-rmassbank	rmassbank	RMassBank is an R package for processing tandem MS files and building of MassBank records.								To update	https://github.com/MassBank/RMassBank	Metabolomics	rmassbank	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	3.0.0	python				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
-rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	1	1	0	67	377
-salmon-kallisto-mtx-to-10x	_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	86	561
-sambamba	sambamba_sample_or_filter	filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM								To update	http://artbio.fr	SAM	sambamba	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba	https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba	0.7.1+galaxy1	sambamba	1.0.1			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	9
-scaffold	scaffold, scaffold_export									To update			scaffold	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold	0.1.0	scaffold				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			27	27	27	0	27	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	0	2185	39356
-scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			1	2	6	0	1	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	16	387
-sccaf	run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out	SCCAF: Single Cell Clustering Assessment Framework.								To update	https://github.com/sccaf/sccaf	Transcriptomics	SCCAF	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf	0.0.9	sccaf	0.0.10			4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	110
-sceasy	sceasy_convert	Convert scRNA data object between popular formats								To update		Transcriptomics	sceasy	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy	0.0.5	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	90	721
-scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	83
-scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	25
-scripting	singularity_scriptrunner	suite_scripting								To update	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	Text Manipulation	scripting tools	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.4.0			14	14	14	11	14	14	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	181	1966
-sgwb	sgwb_astro_tool	SGWB								To update		Astronomy	sgwb_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb	0.0.1+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-shift-longitudes	shyft_longitudes	Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/	Climate Analysis	shift_longitudes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	63
-sixgill	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	24	293
-small_rna_clusters	small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-small_rna_maps	small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-small_rna_signatures	overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0
-smithsonian-volcanoes	smithsonian_volcanoes	Retrieve data from Volcanoes of the World (VOTW) Database								To update	https://volcano.si.edu/gvp_votw.cfm	Retrieve Data	smithsonian_volcanoes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	0.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-snv_matrix	snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-snvtocnv	sequenzaindex, snvtocnv	infer copy number variations from a vcf file with SNVs using R sequenza								To update	http://artbio.fr	Variant Analysis	snvtocnv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv	https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv	3.0.0+galaxy1	sequenza-utils	3.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spec2vec	spec2vec_similarity, spec2vec_training	Mass spectra similarity scoring using a trained Spec2Vec model.	spec2vec	spec2vec		Spec2Vec	Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	Up-to-date	https://github.com/iomega/spec2vec	Metabolomics	spec2vec	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	0.8.0	spec2vec	0.8.0	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spectrast2spectrast_irt	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spectrast2tsv	gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	56	769
-sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-sr_bowtie_dataset_annotation	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	7	4	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	21	225
-stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	10	325
-suite_snvphyl		SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-topologyeditors	gromacs_modify_topology, gromacs_extract_topology	Set of python scripts and associated tool files that can be used to modify topology files.								To update	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	Molecular Dynamics, Computational chemistry	topologyeditors	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	0	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	8	50
-translate_bed	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	49	643
-translate_bed_sequences	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	57
-ucsc-cell-browser	ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets								To update	https://cells.ucsc.edu/	Transcriptomics	ucsc_cell_browser	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser	1.0.0+galaxy1	ucsc-cell-browser	1.2.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	78	941
-unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115	5005
-uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	79	1360
-upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	86
-varscan_vaf	varscan_vaf	Compute variant allele frequency in vcf files generated by varscan.								To update	http://artbio.fr	Variant Analysis	varscan_vaf	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf	https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vcf2snvalignment	vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-verify_map	verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vibrant	vibrant	Virus Identification By iteRative ANnoTation	VIBRANT	VIBRANT		VIBRANT	Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	Up-to-date	https://github.com/AnantharamanLab/VIBRANT	Metagenomics	vibrant	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant	1.2.1	vibrant	1.2.1	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	351	12203
-virsorter	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	virsorter	virsorter		virsorter	Identify DNA and RNA virus sequences.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/jiarong/VirSorter2/	Metagenomics	virsorter	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter	2.2.4	virsorter	2.2.4	Taxonomic classification	Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vmd		vmd is a package for  visualizing and analyzing trajectories from molecular dynamics (MD) simulations								To update	https://www.ks.uiuc.edu/Research/vmd/	Computational chemistry	vmd	chemteam	https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-waveica	waveica	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.	waveica	waveica		WaveICA	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.	Standardisation and normalisation	Metabolomics	Up-to-date	https://github.com/RECETOX/WaveICA	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	0.2.0	r-recetox-waveica	0.2.0	Standardisation and normalisation	Metabolomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	6
-xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	5	5	2	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	175	5876
-xmlstarlet	xmlstarlet	Tool to convert a xml file from one metadata standard to another								To update		Convert Formats	xmlstarlet	ecology	https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet	https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet	1.6.1	xmlstarlet				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	14
-xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-xtb	xtb_molecular_optimization	Performs semiempirical molecular optimization.								To update	https://github.com/grimme-lab/xtb	Metabolomics	xtb_molecular_optimization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	6.6.1	xtb				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
-zeiss_lmd_converter	ZeissLMDconverter	Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	2.0.4	shapely				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	5462	5462	334	334	0	0	0	0	309	309	52	52	5771	5771	386	386
+phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	0	0	1	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	1199	1199	193	193	0	0	0	0	6	6	1	1	1205	1205	194	194
+phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1975	2034	246	258	0	0	0	0	553	564	140	144	2528	2598	386	402
+picard	picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile	Picard SAM/BAM manipulation tools.	picard_samtofastq	picard_samtofastq, picard_replacesamheader, picard_fastqtosam, picard_reordersam		picard_samtofastq	Create a FASTQ file.	Formatting	Sequencing	To update	http://broadinstitute.github.io/picard/	SAM	picard	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard	3.1.1	picard	3.2.0	Formatting	Sequencing	31	31	31	0	31	31	31	0	0	0	0	0	0	0	0	0	0	31	4	31	0	0	31	0	0	0	31	0	0	0	0	0	0	31	31	31	0	386934	399039	11024	11956	366646	589980	32000	57111	56622	62258	2845	3398	810202	1051277	45869	72465
+pick_value	pick_value	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	pick_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1607	1607	41	41	490	490	53	53	127	127	4	4	2224	2224	98	98
+picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	867	1128	144	165	0	0	0	0	2106	2106	121	121	2973	3234	265	286
+picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	2532	2532	382	382	1	1	1	1	1311	1311	83	83	3844	3844	466	466
+pilon	pilon	pilon is a tool for assembly improvement and variant analysis in bacteria	pilon	pilon		pilon	Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.	Sequence assembly, Analysis, Read alignment	Assembly	To update	https://github.com/broadinstitute/pilon/wiki	Variant Analysis	pilon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon	1.20.1	pilon	1.24	Sequence assembly, Analysis	Assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9045	9458	1115	1144	7989	7989	1070	1070	3945	4137	726	741	20979	21584	2911	2955
+pipelign	pipelign	Multipe sequence alignment								Up-to-date	https://github.com/asmmhossain/pipelign/	Next Gen Mappers	pipelign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign	0.2	pipelign	0.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1245	1245	231	231	9046	9046	630	630	0	0	0	0	10291	10291	861	861
+pizzly	pizzly	Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.								To update	https://github.com/pmelsted/pizzly/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly	0.37.3.1	pizzly	0.37.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	201	210	23	24	998	998	76	76	0	0	0	0	1199	1208	99	100
+plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37086	37272	711	734	6346	6346	583	583	3065	3065	61	61	46497	46683	1355	1378
+plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14652	14652	251	251	0	0	0	0	101	101	18	18	14753	14753	269	269
+plink	plink	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	plink	plink		PLINK	Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	Genetic variation analysis	GWAS study	Up-to-date	https://www.cog-genomics.org/plink	Genome-Wide Association Study	plink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink	1.90b6.21	plink	1.90b6.21	Genetic variation analysis	GWAS study	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	851	851	127	127	249	249	43	43	0	0	0	0	1100	1100	170	170
+polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	731	731	86	86	0	0	0	0	42	42	4	4	773	773	90	90
+porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	262015	262852	2627	2711	83623	83623	1918	1918	52558	52558	1037	1037	398196	399033	5582	5666
+poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	13	0	19942	20587	1055	1245	33619	40808	2183	2594	9261	9261	365	365	62822	70656	3603	4204
+presto	presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	63244	65177	1392	1599	0	0	0	0	63244	65177	1392	1599
+pretext	pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6			3	2	3	0	3	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	3463	3463	538	538	1853	1853	256	256	1097	1097	70	70	6413	6413	864	864
+prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10152	10626	253	281	10581	10581	1240	1240	0	0	0	0	20733	21207	1493	1521
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1902	1902	167	167	0	0	0	0	0	0	0	0	1902	1902	167	167
+progressivemauve	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update	http://darlinglab.org/mauve/user-guide/progressivemauve.html	Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2064	2173	678	695	2900	2900	1034	1034	0	0	0	0	4964	5073	1712	1729
+prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	464359	476554	7475	7721	313285	331256	11243	12384	131211	141875	4358	4947	908855	949685	23076	25052
+prot-scriber	prot_scriber	Protein annotation of short human readable descriptions								Up-to-date	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.6	prot-scriber	0.1.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	10	7	7	0	0	0	0	0	0	0	0	10	10	7	7
+proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3962	3962	501	501	0	0	0	0	0	0	0	0	3962	3962	501	501
+psiclass	psiclass	PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.	psiclass	psiclass		PsiCLASS	Reference-based transcriptome assembler for single or multiple RNA-seq samples	Transcriptome assembly	Sequence assembly	Up-to-date	https://github.com/splicebox/PsiCLASS	Transcriptomics	psiclass	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass	https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass	1.0.3	psiclass	1.0.3	Transcriptome assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	24	5	5	0	0	0	0	0	0	0	0	24	24	5	5
+pureclip	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1319	1507	81	92	0	0	0	0	0	0	0	0	1319	1507	81	92
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17782	17782	287	287	853	853	65	65	2224	2224	65	65	20859	20859	417	417
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22742	22742	557	557	2159	2159	716	716	776	776	448	448	25677	25677	1721	1721
+pyega3	pyega3	EGA python client uses the EGA REST API to download authorized datasets and files.								To update	https://github.com/EGA-archive/ega-download-client	Data Source	ega_download_client	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3	5.0.2	pyega3	5.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2716	2716	104	104	134	134	43	43	40	40	1	1	2890	2890	148	148
+pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12858	13232	986	996	8092	8092	943	943	3238	3238	124	124	24188	24562	2053	2063
+pysradb	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.2	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	163	163	35	35	0	0	0	0	0	0	0	0	163	163	35	35
+qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2092	2342	209	238	0	0	0	0	2	2	1	1	2094	2344	210	239
+qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	0	0	0	32	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	31825	34677	3375	3785	1	1	1	1	14	14	4	4	31840	34692	3380	3790
+qiime_extract_viz	qiime_extract_viz	Extract vizualization from QIIME artifacts								To update	http://www.qiime.org	Metagenomics	qiime_extract_viz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz	0.1.0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	8	8	0	0	0	0	0	0	0	0	17	17	8	8
+qq_tools	qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	0	4	4	4	0	684820	684820	3239	3239	90503	90503	3881	3881	29018	29018	826	826	804341	804341	7946	7946
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	67737	69738	7787	7971	51925	56602	9692	10646	32003	34145	3890	4127	151665	160485	21369	22744
+query_impc	query_impc	Contains a tool to query the IMPC database.								To update	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	Convert Formats, Web Services	query_impc	iuc	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc	0.9.0	requests				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	2	0	0	0	0	0	0	0	0	3	3	2	2
+query_tabular	filter_tabular, query_tabular, sqlite_to_tabular	Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular	3.3.1	python				3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	3	2	0	0	0	0	0	0	1	0	0	0	0	0	0	3	3	3	0	130124	135361	1265	1305	11135	11135	922	922	5939	5939	153	153	147198	152435	2340	2380
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3077	4581	395	518	2856	2856	1093	1093	1977	1977	19	19	7910	9414	1507	1630
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4844	4844	480	480	0	0	0	0	7	7	3	3	4851	4851	483	483
+rapidnj	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2		Phylogeny	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	339	339	30	30	1737	1737	256	256	6	6	1	1	2082	2082	287	287
+rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	42	42	9	9	0	0	0	0	0	0	0	0	42	42	9	9
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9477	9477	438	438	0	0	0	0	10585	10585	182	182	20062	20062	620	620
+raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10905	10905	966	966	5100	5114	587	587	4955	6094	765	892	20960	22113	2318	2445
+rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	655	655	57	57	0	0	0	0	0	0	0	0	655	655	57	57
+read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3710	3710	80	80	7	7	6	6	0	0	0	0	3717	3717	86	86
+recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.15.0	recentrifuge	1.15.0	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	472	472	92	92	32	32	13	13	6	6	4	4	510	510	109	109
+red	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	859	859	203	203	305	305	142	142	227	227	58	58	1391	1391	403	403
+repeatmasker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.0.9_p2	Genome annotation	Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5998	5998	810	810	7618	7618	803	803	3135	3135	292	292	16751	16751	1905	1905
+repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7963	7963	413	413	1485	1485	220	220	8402	8402	168	168	17850	17850	801	801
+repmatch_gff3	repmatch_gff3	Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.								To update		ChIP-seq	repmatch_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3		matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	415	721	128	219	0	0	0	0	415	721	128	219
+reshape2	cast, melt	Flexibly restructure and aggregate data using just the two functions melt and dcast								To update	https://cran.r-project.org/web/packages/reshape2/index.html	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2	1.4.2	r-reshape2				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	3543	3619	108	111	536	536	157	157	0	0	0	0	4079	4155	265	268
+resize_coordinate_window	resize_coordinate_window	Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.								To update		Genomic Interval Operations	resize_coordinate_window	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window	https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window	1.0.2	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	75	86	8	9	138	216	30	57	0	0	0	0	213	302	38	66
+revoluzer	revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	Structural variation detection	Molecular evolution, Phylogeny	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2444	2444	52	52	0	0	0	0	0	0	0	0	2444	2444	52	52
+rgcca	rgcca	multi-block analysis								To update	https://github.com/rgcca-factory/RGCCA	Statistics	rgcca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca	3.0.2	rgccacmd	3.0.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	44	44	6	6	77	77	35	35	0	0	0	0	121	121	41	41
+rgrnastar	rna_star, rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	star	star		STAR	Ultrafast universal RNA-seq data aligner	Sequence alignment	RNA-Seq, Transcriptomics	To update	https://github.com/alexdobin/STAR	Next Gen Mappers, Transcriptomics	rgrnastar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar	2.7.11a	star	2.7.11b	Sequence alignment	RNA-Seq, Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	2	0	0	0	2	0	0	0	0	0	1	2	2	2	0	438078	473957	10142	10900	325474	403925	15284	18791	49662	53138	1359	1449	813214	931020	26785	31140
+ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	171	171	20	20	0	0	0	0	0	0	0	0	171	171	20	20
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1522	1522	254	254	372	372	75	75	5	5	1	1	1899	1899	330	330
+roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15196	15685	1459	1501	12188	12188	1768	1768	4881	5539	518	555	32265	33412	3745	3824
+rp2biosensor	rp2biosensor	Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output								To update	https://github.com/brsynth/rp2biosensor	Synthetic Biology	rp2biosensor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor	3.2.1	rp2biosensor				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rp2paths	rp2paths	Enumerate and seperate the different pathways generated by RetroPath2.0								To update	https://github.com/brsynth/rp2paths	Synthetic Biology	rp2paths	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths	1.5.1	rp2paths				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rpbasicdesign	rpbasicdesign	Extracting enzyme IDs from rpSBML files								To update	https://github.com/brsynth/rpbasicdesign	Synthetic Biology	rpbasicdesign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign	1.2.2	rpbasicdesign				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rpfba	rpfba	Perform FBA for the RetroPath2.0 heterologous pathways								To update	https://github.com/brsynth/rptools/releases	Synthetic Biology	rpfba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba	5.12.3	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rptools	rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz	Suite of tools that work on rpSBML format								To update	https://github.com/brsynth/rptools	Synthetic Biology	rptools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools	5.13.1	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rrparser	rrparser	Reaction Rules Parser								To update	https://github.com/brsynth/RRParser	Synthetic Biology	rrparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser	2.5.2	rrparser				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	0	22	22	22	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	0	22	22	22	0	136315	147595	8341	9385	138707	161046	10696	12789	22718	23767	1593	1695	297740	332408	20630	23869
+ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1286	1364	178	193	2220	2220	299	299	0	0	0	0	3506	3584	477	492
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	463	463	119	119	1038	1038	87	87	410	410	24	24	1911	1911	230	230
+samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	Up-to-date	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.26	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+samtools										To update	https://github.com/samtools/samtools	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools	1.20	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+sansa	sansa_annotate	Sansa is a tool for structural variant annotation.								To update	https://github.com/dellytools/sansa	Variant Analysis	sansa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa	0.2.1	sansa	0.2.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	138	138	36	36	0	0	0	0	0	0	0	0	138	138	36	36
+sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	174	174	16	16	399	399	29	29	0	0	0	0	573	573	45	45
+sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	140	140	5	5	253	253	6	6	0	0	0	0	393	393	11	11
+sbml2sbol	sbml2sbol	Convert SBML to SBOL format								To update	https://github.com/neilswainston/SbmlToSbol	Synthetic Biology	sbml2sbol	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol	0.1.13	sbml2sbol				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	63789	64034	2543	2547	29962	29962	1185	1185	18028	18028	379	379	111779	112024	4107	4111
+scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	1345	1371	350	351	0	0	0	0	903	903	29	29	2248	2274	379	380
+sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1059	1059	222	222	426	426	71	71	1	1	1	1	1486	1486	294	294
+schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	809	809	78	78	3	3	2	2	105	105	16	16	917	917	96	96
+scikit-bio	scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1503	1955	283	402	0	0	0	0	1504	1956	284	403
+scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	901	901	90	90	0	0	0	0	0	0	0	0	901	901	90	90
+scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	284	632	34	38	786	786	61	61	1	1	1	1	1071	1419	96	100
+seacr	seacr	SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.								Up-to-date	https://github.com/FredHutch/SEACR	Epigenetics, ChIP-seq	seacr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr	1.3	seacr	1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5106	5106	116	116	6419	6419	241	241	0	0	0	0	11525	11525	357	357
+selenzy_wrapper	selenzy_wrapper	Performs enzyme selection from a reaction query.								Up-to-date	https://github.com/brsynth/selenzy-wrapper	Synthetic Biology	selenzy_wrapper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper	0.3.0	selenzy_wrapper	0.3.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	931	931	93	93	0	0	0	0	0	0	0	0	931	931	93	93
+seq2hla	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	342	342	40	40	0	0	0	0	0	0	0	0	342	342	40	40
+seqcomplexity	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	70	70	19	19	109	109	47	47	0	0	0	0	179	179	66	66
+seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	0	0	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3364	3364	247	247	0	0	0	0	244	244	33	33	3608	3608	280	280
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2424	2424	102	102	0	0	0	0	0	0	0	0	2424	2424	102	102
+seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4182	4182	42	42	0	0	0	0	0	0	0	0	4182	4182	42	42
+seqtk	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	Data handling, Sequence file editing		15	15	15	0	15	15	15	0	0	0	0	0	0	0	0	0	0	14	0	14	0	0	14	0	0	0	15	0	0	0	0	0	0	14	14	14	14	72816	73514	2210	2300	102777	107831	2313	2669	154613	154613	682	682	330206	335958	5205	5651
+seqwish	seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	271	271	2	2	0	0	0	0	0	0	0	0	271	271	2	2
+seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	0	1	1	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	121	121	11	11	32	32	5	5	0	0	0	0	153	153	16	16
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	913	913	308	308	0	0	0	0	568	568	73	73	1481	1481	381	381
+shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46125	47376	2273	2356	40577	40577	3971	3971	19960	21130	1085	1199	106662	109083	7329	7526
+sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	0	18184	18937	555	608	10514	10514	1063	1063	0	0	0	0	28698	29451	1618	1671
+simtext	abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix	A text mining framework for interactive analysis and visualization of similarities among biomedical entities.								To update	https://github.com/dlal-group/simtext	Text Manipulation	simtext	iuc	https://github.com/galaxyproject/tools-iuc/tools/simtext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext	0.0.2	r-argparse	1.0.1			0	2	4	0	0	2	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	220	220	68	68	0	0	0	0	416	416	10	10	636	636	78	78
+sina	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1369	1369	125	125	2398	2398	420	420	0	0	0	0	3767	3767	545	545
+sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								Up-to-date	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.10.1	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	284	284	70	70	165	165	38	38	14	14	2	2	463	463	110	110
+slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	346	362	16	16	872	872	67	67	0	0	0	0	1218	1234	83	83
+sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	141	141	26	26	0	0	0	0	0	0	0	0	141	141	26	26
+smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	158	158	8	8	0	0	0	0	0	0	0	0	158	158	8	8
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	325	325	61	61	137	137	54	54	843	843	63	63	1305	1305	178	178
+snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	1638	331	358	779	779	244	244	467	467	83	83	2745	2884	658	685
+snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1817	1817	14	14	4	4	2	2	136	136	4	4	1957	1957	20	20
+sniffles	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	Up-to-date	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	2.4	sniffles	2.4	Sequence analysis, Structural variation detection	Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1141	1141	134	134	606	606	156	156	2267	2267	80	80	4014	4014	370	370
+snipit	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	Base position variability plotting	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	905	905	44	44	0	0	0	0	0	0	0	0	905	905	44	44
+snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	0	121363	124773	3448	3602	92504	92504	3945	3945	48068	52034	2705	3073	261935	269311	10098	10620
+snp-dists	snp_dists	Compute pairwise SNP distance matrix from a FASTA sequence alignment								Up-to-date	https://github.com/tseemann/snp-dists	Variant Analysis	snp_dists	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists	0.8.2	snp-dists	0.8.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6555	6555	807	807	5336	5336	171	171	1143	1143	182	182	13034	13034	1160	1160
+snp-sites	snp_sites	Finds SNP sites from a multi-FASTA alignment file								Up-to-date	https://github.com/sanger-pathogens/snp-sites	Variant Analysis	snp_sites	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites	2.5.1	snp-sites	2.5.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6597	6597	663	663	1467	1467	256	256	1279	1279	114	114	9343	9343	1033	1033
+snpeff	snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names	SnpEff is a genetic variant annotation and effect prediction toolbox								To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff		biopython	1.70			5	5	5	0	5	5	5	0	0	0	0	0	0	0	1	0	0	0	5	5	0	0	5	0	0	0	5	0	0	0	0	0	0	5	5	5	0	103826	108296	7181	7908	115727	178110	15871	22769	11817	13155	2148	2321	231370	299561	25200	32998
+snpeff-covid19	snpeff_sars_cov_2	SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox	snpeff	snpeff		snpEff	Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).	SNP detection	DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs	To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff_sars_cov_2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19				SNP detection	DNA polymorphism, Nucleic acid sites, features and motifs	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	764895	764895	1276	1276	94572	94572	1636	1636	26990	26990	561	561	886457	886457	3473	3473
+snpfreqplot	snpfreqplot	A plotting app to visualise the SNPs across a region								To update	https://github.com/BrownfieldPlantLab/SNPFreqPlot	Variant Analysis	snpfreqplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot	1.0	r-base				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	3683	3683	338	338	1401	1401	433	433	1029	1029	95	95	6113	6113	866	866
+snpsift	snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck	snpEff SnpSift tools from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html	Variant Analysis	snpsift	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift		snpsift	5.2			8	8	8	0	8	8	8	0	0	0	0	0	0	0	8	0	0	0	0	8	0	0	8	0	0	0	8	0	0	0	0	0	0	8	8	8	0	5142904	5146618	3602	4283	382391	421190	7013	9678	104030	105024	960	1184	5629325	5672832	11575	15145
+snpsift_dbnsfp	snpSift_dbnsfp	snpEff SnpSift dbnsfp tool from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html#dbNSFP	Variant Analysis	snpsift_dbnsfp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	52	55	23	24	421	421	75	75	0	0	0	0	473	476	98	99
+snpsift_genesets	snpSift_geneSets	Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome								To update	http://snpeff.sourceforge.net/SnpSift.html#geneSets	Variant Analysis	snpsift_genesets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	509	554	107	128	474	474	190	190	0	0	0	0	983	1028	297	318
+socru	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	659	659	42	42	296	296	92	92	0	0	0	0	955	955	134	134
+sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	3	9	3	0	82716	87113	8209	8526	120471	120475	14787	14790	54067	61541	5817	6653	257254	269129	28813	29969
+spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	450	491	91	100	4270	4270	288	288	0	0	0	0	4720	4761	379	388
+spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	23	23	0	0	0	0	0	0	0	0	1436	1436	23	23
+spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	142	142	5	5	0	0	0	0	0	0	0	0	142	142	5	5
+sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	0	3	3	3	0	364871	376580	16710	17342	583675	678448	53271	59638	48131	50455	5910	6181	996677	1105483	75891	83161
+srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41
+stacks	stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	Data handling	Mapping, Population genetics	0	13	13	0	0	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	13	0	6440	11998	465	593	0	0	0	0	4070	4070	76	76	10510	16068	541	669
+stacks2	stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65			0	12	12	0	0	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	8437	8592	626	646	0	0	0	0	18016	18016	270	270	26453	26608	896	916
+star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update	https://github.com/STAR-Fusion/STAR-Fusion	Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1312	1383	82	95	2198	3076	234	303	173	173	3	3	3683	4632	319	401
+straindesign	straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion	Toolbox to optimize biological model								To update	https://github.com/brsynth/straindesign	Systems Biology, Synthetic Biology	straindesign	iuc	https://github.com/brsynth/straindesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign	3.2.2	straindesign	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+strelka	strelka_germline, strelka_somatic	Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision.								Up-to-date	https://github.com/Illumina/strelka/	Variant Analysis	strelka	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka	2.9.10	strelka	2.9.10			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	669	669	112	112	1261	1261	417	417	0	0	0	0	1930	1930	529	529
+stringtie	stringtie, stringtie_merge	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	stringtie	stringtie		StringTie	Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.	Transcriptome assembly, RNA-Seq analysis	Transcriptomics, RNA-seq	Up-to-date	http://ccb.jhu.edu/software/stringtie/	Transcriptomics	stringtie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie	2.2.3	stringtie	2.2.3	Transcriptome assembly, RNA-Seq analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	178677	187728	4972	5347	320780	407379	10825	15171	26375	28921	1032	1167	525832	624028	16829	21685
+structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2858	3001	118	123	0	0	0	0	0	0	0	0	2858	3001	118	123
+structureharvester	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date	http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/	Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+swift	swiftlink	Parallel MCMC Linkage Analysis								Up-to-date	https://github.com/ajm/swiftlink	Variant Analysis	swiftlink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift	1.0	swiftlink	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+syndiva	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	30	30	2	2	0	0	0	0	0	0	0	0	30	30	2	2
+table_compute	table_compute	Perform general-purpose table operations								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	Text Manipulation	table_compute	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute	1.2.4	pandas				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	216072	216115	1811	1814	12326	12326	1558	1558	16136	16136	256	256	244534	244577	3625	3628
+tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7011	8135	449	482	9473	28494	626	2183	850	1090	80	104	17334	37719	1155	2769
+tag_pileup_frequency	tag_pileup_frequency	Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup	Statistics, SAM, Genomic Interval Operations	tag_pileup_frequency	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency	1.0.2	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	158	164	15	16	722	865	40	73	0	0	0	0	880	1029	55	89
+tasmanian_mismatch	tasmanian_mismatch	Analysis of positional mismatches								Up-to-date	https://github.com/nebiolabs/tasmanian-mismatch	Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	4	61	61	7	7	0	0	0	0	65	65	11	11
+taxonkit	name2taxid, profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	taxonkit	taxonkit		TaxonKit	TaxonKit is a practical and efficient NCBI taxonomy toolkit.	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	Up-to-date	https://bioinf.shenwei.me/taxonkit/	Metagenomics	taxonkit	iuc	https://github.com/shenwei356/taxonkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit	0.17.0	taxonkit	0.17.0	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	36069	36922	5257	5431	25255	30822	5066	5826	7949	7949	1584	1584	69273	75693	11907	12841
+taxpasta	taxpasta	standardise taxonomic profiles	taxpasta	taxpasta		taxpasta	TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	Up-to-date	https://taxpasta.readthedocs.io/en/latest/	Sequence Analysis	taxpasta	iuc	https://github.com/taxprofiler/taxpasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta	0.7.0	taxpasta	0.7.0	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	34	34	5	5	0	0	0	0	0	0	0	0	34	34	5	5
+tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6372	6395	372	379	7339	7339	378	378	6966	6966	154	154	20677	20700	904	911
+tb_variant_filter	tb_variant_filter	M. tuberculosis H37Rv VCF filter								Up-to-date	https://github.com/COMBAT-TB/tb_variant_filter	Variant Analysis	tb_variant_filter	iuc	https://github.com/COMBAT-TB/tb_variant_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter	0.4.0	tb_variant_filter	0.4.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22977	22977	461	461	3888	3888	274	274	3611	3611	80	80	30476	30476	815	815
+tbl2gff3	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1941	1941	466	466	0	0	0	0	463	463	112	112	2404	2404	578	578
+tbvcfreport	tbvcfreport	Generate HTML report from SnpEff M.tuberculosis VCF(s)								Up-to-date	https://github.com/COMBAT-TB/tbvcfreport	Variant Analysis	tbvcfreport	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport	1.0.1	tbvcfreport	1.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2955	2955	335	335	6090	6090	348	348	2347	2347	72	72	11392	11392	755	755
+te_finder	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.21	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	20	20	0	0	0	0	0	0	0	0	203	203	20	20
+telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+tetoolkit	tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1013	1013	74	74	0	0	0	0	70	70	4	4	1083	1083	78	78
+tetyper	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	106	106	16	16	155	155	47	47	0	0	0	0	261	261	63	63
+tn93	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								Up-to-date	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.14	tn93	1.0.14			4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1915	1915	42	42	1972	1972	225	225	0	0	0	0	3887	3887	267	267
+tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9.1	tooldistillator	0.9.1	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	9	9	6	6	5	5	0	0	0	0	71	71	14	14
+tracegroomer	tracegroomer	TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.								Up-to-date	https://github.com/cbib/TraceGroomer	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer	0.1.4	tracegroomer	0.1.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	1	1	0	0	0	0	0	0	0	0	7	7	1	1
+tracy	tracy_align, tracy_assemble, tracy_basecall, tracy_decompose									To update				iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy	0.6.1	tracy	0.7.8			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	3314	3314	124	124	0	0	0	0	0	0	0	0	3314	3314	124	124
+transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5964	6418	944	970	5450	5450	1066	1066	2610	2796	317	344	14024	14664	2327	2380
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	1039	1039	189	189	2672	3349	467	485	358	358	47	47	4069	4746	703	721
+transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	250	254	31	31	174	174	45	45	0	0	0	0	424	428	76	76
+trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	1	1	1	0	352353	383014	14547	15408	632385	839058	39323	49850	125340	139097	5268	5975	1110078	1361169	59138	71233
+trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	To update	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.2	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	0	9	13	13	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	0	11	13	12	0	35698	39132	4376	4632	44509	44509	6714	6714	21883	23889	1924	2070	102090	107530	13014	13416
+trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1968	2080	374	390	1825	1825	527	527	862	1060	161	195	4655	4965	1062	1112
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	14681	14681	265	265	0	0	0	0	4488	4488	147	147	19169	19169	412	412
+tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	7	7	0	0	0	0	0	0	0	0	17	17	7	7
+tsne	tsne	T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation								To update	https://cran.r-project.org/web/packages/Rtsne/	Text Manipulation	tsne	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne	0.0.2	r-rtsne	0.13			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	379	31	37	281	281	64	64	0	0	0	0	536	660	95	101
+twobittofa	ucsc-twobittofa	twoBitToFa is a tool to convert all or part of .2bit file to FASTA	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenpath/help/twoBit.html	Convert Formats	ucsc_twobittofa	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	469	ucsc-twobittofa	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	413	511	84	118	441	441	123	123	21	21	2	2	875	973	209	243
+tximport	tximport	Wrapper for the Bioconductor package tximport	tximport	tximport		tximport	An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	Up-to-date	http://bioconductor.org/packages/tximport/	Transcriptomics	tximport	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport	1.30.0	bioconductor-tximport	1.30.0	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1802	1802	225	225	6963	6963	904	904	0	0	0	0	8765	8765	1129	1129
+ucsc_axtchain	ucsc_axtchain	Chain together genome alignments	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_axtchain	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain	469	ucsc-axtchain	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_axttomaf	ucsc_axtomaf	Convert dataset from axt to MAF format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_axttomaf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf	469	ucsc-axttomaf	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_blat	ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	Up-to-date	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	469	ucsc-blat	469	Sequence alignment	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_chainnet	ucsc_chainnet	Make alignment nets out of chains	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainnet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	469	ucsc-chainnet	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_chainprenet	ucsc_chainprenet	Remove chains that don't have a chance of being netted	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainprenet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet	469	ucsc-chainprenet	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_chainsort	ucsc_chainsort	Sort chains. By default sorts by score.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainsort	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort	469	ucsc-chainsort	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_netfilter	ucsc_netfilter	Filter out parts of net	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netfilter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter	469	ucsc-netfilter	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_netsyntenic	ucsc_netsyntenic	Add synteny info to a net dataset	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netsyntenic	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic	469	ucsc-netsyntenic	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ucsc_nettoaxt	ucsc_nettoaxt	Convert net (and chain) to axt format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_nettoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt	469	ucsc-nettoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	0	3	5	5	0	55050	68123	1090	1223	9001	9001	906	906	12444	12444	187	187	76495	89568	2183	2316
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	74120	77648	3798	3963	64946	90075	5451	7380	19516	20422	2010	2080	158582	188145	11259	13423
+usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1060	1060	5	5	0	0	0	0	0	0	0	0	1060	1060	5	5
+valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	518	677	75	87	234	234	65	65	0	0	0	0	752	911	140	152
+vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5936	5936	147	147	523	523	15	15	0	0	0	0	6459	6459	162	162
+vardict	vardict_java	VarDict - calls SNVs and indels for tumour-normal pairs								To update	https://github.com/AstraZeneca-NGS/VarDictJava	Variant Analysis	vardict_java	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict	1.8.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	381	381	37	37	0	0	0	0	0	0	0	0	381	381	37	37
+variant_analyzer	mut2read, mut2sscs, read2mut	Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data								To update		Variant Analysis	variant_analyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer	2.0.0	matplotlib				3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	95	95	14	14	516	516	67	67	0	0	0	0	611	611	81	81
+varscan	varscan_copynumber, varscan_mpileup, varscan_somatic	VarScan is a variant caller for high-throughput sequencing data								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/varscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan	2.4.3	varscan	2.4.6			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	10711	11502	1442	1560	16705	16705	3135	3135	1036	1036	100	100	28452	29243	4677	4795
+varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	273	273	12	12	0	0	0	0	0	0	0	0	273	273	12	12
+vcf2maf	vcf2maf	vcf2maf: Convert VCF into MAF								To update	https://github.com/mskcc/vcf2maf	Convert Formats	vcf2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf	1.6.21	vcf2maf	1.6.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1097	1097	46	46	0	0	0	0	65	65	5	5	1162	1162	51	51
+vcf2tsv	vcf2tsv	Converts VCF files into tab-delimited format								To update	https://github.com/ekg/vcflib	Variant Analysis, Convert Formats	vcf2tsv	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	169090	169679	823	874	16304	42215	1141	2594	2485	2511	169	172	187879	214405	2133	3640
+vcfaddinfo	vcfaddinfo	Adds info fields from the second dataset which are not present in the first dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfaddinfo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	882	888	30	32	6118	8261	36	114	175	184	6	6	7175	9333	72	152
+vcfallelicprimitives	vcfallelicprimitives	Splits alleleic primitives (gaps or mismatches) into multiple VCF lines								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfallelicprimitives	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6879	17157	897	1219	7585	14509	1245	1925	1648	1681	225	229	16112	33347	2367	3373
+vcfanno	vcfanno	Annotate VCF files	vcfanno	vcfanno		vcfanno	Fast, flexible annotation of genetic variants.	SNP annotation	Genetic variation, Data submission, annotation and curation	Up-to-date	https://github.com/brentp/vcfanno	Variant Analysis	vcfanno	iuc	https://github.com/galaxyproject/tools-iuc/vcfanno/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno	0.3.5	vcfanno	0.3.5	SNP annotation	Genetic variation, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1139	1139	174	174	0	0	0	0	0	0	0	0	1139	1139	174	174
+vcfannotate	vcfannotate	Intersect VCF records with BED annotations								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotate	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2797	2850	157	181	3668	14532	652	1392	494	507	61	63	6959	17889	870	1636
+vcfannotategenotypes	vcfannotategenotypes	Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotategenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	203	62	66	497	1828	155	387	184	197	11	11	870	2228	228	464
+vcfbedintersect	vcfbedintersect	Intersect VCF and BED datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbedintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3017	4049	185	210	4709	20250	406	1147	507	527	40	42	8233	24826	631	1399
+vcfbreakcreatemulti	vcfbreakcreatemulti	Break multiple alleles into multiple records, or combine overallpoing alleles into a single record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbreakcreatemulti	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	416	478	35	40	3969	10457	82	309	362	378	8	8	4747	11313	125	357
+vcfcheck	vcfcheck	Verify that the reference allele matches the reference genome								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcheck	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	745	767	96	106	803	1895	222	627	241	256	16	17	1789	2918	334	750
+vcfcombine	vcfcombine	Combine multiple VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcombine	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1422	2020	284	505	4951	19530	1021	2669	493	516	60	62	6866	22066	1365	3236
+vcfcommonsamples	vcfcommonsamples	Output records belonging to samples commong between two datasets.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcommonsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	233	253	37	42	234	1839	79	287	199	214	11	12	666	2306	127	341
+vcfdistance	vcfdistance	Calculate distance to the nearest variant.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfdistance	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	572	585	90	92	2063	2427	139	296	272	290	19	22	2907	3302	248	410
+vcffilter	vcffilter2	Tool for filtering VCF files								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffilter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37489	47142	2113	2218	75128	162296	5730	10533	2626	2736	320	331	115243	212174	8163	13082
+vcffixup	vcffixup	Count the allele frequencies across alleles present in each record in the VCF file.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffixup	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	926	957	155	173	2291	5323	313	985	251	265	28	31	3468	6545	496	1189
+vcfflatten	vcfflatten2	Removes multi-allelic sites by picking the most common alternate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfflatten	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	172	183	21	25	351	879	67	201	312	342	15	16	835	1404	103	242
+vcfgeno2haplo	vcfgeno2haplo	Convert genotype-based phased alleles into haplotype alleles								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgeno2haplo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	778	794	107	112	2414	3721	179	508	209	225	20	21	3401	4740	306	641
+vcfgenotypes	vcfgenotypes	Convert numerical representation of genotypes to allelic.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	502	555	134	143	3428	6338	266	858	220	235	23	24	4150	7128	423	1025
+vcfhethom	vcfhethom	Count the number of heterozygotes and alleles, compute het/hom ratio.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfhethom	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1964	1991	182	186	1937	3846	188	644	567	601	26	27	4468	6438	396	857
+vcfleftalign	vcfleftalign	Left-align indels and complex variants in VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfleftalign	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	269	310	38	42	358	1071	89	287	179	213	12	14	806	1594	139	343
+vcfprimers	vcfprimers	Extract flanking sequences for each VCF record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfprimers	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	590	711	28	33	403	831	75	200	190	214	10	12	1183	1756	113	245
+vcfrandomsample	vcfrandomsample	Randomly sample sites from VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfrandomsample	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	161	168	13	15	153	350	27	75	184	192	6	6	498	710	46	96
+vcfselectsamples	vcfselectsamples	Select samples from a VCF file								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfselectsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	830	900	69	88	1315	6257	237	959	344	363	20	21	2489	7520	326	1068
+vcfsort	vcfsort	Sort VCF dataset by coordinate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfsort	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1868	1904	174	185	18378	24175	422	1279	537	674	70	73	20783	26753	666	1537
+vcfvcfintersect	vcfvcfintersect	Intersect two VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfvcfintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	976544	977015	703	748	64155	81830	981	2103	11044	11069	225	229	1051743	1069914	1909	3080
+vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	2157	2287	198	209	3930	5591	446	744	0	0	0	0	6087	7878	644	953
+velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	4	4	22	22	6	6	16	16	1	1	45	45	11	11
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	25171	27943	3899	4270	51187	51187	7557	7557	28546	28619	3585	3613	104904	107749	15041	15440
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4715	5343	888	965	9575	9576	2117	2117	3271	5524	1050	1397	17561	20443	4055	4479
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	48	25	25	0	0	0	0	0	0	0	0	48	48	25	25
+vg	vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.59.0			0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	478	478	17	17	0	0	0	0	0	0	0	0	478	478	17	17
+virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	94	94	16	16	0	0	0	0	0	0	0	0	94	94	16	16
+virheat	virheat	generates a heatmap of allele frequencies from vcf files	virheat	virheat		virHEAT	VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.			Up-to-date	https://github.com/jonas-fuchs/virHEAT	Visualization, Variant Analysis	virheat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat	0.7.1	virheat	0.7.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	2	2	0	0	0	0	0	0	0	0	12	12	2	2
+virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	574	574	76	76	0	0	0	0	0	0	0	0	574	574	76	76
+volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	34917	36852	3670	3786	54931	54931	5597	5597	7183	7183	905	905	97031	98966	10172	10288
+vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.29.0	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	0	8	8	8	0	9694	10338	559	628	12282	53546	1031	2007	5334	5672	246	277	27310	69556	1836	2912
+vsnp	vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+weather_app	simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+weblogo3	rgweblogo3	Sequence Logo generator for fasta	weblogo	weblogo		WebLogo	Web-based application designed to make generate sequence logos.	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	To update		Graphics	weblogo3	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3	3.5.0	weblogo	3.7.9	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2720	2818	206	228	10299	30578	1354	3657	1226	1285	50	59	14245	34681	1610	3944
+wigtobigwig	ucsc_wigtobigwig	converts bedGraph (wig) files into binary bigwig	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenPath/help/bigWig.html	Convert Formats	ucsc_wigtobigwig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig	469	ucsc-wigtobigwig	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1601	1601	106	106	1108	1108	172	172	200	200	15	15	2909	2909	293	293
+windowmasker	windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.16.0			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	537	537	19	19	12	12	7	7	297	297	2	2	846	846	28	28
+winnowmap	winnowmap	A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.								Up-to-date	https://github.com/marbl/Winnowmap	Next Gen Mappers	winnowmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap	2.03	winnowmap	2.03			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	279	279	46	46	12	12	4	4	0	0	0	0	291	291	50	50
+xpath	xpath	XPath XML querying tool								To update	http://search.cpan.org/dist/XML-XPath/	Text Manipulation	xpath	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath	https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath		perl-xml-xpath	1.47			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	128	235	7	8	0	1	0	1	0	0	0	0	128	236	7	9
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	618	618	176	176	336	336	62	62	588	588	25	25	1542	1542	263	263
+zerone	zerone	ChIP-seq discretization and quality control								Up-to-date	https://github.com/nanakiksc/zerone	ChIP-seq	zerone	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone	https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone	1.0	zerone	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	83	96	9	12	0	0	0	0	0	0	0	0	83	96	9	12
+EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	516	516	128	128	0	0	0	0	0	0	0	0	516	516	128	128
+Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	352	352	36	36	0	0	0	0	0	0	0	0	352	352	36	36
+Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	53	53	18	18	0	0	0	0	0	0	0	0	53	53	18	18
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	1038	1038	146	146	0	0	0	0	849	849	38	38	1887	1887	184	184
+ThermoRawFileParser	thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2467	2959	88	124	0	0	0	0	1097	1097	18	18	3564	4056	106	142
+ab1_fastq	ab1_fastq_converter	Tool to convert ab1 files into FASTQ files								To update		Convert Formats	ab1fastq	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq	1.20.0	bioconductor-sangerseqr	1.38.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	49465	49465	281	281	0	0	0	0	0	0	0	0	49465	49465	281	281
+ambertools	ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap	Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.								To update	http://ambermd.org/AmberTools.php	Molecular Dynamics, Computational chemistry	ambertools	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools	21.10	ambertools				7	2	7	0	7	2	7	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	5	0	41793	41881	510	511	1126	1126	159	159	1552	1552	85	85	44471	44559	754	755
+appendfdr	append_fdr									To update			appendfdr	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr	0.2.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	75	75	9	9	0	0	0	0	0	0	0	0	75	75	9	9
+artbio_bam_cleaning	artbio_bam_cleaning	filter bam files before somatic-varscan or lumpy-smoove analysis								To update	http://artbio.fr	SAM, Variant Analysis	artbio_bam_cleaning	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	1.10+galaxy0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+astropytools	astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo	AstropyTools library contains Galaxy tools for elementary Astrophysical operations								To update	https://github.com/astropy/astropy	Astronomy	astropytools	volodymyrss	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	0.1.0+galaxy0	astropy				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	13	13	5	5	0	0	0	0	0	0	0	0	13	13	5	5
+bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+bed_to_protein_map	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	410	419	134	137	363	363	99	99	158	158	13	13	931	940	246	249
+bigwig_to_bedgraph	bigwig_to_bedgraph	Converts a bigWig file to bedGraph format								To update	http://artbio.fr	Convert Formats	bigwig_to_bedgraph	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	377+galaxy1	ucsc-bigwigtobedgraph	469			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5769	6802	567	650	0	0	0	0	0	3	0	1	5769	6805	567	651
+bigwig_to_wig	bigwig_to_wig	Converts a bigWig file to Wiggle (WIG) format								To update	https://artbio.fr	Convert Formats	bigwig_to_wig	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	3+galaxy0	ucsc-bigwiginfo	469			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+bio3d	bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize	Bio3d is a program that can be used to analyse molecular dynamics trajectories.								To update	http://thegrantlab.org/bio3d/index.php	Computational chemistry	bio3d	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	2.4_1	r-bio3d	2.3_3			5	4	5	0	5	4	5	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	5	5	0	10600	10729	1150	1159	1042	1042	255	255	2756	2756	215	215	14398	14527	1620	1629
+biomoldyn	biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering	Tools for MD analysis								To update	https://github.com/moldyn/	Molecular Dynamics, Computational chemistry	biomoldyn	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn	1.5.2	scipy				4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	3	0	493	493	119	119	441	441	148	148	0	0	0	0	934	934	267	267
+biotransformer	biotransformer	BioTransformer is a tool for prediction of small molecule metabolism in mammals.	biotransformer	biotransformer		BioTransformer	BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	Up-to-date	https://bitbucket.org/djoumbou/biotransformerjar/src/master/	Metabolomics	biotransformer	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	3.0.20230403	biotransformer	3.0.20230403	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	48	48	1	1	48	48	1	1
+blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1063	1237	257	300	0	0	0	0	0	0	0	0	1063	1237	257	300
+blast_plus_remote_blastp	blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.16.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24916	27120	283	347	0	0	0	0	0	0	0	0	24916	27120	283	347
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1
+blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	264392	265217	483	552	0	0	0	0	0	0	0	0	264392	265217	483	552
+bumbershoot	idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	1186	1356	21	32	0	0	0	0	0	0	0	0	1186	1356	21	32
+c3s	c3s	Copernicus Climate Change Service (C3S)								To update	https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset	Climate Analysis	c3s	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	0.3.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	234	234	11	11	4	4	4	4	92	92	3	3	330	330	18	18
+cads	cads	Copernicus Atmosphere Data Store (ADS)								To update	https://ads.atmosphere.copernicus.eu/#!/home	Climate Analysis	cads	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	52	52	1	1	0	0	0	0	0	0	0	0	52	52	1	1
+calisp	calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	9869	9869	158	158	0	0	0	0	6886	6886	146	146	16755	16755	304	304
+cardinal	cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								Up-to-date	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	3.4.3	bioconductor-cardinal	3.4.3			0	9	11	0	0	9	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	0	9	11	9	0	41875	50702	663	713	12	12	1	1	7512	7512	231	231	49399	58226	895	945
+cdo	cdo_info, cdo_operations	CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.								To update	https://code.mpimet.mpg.de/projects/cdo/	Climate Analysis		climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	2.0.0					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	218	218	17	17	0	0	0	0	0	0	0	0	218	218	17	17
+cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	4	4	0	0	0	0	0	0	0	0	8	8	4	4
+cesm	cesm	Community Earth System Model (CESM)								Up-to-date	https://www.cesm.ucar.edu/	Climate Analysis	cesm	climate	https://github.com/ESCOMP/CESM	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm	2.1.3	cesm	2.1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	14	2	2	0	0	0	0	0	0	0	0	14	14	2	2
+champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	183	183	20	20	0	0	0	0	0	0	0	0	183	183	20	20
+checkv	checkv_end_to_end	Assess quality of single-contig viral genomes	checkv	checkv		CheckV	CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	Up-to-date	https://bitbucket.org/berkeleylab/checkv/	Metagenomics	checkv	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv	1.0.3	checkv	1.0.3	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+climate-stripes	climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	239	239	35	35	16	16	2	2	182	182	3	3	437	437	40	40
+concat_multi_datasets	cat_multi_datasets	Concatenate multiple datasets tail-to-head, including collection datasets.								To update	http://artbio.fr	Text Manipulation	concatenate_multiple_datasets	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	1.4.3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	4822	4824	613	614	1317	1317	204	204	3088	3795	252	289	9227	9936	1069	1107
+consensus_from_alignments	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1184	1184	154	154	0	0	0	0	0	0	0	0	1184	1184	154	154
+consolidate_vcfs	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cooler	cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify	cooler different tools to process Hi-C from mirnylab								To update	https://github.com/open2c/cooler	Epigenetics	cooler	lldelisle	https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler	0.9.3	htslib	1.21			4	0	5	0	4	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	170	170	26	26	195	195	39	39	0	0	0	0	365	365	65	65
+cpm_tpm_rpk	cpm_tpm_rpk	Generate CPM,TPM or RPK from raw counts								To update	http://artbio.fr	Transcriptomics	cpm_tpm_rpk	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	0.6.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cta	cta_astro_tool	Basic simulation of CTA telescope observations using gammapy package								To update		Astronomy	cta_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta	0.0.1+galaxy0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+custom_pro_db	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1729	1744	144	146	450	450	72	72	361	361	12	12	2540	2555	228	230
+custom_pro_db_annotation_data_manager		CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	441	451	83	87	3	3	2	2	0	0	0	0	444	454	85	89
+data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	867	877	213	216	339	339	94	94	64	64	5	5	1270	1280	312	315
+data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	967	967	308	308	0	0	0	0	0	0	0	0	967	967	308	308
+data_manager_eggnog_mapper		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+data_manager_eggnog_mapper_abspath		download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dbbuilder	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4813	5555	687	805	0	0	0	0	961	961	87	87	5774	6516	774	892
+decoupler	score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk	decoupler - Ensemble of methods to infer biological activities								To update	https://decoupler-py.readthedocs.io/en/latest/	Transcriptomics	suite_decoupler	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler	1.4.0+galaxy3	decoupler	1.5.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	54	6	6	0	0	0	0	0	0	0	0	54	54	6	6
+decoyfasta		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dia_umpire	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	28	33	4	4	0	0	0	0	134	134	4	4	162	167	8	8
+dialignr	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	40	2	2	0	0	0	0	0	0	0	0	40	40	2	2
+diann	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	72	72	14	14	0	0	0	0	171	171	14	14	243	243	28	28
+diapysef	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	262	262	38	38	0	0	0	0	256	256	6	6	518	518	44	44
+diffacto	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	11	7	7	0	0	0	0	0	0	0	0	11	11	7	7
+digestdb	digestdb									To update			digestdb	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+directag_and_tagrecon										To update			directag_and_tagrecon	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+droplet-barcode-plot	_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1151	1151	184	184	356	356	77	77	3	3	1	1	1510	1510	262	262
+dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1900	1901	412	413	609	609	131	131	0	0	0	0	2509	2510	543	544
+eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	1	3	1	0	34432	34437	1149	1152	42	42	2	2	21027	21027	413	413	55501	55506	1564	1567
+embl2fa	embl2fa	Converts EMBL flat format to fasta format								To update	http://artbio.fr	Text Manipulation	embl2fa	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+encyclopedia	encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30			2	4	7	0	2	4	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	738	738	98	98	1	1	1	1	42	42	4	4	781	781	103	103
+eodie	eodie	Earth Observation Data Information Extractor								To update	https://eodie.readthedocs.io/	Climate Analysis	eodie	climate	https://gitlab.com/eetun-tiimi/EODIE	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie	1.0.2	eodie				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	45	45	4	4	0	0	0	0	0	0	0	0	45	45	4	4
+essential_climate_variables	cds_essential_variability	Get Copernicus Essential Climate Variables for assessing climate variability								To update	https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview	Climate Analysis, Data Source	cds_essential_variability	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	232	336	39	40	0	0	0	0	0	0	0	0	232	336	39	40
+ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	30917	32191	1142	1257	36869	36869	1346	1346	5236	5236	230	230	73022	74296	2718	2833
+fastg2protlib	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	29	29	8	8	0	0	0	0	0	0	0	0	29	29	8	8
+fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fates-emerald	ctsm_fates	EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model								To update	https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api	Climate Analysis	ctsm_fates	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	2.0	fates-emerald				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	264	264	69	69	34	34	11	11	103	103	1	1	401	401	81	81
+feature_alignment	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	18	18	1	1	0	0	0	0	0	0	0	0	18	18	1	1
+fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	1	1	1	1
+filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	26717	29932	1026	1072	42990	42990	1176	1176	9619	9619	230	230	79326	82541	2432	2478
+filter_compounds	filter_orgmet_anorg	Tool for filtering organometallics/anorganic compounds from a list of compounds.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	filter_compounds	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	3.1.1	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+filter_density	filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+filter_stats	filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+filter_vcf	filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+find_repeats	findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fisher_test	fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	661	715	52	54	0	0	0	0	167	167	15	15	828	882	67	69
+fragpipe	fragpipe	Data analysis for mass spectrometry-based proteomics.								Up-to-date	https://fragpipe.nesvilab.org/	Proteomics	fragpipe	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	20.0	fragpipe	20.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	64	64	9	9	0	0	0	0	0	0	0	0	64	64	9	9
+free_energy		Free energy tools of BRIDGE.								To update		Molecular Dynamics, Computational chemistry	freeenergy	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fromHicupToJuicebox	fromHicupToJuicebox	Convert the output of hicup (as sam or bam) to the input of juicebox.								To update		Epigenetics	from_hicup_to_juicebox	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fromgtfTobed12	fromgtfTobed12	Convert GTF files to BED12 format								To update	https://pythonhosted.org/gffutils/contents.html	Convert Formats	fromgtftobed12	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	0.11.1+galaxy1	gffutils	0.13			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	11	11	0	0	0	0	0	0	0	0	27	27	11	11
+gatk4	filtermutectcalls, mergemutectstats, mutect2	Find somatic variations								To update	http://artbio.fr	Variant Analysis	gatk4	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gc_derivatization	gc_derivatization	In silico derivatization for GC.								Up-to-date	https://github.com/RECETOX/gc-meox-tms	Metabolomics	gc_derivatization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	1.0.1	gc-meox-tms	1.0.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	1409	1498	39	42	0	0	0	0	0	0	0	0	1409	1498	39	42
+genomad	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	genomad	genomad		geNomad	geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.	Sequence annotation, Taxonomic classification	Sequence analysis	To update	https://github.com/apcamargo/genomad/	Metagenomics	genomad	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad	1.8.0	genomad	1.8.1	Sequence annotation, Taxonomic classification	Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+getTn5ExtendedCoverage	getTn5ExtendedCoverage	Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension								To update		Epigenetics	gettn5extendedcoverage	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gffcompare_to_bed	gffcompare_to_bed	Filter and convert a gffCompare GTF to BED								To update	https://github.com/gpertea/gffcompare/	Convert Formats	gffcompare_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	0.2.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1375	2230	329	347	1071	1071	362	362	492	492	64	64	2938	3793	755	773
+gromacs	gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj	GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.								To update	https://github.com/gromacs	Molecular Dynamics, Computational chemistry	gromacs	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	2022	gromacs	2021.3			14	8	15	0	14	8	15	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	15	9	0	184067	184203	3441	3451	9382	9382	1438	1438	10325	10325	648	648	203774	203910	5527	5537
+gsc_center_scale	center_scale	Center or scale (standardize) data								To update	http://artbio.fr	Statistics	gsc_center_scale	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gsc_filter_cells	filter_cells	Filter single cell RNAseq data on libray depth and number of detected genes								To update	http://artbio.fr	Transcriptomics	gsc_filter_cells	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gsc_filter_genes	filter_genes	Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_filter_genes	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gsc_gene_expression_correlations	single_cell_gene_expression_correlations	Compute single-cell paire-wise gene expressions correlations								To update	http://artbio.fr	Transcriptomics	gsc_gene_expression_correlations	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gsc_mannwhitney_de	mannwhitney_de	Perform a mann-whitney differential testing between two sets of gene expression data								To update	http://artbio.fr	Transcriptomics	gsc_mannwhitney_de	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	4.1.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gsc_scran_normalize	scran_normalize	Normalize raw counts using scran								To update	http://artbio.fr	Transcriptomics	gsc_scran_normalize	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	1.28.1+galaxy0	bioconductor-scran	1.30.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	24	24	3	3	2	2	10	10	2	2	102	102	28	28
+gsc_signature_score	signature_score	Compute signature scores from single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_signature_score	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	2.3.9+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gtf-2-gene-list	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1982	1983	323	324	1040	1040	343	343	205	205	38	38	3227	3228	704	705
+guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	1	1	7	7	1	1
+hardklor	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	98	111	5	8	0	0	0	0	0	0	0	0	98	111	5	8
+hess	hess_astro_tool	Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope								To update		Astronomy	hess_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess	0.0.2+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1
+high_dim_heatmap	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	2	2	0	0	0	0	0	0	0	0	18	18	2	2
+hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+idconvert	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	241	276	24	33	0	0	0	0	0	0	0	0	241	276	24	33
+incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	70	7	7	0	0	0	0	0	0	0	0	70	70	7	7
+isolib	isolib	Create an isotopic pattern library for given compounds and adducts.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	isolib	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	1.0.1+galaxy0	bioconductor-metabocoreutils	1.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+justdiff	justdiff	Unix diff								To update	http://artbio.fr	Text Manipulation	justdiff	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	3.10+galaxy0	diffutils				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+justgzip	justgzip	Compress fastq sequence files								To update	http://artbio.fr	Convert Formats	justgzip	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	2.8+galaxy0	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+lfq_protein_quant	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	78	116	12	19	0	0	0	0	0	0	0	0	78	116	12	19
+longorf	longORF	obtain longest ORF in six-frame translations								To update		Sequence Analysis	longorf	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf	0.3.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ltq_iquant_cli										To update			ltq_iquant_cli	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+lumpy_smoove	lumpy_smoove, vcf2hrdetect	Galaxy wrapper of the lumpy-using smoove workflow								To update	http://artbio.fr	Variant Analysis	lumpy_smoove	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	0.2.8+galaxy1	svtyper	0.7.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+lumpy_sv	lumpy	Find structural variations								To update	http://artbio.fr	Variant Analysis	lumpy_sv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv	1.3	lumpy-sv	0.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+maldiquant	maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base				0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1452	3822	61	68	0	0	0	0	1065	1065	39	39	2517	4887	100	107
+manta	manta	Structural variant and indel caller for mapped sequencing data								To update	http://artbio.fr	Variant Analysis	manta	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/manta	https://github.com/ARTbio/tools-artbio/tree/main/tools/manta	1.6	manta	1.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	218	218	34	34	0	0	0	0	0	0	0	0	218	218	34	34
+map_peptides_to_bed	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	38	44	6	7	0	0	0	0	0	0	0	0	38	44	6	7
+mapping_quality_stats	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	51	51	4	4	0	0	0	0	0	0	0	0	51	51	4	4
+matchms	matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting	Searching, filtering and converting mass spectral libraries.	matchms	matchms		Matchms	Tool to import, process, clean, and compare mass spectrometry data.	Spectral library search, Format validation, Filtering	Metabolomics	Up-to-date	https://github.com/matchms/matchms	Metabolomics	matchms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	0.27.0	matchms	0.27.0	Spectral library search, Format validation, Filtering	Metabolomics	2	14	14	0	2	14	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	1620	1620	70	70	27	27	8	8	1685	1685	12	12	3332	3332	90	90
+maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6863	7021	1251	1264	2798	2798	543	543	3189	3189	352	352	12850	13008	2146	2159
+mdanalysis	mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf	MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations								To update	https://github.com/MDAnalysis/mdanalysis	Computational chemistry	mdanalysis	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis	1.0.0	mdanalysis				10	5	10	0	10	5	10	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	3209	3268	318	326	182	182	51	51	397	397	39	39	3788	3847	408	416
+mdfileconverter	md_converter	A tool for interconverting between different MD structure and trajectory file formats.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter	1.9.7	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26720	26762	251	253	784	784	54	54	977	977	53	53	28481	28523	358	360
+mdslicer	md_slicer	A tool for slicing trajectory files using MDTraj.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer	1.9.9	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	174	174	19	19	6	6	4	4	441	441	7	7	621	621	30	30
+mdtraj	traj_selections_and_merge	MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories								To update	https://github.com/mdtraj/mdtraj	Computational chemistry	mdtraj	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj	1.9.7	mdtraj				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	36	8	8	63	63	4	4	0	0	0	0	99	99	12	12
+mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	3	3	0	0	0	0	0	0	0	0	20	25	3	3
+measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	9	9	0	0	0	0	0	0	0	0	27	27	9	9
+meta_proteome_analyzer	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	126	126	20	20	0	0	0	0	0	0	0	0	126	126	20	20
+metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	980	980	323	323	0	0	0	0	0	0	0	0	980	980	323	323
+metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4471	4471	29	29	0	0	0	0	0	0	0	0	4471	4471	29	29
+metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	2730	2831	260	262	0	0	0	0	1540	1540	71	71	4270	4371	331	333
+mfassignr	mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot	The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements	mfassignr	mfassignr		MFAssignR	Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements.	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	Up-to-date	https://github.com/RECETOX/MFAssignR	Metabolomics	MFAssignR	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	1.1.1	r-mfassignr	1.1.1	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	8	8	0	0	0	0	0	0	0	0	10	10	8	8
+mgf_formatter	mgf_formatter									Up-to-date			mgf_formatter	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter	1.0.0	mgf-formatter	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1458	1458	36	36	1458	1458	36	36
+misc	target_screen, use_theoretical_mz_annotations									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	1.0.0	pandas				0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	2	2	0	0	0	0	0	0	0	0	6	6	2	2
+moFF	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	331	762	20	34	0	0	0	0	137	137	4	4	468	899	24	38
+monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3610	3610	559	559	1728	1728	434	434	0	0	0	0	5338	5338	993	993
+morpheus	morpheus	Morpheus MS Search Application	morpheus	morpheus		Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.	Peptide database search	Proteomics	To update	https://cwenger.github.io/Morpheus	Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	288	morpheus	290	Peptide database search	Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	105	153	12	19	0	0	0	0	833	833	93	93	938	986	105	112
+mqppep	mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	13	13	3	3	0	0	0	0	0	0	0	0	13	13	3	3
+ms2deepscore	ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training	Mass spectra similarity scoring using a trained ms2deepscore model.	ms2deepscore	ms2deepscore		MS2DeepScore	MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	To update	https://github.com/matchms/ms2deepscore	Metabolomics	ms2deepscore	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	2.0.0	ms2deepscore	2.1.0	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20749	22184	455	469	1239	1239	71	71	2666	2666	53	53	24654	26089	579	593
+msgfplus	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	473	529	33	43	0	0	0	0	0	0	0	0	473	529	33	43
+msmetaenhancer	msmetaenhancer		msmetaenhancer	msmetaenhancer		MSMetaEnhancer	Tool for mass spectra metadata annotation.	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/MSMetaEnhancer	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	0.4.0	msmetaenhancer	0.4.0	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	10	10	0	0	0	0	48	48	1	1	251	251	11	11
+msms_extractor	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	110	110	11	11	0	0	0	0	0	0	0	0	110	110	11	11
+msp_merge	msp_merge									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	0.1.0	matchms	0.27.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+msstats	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2353	2353	559	559	1122	1122	211	211	1091	1091	35	35	4566	4566	805	805
+msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	795	795	104	104	0	0	0	0	461	461	12	12	1256	1256	116	116
+mt2mq	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	275	275	38	38	0	0	0	0	0	0	0	0	275	275	38	38
+mutational_patterns	mutational_patterns	Mutational patterns and signatures in base substitution catalogs								Up-to-date	http://artbio.fr	Variant Analysis	mutational_patterns	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	3.12.0	bioconductor-mutationalpatterns	3.12.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	854	860	110	111	79	79	15	15	274	274	13	13	1207	1213	138	139
+mzml_validator	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	15	16	16	15	0	391141	443752	9760	10546	306361	350178	11767	13684	227235	244814	3192	3617	924737	1038744	24719	27847
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	352	352	42	42	8	8	6	6	0	0	0	0	360	360	48	48
+ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	54	6	6	0	0	0	0	0	0	0	0	54	54	6	6
+ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	98	6	6	0	0	0	0	0	0	0	0	98	98	6	6
+ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	57	57	4	4	0	0	0	0	0	0	0	0	57	57	4	4
+omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+openmm	pdbfixer	OpenMM is a toolkit for molecular simulation using high performance GPU code.								To update	https://github.com/openmm	Molecular Dynamics, Computational chemistry	openmm	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	1.8.1	pdbfixer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	491	491	52	52	0	0	0	0	0	0	0	0	491	491	52	52
+openms	AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	3.1	openms	3.2.0			8	34	144	0	8	34	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	141	124	0	32169	108654	3316	4889	50	50	15	15	940	940	245	245	33159	109644	3576	5149
+packmol	packmol	PACKMOL is a package for creating starting structures for Molecular Dynamics simulations								To update	http://m3g.iqm.unicamp.br/packmol/home.shtml	Molecular Dynamics, Computational chemistry	packmol	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol	18.169.1	packmol				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	282	295	32	33	420	420	8	8	0	0	0	0	702	715	40	41
+pathifier	pathifier	pathifier								Up-to-date	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	1.40.0	bioconductor-pathifier	1.40.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	245	245	10	10	0	0	0	0	0	0	0	0	245	245	10	10
+pathwaymatcher	reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	174	244	65	76	0	0	0	0	0	0	0	0	174	244	65	76
+pep_pointer	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	506	511	54	55	21	21	12	12	163	163	8	8	690	695	74	75
+pepquery	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7047	7047	76	76	0	0	0	0	0	0	0	0	7047	7047	76	76
+pepquery2	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2			0	1	3	0	0	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1222	1222	28	28	0	0	0	0	0	0	0	0	1222	1222	28	28
+peptide_genomic_coordinate	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	472	472	56	56	16	16	10	10	149	149	5	5	637	637	71	71
+peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.11			4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	2	0	11986	17898	1046	1153	1314	1314	389	389	3034	3034	118	118	16334	22246	1553	1660
+pepxml_to_xls		Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+percolator	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.7.1			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	338	378	15	16	0	0	0	0	1059	1059	13	13	1397	1437	28	29
+pi_db_tools	calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pindel	pindel	Pindel detects genome-wide structural variation.								Up-to-date	http://artbio.fr	Variant Analysis	pindel	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel	https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel	0.2.5b9	pindel	0.2.5b9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pmd_fdr	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+positions2snv_alignment	positions2snv_alignment	Generate alignment of SNVs from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+positions2snv_invariant_alignment	positions2snv_invariant_alignment	Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_invariant_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+probecoverage	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+proteinpilot	convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml									To update			proteinpilot	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+proteomiqon_joinquantpepionswithproteins	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	366	366	4	4	0	0	0	0	0	0	0	0	366	366	4	4
+proteomiqon_labeledproteinquantification	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	8	8	0	0	0	0	0	0	0	0	16	16	8	8
+proteomiqon_labelfreeproteinquantification	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	6	4	4	0	0	0	0	0	0	0	0	6	6	4	4
+proteomiqon_mzmltomzlite	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	721	721	8	8	0	0	0	0	0	0	0	0	721	721	8	8
+proteomiqon_peptidedb	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	96	96	12	12	0	0	0	0	0	0	0	0	96	96	12	12
+proteomiqon_peptidespectrummatching	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	686	686	5	5	0	0	0	0	0	0	0	0	686	686	5	5
+proteomiqon_proteininference	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	6	6	0	0	0	0	0	0	0	0	89	89	6	6
+proteomiqon_psmbasedquantification	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	604	604	4	4	0	0	0	0	0	0	0	0	604	604	4	4
+proteomiqon_psmstatistics	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	694	694	6	6	0	0	0	0	0	0	0	0	694	694	6	6
+proteore_venn_diagram	proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	1	1	0	0	0	0	0	0	0	0	15	15	1	1
+protxml_to_xls	protxml_to_xls									To update			protxml_to_xls	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+psm2sam	PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+psm_eval	psm_eval									To update			psm_eval	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval	0.1.0	binaries_for_psm_eval				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+psm_validation	psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	20	20	4	4	0	0	0	0	0	0	0	0	20	20	4	4
+psy-maps	psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.3.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	333	502	62	62	0	0	0	0	0	0	0	0	333	502	62	62
+pyprophet	pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5			0	5	6	0	0	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	6	6	0	2626	2626	150	150	0	0	0	0	609	609	9	9	3235	3235	159	159
+pyscenic	pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/								To update		Transcriptomics, RNA, Sequence Analysis	suite_pyscenic	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic	0.12.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pyteomics	mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.4	Protein identification	Proteomics, Proteomics experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	92	92	4	4	0	0	0	0	0	0	0	0	92	92	4	4
+pyvo_integration	astronomical_archives	Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy								To update		Data Source	astronomicalarchivestool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration	0.10.0	astropy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	53	6	6	0	0	0	0	0	0	0	0	53	53	6	6
+qcxms	qcxms_getres, qcxms_neutral_run, qcxms_production_run	QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).								To update	https://github.com/grimme-lab/QCxMS	Computational chemistry, Molecular Dynamics	QCxMS	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	5.2.1					0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11246	11246	13	13	0	0	0	0	0	0	0	0	11246	11246	13	13
+quantp	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	197	241	17	22	0	0	0	0	0	0	0	0	197	241	17	22
+quantwiz_iq	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	32	3	3	0	0	0	0	0	0	0	0	32	32	3	3
+query	query	Execute an SQL statement on a set of tables								To update		Text Manipulation	query	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/query	https://github.com/RECETOX/galaxytools/tree/master/tools/query	0.2	click				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	172	172	9	9	0	0	0	0	0	0	0	0	172	172	9	9
+ramclustr	ramclustr, ramclustr_define_experiment		ramclustr	ramclustr		RAMClustR	A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	To update	https://rdrr.io/cran/RAMClustR/	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	1.3.0	r-ramclustr	1.3.1	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	58	58	22	22	29	29	14	14	344	344	4	4	431	431	40	40
+rawtools	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	166	179	32	33	0	0	0	0	414	414	13	13	580	593	45	46
+rcx-tk	rcx-tk	Tools to process metadata or alkane files.								To update	https://github.com/RECETOX/rcx-tk	Metabolomics	rcx_tk	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk	0.1.0+galaxy0	rcx-tk	0.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+recetox_aplcms	recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise	Peak detection tool for HRMS profile data.	recetox-aplcms	recetox-aplcms		recetox-aplcms	recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	Up-to-date	https://github.com/RECETOX/recetox-aplcms	Metabolomics	recetox-aplcms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	0.13.3	r-recetox-aplcms	0.13.3	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	862	862	12	12	0	0	0	0	48	48	1	1	910	910	13	13
+recetox_msfinder	recetox_msfinder		recetox-msfinder	recetox-msfinder		recetox-msfinder	This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.	Annotation	Metabolomics	To update	https://github.com/RECETOX/recetox-msfinder	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	v3.5.2			Annotation	Metabolomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47	47	4	4	0	0	0	0	0	0	0	0	47	47	4	4
+recetox_xmsannotator	recetox_xmsannotator_advanced		recetox-xmsannotator	recetox-xmsannotator		recetox-xMSannotator	Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		Up-to-date	https://github.com/RECETOX/recetox-xMSannotator	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator	0.10.0	r-recetox-xmsannotator	0.10.0	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	93	93	2	2	93	93	2	2
+regex_find_replace	regex1, regexColumn1	Use python regular expressions to find and replace text								To update		Text Manipulation	regex_find_replace	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	1.0.3	python				2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	78648	78834	1144	1156	18063	18063	870	870	4455	6051	194	289	101166	102948	2208	2315
+regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	438	542	128	157	0	0	0	0	0	0	0	0	438	542	128	157
+rem_complex	rem_complex	Removes molecular coordination complexes.								To update	https://github.com/RECETOX/galaxytools	Metabolomics	rem_complex	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	2	2	0	0	0	0	0	0	0	0	18	18	2	2
+rename_annotated_feature	rename_annotated_feature	Update column names in an abundance table using a annotation table with spectral matching results								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	rename_annotated_feature	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+repenrich	edger-repenrich, repenrich	Repeat element profiling								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	Transcriptomics	repenrich	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	2.31.1					0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1725	1790	56	57	1725	1790	56	57
+repenrich2	edger-repenrich2, repenrich2	Repeat element profiling using bowtie2 aligner								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	Transcriptomics	repenrich2	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	2.31.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+retip	retip_apply, retip_descriptors, retip_filter_rt, retip_train		retip	retip		Retip	Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.	Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	To update	https://github.com/PaoloBnn/Retip	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	0.5.4			Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1
+retrieve_ensembl_bed	retrieve_ensembl_bed	Retrieve cDNA features from Ensembl REST API in BED format								To update	http://rest.ensembl.org/	Data Source	retrieve_ensembl_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+revertR2orientationInBam	revertR2orientationInBam	Revert the mapped orientation of R2 mates in a bam.								To update		SAM	revertr2orientationinbam	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	0.0.2	samtools	1.21			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	40	11	11	520	520	31	31	0	0	0	0	560	560	42	42
+riassigner	riassigner, riassigner_from_comment		riassigner	riassigner		RIAssigner	RIAssigner is a python tool for retention index (RI) computation for GC-MS data.	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/RIAssigner	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	0.4.1	riassigner	0.4.1	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	46	46	19	19	15	15	4	4	1	1	1	1	62	62	24	24
+rmassbank	rmassbank	RMassBank is an R package for processing tandem MS files and building of MassBank records.								To update	https://github.com/MassBank/RMassBank	Metabolomics	rmassbank	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	3.0.0	python				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	48	48	1	1	48	48	1	1
+rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	1	1	0	363	430	158	183	0	0	0	0	67	146	13	39	430	576	171	222
+salmon-kallisto-mtx-to-10x	_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	682	682	172	172	322	322	74	74	3	3	3	3	1007	1007	249	249
+sambamba	sambamba_sample_or_filter	filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM								To update	http://artbio.fr	SAM	sambamba	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba	https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba	0.7.1+galaxy1	sambamba	1.0.1			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	684	684	17	17	684	684	17	17
+sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	10	10	0	0	0	0	0	0	0	0	13	13	10	10
+scaffold	scaffold, scaffold_export									To update			scaffold	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold	0.1.0	scaffold				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			27	27	27	0	27	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	0	45501	45666	4832	4868	7304	7304	1846	1846	3106	3106	457	457	55911	56076	7135	7171
+scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			1	2	6	0	1	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	381	388	99	100	0	0	0	0	297	297	9	9	678	685	108	109
+sccaf	run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out	SCCAF: Single Cell Clustering Assessment Framework.								To update	https://github.com/sccaf/sccaf	Transcriptomics	SCCAF	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf	0.0.9	sccaf	0.0.10			4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	110	110	19	19	0	0	0	0	0	0	0	0	110	110	19	19
+sceasy	sceasy_convert	Convert scRNA data object between popular formats								To update		Transcriptomics	sceasy	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy	0.0.5	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1059	1059	222	222	426	426	71	71	1	1	1	1	1486	1486	294	294
+scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	97	97	41	41	0	0	0	0	0	0	0	0	97	97	41	41
+scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	25	5	5	0	0	0	0	0	0	0	0	25	25	5	5
+scripting	singularity_scriptrunner	suite_scripting								To update	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	Text Manipulation	scripting tools	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1
+sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.4.0			14	14	14	0	14	14	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	0	2296	2328	673	676	141	141	39	39	0	0	0	0	2437	2469	712	715
+sgwb	sgwb_astro_tool	SGWB								To update		Astronomy	sgwb_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb	0.0.1+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	2	2	0	0	0	0	0	0	0	0	5	5	2	2
+shift-longitudes	shyft_longitudes	Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/	Climate Analysis	shift_longitudes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	54	64	4	4	0	0	0	0	0	0	0	0	54	64	4	4
+sixgill	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	312	312	71	71	0	0	0	0	0	0	0	0	312	312	71	71
+small_rna_clusters	small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+small_rna_maps	small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+small_rna_signatures	overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+smithsonian-volcanoes	smithsonian_volcanoes	Retrieve data from Volcanoes of the World (VOTW) Database								To update	https://volcano.si.edu/gvp_votw.cfm	Retrieve Data	smithsonian_volcanoes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	0.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+snv_matrix	snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+snvtocnv	sequenzaindex, snvtocnv	infer copy number variations from a vcf file with SNVs using R sequenza								To update	http://artbio.fr	Variant Analysis	snvtocnv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv	https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv	3.0.0+galaxy1	sequenza-utils	3.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+spec2vec	spec2vec_similarity, spec2vec_training	Mass spectra similarity scoring using a trained Spec2Vec model.	spec2vec	spec2vec		Spec2Vec	Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	Up-to-date	https://github.com/iomega/spec2vec	Metabolomics	spec2vec	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	0.8.0	spec2vec	0.8.0	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1
+spectrast2spectrast_irt	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+spectrast2tsv	gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	789	840	130	134	0	0	0	0	0	0	0	0	789	840	130	134
+sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	80	80	1	1	0	0	0	0	80	80	1	1
+sr_bowtie_dataset_annotation	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	0	4	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	239	239	34	34	44	44	13	13	0	0	0	0	283	283	47	47
+stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	328	328	38	38	0	0	0	0	0	0	0	0	328	328	38	38
+suite_snvphyl		SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+topologyeditors	gromacs_modify_topology, gromacs_extract_topology	Set of python scripts and associated tool files that can be used to modify topology files.								To update	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	Molecular Dynamics, Computational chemistry	topologyeditors	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	0	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	57	57	10	10	20	20	8	8	0	0	0	0	77	77	18	18
+translate_bed	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	649	685	138	142	473	473	105	105	761	761	18	18	1883	1919	261	265
+translate_bed_sequences	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	69	16	21	0	0	0	0	0	0	0	0	57	69	16	21
+ucsc-cell-browser	ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets								To update	https://cells.ucsc.edu/	Transcriptomics	ucsc_cell_browser	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser	1.0.0+galaxy1	ucsc-cell-browser	1.2.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	965	975	178	181	0	0	0	0	0	0	0	0	965	975	178	181
+unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4900	5146	257	270	251	251	81	81	1069	1069	29	29	6220	6466	367	380
+uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1488	1596	230	266	0	0	0	0	743	743	35	35	2231	2339	265	301
+upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	112	38	38	0	0	0	0	0	0	0	0	112	112	38	38
+varscan_vaf	varscan_vaf	Compute variant allele frequency in vcf files generated by varscan.								To update	http://artbio.fr	Variant Analysis	varscan_vaf	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf	https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vcf2snvalignment	vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+verify_map	verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vibrant	vibrant	Virus Identification By iteRative ANnoTation	VIBRANT	VIBRANT		VIBRANT	Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	Up-to-date	https://github.com/AnantharamanLab/VIBRANT	Metagenomics	vibrant	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant	1.2.1	vibrant	1.2.1	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	14412	14590	722	732	0	0	0	0	0	0	0	0	14412	14590	722	732
+virsorter	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	virsorter	virsorter		virsorter	Identify DNA and RNA virus sequences.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/jiarong/VirSorter2/	Metagenomics	virsorter	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter	2.2.4	virsorter	2.2.4	Taxonomic classification	Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vmd		vmd is a package for  visualizing and analyzing trajectories from molecular dynamics (MD) simulations								To update	https://www.ks.uiuc.edu/Research/vmd/	Computational chemistry	vmd	chemteam	https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+waveica	waveica	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.	waveica	waveica		WaveICA	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.	Standardisation and normalisation	Metabolomics	Up-to-date	https://github.com/RECETOX/WaveICA	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	0.2.0	r-recetox-waveica	0.2.0	Standardisation and normalisation	Metabolomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	39	6	6	4	4	3	3	0	0	0	0	43	43	9	9
+xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	0	5	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	5995	5995	275	275	66	66	23	23	295	295	3	3	6356	6356	301	301
+xmlstarlet	xmlstarlet	Tool to convert a xml file from one metadata standard to another								To update		Convert Formats	xmlstarlet	ecology	https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet	https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet	1.6.1	xmlstarlet				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	59	59	17	17	0	0	0	0	0	0	0	0	59	59	17	17
+xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+xtb	xtb_molecular_optimization	Performs semiempirical molecular optimization.								To update	https://github.com/grimme-lab/xtb	Metabolomics	xtb_molecular_optimization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	6.6.1	xtb				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	143	143	4	4	0	0	0	0	0	0	0	0	143	143	4	4
+yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+zeiss_lmd_converter	ZeissLMDconverter	Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	2.0.4	shapely				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	1	1	0	0	0	0	0	0	0	0	4	4	1	1
+zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	4	4	0	0	0	0	0	0	0	0	26	26	4	4
diff --git a/communities/all/resources/tools_wordcloud.png b/communities/all/resources/tools_wordcloud.png
index 046e0b2c..5c73cafb 100644
Binary files a/communities/all/resources/tools_wordcloud.png and b/communities/all/resources/tools_wordcloud.png differ
diff --git a/communities/all/resources/tutorials.json b/communities/all/resources/tutorials.json
index 02264a97..e76a3dc8 100644
--- a/communities/all/resources/tutorials.json
+++ b/communities/all/resources/tutorials.json
@@ -86,7 +86,7 @@
             "Use an Ansible playbook for all of the above.",
             "Monitor a Celery task using the Flower dashboard"
         ],
-        "pageviews": 3076381,
+        "pageviews": 3107984,
         "pub_date": "2022-07-16",
         "questions": null,
         "requirements": [
@@ -106,6 +106,7 @@
         "slides_recordings": false,
         "subtopic": "data",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "tags": [
             "ansible",
@@ -133,8 +134,8 @@
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-        "visit_duration": 228,
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+        "visit_duration": 229,
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     {
@@ -227,7 +228,7 @@
             "be familiar with configuring Galaxy to use an upstream (proxy) authentication provider",
             "be able to log in to your Galaxy server with a file-configured user."
         ],
-        "pageviews": 5898193,
+        "pageviews": 5929797,
         "pub_date": "2019-01-28",
         "questions": [
             "How can I connect Galaxy with CAS, SAML, etc."
@@ -253,6 +254,7 @@
         "slides_recordings": false,
         "subtopic": "features",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
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@@ -280,7 +282,7 @@
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     {
         "admin_install": {
@@ -374,7 +376,7 @@
             "Manage permissions",
             "Import data from disk"
         ],
-        "pageviews": 5831294,
+        "pageviews": 5862935,
         "pub_date": "2021-01-14",
         "questions": [
             "How do data libraries work?",
@@ -414,6 +416,7 @@
         "slides_recordings": false,
         "subtopic": "data",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "tags": [
             "ansible",
@@ -442,8 +445,8 @@
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-        "visit_duration": 275,
-        "visitors": 2114956
+        "visit_duration": 274,
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@@ -493,7 +496,7 @@
         "license": "CC-BY-4.0",
         "logo": "assets/images/gat.png",
         "mod_date": "2022-03-01",
-        "pageviews": 5897141,
+        "pageviews": 5928745,
         "pub_date": "2019-01-28",
         "short_id": "S00028",
         "short_tools": [],
@@ -501,6 +504,7 @@
         "slides_recordings": false,
         "subtopic": "deprecated",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "title": "uWSGI",
         "tools": [],
@@ -524,7 +528,7 @@
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@@ -632,13 +636,14 @@
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         "logo": "assets/images/gat.png",
         "mod_date": "2022-06-16",
-        "pageviews": 5897142,
+        "pageviews": 5928745,
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         "short_id": "S00008",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "title": "Galactic Database",
         "tools": [],
@@ -662,7 +667,7 @@
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@@ -801,7 +806,7 @@
         "license": "CC-BY-4.0",
         "logo": "assets/images/gat.png",
         "mod_date": "2024-07-10",
-        "pageviews": 301227,
+        "pageviews": 332830,
         "pub_date": "2024-07-10",
         "short_id": "S00122",
         "short_tools": [],
@@ -809,6 +814,7 @@
         "slides_recordings": false,
         "subtopic": "maintenance",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "tags": [
             "deploying",
@@ -836,8 +842,8 @@
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-        "visit_duration": 149,
-        "visitors": 124234
+        "visit_duration": 156,
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@@ -943,7 +949,7 @@
             "Extract a list of tools from a workflow",
             "Install these tools on a given Galaxy"
         ],
-        "pageviews": 5899224,
+        "pageviews": 5930838,
         "pub_date": "2019-01-27",
         "questions": [
             "How to install, update, and maintain Galaxy tools?",
@@ -994,6 +1000,7 @@
         ],
         "subtopic": "features",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "tags": [
             "tools",
@@ -1021,8 +1028,8 @@
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-        "visit_duration": 384,
-        "visitors": 2134981
+        "visit_duration": 382,
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         "admin_install": {
@@ -1141,7 +1148,7 @@
             "Learn about different monitoring strategies.",
             "Setup and start the Galaxy reports app."
         ],
-        "pageviews": 5897142,
+        "pageviews": 5928746,
         "pub_date": "2018-01-07",
         "questions": [
             "How to monitor a Galaxy service?"
@@ -1151,6 +1158,7 @@
         "slides": true,
         "slides_recordings": false,
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "tags": [
             "work-in-progress"
@@ -1178,7 +1186,7 @@
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@@ -1319,7 +1327,7 @@
             "Configure your Galaxy to serve Interactive Tools using an Ansible Playbook",
             "Start, run, and use an Interactive Tool"
         ],
-        "pageviews": 5900082,
+        "pageviews": 5931692,
         "pub_date": "2020-02-27",
         "questions": [
             "What are Galaxy Interactive Tools?",
@@ -1358,6 +1366,7 @@
         "slides_recordings": false,
         "subtopic": "features",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "tags": [
             "ansible",
@@ -1385,8 +1394,8 @@
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-        "visit_duration": 317,
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+        "visit_duration": 318,
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     {
@@ -1503,7 +1512,7 @@
             "Setup cleanups",
             "Learn what to back up and how to recover"
         ],
-        "pageviews": 5897653,
+        "pageviews": 5929263,
         "pub_date": "2019-01-31",
         "questions": [
             "How can I back up my Galaxy?",
@@ -1531,6 +1540,7 @@
         "slides_recordings": false,
         "subtopic": "maintenance",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "tags": [
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@@ -1559,8 +1569,8 @@
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-        "visit_duration": 755,
-        "visitors": 2133958
+        "visit_duration": 745,
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         "admin_install": {
@@ -1647,7 +1657,7 @@
         "objectives": [
             "Setup Galaxy with both the Hierarachical and Distributed Object Storages"
         ],
-        "pageviews": 5899105,
+        "pageviews": 5930711,
         "pub_date": "2019-01-28",
         "questions": [
             "How does Galaxy locate data?",
@@ -1682,6 +1692,7 @@
         ],
         "subtopic": "data",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
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@@ -1710,7 +1721,7 @@
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@@ -1797,13 +1808,14 @@
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         "logo": "assets/images/gat.png",
         "mod_date": "2021-04-06",
-        "pageviews": 5897143,
+        "pageviews": 5928747,
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         "short_id": "S00009",
         "short_tools": [],
         "slides": true,
         "slides_recordings": false,
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "title": "Empathy",
         "tools": [],
@@ -1827,7 +1839,7 @@
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@@ -1866,7 +1878,7 @@
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         "logo": "assets/images/gat.png",
         "mod_date": "2022-03-01",
-        "pageviews": 5897143,
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         "short_id": "S00004",
         "short_tools": [],
@@ -1874,6 +1886,7 @@
         "slides_recordings": false,
         "subtopic": "cloud",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "title": "Galaxy on the Cloud",
         "tools": [],
@@ -1897,7 +1910,7 @@
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     {
         "admin_install": {
@@ -2002,10 +2015,10 @@
         ],
         "dir": "topics/admin/tutorials/reference-genomes",
         "edam_operation": [
-            "Generation",
             "Sequence alignment",
             "Genome indexing",
-            "Read mapping"
+            "Read mapping",
+            "Generation"
         ],
         "edam_topic": [],
         "feedback_mean_note": null,
@@ -2029,7 +2042,7 @@
             "Be able to download and use data managers to add a reference genome and its pre-calculated indices into the Galaxy reference data system",
             "Use an Ansible playbook for all of the above"
         ],
-        "pageviews": 5897655,
+        "pageviews": 5929261,
         "pub_date": "2019-01-28",
         "questions": null,
         "requirements": [
@@ -2045,13 +2058,14 @@
         "short_id": "T00329",
         "short_tools": [
             "bwa",
-            "data_manager_fetch_genome_all_fasta_dbkey",
-            "bwa_mem_index_builder_data_manager"
+            "bwa_mem_index_builder_data_manager",
+            "data_manager_fetch_genome_all_fasta_dbkey"
         ],
         "slides": true,
         "slides_recordings": false,
         "subtopic": "data",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "1h",
         "title": "Reference Data with Data Managers",
@@ -2079,8 +2093,8 @@
         "video": false,
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-        "visit_duration": 447,
-        "visitors": 2133965,
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     },
     {
@@ -2153,7 +2167,7 @@
             "Setup Grafana",
             "Create several charts"
         ],
-        "pageviews": 5902242,
+        "pageviews": 5933848,
         "pub_date": "2019-01-31",
         "questions": [
             "How to monitor Galaxy with Telegraf",
@@ -2204,6 +2218,7 @@
         ],
         "subtopic": "monitoring",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "tags": [
             "ansible",
@@ -2233,7 +2248,7 @@
         "video_versions": 1,
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         "visit_duration": 203,
-        "visitors": 2136259
+        "visitors": 2146666
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     {
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@@ -2310,7 +2325,7 @@
         "license": "CC-BY-4.0",
         "logo": "assets/images/gat.png",
         "mod_date": "2023-04-16",
-        "pageviews": 5897146,
+        "pageviews": 5928747,
         "pub_date": "2019-01-28",
         "short_id": "S00019",
         "short_tools": [],
@@ -2318,6 +2333,7 @@
         "slides_recordings": false,
         "subtopic": "maintenance",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "title": "Gearing towards production",
         "tools": [],
@@ -2341,7 +2357,7 @@
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         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2133582
+        "visitors": 2143985
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     {
         "admin_install": {
@@ -2454,7 +2470,7 @@
             "Learn the Galaxy user/group management and assign Quotas.",
             "Understand the Role Based Access Control (RBAC) of Galaxy."
         ],
-        "pageviews": 5897146,
+        "pageviews": 5928747,
         "pub_date": "2018-01-07",
         "questions": [
             "How does Galaxy manage users and groups?",
@@ -2497,6 +2513,7 @@
         ],
         "subtopic": "maintenance",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "15m",
         "title": "User, Role, Group, Quota, and Authentication managment",
@@ -2521,7 +2538,7 @@
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-        "visitors": 2133582,
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     {
@@ -2632,7 +2649,7 @@
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         "logo": "assets/images/gat.png",
         "mod_date": "2023-04-17",
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+                                "4.6.3",
+                                "4.1",
+                                "5.0.2"
+                            ]
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+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
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+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
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+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
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+                        },
+                        {
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+                            "state": "missing"
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+                    "version": "5.2.0+galaxy1"
                 }
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@@ -8024,8 +9856,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 319,
-        "visitors": 2161888,
+        "visit_duration": 320,
+        "visitors": 2172483,
         "workflows": [
             {
                 "creators": [],
@@ -8181,7 +10013,7 @@
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Intro to Genome Assembly",
                 "outputs": [
                     {
@@ -8788,24 +10620,24 @@
         ],
         "dir": "topics/assembly/tutorials/chloroplast-assembly",
         "edam_operation": [
-            "Scatter plot plotting",
-            "Genome annotation",
-            "Sequence alignment",
-            "Cross-assembly",
-            "Read mapping",
-            "Genome visualisation",
+            "Coding region prediction",
             "Genome assembly",
+            "Genome indexing",
+            "Sequence assembly visualisation",
             "De-novo assembly",
-            "Box-Whisker plot plotting",
-            "Analysis",
-            "Sequence assembly",
-            "Generation",
-            "Gene prediction",
             "Mapping assembly",
-            "Sequence assembly visualisation",
+            "Genome visualisation",
             "Read alignment",
-            "Genome indexing",
-            "Coding region prediction"
+            "Generation",
+            "Sequence assembly",
+            "Box-Whisker plot plotting",
+            "Scatter plot plotting",
+            "Genome annotation",
+            "Gene prediction",
+            "Read mapping",
+            "Cross-assembly",
+            "Sequence alignment",
+            "Analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -8819,7 +10651,6 @@
             "GalaxyTrakr",
             "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)"
         ],
@@ -8842,7 +10673,7 @@
             "Annotate the assembly and view",
             "Map reads to the assembly and view"
         ],
-        "pageviews": 9814,
+        "pageviews": 9850,
         "pub_date": "2020-12-04",
         "questions": [
             "How can we assemble a chloroplast genome?"
@@ -8876,16 +10707,16 @@
         ],
         "short_id": "T00030",
         "short_tools": [
-            "bwa_mem",
-            "prokka",
-            "jbrowse",
             "bandage_image",
-            "upload1",
-            "bandage_info",
+            "jbrowse",
             "fasta-stats",
-            "flye",
+            "pilon",
+            "bandage_info",
+            "bwa_mem",
             "nanoplot",
-            "pilon"
+            "upload1",
+            "prokka",
+            "flye"
         ],
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         "slides_recordings": false,
@@ -8914,10 +10745,136 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
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+                },
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+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -8927,6 +10884,2114 @@
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.9.4+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "2.6"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "inexact",
+                            "versions": [
+                                "2.9.1+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
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+                        },
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+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
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+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
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+                            "state": "exact",
+                            "version": "2.6"
+                        },
+                        {
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+                            "state": "exact",
+                            "version": "2.6"
+                        },
+                        {
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+                            "state": "exact",
+                            "version": "2.6"
+                        },
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+                            "state": "exact",
+                            "version": "2.6"
+                        },
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+                            "state": "exact",
+                            "version": "2.6"
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+                        {
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+                            "state": "exact",
+                            "version": "2.6"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
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+                    "version": "2.6"
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+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
                 }
             ]
         },
@@ -8973,8 +13038,8 @@
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 172,
-        "visitors": 6133,
+        "visit_duration": 173,
+        "visitors": 6160,
         "workflows": [
             {
                 "creators": [],
@@ -9117,7 +13182,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina_reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nNanopore_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTiny_set_illumina_read\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nTiny_set_nanopore_reads\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Flye assembly\"];\n  1 -->|output| 4;\n  5[\"NanoPlot\"];\n  1 -->|output| 5;\n  6[\"Map with BWA-MEM\"];\n  0 -->|output| 6;\n  4 -->|consensus| 6;\n  7[\"Fasta Statistics\"];\n  4 -->|consensus| 7;\n  8[\"Bandage Info\"];\n  4 -->|assembly_gfa| 8;\n  9[\"Bandage Image\"];\n  4 -->|assembly_gfa| 9;\n  10[\"pilon\"];\n  6 -->|bam_output| 10;\n  4 -->|consensus| 10;\n  11[\"Fasta Statistics\"];\n  10 -->|output_fasta| 11;\n  12[\"Map with BWA-MEM\"];\n  2 -->|output| 12;\n  10 -->|output_fasta| 12;\n  13[\"Map with BWA-MEM\"];\n  3 -->|output| 13;\n  10 -->|output_fasta| 13;\n  14[\"Prokka\"];\n  10 -->|output_fasta| 14;\n  15[\"JBrowse\"];\n  10 -->|output_fasta| 15;\n  12 -->|bam_output| 15;\n  13 -->|bam_output| 15;\n  16[\"JBrowse\"];\n  10 -->|output_fasta| 16;\n  14 -->|out_gff| 16;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Chloroplast-genome-assembly-and-annotation",
                 "outputs": [
                     {
@@ -10138,19 +14203,18 @@
         ],
         "dir": "topics/assembly/tutorials/assembly-quality-control",
         "edam_operation": [
-            "Visualisation",
             "Genome assembly",
+            "Transcriptome assembly",
             "De-novo assembly",
             "Phasing",
+            "k-mer counting",
             "Sequence assembly validation",
             "Scaffolding",
-            "k-mer counting",
-            "Transcriptome assembly"
+            "Visualisation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org.au"
         ],
         "feedback_mean_note": null,
@@ -10184,7 +14248,7 @@
         "objectives": [
             "Assess assembly quality"
         ],
-        "pageviews": 2940854,
+        "pageviews": 2972501,
         "pub_date": "2022-08-26",
         "questions": [
             "Is my genome assembly ready for annotation and/or scaffolding?"
@@ -10192,10 +14256,10 @@
         "short_id": "T00028",
         "short_tools": [
             "merqury",
+            "meryl",
             "busco",
-            "quast",
             "chromeister",
-            "meryl"
+            "quast"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -10206,11 +14270,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
@@ -10225,6 +14284,870 @@
                 }
             ]
         },
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
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+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
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+                    "usegalaxy": false
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                                "5.0.2+galaxy4",
+                                "5.0.2+galaxy5",
+                                "4.1",
+                                "5.0.2",
+                                "5.0.2+galaxy2",
+                                "5.0.2+galaxy3"
+                            ]
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+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy0"
+                        },
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+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy0"
+                        },
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+                            "state": "exact",
+                            "version": "5.2.0+galaxy0"
+                        },
+                        {
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+                            "state": "missing"
+                        }
+                    ],
+                    "version": "5.2.0+galaxy0"
+                }
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         "tags": [
             "assembly",
@@ -10258,8 +15181,8 @@
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         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 271,
-        "visitors": 1228609,
+        "visit_duration": 273,
+        "visitors": 1239004,
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@@ -10414,7 +15337,7 @@
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Genome Assembly Quality Control",
                 "outputs": [],
                 "parent_id": "assembly/assembly-quality-control",
@@ -10558,8 +15481,8 @@
         ],
         "dir": "topics/assembly/tutorials/assembly-decontamination",
         "edam_operation": [
-            "Taxonomic classification",
-            "Data handling"
+            "Data handling",
+            "Taxonomic classification"
         ],
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@@ -10589,7 +15512,7 @@
             "Identify contaminant species",
             "Remove Mitochondrial DNA from an assembly"
         ],
-        "pageviews": 71,
+        "pageviews": 104,
         "pub_date": "2024-09-04",
         "questions": [
             "How to remove contaminant sequences from your assembly?"
@@ -10611,15 +15534,15 @@
         ],
         "short_id": "T00452",
         "short_tools": [
+            "Cut1",
             "tp_sed_tool",
+            "gfastats",
             "tp_cat",
-            "Filter1",
+            "parse_mito_blast",
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             "kraken2",
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-            "gfastats",
-            "parse_mito_blast",
-            "ncbi_blastn_wrapper"
+            "ncbi_blastn_wrapper",
+            "Filter1"
         ],
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         "slides_recordings": false,
@@ -10649,6 +15572,2239 @@
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+                            "state": "inexact",
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+                                "2.1.1+galaxy0",
+                                "2.0.8_beta+galaxy0"
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+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
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+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
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+                },
+                {
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+                    "servers": [
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+                            "state": "missing"
+                        },
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+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
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+                        {
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+                            "state": "missing"
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+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
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+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.0.2+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.0.2+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.0.2+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.0.2+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.0.2+galaxy0"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "1H30M",
         "title": "Decontamination of a genome assembly",
@@ -10687,8 +17843,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 278,
-        "visitors": 59,
+        "visit_duration": 302,
+        "visitors": 83,
         "workflows": [
             {
                 "creators": [
@@ -10795,7 +17951,7 @@
                 ],
                 "license": "BSD-3-Clause",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nScaffolded assembly fasta\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nDatabase for Kraken2\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"soft-masking \"];\n  0 -->|output| 2;\n  3[\"hard-masking\"];\n  2 -->|outfile| 3;\n  4[\"ID non-target contaminants\"];\n  1 -->|output| 4;\n  3 -->|output| 4;\n  c380857b-5180-4e82-a14f-8b575f10abaa[\"Output\\nKraken2 classification scores\"];\n  4 --> c380857b-5180-4e82-a14f-8b575f10abaa;\n  style c380857b-5180-4e82-a14f-8b575f10abaa stroke:#2c3143,stroke-width:4px;\n  5[\"blast mitochondria DB\"];\n  3 -->|output| 5;\n  6[\"Cut\"];\n  4 -->|output| 6;\n  7[\"parsing blast output\"];\n  5 -->|output1| 7;\n  1478af1e-52f4-48fe-b966-0a61e2014a58[\"Output\\nmito_scaff_names\"];\n  7 --> 1478af1e-52f4-48fe-b966-0a61e2014a58;\n  style 1478af1e-52f4-48fe-b966-0a61e2014a58 stroke:#2c3143,stroke-width:4px;\n  8[\"Filter\"];\n  6 -->|out_file1| 8;\n  64156e28-aaf0-4578-9a7e-d6d21774c2c8[\"Output\\ncontaminants_table\"];\n  8 --> 64156e28-aaf0-4578-9a7e-d6d21774c2c8;\n  style 64156e28-aaf0-4578-9a7e-d6d21774c2c8 stroke:#2c3143,stroke-width:4px;\n  9[\"Cut\"];\n  8 -->|out_file1| 9;\n  10[\"concatenate scaffold lists\"];\n  7 -->|mito_scaff_names| 10;\n  9 -->|out_file1| 10;\n  77084ec5-a145-40c1-9cfc-476d091105ae[\"Output\\nfull contaminant + mito scaffold list\"];\n  10 --> 77084ec5-a145-40c1-9cfc-476d091105ae;\n  style 77084ec5-a145-40c1-9cfc-476d091105ae stroke:#2c3143,stroke-width:4px;\n  11[\"removing scaffolds \"];\n  0 -->|output| 11;\n  10 -->|out_file1| 11;\n  88a8e9ed-d92c-4340-aaad-c6d450a336aa[\"Output\\nfinal decontaminated assembly\"];\n  11 --> 88a8e9ed-d92c-4340-aaad-c6d450a336aa;\n  style 88a8e9ed-d92c-4340-aaad-c6d450a336aa stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Assembly-decontamination-VGP9",
                 "outputs": [
                     {
@@ -11230,6 +18386,13 @@
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "2babe6d5c561",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "bwa_mem2",
                     "owner": "iuc",
@@ -11272,6 +18435,13 @@
                     "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "pretext_map",
+                    "owner": "iuc",
+                    "revisions": "79b48f02db49",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "pretext_snapshot",
                     "owner": "iuc",
@@ -11288,7 +18458,7 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 7d9ee8cd14b8\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 8c2167481e72\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 5799092ffdff\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 3ef480892a9f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 3a0efe14891f\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: smudgeplot\n  owner: galaxy-australia\n  revisions: 5e0825476fb7\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bellerophon\n  owner: iuc\n  revisions: 25ca5d73aedf\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: bb935709506a\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: b4a22d90cce9\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 01210c4e9144\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n  owner: iuc\n  revisions: f8113c25bc6b\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 5cc34c3f440d\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n  owner: iuc\n  revisions: dfb8a4497339\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_snapshot\n  owner: iuc\n  revisions: 44c66e8d21e6\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
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         "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json",
         "contributors": [
             {
@@ -11319,24 +18489,33 @@
                 "orcid": "0000-0001-8293-4816",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tbrown91/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/tbrown91.json"
+            },
+            {
+                "email": "delphine.lariviere@galaxy.org",
+                "id": "delphine-l",
+                "joined": "2017-09",
+                "name": "Delphine Lariviere",
+                "orcid": "0000-0001-6421-3484",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
             }
         ],
         "dir": "topics/assembly/tutorials/ERGA-post-assembly-QC",
         "edam_operation": [
-            "Data handling",
-            "Sequence alignment",
-            "Sequence trimming",
+            "Genotyping",
+            "Sequence alignment analysis",
             "Genome assembly",
+            "Transcriptome assembly",
+            "Data handling",
+            "Sequence assembly visualisation",
             "De-novo assembly",
-            "Sequence alignment analysis",
             "Phasing",
+            "k-mer counting",
             "Sequence assembly validation",
             "Scaffolding",
-            "Sequence assembly visualisation",
-            "Pairwise sequence alignment",
-            "k-mer counting",
-            "Transcriptome assembly",
-            "Genotyping"
+            "Sequence trimming",
+            "Sequence alignment",
+            "Pairwise sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -11360,40 +18539,55 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-09-06",
+        "mod_date": "2024-10-08",
         "objectives": [
             "Apply the post-assembly-QC-workflow using the necessary tools",
             "Analyse and evaluate the results of the workflow"
         ],
-        "pageviews": 1211,
+        "pageviews": 1260,
         "pub_date": "2023-06-23",
         "questions": [
             "What combination of tools can assess the quality of a genome assembly?",
-            "What metrics can help to analyse the quality of an asembly?",
+            "What metrics can help to analyse the quality of an assembly?",
             "How do we evaluate the outputs?"
         ],
+        "recordings": [
+            {
+                "bot-timestamp": 1728229662,
+                "captioners": [
+                    "delphine-l"
+                ],
+                "date": "2024-10-06",
+                "galaxy_version": "24.1.3.dev0",
+                "length": "44M",
+                "speakers": [
+                    "delphine-l"
+                ],
+                "youtube_id": "n4PNTTa2d6U"
+            }
+        ],
         "short_id": "T00355",
         "short_tools": [
-            "merqury",
-            "minimap2",
             "busco",
-            "tp_find_and_replace",
+            "CONVERTER_gz_to_uncompressed",
             "pretext_snapshot",
-            "bwa_mem2",
-            "gfastats",
             "bg_diamond",
-            "pretext_map",
-            "__EXTRACT_DATASET__",
             "samtools_stats",
-            "genomescope",
-            "bandage_image",
-            "blobtoolkit",
-            "interactive_tool_blobtoolkit",
             "bellerophon",
+            "__EXTRACT_DATASET__",
+            "smudgeplot",
             "collapse_dataset",
             "meryl",
-            "smudgeplot",
-            "CONVERTER_gz_to_uncompressed"
+            "interactive_tool_blobtoolkit",
+            "blobtoolkit",
+            "bandage_image",
+            "minimap2",
+            "tp_find_and_replace",
+            "pretext_map",
+            "bwa_mem2",
+            "merqury",
+            "gfastats",
+            "genomescope"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -11418,6 +18612,3537 @@
                 }
             ]
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+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
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+                },
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+                },
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                },
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+                },
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+                },
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+                },
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+                    "url": "https://usegalaxy.be/",
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+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
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+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
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+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
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+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
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+                    "servers": [
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+                            "state": "missing"
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+                            "state": "missing"
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+                            "state": "local"
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+                        {
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+                            "state": "local"
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+                            "state": "local"
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+                        {
+                            "server": "https://galaxytrakr.org/",
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+                            "state": "missing"
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+                            "state": "missing"
+                        },
+                        {
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+                            "state": "local"
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+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
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+                        {
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+                        {
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+                            "state": "missing"
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+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
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+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
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+                        {
+                            "server": "https://usegalaxy.org",
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+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
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+                            "state": "missing"
+                        }
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+                    "version": "local"
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+                            "state": "local"
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
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+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
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+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
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+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
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+                        {
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@@ -11467,12 +22194,12 @@
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             "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json"
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-        "visitors": 918,
+        "visit_duration": 105,
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@@ -11795,7 +22522,7 @@
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Post-assembly workflow",
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                     {
@@ -12408,7 +23135,7 @@
             "Generate Mitochondrial assembly",
             "Understand the outputs of MitoHifi"
         ],
-        "pageviews": 78,
+        "pageviews": 93,
         "pub_date": "2024-09-03",
         "questions": [
             "How to assemble the mitochondrial genome from PacBio Hifi Reads"
@@ -12430,8 +23157,8 @@
         ],
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-            "compress_file",
-            "mitohifi"
+            "mitohifi",
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         "slides_recordings": false,
@@ -12460,6 +23187,417 @@
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+                    "version": "0.1.0"
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+        },
         "symlink": null,
         "time_estimation": "1H",
         "title": "Assembly of the mitochondrial genome from PacBio HiFi reads",
@@ -12486,8 +23624,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 189,
-        "visitors": 64,
+        "visit_duration": 164,
+        "visitors": 76,
         "workflows": [
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                 "creators": [
@@ -12622,7 +23760,7 @@
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Mitogenome-Assembly-VGP0",
                 "outputs": [
                     {
@@ -13111,14 +24249,14 @@
             "topic_3301"
         ],
         "edam_operation": [
-            "Sequence assembly validation",
-            "Statistical calculation",
-            "Sequence assembly visualisation",
-            "Visualisation",
+            "Sequence contamination filtering",
             "Genome assembly",
+            "Sequence assembly validation",
             "Sequencing quality control",
+            "Visualisation",
+            "Sequence assembly visualisation",
             "Sequence composition calculation",
-            "Sequence contamination filtering"
+            "Statistical calculation"
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@@ -13130,7 +24268,6 @@
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             "UseGalaxy.eu",
-            "UseGalaxy.fr",
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@@ -13178,7 +24315,7 @@
             "Run tools to assess the quality of an assembly",
             "Understand the outputs of tools to assess the quality of an assembly"
         ],
-        "pageviews": 10837,
+        "pageviews": 10915,
         "pub_date": "2021-03-24",
         "questions": [
             "How to check the quality of the MiSeq data?",
@@ -13202,13 +24339,13 @@
         ],
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-            "fastp",
             "bandage_image",
-            "upload1",
-            "bandage_info",
-            "quast",
+            "shovill",
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+            "bandage_info",
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@@ -13224,11 +24361,6 @@
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-                    "url": "https://usegalaxy.fr/",
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                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -13258,6 +24390,1333 @@
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+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
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+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
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+                                "0.8.0",
+                                "0.9.0",
+                                "1.0.4+galaxy0"
+                            ]
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+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.1.0+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.1.0+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.1.0+galaxy1",
+                                "1.1.0+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.1.0+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.1.0+galaxy2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
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+                },
+                {
+                    "id": "upload1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "illumina",
@@ -13296,7 +25755,7 @@
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         "video_view": 0,
         "visit_duration": 227,
-        "visitors": 6735,
+        "visitors": 6791,
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@@ -13318,7 +25777,7 @@
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                 "name": "Genome Assembly of MRSA using Illumina MiSeq Data",
                 "outputs": [
                     {
@@ -13488,7 +25947,7 @@
                             {
                                 "label": "fastp_json",
                                 "output_name": "report_json",
-                                "uuid": "45c8ff4e-7e47-4c69-8e46-863dc3a688d3"
+                                "uuid": "bedb2db6-817e-45da-838f-b10988c6d3ca"
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                         ]
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@@ -13545,7 +26004,7 @@
                             {
                                 "label": "shovill_log",
                                 "output_name": "shovill_std_log",
-                                "uuid": "cec0f15e-2836-442a-bfef-55106e8a5d18"
+                                "uuid": "cb0b1f9d-0218-4b57-8b5e-789b06bc97a2"
                             }
                         ]
                     },
@@ -13590,7 +26049,7 @@
                             {
                                 "label": "quast_output",
                                 "output_name": "report_html",
-                                "uuid": "14ee7f86-cd67-47ad-825e-cbbb5737fbda"
+                                "uuid": "4570780a-41b4-4135-8454-5d6b7236b61b"
                             }
                         ]
                     },
@@ -13635,7 +26094,7 @@
                             {
                                 "label": "bandage_info_output",
                                 "output_name": "outfile",
-                                "uuid": "a1b831a6-24a3-4643-b0d2-fafac0deba79"
+                                "uuid": "56d4d8fb-3c04-4eb5-9beb-565e39f25641"
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                         ]
                     }
@@ -13773,7 +26232,6 @@
             "MISSISSIPPI",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
@@ -13797,12 +26255,12 @@
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-09-19",
+        "mod_date": "2024-10-08",
         "objectives": [
             "Learn the tools necessary to perform a de novo assembly of a vertebrate genome",
             "Evaluate the quality of the assembly"
         ],
-        "pageviews": 3049,
+        "pageviews": 3079,
         "pub_date": "2022-04-06",
         "questions": [
             "What combination of tools can produce the highest quality assembly of vertebrate genomes?",
@@ -13820,7 +26278,7 @@
                 "speakers": [
                     "abueg"
                 ],
-                "youtube_id": "LO-migvwcM"
+                "youtube_id": "_LO-migvwcM"
             }
         ],
         "short_id": "T00040",
@@ -13856,11 +26314,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -13890,6 +26343,296 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
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+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
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+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
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+                            "state": "exact",
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+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
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+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
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+                                "5.0.2+galaxy1",
+                                "4.6.3",
+                                "4.1",
+                                "5.0.2"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "5.2.0+galaxy1"
+                }
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         "tags": [
             "pacbio",
@@ -13916,12 +26659,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_workflow_training/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/vgp_workflow_training/tutorial.json"
         },
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+        "version": 23,
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         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 164,
-        "visitors": 2135,
+        "visit_duration": 163,
+        "visitors": 2157,
         "zenodo_link": "https://zenodo.org/record/5887339"
     },
     {
@@ -14182,23 +26925,23 @@
             "topic_4013"
         ],
         "edam_operation": [
-            "Scatter plot plotting",
+            "Genome assembly",
             "Sequencing error detection",
-            "Sequence alignment",
+            "Sequence assembly visualisation",
+            "De-novo assembly",
+            "Filtering",
+            "Mapping assembly",
+            "Scatter plot plotting",
+            "Sequence assembly validation",
             "Visualisation",
             "Cross-assembly",
-            "Read mapping",
-            "Sequencing quality control",
-            "Genome assembly",
-            "De-novo assembly",
+            "Sequence alignment",
+            "Sequence composition calculation",
             "Box-Whisker plot plotting",
+            "Sequencing quality control",
+            "Read mapping",
             "Sequence contamination filtering",
-            "Sequence assembly validation",
-            "Mapping assembly",
-            "Statistical calculation",
-            "Sequence assembly visualisation",
-            "Filtering",
-            "Sequence composition calculation"
+            "Statistical calculation"
         ],
         "edam_topic": [
             "Sequence assembly",
@@ -14254,7 +26997,7 @@
             "Run tools to assess the quality of an assembly",
             "Understand the outputs of tools to assess the quality of an assembly"
         ],
-        "pageviews": 10976,
+        "pageviews": 11067,
         "pub_date": "2021-03-24",
         "questions": [
             "How to check the quality of the MinION data (together with Illumina data)?",
@@ -14263,18 +27006,18 @@
         ],
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-            "CONVERTER_bz2_to_uncompressed",
-            "fastp",
-            "filtlong",
             "bandage_image",
-            "porechop",
-            "upload1",
-            "quast",
-            "flye",
+            "polypolish",
+            "filtlong",
+            "fastqc",
             "nanoplot",
+            "upload1",
             "bwa_mem2",
-            "polypolish",
-            "fastqc"
+            "fastp",
+            "porechop",
+            "CONVERTER_bz2_to_uncompressed",
+            "quast",
+            "flye"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -14294,6 +27037,2040 @@
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             ]
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+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
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+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
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+                    "url": "http://dintor.eurac.edu/"
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
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+                    "url": "https://www.immportgalaxy.org/"
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+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "nanopore",
@@ -14339,8 +29116,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 204,
-        "visitors": 7147,
+        "visit_duration": 203,
+        "visitors": 7215,
         "workflows": [
             {
                 "creators": [
@@ -14457,7 +29234,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNanopore raw reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina forward raw reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nIllumina reverse raw reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Convert compressed file to uncompressed.\"];\n  0 -->|output| 3;\n  4[\"FastQC\"];\n  0 -->|output| 4;\n  5[\"fastp\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  6[\"NanoPlot\"];\n  3 -->|output1| 6;\n  a97e6f33-8182-4a33-86dd-6cfbb83a842d[\"Output\\nnanoplot_before_filtering\"];\n  6 --> a97e6f33-8182-4a33-86dd-6cfbb83a842d;\n  style a97e6f33-8182-4a33-86dd-6cfbb83a842d stroke:#2c3143,stroke-width:4px;\n  7[\"filtlong\"];\n  5 -->|out1| 7;\n  5 -->|out2| 7;\n  0 -->|output| 7;\n  8[\"Flye\"];\n  7 -->|outfile| 8;\n  f12e718f-1bd5-490d-bd41-f0747aaa41a6[\"Output\\nflye_assembly_info\"];\n  8 --> f12e718f-1bd5-490d-bd41-f0747aaa41a6;\n  style f12e718f-1bd5-490d-bd41-f0747aaa41a6 stroke:#2c3143,stroke-width:4px;\n  9[\"NanoPlot\"];\n  7 -->|outfile| 9;\n  89524090-f590-434d-89e2-66f0b1a23c7c[\"Output\\nnanoplot_after_filtering\"];\n  9 --> 89524090-f590-434d-89e2-66f0b1a23c7c;\n  style 89524090-f590-434d-89e2-66f0b1a23c7c stroke:#2c3143,stroke-width:4px;\n  10[\"Bandage Image\"];\n  8 -->|assembly_gfa| 10;\n  11[\"BWA-MEM2\"];\n  5 -->|out2| 11;\n  8 -->|consensus| 11;\n  12[\"Quast\"];\n  8 -->|consensus| 12;\n  dabfb8fd-8791-4959-a9dc-9b3c1e57a69c[\"Output\\nquast_report_before_polishing\"];\n  12 --> dabfb8fd-8791-4959-a9dc-9b3c1e57a69c;\n  style dabfb8fd-8791-4959-a9dc-9b3c1e57a69c stroke:#2c3143,stroke-width:4px;\n  13[\"BWA-MEM2\"];\n  5 -->|out1| 13;\n  8 -->|consensus| 13;\n  14[\"Polypolish\"];\n  8 -->|consensus| 14;\n  13 -->|bam_output| 14;\n  11 -->|bam_output| 14;\n  15[\"Quast\"];\n  14 -->|polished_fasta| 15;\n  8 -->|consensus| 15;\n  4e465b51-68bf-4203-9a7c-897f46c70277[\"Output\\nquast_report_after_polishing\"];\n  15 --> 4e465b51-68bf-4203-9a7c-897f46c70277;\n  style 4e465b51-68bf-4203-9a7c-897f46c70277 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)",
                 "outputs": [
                     {
@@ -15138,21 +29915,21 @@
         "dir": "topics/assembly/tutorials/vgp_genome_assembly",
         "edam_operation": [
             "Data handling",
-            "Sequence alignment",
-            "Visualisation",
-            "Sequence trimming",
             "Genome assembly",
+            "Transcriptome assembly",
+            "Read binning",
             "De-novo assembly",
+            "Primer removal",
             "Phasing",
+            "k-mer counting",
             "Sequence assembly validation",
             "Scaffolding",
-            "Read binning",
-            "Pairwise sequence alignment",
-            "k-mer counting",
-            "Transcriptome assembly",
-            "Mapping",
+            "Visualisation",
             "Read pre-processing",
-            "Primer removal"
+            "Sequence trimming",
+            "Sequence alignment",
+            "Pairwise sequence alignment",
+            "Mapping"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -15177,7 +29954,7 @@
             "Learn the tools necessary to perform a de novo assembly of a vertebrate genome",
             "Evaluate the quality of the assembly"
         ],
-        "pageviews": 17734,
+        "pageviews": 17815,
         "pub_date": "2021-06-04",
         "questions": [
             "What combination of tools can produce the highest quality assembly of vertebrate genomes?",
@@ -15199,34 +29976,34 @@
         ],
         "short_id": "T00039",
         "short_tools": [
-            "merqury",
-            "bionano_scaffold",
-            "minimap2",
+            "cat1",
             "busco",
-            "quast",
-            "tp_find_and_replace",
+            "tp_grep_tool",
             "pretext_snapshot",
+            "bellerophon",
+            "gfa_to_fa",
+            "sort1",
+            "collapse_dataset",
+            "meryl",
+            "cutadapt",
+            "hifiasm",
+            "bedtools_bamtobed",
+            "bionano_scaffold",
+            "quast",
+            "minimap2",
             "yahs",
+            "tp_find_and_replace",
             "collection_column_join",
+            "pretext_map",
             "bwa_mem2",
-            "purge_dups",
+            "Add_a_column1",
+            "tp_cut_tool",
             "salsa",
+            "merqury",
             "gfastats",
-            "tp_cut_tool",
-            "pretext_map",
-            "hifiasm",
-            "genomescope",
-            "cutadapt",
-            "bellerophon",
-            "collapse_dataset",
-            "meryl",
-            "cat1",
-            "sort1",
             "Convert characters1",
-            "tp_grep_tool",
-            "Add_a_column1",
-            "bedtools_bamtobed",
-            "gfa_to_fa"
+            "genomescope",
+            "purge_dups"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -15234,6 +30011,5976 @@
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             "inexact": []
         },
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
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+                },
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+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
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+                    "name": "ChemFlow",
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+                },
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+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
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+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
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+                    "usegalaxy": false
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+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
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+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
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+                {
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+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
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+                },
+                {
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+                            "server": "https://galaxytrakr.org/",
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+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
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+                        {
+                            "server": "https://galaxytrakr.org/",
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+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
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+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
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+                            "server": "https://galaxy-web.ipk-gatersleben.de",
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+                            "server": "https://www.immportgalaxy.org/",
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+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
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+                            "server": "https://mississippi.sorbonne-universite.fr",
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+                            "server": "https://palfinder.ls.manchester.ac.uk/",
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+                        },
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+                            "server": "https://usegalaxy.be/",
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+                                "4.2",
+                                "4.0"
+                            ]
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+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
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+                        },
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+                            "server": "https://usegalaxy.no/",
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+                            "server": "https://usegalaxy.org",
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+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
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+                            "server": "https://viralvariant.anses.fr/",
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+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
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+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.2.1+galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "pacbio",
@@ -15305,7 +36052,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 119,
-        "visitors": 11232,
+        "visitors": 11301,
         "workflows": [
             {
                 "creators": [],
@@ -15483,7 +36230,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nBionano_dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nHi-C_dataset_R\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nHi-C_dataset_F\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"GFA to FASTA\"];\n  5[\"GFA to FASTA\"];\n  6[\"Cutadapt\"];\n  3 -->|output| 6;\n  7[\"Busco\"];\n  4 -->|out_fa| 7;\n  8[\"Busco\"];\n  5 -->|out_fa| 8;\n  9[\"Purge overlaps\"];\n  5 -->|out_fa| 9;\n  10[\"Collapse Collection\"];\n  6 -->|out1| 10;\n  11[\"Meryl\"];\n  6 -->|out1| 11;\n  12[\"Map with minimap2\"];\n  6 -->|out1| 12;\n  5 -->|out_fa| 12;\n  13[\"Quast\"];\n  5 -->|out_fa| 13;\n  4 -->|out_fa| 13;\n  6 -->|out1| 13;\n  14[\"Map with minimap2\"];\n  9 -->|split_fasta| 14;\n  9 -->|split_fasta| 14;\n  15[\"Meryl\"];\n  11 -->|read_db| 15;\n  16[\"Purge overlaps\"];\n  12 -->|alignment_output| 16;\n  17[\"Meryl\"];\n  15 -->|read_db| 17;\n  18[\"Merqury\"];\n  5 -->|out_fa| 18;\n  4 -->|out_fa| 18;\n  15 -->|read_db| 18;\n  19[\"Purge overlaps\"];\n  16 -->|pbcstat_cov| 19;\n  16 -->|calcuts_cutoff| 19;\n  14 -->|alignment_output| 19;\n  20[\"GenomeScope\"];\n  17 -->|read_db_hist| 20;\n  21[\"Purge overlaps\"];\n  19 -->|purge_dups_bed| 21;\n  5 -->|out_fa| 21;\n  22[\"Replace\"];\n  20 -->|summary| 22;\n  23[\"Compute\"];\n  20 -->|model_params| 23;\n  24[\"Bionano Hybrid Scaffold\"];\n  0 -->|output| 24;\n  21 -->|get_seqs_purged| 24;\n  25[\"Concatenate datasets\"];\n  21 -->|get_seqs_hap| 25;\n  4 -->|out_fa| 25;\n  26[\"Busco\"];\n  21 -->|get_seqs_purged| 26;\n  27[\"Replace\"];\n  22 -->|outfile| 27;\n  28[\"Compute\"];\n  23 -->|out_file1| 28;\n  29[\"Concatenate datasets\"];\n  24 -->|ngs_contigs_scaffold_trimmed| 29;\n  24 -->|ngs_contigs_not_scaffolded_trimmed| 29;\n  30[\"Purge overlaps\"];\n  25 -->|out_file1| 30;\n  31[\"Map with minimap2\"];\n  10 -->|output| 31;\n  25 -->|out_file1| 31;\n  32[\"Search in textfiles\"];\n  27 -->|outfile| 32;\n  33[\"Advanced Cut\"];\n  28 -->|out_file1| 33;\n  34[\"Advanced Cut\"];\n  28 -->|out_file1| 34;\n  35[\"BWA-MEM2\"];\n  1 -->|output| 35;\n  29 -->|out_file1| 35;\n  36[\"BWA-MEM2\"];\n  2 -->|output| 36;\n  29 -->|out_file1| 36;\n  37[\"Replace\"];\n  29 -->|out_file1| 37;\n  38[\"Quast\"];\n  29 -->|out_file1| 38;\n  10 -->|output| 38;\n  39[\"Busco\"];\n  29 -->|out_file1| 39;\n  40[\"Map with minimap2\"];\n  30 -->|split_fasta| 40;\n  30 -->|split_fasta| 40;\n  41[\"Purge overlaps\"];\n  31 -->|alignment_output| 41;\n  42[\"Convert\"];\n  32 -->|output| 42;\n  43[\"Filter and merge\"];\n  36 -->|bam_output| 43;\n  35 -->|bam_output| 43;\n  44[\"Purge overlaps\"];\n  41 -->|pbcstat_cov| 44;\n  41 -->|calcuts_cutoff| 44;\n  40 -->|alignment_output| 44;\n  45[\"Advanced Cut\"];\n  42 -->|out_file1| 45;\n  46[\"bedtools BAM to BED\"];\n  43 -->|outfile| 46;\n  47[\"PretextMap\"];\n  43 -->|outfile| 47;\n  48[\"Purge overlaps\"];\n  44 -->|purge_dups_bed| 48;\n  25 -->|out_file1| 48;\n  49[\"Sort\"];\n  46 -->|output| 49;\n  50[\"Pretext Snapshot\"];\n  47 -->|pretext_map_out| 50;\n  51[\"Busco\"];\n  48 -->|get_seqs_purged| 51;\n  52[\"Quast\"];\n  21 -->|get_seqs_purged| 52;\n  48 -->|get_seqs_purged| 52;\n  10 -->|output| 52;\n  53[\"SALSA\"];\n  49 -->|out_file1| 53;\n  37 -->|outfile| 53;\n  54[\"BWA-MEM2\"];\n  1 -->|output| 54;\n  53 -->|scaffolds_fasta| 54;\n  55[\"BWA-MEM2\"];\n  2 -->|output| 55;\n  53 -->|scaffolds_fasta| 55;\n  56[\"Busco\"];\n  53 -->|scaffolds_fasta| 56;\n  57[\"Quast\"];\n  53 -->|scaffolds_fasta| 57;\n  10 -->|output| 57;\n  58[\"Filter and merge\"];\n  55 -->|bam_output| 58;\n  54 -->|bam_output| 58;\n  59[\"PretextMap\"];\n  58 -->|outfile| 59;\n  60[\"Pretext Snapshot\"];\n  59 -->|pretext_map_out| 60;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "VGP assembly: training workflow",
                 "outputs": [],
                 "parent_id": "assembly/vgp_genome_assembly",
@@ -15673,19 +36420,18 @@
         ],
         "dir": "topics/assembly/tutorials/flye-assembly",
         "edam_operation": [
-            "Cross-assembly",
-            "Visualisation",
             "Genome assembly",
+            "Transcriptome assembly",
             "De-novo assembly",
-            "Sequence assembly validation",
             "Mapping assembly",
+            "Sequence assembly validation",
             "Scaffolding",
-            "Transcriptome assembly"
+            "Visualisation",
+            "Cross-assembly"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
@@ -15724,7 +36470,7 @@
             "Assemble a Genome with PacBio data",
             "Assess assembly quality"
         ],
-        "pageviews": 4626,
+        "pageviews": 4643,
         "pub_date": "2021-11-29",
         "questions": [
             "How to perform a genome assembly with PacBio data ?",
@@ -15732,10 +36478,10 @@
         ],
         "short_id": "T00033",
         "short_tools": [
-            "flye",
-            "busco",
             "fasta-stats",
-            "quast"
+            "busco",
+            "quast",
+            "flye"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -15746,11 +36492,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -15785,6 +36526,889 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
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                 "outputs": [
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@@ -18685,26 +42826,26 @@
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@@ -18735,7 +42876,7 @@
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@@ -18756,21 +42897,21 @@
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@@ -18795,6 +42936,2419 @@
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "5.0.2+galaxy5"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "5.0.2+galaxy0",
+                                "5.0.2+galaxy1",
+                                "4.6.3",
+                                "4.1",
+                                "5.0.2"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "5.2.0+galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "assembly",
@@ -18841,7 +45395,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 127,
-        "visitors": 4015,
+        "visitors": 4068,
         "workflows": [
             {
                 "creators": [
@@ -19016,7 +45570,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with long reads, x4 - upgraded\"];\n  style 4 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 4;\n  1 -->|output| 4;\n  2 -->|output| 4;\n  5[\"Medaka polish\"];\n  4 -->|Assembly polished by long reads using Racon| 5;\n  1 -->|output| 5;\n  e3136060-bce7-4af3-87c4-9dcbb0d1f531[\"Output\\nAssembly polished by long reads using Medaka\"];\n  5 --> e3136060-bce7-4af3-87c4-9dcbb0d1f531;\n  style e3136060-bce7-4af3-87c4-9dcbb0d1f531 stroke:#2c3143,stroke-width:4px;\n  6[\"Fasta statistics after Racon long read polish\"];\n  4 -->|Assembly polished by long reads using Racon| 6;\n  7[\"Fasta statistics after Medaka polish\"];\n  5 -->|out_consensus| 7;\n  8[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with Illumina reads R1 only, x2 - upgraded\"];\n  style 8 fill:#edd,stroke:#900,stroke-width:4px;\n  5 -->|out_consensus| 8;\n  3 -->|output| 8;\n  9[\"Fasta statistics after Racon short read polish\"];\n  8 -->|Assembly polished by short reads using Racon| 9;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Assembly polishing - upgraded",
                 "outputs": [
                     {
@@ -19854,7 +46408,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Flye: assembly\"];\n  0 -->|output| 1;\n  3960e31d-7a9e-400c-bb21-f6e47b75e649[\"Output\\nFlye assembly on input dataset(s) (consensus)\"];\n  1 --> 3960e31d-7a9e-400c-bb21-f6e47b75e649;\n  style 3960e31d-7a9e-400c-bb21-f6e47b75e649 stroke:#2c3143,stroke-width:4px;\n  e524f295-a957-4c91-838c-f8e98e809b6c[\"Output\\nFlye assembly on input dataset(s) (assembly_graph)\"];\n  1 --> e524f295-a957-4c91-838c-f8e98e809b6c;\n  style e524f295-a957-4c91-838c-f8e98e809b6c stroke:#2c3143,stroke-width:4px;\n  48b854e2-dd6e-4345-8d05-09abca6659da[\"Output\\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)\"];\n  1 --> 48b854e2-dd6e-4345-8d05-09abca6659da;\n  style 48b854e2-dd6e-4345-8d05-09abca6659da stroke:#2c3143,stroke-width:4px;\n  8672c172-71a7-432c-9679-a8e37f36cf53[\"Output\\nFlye assembly on input dataset(s) (assembly_info)\"];\n  1 --> 8672c172-71a7-432c-9679-a8e37f36cf53;\n  style 8672c172-71a7-432c-9679-a8e37f36cf53 stroke:#2c3143,stroke-width:4px;\n  2[\"Fasta statistics\"];\n  1 -->|consensus| 2;\n  3[\"Quast genome report\"];\n  1 -->|consensus| 3;\n  17cdf8e0-8ad4-4570-afae-1861934fc678[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  3 --> 17cdf8e0-8ad4-4570-afae-1861934fc678;\n  style 17cdf8e0-8ad4-4570-afae-1861934fc678 stroke:#2c3143,stroke-width:4px;\n  4[\"Bandage image: Flye assembly\"];\n  1 -->|assembly_gfa| 4;\n  e66bd129-146f-48dc-95b8-39a2a1ffb68d[\"Output\\nBandage Image on input dataset(s): Assembly Graph Image\"];\n  4 --> e66bd129-146f-48dc-95b8-39a2a1ffb68d;\n  style e66bd129-146f-48dc-95b8-39a2a1ffb68d stroke:#2c3143,stroke-width:4px;\n  5[\"Bar chart: show contig sizes\"];\n  1 -->|assembly_info| 5;\n  6d0a4e23-d631-4e37-8930-3d22fc91369b[\"Output\\nBar chart showing contig sizes\"];\n  5 --> 6d0a4e23-d631-4e37-8930-3d22fc91369b;\n  style 6d0a4e23-d631-4e37-8930-3d22fc91369b stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Assembly with Flye - upgraded",
                 "outputs": [
                     {
@@ -20199,7 +46753,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPolished assembly\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Busco: assess assembly\"];\n  0 -->|output| 2;\n  219e4952-36e0-4b01-a407-e774b5b02dca[\"Output\\nBusco short summary\"];\n  2 --> 219e4952-36e0-4b01-a407-e774b5b02dca;\n  style 219e4952-36e0-4b01-a407-e774b5b02dca stroke:#2c3143,stroke-width:4px;\n  3[\"Quast: assess assembly\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  77ab0186-4cfd-460f-b71e-39a923414ef4[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  3 --> 77ab0186-4cfd-460f-b71e-39a923414ef4;\n  style 77ab0186-4cfd-460f-b71e-39a923414ef4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Assess genome quality - upgraded",
                 "outputs": [
                     {
@@ -20530,7 +47084,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nR1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nR2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nminimap settings for long reads\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nReference genome for Quast\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\ud83d\udee0\ufe0f Subworkflow\\nkmer counting - meryl - upgraded\"];\n  style 5 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 5;\n  6[\"\ud83d\udee0\ufe0f Subworkflow\\nData QC - upgraded\"];\n  style 6 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 6;\n  2 -->|output| 6;\n  0 -->|output| 6;\n  7[\"\ud83d\udee0\ufe0f Subworkflow\\nTrim and filter reads - fastp - upgraded \"];\n  style 7 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  0 -->|output| 7;\n  8[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly with Flye - upgraded\"];\n  style 8 fill:#edd,stroke:#900,stroke-width:4px;\n  7 -->|fastp filtered long reads| 8;\n  9[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly polishing - upgraded\"];\n  style 9 fill:#edd,stroke:#900,stroke-width:4px;\n  8 -->|Flye assembly on input datasets consensus| 9;\n  7 -->|fastp filtered R1 reads| 9;\n  7 -->|fastp filtered long reads| 9;\n  3 -->|output| 9;\n  10[\"\ud83d\udee0\ufe0f Subworkflow\\nAssess genome quality - upgraded\"];\n  style 10 fill:#edd,stroke:#900,stroke-width:4px;\n  9 -->|Assembly polished by long reads using Medaka| 10;\n  4 -->|output| 10;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Combined workflows for large genome assembly - upgraded ",
                 "outputs": [
                     {
@@ -22066,7 +48620,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput file: long reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Nanoplot: long reads\"];\n  0 -->|output| 3;\n  73d0e4cf-366e-41c1-810a-b269638826b3[\"Output\\nNanoPlot on input dataset(s): HTML report\"];\n  3 --> 73d0e4cf-366e-41c1-810a-b269638826b3;\n  style 73d0e4cf-366e-41c1-810a-b269638826b3 stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC on R1\"];\n  1 -->|output| 4;\n  5[\"FastQC on R2\"];\n  2 -->|output| 5;\n  6[\"MultiQC: combine fastQC reports\"];\n  4 -->|text_file| 6;\n  5 -->|text_file| 6;\n  8baf8700-876e-4a74-ad99-6e656f3ba618[\"Output\\nMultiQC on input dataset(s): Webpage\"];\n  6 --> 8baf8700-876e-4a74-ad99-6e656f3ba618;\n  style 8baf8700-876e-4a74-ad99-6e656f3ba618 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Data QC - upgraded",
                 "outputs": [
                     {
@@ -22339,7 +48893,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina reads, R1, in fastq.gz format\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Minimap2 round 1: map reads to assembly\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Racon round 1: polish assembly\"];\n  0 -->|output| 3;\n  2 -->|alignment_output| 3;\n  1 -->|output| 3;\n  4[\"Minimap2 round 2: map reads to assembly\"];\n  1 -->|output| 4;\n  3 -->|consensus| 4;\n  5[\"Racon round 2: polish assembly\"];\n  3 -->|consensus| 5;\n  4 -->|alignment_output| 5;\n  1 -->|output| 5;\n  594819c3-668e-4575-b9a6-4459ffacf952[\"Output\\nAssembly polished by short reads using Racon\"];\n  5 --> 594819c3-668e-4575-b9a6-4459ffacf952;\n  style 594819c3-668e-4575-b9a6-4459ffacf952 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
                 "outputs": [
                     {
@@ -22574,7 +49128,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads \"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"Minimap2: map long reads to assembly\"];\n  2 -->|output| 3;\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Racon: polish 1\"];\n  0 -->|output| 4;\n  3 -->|alignment_output| 4;\n  1 -->|output| 4;\n  5[\"Minimap2: map long reads to polished assembly 1\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  4 -->|consensus| 5;\n  6[\"Racon: polish 2\"];\n  4 -->|consensus| 6;\n  5 -->|alignment_output| 6;\n  1 -->|output| 6;\n  7[\"Minimap2: map long reads to polished assembly 2\"];\n  2 -->|output| 7;\n  1 -->|output| 7;\n  6 -->|consensus| 7;\n  8[\"Racon: polish 3\"];\n  6 -->|consensus| 8;\n  7 -->|alignment_output| 8;\n  1 -->|output| 8;\n  9[\"Minimap2: map long reads to polished assembly 3\"];\n  2 -->|output| 9;\n  1 -->|output| 9;\n  8 -->|consensus| 9;\n  10[\"Racon: polish 4\"];\n  8 -->|consensus| 10;\n  9 -->|alignment_output| 10;\n  1 -->|output| 10;\n  bcf0f03c-5951-46a7-aa38-545aed9bc183[\"Output\\nAssembly polished by long reads using Racon\"];\n  10 --> bcf0f03c-5951-46a7-aa38-545aed9bc183;\n  style bcf0f03c-5951-46a7-aa38-545aed9bc183 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Racon polish with long reads, x4 - upgraded",
                 "outputs": [
                     {
@@ -22836,7 +49390,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina reads R2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"fastp on short reads\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  656e4138-41ab-4561-8989-33de9ac9a2f3[\"Output\\nfastp report on short reads html\"];\n  3 --> 656e4138-41ab-4561-8989-33de9ac9a2f3;\n  style 656e4138-41ab-4561-8989-33de9ac9a2f3 stroke:#2c3143,stroke-width:4px;\n  0d53f347-0368-47cb-953a-2e4dac57e013[\"Output\\nfastp filtered R1 reads\"];\n  3 --> 0d53f347-0368-47cb-953a-2e4dac57e013;\n  style 0d53f347-0368-47cb-953a-2e4dac57e013 stroke:#2c3143,stroke-width:4px;\n  10fbe1e5-400c-4ffe-8794-9b776b0d7322[\"Output\\nfastp report on short reads json\"];\n  3 --> 10fbe1e5-400c-4ffe-8794-9b776b0d7322;\n  style 10fbe1e5-400c-4ffe-8794-9b776b0d7322 stroke:#2c3143,stroke-width:4px;\n  639ed3f7-0e51-4e5d-b6f8-081378962109[\"Output\\nfastp filtered R2 reads\"];\n  3 --> 639ed3f7-0e51-4e5d-b6f8-081378962109;\n  style 639ed3f7-0e51-4e5d-b6f8-081378962109 stroke:#2c3143,stroke-width:4px;\n  4[\"fastp on long reads\"];\n  2 -->|output| 4;\n  5e0d2c3d-41a4-4823-ae9c-b1e4d2826541[\"Output\\nfastp report on long reads html\"];\n  4 --> 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541;\n  style 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541 stroke:#2c3143,stroke-width:4px;\n  e6018ad6-86f4-4e78-8cf2-ccc8b97022fe[\"Output\\nfastp filtered long reads\"];\n  4 --> e6018ad6-86f4-4e78-8cf2-ccc8b97022fe;\n  style e6018ad6-86f4-4e78-8cf2-ccc8b97022fe stroke:#2c3143,stroke-width:4px;\n  69f8383b-a1be-4a74-95f4-3dba35e01426[\"Output\\nfastp report on long reads json\"];\n  4 --> 69f8383b-a1be-4a74-95f4-3dba35e01426;\n  style 69f8383b-a1be-4a74-95f4-3dba35e01426 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Trim and filter reads - fastp - upgraded ",
                 "outputs": [
                     {
@@ -23163,7 +49717,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Meryl - count kmers\"];\n  0 -->|output| 1;\n  899ddd93-4c0f-4f81-a973-8120494ed983[\"Output\\nMeryl on input dataset(s): read-db.meryldb\"];\n  1 --> 899ddd93-4c0f-4f81-a973-8120494ed983;\n  style 899ddd93-4c0f-4f81-a973-8120494ed983 stroke:#2c3143,stroke-width:4px;\n  2[\"Meryl - generate histogram\"];\n  1 -->|read_db| 2;\n  3[\"Genomescope\"];\n  2 -->|read_db_hist| 3;\n  efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac[\"Output\\nGenomeScope on input dataset(s) Transformed log plot\"];\n  3 --> efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac;\n  style efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac stroke:#2c3143,stroke-width:4px;\n  701df341-5767-44bc-ade2-6af498ab7467[\"Output\\nGenomeScope on input dataset(s) Transformed linear plot\"];\n  3 --> 701df341-5767-44bc-ade2-6af498ab7467;\n  style 701df341-5767-44bc-ade2-6af498ab7467 stroke:#2c3143,stroke-width:4px;\n  85fa4004-b351-47b3-84aa-6788d338037a[\"Output\\nGenomeScope on input dataset(s) Log plot\"];\n  3 --> 85fa4004-b351-47b3-84aa-6788d338037a;\n  style 85fa4004-b351-47b3-84aa-6788d338037a stroke:#2c3143,stroke-width:4px;\n  c71ce055-98f0-4354-9397-2f8833b90cc4[\"Output\\nGenomeScope on input dataset(s) Linear plot\"];\n  3 --> c71ce055-98f0-4354-9397-2f8833b90cc4;\n  style c71ce055-98f0-4354-9397-2f8833b90cc4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "kmer counting - meryl - upgraded",
                 "outputs": [
                     {
@@ -23503,9 +50057,9 @@
         ],
         "dir": "topics/assembly/tutorials/debruijn-graph-assembly",
         "edam_operation": [
+            "Sequence assembly",
             "Genome assembly",
-            "Optimisation and refinement",
-            "Sequence assembly"
+            "Optimisation and refinement"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -23542,7 +50096,7 @@
             "Compare this assembly with those we did in the basic tutorial",
             "Perform an assembly using the SPAdes assembler."
         ],
-        "pageviews": 5905570,
+        "pageviews": 5937219,
         "pub_date": "2017-05-24",
         "questions": [
             "What are the factors that affect genome assembly?",
@@ -23550,8 +50104,8 @@
         ],
         "short_id": "T00031",
         "short_tools": [
-            "spades",
             "fasta-stats",
+            "spades",
             "velvetoptimiser"
         ],
         "slides": true,
@@ -23597,6 +50151,576 @@
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+                            "server": "http://galaxy.interactomix.com/",
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+                        {
+                            "server": "https://neo.engr.uconn.edu/",
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+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
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+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
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+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "2.2.6"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "2.2.6"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.2.6"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "2.2.6"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2.2.6"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.2.6"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.2.6"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "2h",
         "title": "De Bruijn Graph Assembly",
@@ -23625,7 +50749,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 299,
-        "visitors": 2138764,
+        "visitors": 2149202,
         "workflows": [
             {
                 "creators": [],
@@ -23723,7 +50847,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmutant_R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nmutant_R2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"VelvetOptimiser\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"SPAdes\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Fasta Statistics\"];\n  2 -->|contigs| 4;\n  dacb84a5-5482-4ab0-81ad-e92af21636cd[\"Output\\nfasta_stats_velvet\"];\n  4 --> dacb84a5-5482-4ab0-81ad-e92af21636cd;\n  style dacb84a5-5482-4ab0-81ad-e92af21636cd stroke:#2c3143,stroke-width:4px;\n  5[\"Fasta Statistics\"];\n  3 -->|out_contigs| 5;\n  ff376be9-7361-48c6-b1c8-d9f951b9c6fa[\"Output\\nfasta_stats_spades\"];\n  5 --> ff376be9-7361-48c6-b1c8-d9f951b9c6fa;\n  style ff376be9-7361-48c6-b1c8-d9f951b9c6fa stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Debruijn Graph",
                 "outputs": [
                     {
@@ -24065,24 +51189,24 @@
             "topic_0196"
         ],
         "edam_operation": [
-            "Data handling",
-            "Visualisation",
-            "Sequence trimming",
-            "Read mapping",
-            "Sequencing quality control",
-            "Genome assembly",
-            "Sequence alignment analysis",
-            "Sequence contamination filtering",
-            "Sequence assembly validation",
             "Variant calling",
-            "Statistical calculation",
+            "Genome assembly",
             "Sequence assembly visualisation",
-            "Sequence file editing",
+            "Sequence assembly validation",
+            "Visualisation",
+            "Sequence trimming",
             "Local alignment",
+            "Sequence file editing",
+            "Data handling",
+            "Sequence alignment analysis",
+            "Primer removal",
+            "Formatting",
             "Sequence composition calculation",
+            "Sequencing quality control",
+            "Read mapping",
             "Read pre-processing",
-            "Primer removal",
-            "Formatting"
+            "Sequence contamination filtering",
+            "Statistical calculation"
         ],
         "edam_topic": [
             "Metagenomics",
@@ -24110,7 +51234,7 @@
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-10-02",
+        "mod_date": "2024-10-08",
         "objectives": [
             "Describe what an assembly is",
             "Describe what de-replication is",
@@ -24122,8 +51246,8 @@
             "Apply appropriate tools for analyzing the quality of metagenomic assembly",
             "Evaluate the Quality of the Assembly with Quast, Bowtie2, and CoverM-Genome"
         ],
-        "pageviews": 7,
-        "pub_date": "2024-10-02",
+        "pageviews": 14,
+        "pub_date": "2024-10-08",
         "questions": [
             "Why metagenomic data should be assembled?",
             "What is the difference between co-assembly and individual assembly?",
@@ -24153,24 +51277,24 @@
         ],
         "short_id": "T00035",
         "short_tools": [
-            "ngsutils_bam_filter",
-            "tp_cat",
-            "bamtools",
             "bandage_image",
-            "filter_tabular",
-            "megahit_contig2fastg",
-            "bandage_info",
-            "bg_uniq",
-            "quast",
             "seqtk_subseq",
+            "megahit_contig2fastg",
             "cutadapt",
             "random_lines1",
-            "collection_column_join",
+            "tp_cat",
             "megahit",
-            "coverm_contig",
             "fastqc",
+            "bg_uniq",
+            "collection_column_join",
+            "bandage_info",
             "metaspades",
-            "bowtie2"
+            "coverm_contig",
+            "bowtie2",
+            "filter_tabular",
+            "quast",
+            "bamtools",
+            "ngsutils_bam_filter"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -24190,6 +51314,3286 @@
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+                            "server": "http://pepsimili.e-nios.com:8080/",
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+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "3.9.0",
+                                "1.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "3.15.4+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "3.15.4+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "3.15.4+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "3.15.4+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "3.15.4+galaxy2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "3.15.4+galaxy2"
+                }
+            ]
+        },
         "symlink": true,
         "tags": [
             "assembly",
@@ -24240,7 +54644,7 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 23,
+        "visit_duration": 426,
         "visitors": 6,
         "workflows": [
             {
@@ -24290,7 +54694,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"metaSPAdes\"];\n  0 -->|output| 1;\n  833d79ff-e16f-414c-9c41-db8dbfa8ed6b[\"Output\\nmetaSPAdes on input dataset(s): Scaffolds\"];\n  1 --> 833d79ff-e16f-414c-9c41-db8dbfa8ed6b;\n  style 833d79ff-e16f-414c-9c41-db8dbfa8ed6b stroke:#2c3143,stroke-width:4px;\n  10319152-d2f9-47d8-be41-f956a57e86d3[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph\"];\n  1 --> 10319152-d2f9-47d8-be41-f956a57e86d3;\n  style 10319152-d2f9-47d8-be41-f956a57e86d3 stroke:#2c3143,stroke-width:4px;\n  b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds\"];\n  1 --> b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633;\n  style b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633 stroke:#2c3143,stroke-width:4px;\n  b6b74c9d-5a16-4725-a1d1-11c1f05ee909[\"Output\\nmetaSPAdes on input dataset(s): Contigs\"];\n  1 --> b6b74c9d-5a16-4725-a1d1-11c1f05ee909;\n  style b6b74c9d-5a16-4725-a1d1-11c1f05ee909 stroke:#2c3143,stroke-width:4px;\n  2[\"MEGAHIT\"];\n  0 -->|output| 2;\n  3[\"Bowtie2\"];\n  0 -->|output| 3;\n  2 -->|output| 3;\n  4[\"megahit contig2fastg\"];\n  2 -->|output| 4;\n  5[\"Quast\"];\n  2 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Bandage Image\"];\n  4 -->|fastg| 6;\n  7[\"Bandage Info\"];\n  4 -->|fastg| 7;\n  8[\"Column join\"];\n  7 -->|outfile| 8;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Metagenomics assembly tutorial workflow",
                 "outputs": [
                     {
@@ -24874,7 +55278,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nERR2231567_1.fastq.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nERR2231567_2.fastq.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Cutadapt\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"MEGAHIT\"];\n  2 -->|out1| 3;\n  2 -->|out2| 3;\n  4[\"Bowtie2\"];\n  2 -->|out1| 4;\n  2 -->|out2| 4;\n  3 -->|output| 4;\n  5[\"BAM filter\"];\n  4 -->|output| 5;\n  6[\"BAM filter\"];\n  4 -->|output| 6;\n  7[\"Convert, Merge, Randomize\"];\n  5 -->|outfile| 7;\n  8[\"Convert, Merge, Randomize\"];\n  6 -->|outfile| 8;\n  9[\"Select random lines\"];\n  7 -->|out_file1| 9;\n  10[\"Select random lines\"];\n  8 -->|out_file1| 10;\n  11[\"Filter Tabular\"];\n  9 -->|out_file1| 11;\n  12[\"Filter Tabular\"];\n  10 -->|out_file1| 12;\n  13[\"Unique\"];\n  11 -->|output| 13;\n  14[\"Unique\"];\n  12 -->|output| 14;\n  15[\"Concatenate datasets\"];\n  13 -->|outfile| 15;\n  14 -->|outfile| 15;\n  16[\"seqtk_subseq\"];\n  2 -->|out1| 16;\n  15 -->|out_file1| 16;\n  17[\"seqtk_subseq\"];\n  2 -->|out2| 17;\n  15 -->|out_file1| 17;\n  18[\"FastQC\"];\n  16 -->|default| 18;\n  19[\"FastQC\"];\n  17 -->|default| 19;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "workflow-generate-dataset-for-assembly-tutorial",
                 "outputs": [
                     {
@@ -25902,17 +56306,17 @@
             "topic_3301"
         ],
         "edam_operation": [
-            "Genome annotation",
-            "Visualisation",
             "Genome assembly",
-            "Sequencing quality control",
+            "Coding region prediction",
+            "Sequence composition calculation",
+            "Genome annotation",
             "Sequence assembly validation",
+            "Validation",
+            "Sequencing quality control",
             "Gene prediction",
-            "Statistical calculation",
+            "Visualisation",
             "Aggregation",
-            "Validation",
-            "Sequence composition calculation",
-            "Coding region prediction"
+            "Statistical calculation"
         ],
         "edam_topic": [
             "Sequence assembly",
@@ -25943,7 +56347,6 @@
             "MISSISSIPPI",
             "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no"
         ],
         "js_requirements": {
@@ -25966,18 +56369,18 @@
             "Evaluate the Quality of the Assembly with Quast",
             "Annotate the assembly with Prokka"
         ],
-        "pageviews": 5917098,
+        "pageviews": 5948759,
         "pub_date": "2017-10-11",
         "questions": [
             "I have short reads and long reads. How do I assemble a genome?"
         ],
         "short_id": "T00038",
         "short_tools": [
-            "prokka",
             "unicycler",
-            "quast",
+            "fastqc",
             "multiqc",
-            "fastqc"
+            "prokka",
+            "quast"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -26026,14 +56429,915 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
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+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "exact",
+                            "version": "0.4.8.0"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "0.5.0+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "0.4.8.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.5.0+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.4.8.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "0.4.8.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.4.8.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.4.8.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.4.8.0"
                 }
             ]
         },
@@ -26070,8 +57374,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 274,
-        "visitors": 2144791,
+        "visit_duration": 275,
+        "visitors": 2155238,
         "workflows": [
             {
                 "creators": [],
@@ -26248,7 +57552,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nForward reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReverse Reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nLong Reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"FastQC\"];\n  0 -->|output| 3;\n  4[\"FastQC\"];\n  1 -->|output| 4;\n  5[\"Create assemblies with Unicycler\"];\n  2 -->|output| 5;\n  0 -->|output| 5;\n  1 -->|output| 5;\n  6[\"MultiQC\"];\n  3 -->|text_file| 6;\n  4 -->|text_file| 6;\n  7[\"Quast\"];\n  5 -->|assembly| 7;\n  8[\"Prokka\"];\n  5 -->|assembly| 8;\n  0d6b33c9-b105-4997-9045-b86e52f00156[\"Output\\ntbl\"];\n  8 --> 0d6b33c9-b105-4997-9045-b86e52f00156;\n  style 0d6b33c9-b105-4997-9045-b86e52f00156 stroke:#2c3143,stroke-width:4px;\n  8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab[\"Output\\ngbk\"];\n  8 --> 8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab;\n  style 8e08b54d-87e1-4269-9b96-8ebf1a9bb4ab stroke:#2c3143,stroke-width:4px;\n  65e4ddf9-f5bc-4078-8b4e-37b332e12ece[\"Output\\nffn\"];\n  8 --> 65e4ddf9-f5bc-4078-8b4e-37b332e12ece;\n  style 65e4ddf9-f5bc-4078-8b4e-37b332e12ece stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Unicycler training",
                 "outputs": [
                     {
@@ -27070,9 +58374,9 @@
             "topic_3301"
         ],
         "edam_operation": [
+            "Read mapping",
             "Sequence alignment",
             "Sequence visualisation",
-            "Read mapping",
             "Genome visualisation",
             "Mapping"
         ],
@@ -27105,7 +58409,7 @@
             "Perform sequence comparison to locate rearrangements",
             "Identify genes located in deletions"
         ],
-        "pageviews": 12166,
+        "pageviews": 12192,
         "pub_date": "2018-06-14",
         "questions": [
             "I just assembled a genome. How does it compare with already sequenced genomes?",
@@ -27122,33 +58426,33 @@
         ],
         "short_id": "T00032",
         "short_tools": [
-            "join1",
+            "cat1",
             "tp_sed_tool",
             "lastz_wrapper_2",
-            "upload1",
-            "fasta_filter_by_length",
-            "bedtools_intersectbed",
-            "datamash_ops",
-            "circos_interval_to_tiles",
             "jbrowse",
-            "tp_cat",
-            "mergeCols1",
-            "Filter1",
-            "bedtools_sortbed",
-            "tp_sort_header_tool",
-            "Grep1",
-            "Cut1",
+            "circos_interval_to_tiles",
+            "tp_grep_tool",
+            "circos",
+            "bedtools_complementbed",
             "collapse_dataset",
-            "cat1",
+            "bedtools_intersectbed",
+            "upload1",
+            "datamash_ops",
             "tp_replace_in_column",
             "addValue",
-            "circos_aln_to_links",
-            "fasta_compute_length",
-            "circos",
-            "tp_grep_tool",
+            "Filter1",
             "tp_replace_in_line",
             "random_lines1",
-            "bedtools_complementbed"
+            "tp_sort_header_tool",
+            "Grep1",
+            "fasta_compute_length",
+            "mergeCols1",
+            "Cut1",
+            "fasta_filter_by_length",
+            "tp_cat",
+            "join1",
+            "bedtools_sortbed",
+            "circos_aln_to_links"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -27156,6 +58460,4276 @@
             "exact": [],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Cut1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
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+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
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+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
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+                        {
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+                            "state": "local"
+                        },
+                        {
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+                        },
+                        {
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+                            "state": "local"
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+                        {
+                            "server": "https://galaxy.pasteur.fr/",
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+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
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+                        {
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+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
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+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
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+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
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+                        {
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+                            "state": "missing"
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+                        },
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+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
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+                        },
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+                        {
+                            "server": "https://usegalaxy.org",
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+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Filter1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
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+                        },
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+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
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+                        {
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+                        },
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+                        {
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+                            "state": "local"
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+                        {
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+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
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+                        },
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+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
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+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
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+                            "server": "http://dintor.eurac.edu/",
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+                        {
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+                        },
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+                        {
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+                        {
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+                        {
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+                            "state": "missing"
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+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                        },
+                        {
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+                        {
+                            "server": "https://usegalaxy.org.au",
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@@ -27216,7 +62790,7 @@
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@@ -27406,7 +62980,7 @@
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Ecoli Comparison",
                 "outputs": [],
                 "parent_id": "assembly/ecoli_comparison",
@@ -27540,7 +63114,7 @@
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         "logo": "GTN",
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@@ -27584,6 +63158,10 @@
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@@ -27797,6 +63375,10 @@
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         "time_estimation": "1h",
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@@ -27922,7 +63504,7 @@
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             "How to run CLM-FATES with the CLM-FATES Galaxy tool?",
@@ -27964,13 +63546,13 @@
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@@ -28002,6 +63584,1101 @@
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@@ -28037,7 +64714,7 @@
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@@ -28158,7 +64835,7 @@
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "CLM-FATES_ ALP1 simulation (5 years)",
                 "outputs": [
                     {
@@ -28765,7 +65442,7 @@
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             "Learn about climate observations, reanalysis, climate predictions and climate projections"
         ],
-        "pageviews": 1202,
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@@ -28773,13 +65450,13 @@
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@@ -28804,6 +65481,1134 @@
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+                            "server": "https://palfinder.ls.manchester.ac.uk/",
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+                            "server": "http://pepsimili.e-nios.com:8080/",
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+                            "state": "inexact",
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+                            ]
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+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.2.1+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.2.1+galaxy2",
+                                "3.3.5+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2.2.1+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
+                                "2.2.1+galaxy2",
+                                "3.4.0+galaxy1",
+                                "3.3.5+galaxy2",
+                                "3.3.5+galaxy0",
+                                "3.4.0+galaxy0",
+                                "3.3.5+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.2.1+galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "1H",
         "title": "Getting your hands-on climate data",
@@ -28836,7 +66641,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 55,
-        "visitors": 852,
+        "visitors": 854,
         "workflows": [
             {
                 "creators": [
@@ -28926,7 +66731,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Copernicus Essential Climate Variables\"];\n  3[\"climate stripes\"];\n  0 -->|output| 3;\n  4[\"Select\"];\n  1 -->|output| 4;\n  5[\"Datamash\"];\n  1 -->|output| 5;\n  6[\"Datamash\"];\n  1 -->|output| 6;\n  7[\"Datamash\"];\n  1 -->|output| 7;\n  8[\"Text reformatting\"];\n  1 -->|output| 8;\n  9[\"map plot\"];\n  2 -->|ofilename| 9;\n  10[\"Datamash\"];\n  8 -->|outfile| 10;\n  11[\"Datamash\"];\n  8 -->|outfile| 11;\n  12[\"Datamash\"];\n  10 -->|out_file| 12;\n  13[\"Datamash\"];\n  10 -->|out_file| 13;\n  14[\"Scatterplot w ggplot2\"];\n  11 -->|out_file| 14;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Climate 101",
                 "outputs": [],
                 "parent_id": "climate/climate-101",
@@ -29079,7 +66884,7 @@
             "Learn to filter, make reduction operations (mean, max, min)",
             "Learn to resample my data"
         ],
-        "pageviews": 3872139,
+        "pageviews": 3903745,
         "pub_date": "2022-02-18",
         "questions": [
             "What Xarray Galaxy Tools can I use in Galaxy and what for?",
@@ -29109,16 +66914,16 @@
         "short_id": "T00044",
         "short_tools": [
             "__EXTRACT_DATASET__",
-            "xarray_metadata_info",
-            "xarray_mapplot",
             "graphicsmagick_image_montage",
-            "xarray_netcdf2netcdf",
-            "ggplot2_point",
-            "xarray_coords_info",
-            "climate_stripes",
+            "xarray_select",
             "regexColumn1",
+            "xarray_coords_info",
+            "ggplot2_point",
             "__MERGE_COLLECTION__",
-            "xarray_select"
+            "xarray_mapplot",
+            "xarray_metadata_info",
+            "climate_stripes",
+            "xarray_netcdf2netcdf"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -29143,6 +66948,1647 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
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+                    "usegalaxy": false
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+                },
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+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                {
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+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
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+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
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+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.org",
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+                    "url": "https://usegalaxy.org.au",
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fill:#ded,stroke:#393,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Parameter\\ntime=4\"];\n  style 9 fill:#ded,stroke:#393,stroke-width:4px;\n  10[\"\u2139\ufe0f Input Parameter\\ntime=0\"];\n  style 10 fill:#ded,stroke:#393,stroke-width:4px;\n  11[\"NetCDF xarray Coordinate Info\"];\n  1 -->|output| 11;\n  12[\"NetCDF xarray Metadata Info\"];\n  1 -->|output| 12;\n  13[\"extract longitude\"];\n  11 -->|output_dir| 13;\n  14[\"extract latitude\"];\n  11 -->|output_dir| 14;\n  15[\"Extract time from coordinate info\"];\n  11 -->|output_dir| 15;\n  3b4968d7-8984-4e66-87a9-a3ab8fc12ca4[\"Output\\ninput dataset(s) (extracted element)\"];\n  15 --> 3b4968d7-8984-4e66-87a9-a3ab8fc12ca4;\n  style 3b4968d7-8984-4e66-87a9-a3ab8fc12ca4 stroke:#2c3143,stroke-width:4px;\n  16[\"NetCDF xarray operations\"];\n  1 -->|output| 16;\n  14 -->|output| 16;\n  13 -->|output| 16;\n  12 -->|output| 16;\n  17[\"NetCDF xarray operations\"];\n  1 -->|output| 17;\n  15 -->|output| 17;\n  12 -->|output| 17;\n  18[\"NetCDF xarray operations\"];\n  1 -->|output| 18;\n  15 -->|output| 18;\n  14 -->|output| 18;\n  13 -->|output| 18;\n  12 -->|output| 18;\n  19[\"PM2.5 CAMS Europe 0 days 00:00 UTC reference time\"];\n  15 -->|output| 19;\n  0 -->|output| 19;\n  1 -->|output| 19;\n  12 -->|output| 19;\n  42483031-21e2-4d88-8898-4a9aa9bb10e5[\"Output\\nPM2.5 reference date Europe\"];\n  19 --> 42483031-21e2-4d88-8898-4a9aa9bb10e5;\n  style 42483031-21e2-4d88-8898-4a9aa9bb10e5 stroke:#2c3143,stroke-width:4px;\n  20[\"PM2.5 CAMS forecast 2 days 12:00 UTC\"];\n  15 -->|output| 20;\n  2 -->|output| 20;\n  1 -->|output| 20;\n  12 -->|output| 20;\n  07ba8141-bad3-4a61-833d-3b3e82b53fdb[\"Output\\nPM2.5 fc 2 days 12:00 UTC Europe\"];\n  20 --> 07ba8141-bad3-4a61-833d-3b3e82b53fdb;\n  style 07ba8141-bad3-4a61-833d-3b3e82b53fdb stroke:#2c3143,stroke-width:4px;\n  21[\"NetCDF xarray Selection\"];\n  16 -->|output_netcdf| 21;\n  12 -->|output| 21;\n  22[\"NetCDF xarray Coordinate Info\"];\n  17 -->|output_netcdf| 22;\n  23[\"NetCDF xarray Coordinate Info\"];\n  18 -->|output_netcdf| 23;\n  24[\"NetCDF xarray Metadata Info\"];\n  18 -->|output_netcdf| 24;\n  25[\"Column Regex Find And Replace\"];\n  21 -->|simpleoutput| 25;\n  26[\"PM2.5 over Naples 4 days forecast\"];\n  21 -->|simpleoutput| 26;\n  8984beb4-e593-42f8-8de5-0e92631061c7[\"Output\\n1D plot PM2.5 over Naples (4 days forecast)\"];\n  26 --> 8984beb4-e593-42f8-8de5-0e92631061c7;\n  style 8984beb4-e593-42f8-8de5-0e92631061c7 stroke:#2c3143,stroke-width:4px;\n  27[\"Extract times from coordinates\"];\n  22 -->|output_dir| 27;\n  28[\"Extract time\"];\n  23 -->|output_dir| 28;\n  29[\" stripes PM2.5 over Naples 4 days forecast\"];\n  25 -->|out_file1| 29;\n  92cad576-78b5-4e07-9a07-6f05ff8f4a56[\"Output\\nPM2.5 stripes Naples for 4 days forecast from reference date\"];\n  29 --> 92cad576-78b5-4e07-9a07-6f05ff8f4a56;\n  style 92cad576-78b5-4e07-9a07-6f05ff8f4a56 stroke:#2c3143,stroke-width:4px;\n  30[\"NetCDF xarray map plotting\"];\n  27 -->|output| 30;\n  0 -->|output| 30;\n  18 -->|output_netcdf| 30;\n  24 -->|output| 30;\n  31[\"NetCDF xarray map plotting\"];\n  28 -->|output| 31;\n  6 -->|output| 31;\n  18 -->|output_netcdf| 31;\n  24 -->|output| 31;\n  32[\"NetCDF xarray map plotting\"];\n  28 -->|output| 32;\n  8 -->|output| 32;\n  18 -->|output_netcdf| 32;\n  24 -->|output| 32;\n  33[\"NetCDF xarray map plotting\"];\n  28 -->|output| 33;\n  5 -->|output| 33;\n  18 -->|output_netcdf| 33;\n  24 -->|output| 33;\n  34[\"NetCDF xarray map plotting\"];\n  28 -->|output| 34;\n  9 -->|output| 34;\n  18 -->|output_netcdf| 34;\n  24 -->|output| 34;\n  35[\"NetCDF xarray map plotting\"];\n  28 -->|output| 35;\n  4 -->|output| 35;\n  18 -->|output_netcdf| 35;\n  24 -->|output| 35;\n  36[\"NetCDF xarray map plotting\"];\n  28 -->|output| 36;\n  7 -->|output| 36;\n  18 -->|output_netcdf| 36;\n  24 -->|output| 36;\n  37[\"NetCDF xarray map plotting\"];\n  28 -->|output| 37;\n  3 -->|output| 37;\n  18 -->|output_netcdf| 37;\n  24 -->|output| 37;\n  38[\"NetCDF xarray map plotting\"];\n  28 -->|output| 38;\n  3 -->|output| 38;\n  18 -->|output_netcdf| 38;\n  24 -->|output| 38;\n  39[\"NetCDF xarray map plotting\"];\n  28 -->|output| 39;\n  4 -->|output| 39;\n  18 -->|output_netcdf| 39;\n  24 -->|output| 39;\n  40[\"NetCDF xarray map plotting\"];\n  28 -->|output| 40;\n  10 -->|output| 40;\n  18 -->|output_netcdf| 40;\n  24 -->|output| 40;\n  41[\"NetCDF xarray map plotting\"];\n  28 -->|output| 41;\n  5 -->|output| 41;\n  18 -->|output_netcdf| 41;\n  24 -->|output| 41;\n  42[\"NetCDF xarray map plotting\"];\n  28 -->|output| 42;\n  6 -->|output| 42;\n  18 -->|output_netcdf| 42;\n  24 -->|output| 42;\n  43[\"NetCDF xarray map plotting\"];\n  28 -->|output| 43;\n  10 -->|output| 43;\n  18 -->|output_netcdf| 43;\n  24 -->|output| 43;\n  44[\"NetCDF xarray map plotting\"];\n  28 -->|output| 44;\n  7 -->|output| 44;\n  18 -->|output_netcdf| 44;\n  24 -->|output| 44;\n  45[\"NetCDF xarray map plotting\"];\n  28 -->|output| 45;\n  9 -->|output| 45;\n  18 -->|output_netcdf| 45;\n  24 -->|output| 45;\n  46[\"NetCDF xarray map plotting\"];\n  28 -->|output| 46;\n  8 -->|output| 46;\n  18 -->|output_netcdf| 46;\n  24 -->|output| 46;\n  47[\"Merge collections\"];\n  30 -->|output_dir| 47;\n  32 -->|output_dir| 47;\n  31 -->|output_dir| 47;\n  33 -->|output_dir| 47;\n  34 -->|output_dir| 47;\n  37 -->|output_dir| 47;\n  35 -->|output_dir| 47;\n  36 -->|output_dir| 47;\n  48[\"Merge collections\"];\n  43 -->|output_dir| 48;\n  46 -->|output_dir| 48;\n  42 -->|output_dir| 48;\n  41 -->|output_dir| 48;\n  45 -->|output_dir| 48;\n  38 -->|output_dir| 48;\n  39 -->|output_dir| 48;\n  44 -->|output_dir| 48;\n  49[\"PM2.5 forecast 10:00 - 17:00 UTC > 30 um/m3\"];\n  47 -->|output| 49;\n  1c16eeb7-dfe1-40de-9be7-3aa2a8568308[\"Output\\nPM2.5 (values > 30 um/m3)  fc 10:00 - 17:00 UTC over Italy\"];\n  49 --> 1c16eeb7-dfe1-40de-9be7-3aa2a8568308;\n  style 1c16eeb7-dfe1-40de-9be7-3aa2a8568308 stroke:#2c3143,stroke-width:4px;\n  50[\"PM2.5 forecast 10:00 - 17:00 UTC \"];\n  48 -->|output| 50;\n  070fe227-b533-4c77-bed0-4d005b174920[\"Output\\nPM2.5 fc 10:00 - 17:00 UTC over Italy\"];\n  50 --> 070fe227-b533-4c77-bed0-4d005b174920;\n  style 070fe227-b533-4c77-bed0-4d005b174920 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "GTN 'Pangeo 101 for everyone - Xarray'",
                 "outputs": [
                     {
@@ -30642,7 +70088,7 @@
             "Learn to resample my data",
             "Learn to cite and contribute to Pangeo"
         ],
-        "pageviews": 3872597,
+        "pageviews": 3904201,
         "pub_date": "2022-02-18",
         "questions": [
             "What is Pangeo notebook?",
@@ -30710,6 +70156,278 @@
             ],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "interactive_tool_pangeo_notebook",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "pangeo",
@@ -30739,8 +70457,8 @@
         "video": true,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 270,
-        "visitors": 1524935,
+        "visit_duration": 271,
+        "visitors": 1535314,
         "workflows": [
             {
                 "creators": [
@@ -30778,7 +70496,7 @@
                 "inputs": [],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"Pangeo Jupyter for Big Data geoscience\"];",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Pangeo Jupyter Notebook",
                 "outputs": [
                     {
@@ -30982,7 +70700,7 @@
             "Learn to get temperature variations.",
             "Learn to use an interactive tool to visualise Argo temperature variable on an interactive map."
         ],
-        "pageviews": 122,
+        "pageviews": 124,
         "pub_date": "2024-03-24",
         "questions": [
             "How to use the Pangeo ecosystem to analyse ocean data?",
@@ -30999,11 +70717,11 @@
         ],
         "short_id": "T00428",
         "short_tools": [
-            "xarray_metadata_info",
-            "argo_getdata",
-            "xarray_coords_info",
             "timeseries_extraction",
-            "interactive_tool_odv"
+            "interactive_tool_odv",
+            "xarray_coords_info",
+            "xarray_metadata_info",
+            "argo_getdata"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -31017,6 +70735,813 @@
             ],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "interactive_tool_odv",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
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-        "visitors": 97,
+        "visit_duration": 113,
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@@ -31084,7 +71609,7 @@
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Analyse Argo data ",
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                 "parent_id": "climate/argo_pangeo",
@@ -31215,7 +71740,7 @@
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             "Learn to visualise gases around a volcano"
         ],
-        "pageviews": 150,
+        "pageviews": 153,
         "pub_date": "2024-01-26",
         "questions": [
             "How to visualise volcanoes with Sentinel 5 data ?",
@@ -31224,9 +71749,9 @@
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         "short_id": "T00396",
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             "interactive_tool_copernicus_notebook",
-            "interactive_tool_copernicus"
+            "interactive_tool_copernicus",
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         "slides_recordings": false,
@@ -31234,6 +71759,538 @@
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
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+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                    "url": "http://galaxy.inf.ethz.ch"
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+                    "url": "https://usegalaxy.no/",
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+                    "url": "https://usegalaxy.org.au",
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+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
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+                        },
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+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
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+                        },
+                        {
+                            "server": "https://usegalaxy.org",
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+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
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+                },
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+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
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+                        {
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+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "earth-system",
@@ -31266,8 +72323,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 39,
-        "visitors": 127,
+        "visit_duration": 37,
+        "visitors": 130,
         "workflows": [
             {
                 "creators": [
@@ -31298,7 +72355,7 @@
                 "inputs": [],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"Copernicus Data Space Ecosystem\"];\n  1[\"Panoply\"];\n  0 -->|output_collection| 1;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Sentinel5 volcanic data",
                 "outputs": [],
                 "parent_id": "climate/sentinel5_data",
@@ -31429,7 +72486,7 @@
             "Deals with ODV collection with data originating from Emodnet chemistry",
             "Visualise ocean variables to study climate changes"
         ],
-        "pageviews": 125,
+        "pageviews": 128,
         "pub_date": "2023-11-29",
         "questions": [
             "How to process extract ocean's variables?",
@@ -31438,9 +72495,9 @@
         ],
         "short_id": "T00376",
         "short_tools": [
-            "divand_full_analysis",
             "interactive_tool_odv",
-            "interactive_tool_divand"
+            "interactive_tool_divand",
+            "divand_full_analysis"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -31454,6 +72511,539 @@
             ],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
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+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
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+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.be/",
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+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
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+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
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+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
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+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
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+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
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@@ -31919,6 +73509,10 @@
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@@ -31992,7 +74479,7 @@
             "Learn to use Panoply in Galaxy to visuallize netCDF geo-referenced data",
             "Learn how Panoply plots are exported to Galaxy"
         ],
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         "questions": [
             "How to start Panoply interactive environment in Galaxy?",
@@ -32023,6 +74510,278 @@
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+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "interactive_tool_panoply",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "interactive-tools"
@@ -32051,8 +74810,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 51,
-        "visitors": 5632,
+        "visit_duration": 50,
+        "visitors": 5648,
         "zenodo_link": "https://doi.org/10.5281/zenodo.3695482"
     },
     {
@@ -32082,7 +74841,6 @@
         "exact_supported_servers": [
             "UseGalaxy.be",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
@@ -32167,17 +74925,284 @@
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
                 }
             ],
-            "inexact": []
+            "tools": [
+                {
+                    "id": "interactive_tool_jupyter_notebook",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
         },
         "symlink": null,
         "tags": [
@@ -32285,8 +75310,7 @@
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -32309,7 +75333,7 @@
             "Deal with netcdf files in ODV",
             "Visualise ocean variables from Argo glider's data"
         ],
-        "pageviews": 260,
+        "pageviews": 266,
         "pub_date": "2023-11-27",
         "questions": [
             "How to process Argo's glider data ?",
@@ -32328,14 +75352,281 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
                 }
             ],
-            "inexact": []
+            "tools": [
+                {
+                    "id": "interactive_tool_odv",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
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+                        "short_hash": "52ea0ed9e",
+                        "unix": "1582108026"
+                    },
+                    {
+                        "hash": "d681f0586063602176dd9f0a0c3b6901e1252c44",
+                        "message": "disabled workflow with testtools",
+                        "num": 5,
+                        "short_hash": "d681f0586",
+                        "unix": "1579166204"
+                    },
+                    {
+                        "hash": "eb4d724e0064c77beb20efa626a0f28fd0500676",
+                        "message": "Workflow renaming",
+                        "num": 4,
+                        "short_hash": "eb4d724e0",
+                        "unix": "1579084895"
+                    },
+                    {
+                        "hash": "7da80b34185f4165852feb3bfe80d692609685db",
+                        "message": "Workflows fix",
+                        "num": 3,
+                        "short_hash": "7da80b341",
+                        "unix": "1578668175"
+                    },
+                    {
+                        "hash": "faf6d298afa752b6676a1533854c634efefe8075",
+                        "message": "unflatten workflows",
+                        "num": 2,
+                        "short_hash": "faf6d298a",
+                        "unix": "1576155753"
+                    },
+                    {
+                        "hash": "aa2ef61fb0b97cf82ea068696454cf18f729f01b",
+                        "message": "initial cheminformatics commit",
+                        "num": 1,
+                        "short_hash": "aa2ef61fb",
+                        "unix": "1560350110"
+                    }
+                ],
+                "inputs": [],
+                "license": null,
+                "mermaid": "flowchart TD\n  11[\"Compound Search\"];\n  5 -->|outfile| 11;\n  13[\"Remove duplicated molecules\"];\n  5 -->|outfile| 13;\n  19[\"Remove counterions and fragments\"];\n  13 -->|outfile| 19;\n  2[\"Online data\"];\n  29[\"Filter\"];\n  19 -->|outfile| 29;\n  30[\"Compound Convert\"];\n  19 -->|outfile| 30;\n  31[\"Molecules to Fingerprints\"];\n  19 -->|outfile| 31;\n  39[\"Natural Product\"];\n  29 -->|outfile| 39;\n  40[\"Molecules to Fingerprints\"];\n  29 -->|outfile| 40;\n  44[\"NxN Clustering\"];\n  40 -->|outfile| 44;\n  5[\"Change Title\"];\n  2 -->|output| 5;",
+                "modified": "2024-10-08 10:05:41 +0000",
+                "name": "CTB Workflow",
+                "outputs": [],
+                "parent_id": "computational-chemistry/cheminformatics",
+                "path": "topics/computational-chemistry/tutorials/cheminformatics/workflows/main_workflow.ga",
+                "tags": [
+                    "computational-chemistry"
+                ],
+                "test_results": null,
+                "tests": false,
+                "title": "CTB Workflow",
+                "topic_id": "computational-chemistry",
+                "trs_endpoint": "https://training.galaxyproject.org/training-material/api/ga4gh/trs/v2/tools/computational-chemistry-cheminformatics/versions/main-workflow",
+                "tutorial_id": "cheminformatics",
+                "url": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/cheminformatics/workflows/main_workflow.ga",
+                "url_html": "https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/cheminformatics/workflows/main_workflow.html",
+                "version": 4,
+                "wfid": "computational-chemistry-cheminformatics",
+                "wfname": "main-workflow",
+                "workflow": "main_workflow.ga",
+                "workflow_tools": [
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+                    "toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/0.4",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_online_data_fetch/0.2",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_change_title/0.0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_compound_convert/0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_filter/1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_obgrep/0.1",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remDuplicates/1.0",
+                    "toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remIons/1.0"
+                ],
+                "workflowhub_id": "1075"
+            }
+        ],
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.json",
+        "contributors": [
+            {
+                "id": "chrisbarnettster",
                 "joined": "2019-05",
                 "name": "Christopher Barnett",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/chrisbarnettster/",
@@ -33127,7 +80161,7 @@
         "objectives": [
             "Learn about the NAMD engine provided in BRIDGE"
         ],
-        "pageviews": 6458,
+        "pageviews": 6470,
         "pub_date": "2019-06-03",
         "questions": [
             "How do I use the NAMD engine in Galaxy?",
@@ -33155,6 +80189,668 @@
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             "inexact": []
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@@ -33186,8 +80882,8 @@
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+        "visit_duration": 71,
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@@ -33285,7 +80981,7 @@
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
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@@ -33461,7 +81157,7 @@
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
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                 "outputs": [],
                 "parent_id": "computational-chemistry/md-simulation-namd",
@@ -33789,7 +81485,7 @@
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         "questions": [
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@@ -33813,24 +81509,24 @@
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@@ -33865,6 +81561,4140 @@
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Workflow constructed from history 'Hsp90-MDAnalysis'",
                 "outputs": [],
                 "parent_id": "computational-chemistry/htmd-analysis",
@@ -34118,7 +85948,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nPDB code e.g. 6hhr\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nLigand name e.g. AG5E\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"Get PDB file\"];\n  0 -->|output| 2;\n  3[\"Search in textfiles\"];\n  2 -->|output| 3;\n  4[\"Search in textfiles\"];\n  2 -->|output| 4;\n  1 -->|output| 4;\n  5[\"GROMACS initial setup\"];\n  3 -->|output| 5;\n  6[\"Compound conversion\"];\n  4 -->|output| 6;\n  7[\"Generate MD topologies for small molecules\"];\n  6 -->|outfile| 7;\n  8[\"Merge GROMACS topologies\"];\n  7 -->|gro_output| 8;\n  5 -->|output1| 8;\n  5 -->|output2| 8;\n  7 -->|output| 8;\n  9[\"GROMACS structure configuration\"];\n  8 -->|complex_gro| 9;\n  10[\"GROMACS solvation and adding ions\"];\n  8 -->|complex_top| 10;\n  9 -->|output| 10;\n  11[\"GROMACS energy minimization\"];\n  10 -->|output2| 11;\n  10 -->|output1| 11;\n  12[\"GROMACS simulation\"];\n  5 -->|output3| 12;\n  10 -->|output2| 12;\n  11 -->|output1| 12;\n  13[\"GROMACS simulation\"];\n  5 -->|output3| 13;\n  10 -->|output2| 13;\n  12 -->|output1| 13;\n  12 -->|output5| 13;\n  14[\"GROMACS simulation\"];\n  10 -->|output2| 14;\n  13 -->|output1| 14;\n  13 -->|output5| 14;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "MD protein-ligand workflow (from PDB structure)",
                 "outputs": [
                     {
@@ -34365,7 +86195,7 @@
             "Understand the structure of the molecular dynamics workflow.",
             "Prepare a short (1 ns) trajectory for a simulation of a protein."
         ],
-        "pageviews": 43562,
+        "pageviews": 43610,
         "pub_date": "2019-06-03",
         "questions": [
             "How do I use the GROMACS engine in Galaxy?",
@@ -34374,11 +86204,11 @@
         "short_id": "T00051",
         "short_tools": [
             "gmx_solvate",
-            "gmx_em",
-            "get_pdb",
-            "tp_grep_tool",
             "gmx_setup",
+            "tp_grep_tool",
             "gmx_editconf",
+            "get_pdb",
+            "gmx_em",
             "gmx_sim"
         ],
         "slides": false,
@@ -34424,6 +86254,1862 @@
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@@ -34527,7 +88213,7 @@
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@@ -34962,7 +88648,7 @@
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@@ -34992,12 +88678,12 @@
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@@ -35033,6 +88719,1104 @@
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+                            "state": "exact",
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+                            "state": "inexact",
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+                            "state": "exact",
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+                            "state": "missing"
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         "tags": [
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@@ -35071,7 +89855,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 148,
-        "visitors": 190,
+        "visitors": 192,
         "workflows": [
             {
                 "creators": [
@@ -35156,7 +89940,7 @@
                 ],
                 "license": "CC-BY-4.0",
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Data management in Medicinal Chemistry workflow",
                 "outputs": [
                     {
@@ -35712,7 +90496,7 @@
             "Learn which analysis tools are available.",
             "Analyse a protein and discuss the meaning behind each analysis."
         ],
-        "pageviews": 54198,
+        "pageviews": 54253,
         "pub_date": "2019-06-03",
         "questions": [
             "Which analysis tools are available?"
@@ -35729,14 +90513,14 @@
         ],
         "short_id": "T00047",
         "short_tools": [
+            "mdanalysis_rdf",
             "bio3d_rmsf",
             "mdanalysis_dihedral",
-            "mdanalysis_rdf",
-            "bio3d_pca",
+            "mdanalysis_ramachandran_plot",
             "bio3d_rmsd",
+            "mdanalysis_cosine_analysis",
             "mdanalysis_distance",
-            "mdanalysis_ramachandran_plot",
-            "mdanalysis_cosine_analysis"
+            "bio3d_pca"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -35776,6 +90560,1718 @@
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+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
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+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Analysis using MDAnalysis",
                 "outputs": [
                     {
@@ -36488,7 +92984,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nprotein_mdsimulation_dcd\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nprotein_pdb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"RMSD Analysis\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  6de2beaf-f80e-4788-8598-229a1c582757[\"Output\\nrmsd_tabular_output\"];\n  2 --> 6de2beaf-f80e-4788-8598-229a1c582757;\n  style 6de2beaf-f80e-4788-8598-229a1c582757 stroke:#2c3143,stroke-width:4px;\n  3[\"RMSF Analysis\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  1f2d715d-230a-4ec5-a509-e8ae501e7634[\"Output\\nrmsf_tabular_output\"];\n  3 --> 1f2d715d-230a-4ec5-a509-e8ae501e7634;\n  style 1f2d715d-230a-4ec5-a509-e8ae501e7634 stroke:#2c3143,stroke-width:4px;\n  4[\"PCA\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5[\"Output\\npca_tabular_output\"];\n  4 --> 92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5;\n  style 92b7a40f-9ffc-4f56-8cf3-deec52e7b8b5 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Simple Analysis",
                 "outputs": [
                     {
@@ -36876,7 +93372,7 @@
             "Replicate the study on a (very) small scale",
             "Gain familiarity with the docking and scoring techniques involved."
         ],
-        "pageviews": 4568,
+        "pageviews": 4577,
         "pub_date": "2020-03-27",
         "questions": [
             "How can candidate ligands be generated and docked to a protein in Galaxy?",
@@ -36894,18 +93390,18 @@
         ],
         "short_id": "T00049",
         "short_tools": [
-            "openbabel_compound_convert",
-            "split_file_to_collection",
-            "enumerate_charges",
-            "rxdock_rbcavity",
-            "sucos_max_score",
+            "rxdock_rbdock",
+            "xchem_transfs_scoring",
             "collapse_dataset",
             "xchem_pose_scoring",
-            "rxdock_rbdock",
-            "ctb_frankenstein_ligand",
             "rdock_rbdock",
+            "rxdock_rbcavity",
+            "sucos_max_score",
+            "ctb_frankenstein_ligand",
+            "openbabel_compound_convert",
+            "enumerate_charges",
             "rdock_rbcavity",
-            "xchem_transfs_scoring"
+            "split_file_to_collection"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -36913,6 +93409,2533 @@
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             "inexact": []
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         "tags": [
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@@ -36959,7 +95982,7 @@
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         "video_view": 0,
         "visit_duration": 179,
-        "visitors": 2706,
+        "visitors": 2713,
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@@ -37101,7 +96124,7 @@
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+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
                 "outputs": [
                     {
@@ -37382,7 +96405,7 @@
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             "Analyze the results of the protein target prediction."
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         "questions": [
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@@ -37390,12 +96413,12 @@
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-            "ctb_alignit",
-            "split_file_to_collection",
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@@ -37419,6 +96442,974 @@
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+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "0.1.1"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "0.1.1"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "exact",
+                            "version": "0.1.1"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "9.3+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.1.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "0.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.1.1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.1.1"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "2H",
         "title": "Protein target prediction of a bioactive ligand with Align-it and ePharmaLib",
@@ -37449,8 +97440,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 148,
-        "visitors": 968,
+        "visit_duration": 147,
+        "visitors": 971,
         "workflows": [
             {
                 "creators": [
@@ -37564,7 +97555,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery ligand\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nPharmacophore library\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Ligand ionization state generation\"];\n  0 -->|output| 2;\n  3[\"Splitting ePharmaLib into individual pharmacophores\"];\n  1 -->|output| 3;\n  4[\" Low-energy ligand conformer search\"];\n  2 -->|outfile| 4;\n  5[\"Pharmacophore alignment\"];\n  4 -->|outfile| 5;\n  3 -->|list_output_generic| 5;\n  6[\"Concatenating the pharmacophore alignment scores\"];\n  5 -->|score_result_file| 6;\n  7[\"Ranking the predicted protein targets according to the Tversky index 10th column\"];\n  6 -->|out_file1| 7;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Zauberkugel",
                 "outputs": [
                     {
@@ -38001,7 +97992,7 @@
             "learn how to set up up a model protein and ligand system (with CHARMM-GUI)",
             "learn how to upload the system to Galaxy"
         ],
-        "pageviews": 2000,
+        "pageviews": 2005,
         "pub_date": "2019-06-03",
         "questions": [
             "How to get started modelling a protein and a ligand?"
@@ -38052,6 +98043,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
+        },
         "symlink": null,
         "time_estimation": "2H",
         "title": "Setting up molecular systems",
@@ -38076,7 +98071,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 105,
-        "visitors": 1465,
+        "visitors": 1469,
         "zenodo_link": "https://zenodo.org/record/2600690"
     },
     {
@@ -38267,11 +98262,11 @@
         ],
         "dir": "topics/contributing/tutorials/create-new-tutorial",
         "edam_operation": [
-            "Data handling",
-            "Sequence trimming",
             "Sequence file editing",
+            "Data handling",
             "Read mapping",
             "Read pre-processing",
+            "Sequence trimming",
             "Primer removal"
         ],
         "edam_topic": [],
@@ -38296,7 +98291,7 @@
             "Create hands-on",
             "Add technical support for a tutorial"
         ],
-        "pageviews": 2148,
+        "pageviews": 2156,
         "pub_date": "2018-06-20",
         "questions": [
             "How to integrate a new tutorial?",
@@ -38318,24 +98313,25 @@
         ],
         "short_id": "T00057",
         "short_tools": [
+            "Cut1",
             "tp_sed_tool",
-            "tp_sorted_uniq",
-            "bam_to_sam",
-            "tp_cat",
-            "c3s",
-            "Filter1",
-            "cutadapt",
             "seqtk_subseq",
+            "cutadapt",
+            "tp_cat",
             "random_lines1",
             "fastq_to_tabular",
-            "Cut1",
+            "tp_sorted_uniq",
+            "bam_to_sam",
+            "c3s",
+            "bowtie2",
             "tp_cut_tool",
-            "bowtie2"
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "writing",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "15m",
         "title": "Creating a new tutorial",
@@ -38373,8 +98369,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 315,
-        "visitors": 1415,
+        "visit_duration": 314,
+        "visitors": 1423,
         "workflows": [
             {
                 "creators": [],
@@ -38472,7 +98468,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSRR891268_R1_20M.fastq.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSRR891268_R2_20M.fastq.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Unique\"];\n  9 -->|out_file1| 10;\n  11[\"Text transformation\"];\n  10 -->|outfile| 11;\n  12[\"Concatenate datasets\"];\n  6 -->|out_file1| 12;\n  11 -->|output| 12;\n  13[\"Unique\"];\n  12 -->|out_file1| 13;\n  14[\"seqtk_subseq\"];\n  0 -->|output| 14;\n  13 -->|outfile| 14;\n  15[\"Text transformation\"];\n  13 -->|outfile| 15;\n  16[\"seqtk_subseq\"];\n  1 -->|output| 16;\n  15 -->|output| 16;\n  2[\"FASTQ to Tabular\"];\n  0 -->|output| 2;\n  3[\"Cutadapt\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Cut\"];\n  2 -->|output_file| 4;\n  5[\"Bowtie2\"];\n  3 -->|out1| 5;\n  3 -->|out2| 5;\n  6[\"Select random lines\"];\n  4 -->|output| 6;\n  7[\"BAM-to-SAM\"];\n  5 -->|output| 7;\n  8[\"Filter\"];\n  7 -->|output1| 8;\n  9[\"Cut\"];\n  8 -->|out_file1| 9;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "MakeAFakeInput",
                 "outputs": [],
                 "parent_id": "contributing/create-new-tutorial",
@@ -38569,7 +98565,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAPI Request file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Copernicus Climate Data Store\"];\n  0 -->|output| 1;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Retrieve climate data from Copernicus",
                 "outputs": [
                     {
@@ -38818,7 +98814,7 @@
             "Create a new set of slides",
             "Add presenter comments"
         ],
-        "pageviews": 5897155,
+        "pageviews": 5928759,
         "pub_date": "2018-06-13",
         "questions": [
             "How to format slides?",
@@ -38859,6 +98855,7 @@
         ],
         "subtopic": "writing",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": null,
         "title": "Creating Slides",
@@ -38883,7 +98880,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2133582
+        "visitors": 2143985
     },
     {
         "admin_install": {
@@ -38937,7 +98934,7 @@
         "license": "CC-BY-4.0",
         "logo": "GTN",
         "mod_date": "2023-01-12",
-        "pageviews": 5897155,
+        "pageviews": 5928759,
         "priority": 1,
         "pub_date": "2017-06-25",
         "redirect_from": [
@@ -38950,6 +98947,7 @@
         "slides": true,
         "slides_recordings": false,
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "title": "Overview of the Galaxy Training Material",
         "tools": [],
@@ -38973,7 +98971,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2133582
+        "visitors": 2143985
     },
     {
         "admin_install": {
@@ -39049,7 +99047,7 @@
             "Create a pull request",
             "Update a pull request"
         ],
-        "pageviews": 5901686,
+        "pageviews": 5933292,
         "pub_date": "2017-06-12",
         "questions": [
             "How can I contribute to an open-source project with GitHub?",
@@ -39061,6 +99059,7 @@
         "slides_recordings": false,
         "subtopic": "contribute",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "30m",
         "title": "Contributing with GitHub via command-line",
@@ -39085,7 +99084,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 196,
-        "visitors": 2136392
+        "visitors": 2146797
     },
     {
         "admin_install": {
@@ -39242,7 +99241,7 @@
             "Explain how learning models can help you improve your teaching in the classroom",
             "List learning strategies and principles suggested by evidence-based research results"
         ],
-        "pageviews": 5094,
+        "pageviews": 5130,
         "pub_date": "2022-09-23",
         "questions": [
             "What are the main principles that drive learning?",
@@ -39296,6 +99295,7 @@
         "slides_recordings": false,
         "subtopic": "pedagogy",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "2h",
         "title": "Principles of learning and how they apply to training and teaching",
@@ -39320,7 +99320,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 49,
-        "visitors": 4241
+        "visitors": 4270
     },
     {
         "admin_install": {
@@ -39432,6 +99432,7 @@
         "slides_recordings": false,
         "subtopic": "writing",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "2h",
         "title": "Teaching Python",
@@ -39519,7 +99520,7 @@
             "Create a pull request",
             "Update a pull request"
         ],
-        "pageviews": 917,
+        "pageviews": 923,
         "pub_date": "2018-06-12",
         "questions": [
             "How can I contribute to an open-source project with GitHub and its interface"
@@ -39530,6 +99531,7 @@
         "slides_recordings": false,
         "subtopic": "contribute",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "20m",
         "title": "Contributing with GitHub via its interface",
@@ -39554,7 +99556,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 135,
-        "visitors": 583
+        "visitors": 586
     },
     {
         "abbreviations": {
@@ -39736,8 +99738,8 @@
         ],
         "dir": "topics/contributing/tutorials/create-new-tutorial-content",
         "edam_operation": [
-            "Sequencing quality control",
-            "Validation"
+            "Validation",
+            "Sequencing quality control"
         ],
         "edam_topic": [],
         "feedback_mean_note": null,
@@ -39759,7 +99761,7 @@
             "Create hands-on",
             "Use the different boxes"
         ],
-        "pageviews": 9192,
+        "pageviews": 9195,
         "pub_date": "2017-06-25",
         "questions": [
             "How to write a tutorial with hands-on?",
@@ -39768,13 +99770,14 @@
         ],
         "short_id": "T00058",
         "short_tools": [
-            "multiqc",
-            "upload1"
+            "upload1",
+            "multiqc"
         ],
         "slides": false,
         "slides_recordings": false,
         "subtopic": "writing",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "15m",
         "title": "Creating content in Markdown",
@@ -39802,7 +99805,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 123,
-        "visitors": 3303
+        "visitors": 3306
     },
     {
         "admin_install": {
@@ -39899,7 +99902,7 @@
             "Create a new topic",
             "Set up the metadata for a topic"
         ],
-        "pageviews": 1259,
+        "pageviews": 1268,
         "pub_date": "2018-06-04",
         "questions": [
             "How to include a new topic?",
@@ -39910,6 +99913,7 @@
         "slides": false,
         "slides_recordings": false,
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "30m",
         "title": "Including a new topic",
@@ -39934,7 +99938,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 27,
-        "visitors": 863
+        "visitors": 872
     },
     {
         "admin_install": {
@@ -40141,6 +100145,7 @@
         "slides_recordings": false,
         "subtopic": "pedagogy",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "60m",
         "title": "Design and plan session, course, materials",
@@ -40224,7 +100229,7 @@
         "objectives": [
             "Know where to find all of the available metadata, so you can reference it later."
         ],
-        "pageviews": 262,
+        "pageviews": 263,
         "pub_date": "2022-06-02",
         "questions": [
             "What metadata is required or possible to set in a Tutorial, Slide, Topic, or FAQ"
@@ -40234,6 +100239,7 @@
         "slides": false,
         "slides_recordings": false,
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "10m",
         "title": "GTN Metadata",
@@ -40258,7 +100264,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 186,
-        "visitors": 192
+        "visitors": 193
     },
     {
         "admin_install": {
@@ -40322,7 +100328,7 @@
             "Preview the GTN website online via GitPod",
             "Make changes to the GTN website and preview those changes"
         ],
-        "pageviews": 1335,
+        "pageviews": 1336,
         "pub_date": "2021-06-24",
         "questions": [
             "How can I get a preview of the GTN website using GitPod?"
@@ -40347,6 +100353,7 @@
         "slides_recordings": false,
         "subtopic": "writing",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "15m",
         "title": "Running the GTN website online using GitPod",
@@ -40371,7 +100378,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 167,
-        "visitors": 930
+        "visitors": 931
     },
     {
         "admin_install": {
@@ -40504,6 +100511,7 @@
         "slides": false,
         "slides_recordings": false,
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "15m",
         "title": "Creating Interactive Galaxy Tours",
@@ -40682,7 +100690,7 @@
             "Creating a Galaxy Docker flavor with the needed tools, data and workflows for a tutorial",
             "Testing the Galaxy Docker flavor of a tutorial"
         ],
-        "pageviews": 601,
+        "pageviews": 603,
         "pub_date": "2017-06-25",
         "questions": [
             "How can we define the technical infrastructure for a tutorial?",
@@ -40698,6 +100706,7 @@
         "slides_recordings": false,
         "subtopic": "writing",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "30m",
         "title": "Tools, Data, and Workflows for tutorials",
@@ -40722,7 +100731,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 109,
-        "visitors": 422
+        "visitors": 424
     },
     {
         "admin_install": {
@@ -40797,6 +100806,7 @@
         "slides": false,
         "slides_recordings": false,
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "5m",
         "title": "Updating diffs in admin training",
@@ -40884,7 +100894,7 @@
         "objectives": [
             "Adding a video to a set of slides"
         ],
-        "pageviews": 319,
+        "pageviews": 322,
         "pub_date": "2020-10-20",
         "questions": [
             "How can we add auto-generated video?",
@@ -40897,6 +100907,7 @@
         "slides_recordings": false,
         "subtopic": "writing",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "20m",
         "title": "Adding auto-generated video to your slides",
@@ -40920,8 +100931,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 258,
-        "visitors": 242
+        "visit_duration": 255,
+        "visitors": 244
     },
     {
         "admin_install": {
@@ -40990,6 +101001,7 @@
         "slides": false,
         "slides_recordings": false,
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "10m",
         "title": "Generating PDF artefacts of the website",
@@ -41136,7 +101148,7 @@
             "Running the GTN material website locally",
             "Tracking changes to the content live in the webbrowser"
         ],
-        "pageviews": 1540,
+        "pageviews": 1544,
         "pub_date": "2017-06-25",
         "questions": [
             "How to setup the infrastructure to build training webpages?"
@@ -41147,6 +101159,7 @@
         "slides_recordings": false,
         "subtopic": "writing",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "15m",
         "title": "Running the GTN website locally",
@@ -41171,7 +101184,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 216,
-        "visitors": 1111
+        "visitors": 1114
     },
     {
         "admin_install": {
@@ -41253,6 +101266,7 @@
         "slides": false,
         "slides_recordings": false,
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "15m",
         "title": "Adding Quizzes to your Tutorial",
@@ -41390,14 +101404,14 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-10-02",
+        "mod_date": "2024-10-08",
         "objectives": [
             "Learn about metadata and findability",
             "Learn how to support system and content curation"
         ],
         "pageviews": 0,
         "priority": 3,
-        "pub_date": "2024-10-02",
+        "pub_date": "2024-10-08",
         "questions": [
             "What are the FAIR training materials?",
             "How to test, reproduce and share your content?",
@@ -41418,6 +101432,7 @@
         "slides_recordings": false,
         "subtopic": "fair-data",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": true,
         "tags": [
             "fair",
@@ -41612,7 +101627,7 @@
             "Replicate the study on a (very) small scale",
             "Gain familiarity with the docking and scoring techniques involved."
         ],
-        "pageviews": 4568,
+        "pageviews": 4577,
         "pub_date": "2020-03-27",
         "questions": [
             "How can candidate ligands be generated and docked to a protein in Galaxy?",
@@ -41630,18 +101645,18 @@
         ],
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-            "openbabel_compound_convert",
-            "split_file_to_collection",
-            "enumerate_charges",
-            "rxdock_rbcavity",
-            "sucos_max_score",
+            "rxdock_rbdock",
+            "xchem_transfs_scoring",
             "collapse_dataset",
             "xchem_pose_scoring",
-            "rxdock_rbdock",
-            "ctb_frankenstein_ligand",
             "rdock_rbdock",
+            "rxdock_rbcavity",
+            "sucos_max_score",
+            "ctb_frankenstein_ligand",
+            "openbabel_compound_convert",
+            "enumerate_charges",
             "rdock_rbcavity",
-            "xchem_transfs_scoring"
+            "split_file_to_collection"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -41649,6 +101664,2533 @@
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             "inexact": []
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@@ -41695,7 +104237,7 @@
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-        "visitors": 2706,
+        "visitors": 2713,
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@@ -41837,7 +104379,7 @@
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
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@@ -42107,7 +104649,7 @@
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             "Submit consensus sequence and metadata to ENA's test server"
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         "questions": [
             "How do you submit raw sequence reads and assembled genomes to the European Nucleotide Archive?"
@@ -42139,6 +104681,597 @@
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+                            "state": "missing"
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+                            "state": "inexact",
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+                            "server": "https://usegalaxy.eu",
+                            "state": "inexact",
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+                                "0.3.1",
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+                                "0.5.3",
+                                "0.6.1",
+                                "0.6.0",
+                                "0.4.1",
+                                "0.3.3",
+                                "0.3.2",
+                                "0.4.3",
+                                "0.6.3+galaxy0"
+                            ]
+                        },
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+                            "server": "https://usegalaxy.no/",
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+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
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+                                "0.7.1+galaxy1",
+                                "0.5.3",
+                                "0.6.1",
+                                "0.6.0",
+                                "0.3.3",
+                                "0.4.3",
+                                "0.6.3+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
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+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "covid19"
@@ -42170,7 +105303,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 236,
-        "visitors": 1810937,
+        "visitors": 1821302,
         "workflows": [
             {
                 "creators": [],
@@ -42194,7 +105327,7 @@
                 "inputs": [],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"ENA Upload tool\"];\n  1[\"ENA Upload tool\"];",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "GTN_ENA_upload_workflow",
                 "outputs": [
                     {
@@ -42382,8 +105515,8 @@
         ],
         "dir": "topics/galaxy-interface/tutorials/workflow-automation",
         "edam_operation": [
-            "Tree-based sequence alignment",
-            "Variant classification"
+            "Variant classification",
+            "Tree-based sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -42397,8 +105530,7 @@
         "hands_on": true,
         "id": "galaxy-interface/workflow-automation",
         "inexact_supported_servers": [
-            "MISSISSIPPI",
-            "UseGalaxy.fr"
+            "MISSISSIPPI"
         ],
         "js_requirements": {
             "mathjax": null,
@@ -42416,7 +105548,7 @@
             "Be able to write simple shell scripts for running multiple workflows concurrently or sequentially.",
             "Learn how to use Pangolin to assign annotated variants to lineages."
         ],
-        "pageviews": 2813,
+        "pageviews": 2825,
         "pub_date": "2021-06-08",
         "questions": [
             "How can I schedule and run tens or hundreds of Galaxy workflows easily?",
@@ -42448,11 +105580,11 @@
         ],
         "short_id": "T00162",
         "short_tools": [
-            "pangolin",
-            "bcftools_consensus",
-            "snpSift_filter",
             "compose_text_param",
-            "collapse_dataset"
+            "bcftools_consensus",
+            "collapse_dataset",
+            "pangolin",
+            "snpSift_filter"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -42485,11 +105617,874 @@
                     "name": "MISSISSIPPI",
                     "url": "https://mississippi.sorbonne-universite.fr",
                     "usegalaxy": false
+                }
+            ]
+        },
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+                    "url": "http://apostl.moffitt.org/"
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                    "usegalaxy": false
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+                    "name": "Mandoiu Lab",
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+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
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+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
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+                    "url": "https://usegalaxy.no/",
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+                    "url": "https://usegalaxy.org.au",
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+                    "url": "https://viralvariant.anses.fr/"
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+                            ]
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+                            "state": "exact",
+                            "version": "4.2"
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+                        {
+                            "server": "https://usegalaxy.no/",
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+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "4.2"
                 }
             ]
         },
@@ -42528,7 +106523,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 120,
-        "visitors": 2277,
+        "visitors": 2288,
         "workflows": [
             {
                 "creators": [
@@ -42661,7 +106656,7 @@
                 ],
                 "license": "MIT",
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "vcf2lineage",
                 "outputs": [
                     {
@@ -43064,16 +107059,15 @@
         ],
         "dir": "topics/sequence-analysis/tutorials/human-reads-removal",
         "edam_operation": [
-            "Generation",
-            "Data handling",
-            "Sequence alignment",
             "Sequence file editing",
+            "Data handling",
+            "Genome indexing",
             "Read mapping",
-            "Genome indexing"
+            "Sequence alignment",
+            "Generation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
@@ -43109,7 +107103,7 @@
             "Preprocess and map the data against the human reference genome",
             "Eliminate reads/read pairs that map to the human genome from the original data"
         ],
-        "pageviews": 4842,
+        "pageviews": 4864,
         "pub_date": "2021-08-04",
         "questions": [
             "How can you remove traces of human sequence data from a sequenced viral sample?"
@@ -43133,24 +107127,19 @@
         ],
         "short_id": "T00236",
         "short_tools": [
-            "bwa_mem",
-            "seqtk_subseq",
             "tp_replace_in_line",
-            "samtools_fastx",
-            "Grep1",
-            "__UNZIP_COLLECTION__",
+            "seqtk_subseq",
             "trimmomatic",
-            "__ZIP_COLLECTION__"
+            "__ZIP_COLLECTION__",
+            "bwa_mem",
+            "Grep1",
+            "samtools_fastx",
+            "__UNZIP_COLLECTION__"
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-                    "url": "https://usegalaxy.fr/",
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-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -43200,6 +107189,1447 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
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+                },
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@@ -43237,7 +108667,7 @@
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-        "visitors": 3422,
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@@ -43307,7 +108737,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data",
                 "outputs": [
                     {
@@ -44022,15 +109452,15 @@
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         "edam_operation": [
             "Data handling",
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
-            "Sequence contamination filtering",
+            "Genome indexing",
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             "Generation",
-            "Validation",
             "SNP detection",
-            "Formatting",
-            "Genome indexing"
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@@ -44045,7 +109475,6 @@
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@@ -44067,7 +109496,7 @@
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             "Understand the analysis steps required to identify and annotate genomic mutations from sequencing data of SARS-CoV-2 samples"
         ],
-        "pageviews": 18698,
+        "pageviews": 18744,
         "pub_date": "2020-06-24",
         "questions": [
             "How can you download public sequencing data deposited in the NCBI Sequence Read Archive (SRA) into a Galaxy history for analysis?",
@@ -44090,20 +109519,20 @@
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-            "picard_MarkDuplicates",
-            "fastp",
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-            "lofreq_viterbi",
+            "lofreq_call",
             "snpeff_sars_cov_2",
             "multiqc",
             "lofreq_indelqual",
+            "snpSift_extractFields",
+            "bwa_mem",
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+            "picard_MarkDuplicates",
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             "fasterq_dump",
-            "lofreq_call",
             "tp_cut_tool",
-            "snpSift_extractFields"
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@@ -44138,19 +109567,2338 @@
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-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.org.au",
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+                                "2.11.0+galaxy0",
+                                "2.10.7+galaxy1",
+                                "2.10.4+galaxy1"
+                            ]
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+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "3.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "3.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.11.0+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "3.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "3.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "3.0.3+galaxy0"
                 }
             ]
         },
@@ -44199,7 +111947,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 174,
-        "visitors": 12309,
+        "visitors": 12340,
         "workflows": [
             {
                 "creators": [],
@@ -44330,7 +112078,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Faster Download and Extract Reads in FASTQ\"];\n  1 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|list_paired| 3;\n  4[\"Map with BWA-MEM\"];\n  3 -->|output_paired_coll| 4;\n  0 -->|output| 4;\n  5[\"MarkDuplicates\"];\n  4 -->|bam_output| 5;\n  6[\"Realign reads\"];\n  5 -->|outFile| 6;\n  0 -->|output| 6;\n  7[\"Samtools stats\"];\n  5 -->|outFile| 7;\n  8[\"Insert indel qualities\"];\n  6 -->|realigned| 8;\n  0 -->|output| 8;\n  2ca7c89b-999f-41dc-8037-e54e25959a7e[\"Output\\nRealigned Alignments with Indel Qualities\"];\n  8 --> 2ca7c89b-999f-41dc-8037-e54e25959a7e;\n  style 2ca7c89b-999f-41dc-8037-e54e25959a7e stroke:#2c3143,stroke-width:4px;\n  9[\"Call variants\"];\n  8 -->|output| 9;\n  0 -->|output| 9;\n  10[\"SnpEff eff:\"];\n  9 -->|variants| 10;\n  11[\"SnpSift Extract Fields\"];\n  10 -->|snpeff_output| 11;\n  06259137-eaa5-404a-923c-70ee5f1d89d4[\"Output\\nSnpSift tabular output\"];\n  11 --> 06259137-eaa5-404a-923c-70ee5f1d89d4;\n  style 06259137-eaa5-404a-923c-70ee5f1d89d4 stroke:#2c3143,stroke-width:4px;\n  12[\"MultiQC\"];\n  3 -->|report_json| 12;\n  7 -->|output| 12;\n  5 -->|metrics_file| 12;\n  10 -->|csvFile| 12;\n  758ffde5-7ddd-482a-88b2-1504f8335488[\"Output\\nMultiQC Report PE\"];\n  12 --> 758ffde5-7ddd-482a-88b2-1504f8335488;\n  style 758ffde5-7ddd-482a-88b2-1504f8335488 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Simple COVID-19 - PE Variation",
                 "outputs": [
                     {
@@ -44906,10 +112654,10 @@
         ],
         "dir": "topics/variant-analysis/tutorials/sars-cov-2-variant-discovery",
         "edam_operation": [
-            "Tree-based sequence alignment",
             "Variant calling",
+            "Methylation analysis",
             "Variant classification",
-            "Methylation analysis"
+            "Tree-based sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -44944,7 +112692,7 @@
             "Know different SARS-CoV-2 lineage classification systems, and use pangolin and Nextclade to assign samples to predefined lineages",
             "Combine information from different analysis steps to be able to draw appropriate conclusions about individual samples and batches of viral data"
         ],
-        "pageviews": 12059,
+        "pageviews": 12082,
         "pub_date": "2021-06-30",
         "questions": [
             "How can a complete analysis, including viral consensus sequence reconstruction and lineage assignment be performed?",
@@ -45008,11 +112756,11 @@
         "short_id": "T00316",
         "short_tools": [
             "pangolin",
-            "Filter1",
+            "nextclade",
             "upload1",
+            "datamash_ops",
             "fasta_regex_finder",
-            "nextclade",
-            "datamash_ops"
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -45038,6 +112786,987 @@
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+                },
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+                        {
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+                            "state": "local"
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+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                }
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         "symlink": null,
         "tags": [
             "covid19",
@@ -45074,7 +113803,7 @@
         "video_versions": 3,
         "video_view": 0,
         "visit_duration": 208,
-        "visitors": 6500
+        "visitors": 6513
     },
     {
         "admin_install": {
@@ -45212,18 +113941,18 @@
         ],
         "dir": "topics/assembly/tutorials/assembly-with-preprocessing",
         "edam_operation": [
-            "Scatter plot plotting",
-            "Data handling",
-            "Read mapping",
-            "Sequencing quality control",
+            "Sequence file editing",
             "Genome assembly",
-            "Box-Whisker plot plotting",
+            "Data handling",
             "Sequence contamination filtering",
-            "Aggregation",
             "Sequence assembly visualisation",
-            "Pairwise sequence alignment",
+            "Box-Whisker plot plotting",
+            "Scatter plot plotting",
             "Validation",
-            "Sequence file editing"
+            "Sequencing quality control",
+            "Read mapping",
+            "Aggregation",
+            "Pairwise sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -45238,7 +113967,6 @@
             "MISSISSIPPI",
             "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)"
         ],
@@ -45261,7 +113989,7 @@
             "Detect and remove human reads",
             "Assemble retained reads and explore the results"
         ],
-        "pageviews": 5905033,
+        "pageviews": 5936667,
         "pub_date": "2020-04-21",
         "questions": [
             "How can a genome of interest be assembled against a background of contaminating reads from other genomes?",
@@ -45306,22 +114034,22 @@
         ],
         "short_id": "T00029",
         "short_tools": [
-            "samtools_stats",
-            "unicycler",
-            "fastp",
-            "minimap2",
+            "fasta_filter_by_length",
             "bandage_image",
+            "minimap2",
             "samtools_view",
-            "fasta_filter_by_length",
-            "bandage_info",
-            "samtools_fastx",
+            "collapse_dataset",
+            "unicycler",
+            "__ZIP_COLLECTION__",
             "multiqc",
             "seqtk_sample",
-            "fasterq_dump",
+            "bandage_info",
             "nanoplot",
-            "collapse_dataset",
-            "__ZIP_COLLECTION__",
-            "bowtie2"
+            "samtools_stats",
+            "bowtie2",
+            "fastp",
+            "samtools_fastx",
+            "fasterq_dump"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -45355,10 +114083,136 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
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+                    "url": "http://apostl.moffitt.org/"
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+                {
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
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+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
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+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
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+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
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+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
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+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
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+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
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+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
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+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
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+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -45368,6 +114222,2398 @@
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
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+                            "state": "exact",
+                            "version": "0.4.8.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "0.4.8.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.4.8.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.4.8.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.4.8.0"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "5.1.0"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "5.1.0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "5.1.0"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "5.1.0",
+                                "1.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "4.2"
                 }
             ]
         },
@@ -45414,8 +116660,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 364,
-        "visitors": 2138036,
+        "visit_duration": 365,
+        "visitors": 2148459,
         "workflows": [
             {
                 "creators": [],
@@ -45501,7 +116747,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nCollection of paired short-reads data\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nCollection of long-reads data\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Samtools fastx\"];\n  7 -->|outputsam| 10;\n  11[\"Samtools fastx\"];\n  9 -->|outputsam| 11;\n  12[\"Collapse Collection\"];\n  10 -->|nonspecific| 12;\n  13[\"Zip Collection\"];\n  11 -->|forward| 13;\n  11 -->|reverse| 13;\n  14[\"Collapse Collection\"];\n  11 -->|forward| 14;\n  15[\"Collapse Collection\"];\n  11 -->|reverse| 15;\n  16[\"seqtk_sample\"];\n  14 -->|output| 16;\n  17[\"seqtk_sample\"];\n  15 -->|output| 17;\n  18[\"Create assemblies with Unicycler\"];\n  12 -->|output| 18;\n  16 -->|default| 18;\n  17 -->|default| 18;\n  19[\"Bandage Info\"];\n  18 -->|assembly_graph| 19;\n  2[\"fastp: Trimmed Illumina Reads\"];\n  0 -->|output| 2;\n  20[\"Filter sequences by length\"];\n  18 -->|assembly| 20;\n  21[\"Bandage Image\"];\n  18 -->|assembly_graph| 21;\n  3[\"NanoPlot\"];\n  1 -->|output| 3;\n  4[\"Map with minimap2\"];\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  2 -->|report_json| 5;\n  6[\"Bowtie2\"];\n  2 -->|output_paired_coll| 6;\n  7[\"Samtools view\"];\n  4 -->|alignment_output| 7;\n  8[\"Samtools stats\"];\n  4 -->|alignment_output| 8;\n  9[\"Samtools view\"];\n  6 -->|output| 9;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "assembly_with_preprocessing",
                 "outputs": [
                     {
@@ -46427,7 +117673,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nList of Illumina accessions\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nList of ONT accessions\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Samtools stats\"];\n  6 -->|alignment_output| 10;\n  11[\"Samtools view\"];\n  8 -->|output| 11;\n  12[\"Samtools fastx\"];\n  9 -->|outputsam| 12;\n  13[\"Samtools fastx\"];\n  11 -->|outputsam| 13;\n  14[\"Collapse Collection\"];\n  12 -->|nonspecific| 14;\n  15[\"Zip Collection\"];\n  13 -->|forward| 15;\n  13 -->|reverse| 15;\n  16[\"Collapse Collection\"];\n  13 -->|forward| 16;\n  17[\"Collapse Collection\"];\n  13 -->|reverse| 17;\n  18[\"seqtk_sample\"];\n  16 -->|output| 18;\n  19[\"seqtk_sample\"];\n  17 -->|output| 19;\n  2[\"Illumina data\"];\n  0 -->|output| 2;\n  20[\"Create assemblies with Unicycler\"];\n  14 -->|output| 20;\n  18 -->|default| 20;\n  19 -->|default| 20;\n  21[\"Bandage Info\"];\n  20 -->|assembly_graph| 21;\n  22[\"Bandage Image\"];\n  20 -->|assembly_graph| 22;\n  23[\"Filter sequences by length\"];\n  20 -->|assembly| 23;\n  3[\"ONT data\"];\n  1 -->|output| 3;\n  4[\"fastp: Trimmed Illumina Reads\"];\n  2 -->|list_paired| 4;\n  5[\"NanoPlot\"];\n  3 -->|output_collection| 5;\n  6[\"Map with minimap2\"];\n  3 -->|output_collection| 6;\n  7[\"MultiQC\"];\n  4 -->|report_json| 7;\n  8[\"Bowtie2\"];\n  4 -->|output_paired_coll| 8;\n  9[\"Samtools view\"];\n  6 -->|alignment_output| 9;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "assembly_with_preprocessing_and_sra_download",
                 "outputs": [
                     {
@@ -47491,8 +118737,8 @@
         ],
         "dir": "topics/galaxy-interface/tutorials/ncbi-sarf",
         "edam_operation": [
-            "SNP detection",
-            "Data handling"
+            "Data handling",
+            "SNP detection"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -47524,7 +118770,7 @@
             "Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content",
             "Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format"
         ],
-        "pageviews": 5142208,
+        "pageviews": 5173816,
         "pub_date": "2021-05-31",
         "questions": [
             "How can I search SRA SARS-CoV-2 metadata from within Galaxy?",
@@ -47556,13 +118802,13 @@
         ],
         "short_id": "T00155",
         "short_tools": [
-            "query_tabular",
-            "tp_cat",
-            "jq",
-            "fastq_dump",
             "snpeff_sars_cov_2",
+            "tp_cat",
+            "query_tabular",
             "fastq_to_fasta_python",
-            "fasterq_dump"
+            "fasterq_dump",
+            "fastq_dump",
+            "jq"
         ],
         "slides": true,
         "slides_recordings": [
@@ -47616,6 +118862,1182 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "0.1.0"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "0.1.0"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.1.1"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "9.3+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "exact",
+                            "version": "0.1.0"
+                        },
+                        {
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+                            "state": "exact",
+                            "version": "0.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "0.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.1.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.1.0"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "1.1.5"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
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         "tags": [
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@@ -47652,7 +120074,7 @@
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         "video_view": 0,
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@@ -47815,19 +120237,18 @@
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         "edam_operation": [
-            "Generation",
-            "Statistical calculation",
-            "Sequence alignment",
-            "Read mapping",
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             "Sequence composition calculation",
+            "Sequencing quality control",
+            "Genome indexing",
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@@ -47861,7 +120282,7 @@
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             "Tap into the interdisciplinary nature of science"
         ],
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+        "pageviews": 961,
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         "questions": [
             "How do I check my data quality?",
@@ -47871,8 +120292,8 @@
         "short_id": "T00356",
         "short_tools": [
             "bwa_mem",
-            "fastqc",
-            "jbrowse"
+            "jbrowse",
+            "fastqc"
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@@ -47883,11 +120304,6 @@
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                     "url": "https://usegalaxy.no/",
@@ -47937,6 +120353,620 @@
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+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.16.9+galaxy0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "covid19",
@@ -47969,8 +120999,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 271,
-        "visitors": 739,
+        "visit_duration": 270,
+        "visitors": 744,
         "zenodo_link": "https://doi.org/10.5281/zenodo.8115178"
     },
     {
@@ -48169,40 +121199,40 @@
         "layout": "tutorial_hands_on",
         "level": "Introductory",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-10-02",
+        "mod_date": "2024-10-08",
         "objectives": [
             "Familiarize yourself with data manipulation tools in Galaxy",
             "Perform basic text manipulation tasks in Galaxy",
             "Become comfortable converting text-based files in a variety of ways.",
             "Reason about the expected outcome of tools"
         ],
-        "pageviews": 0,
-        "pub_date": "2024-10-02",
+        "pageviews": 1,
+        "pub_date": "2024-10-08",
         "questions": [
             "How can I do basic data manipulation in Galaxy?",
             "Which tools are available to convert, reformat, filter, sort etc my text-based data?"
         ],
         "short_id": "T00077",
         "short_tools": [
+            "cat1",
             "",
-            "join1",
-            "Count1",
-            "upload1",
+            "regexColumn1",
             "wc_gnu",
-            "datamash_ops",
-            "Grouping1",
+            "Remove beginning1",
             "tp_sorted_uniq",
-            "tabular_to_csv",
-            "tp_cat",
+            "upload1",
+            "datamash_ops",
             "Filter1",
+            "Count1",
             "tp_sort_header_tool",
-            "tp_split_on_column",
+            "Add_a_column1",
             "Cut1",
-            "Remove beginning1",
-            "cat1",
+            "tp_split_on_column",
+            "tabular_to_csv",
+            "tp_cat",
             "Show beginning1",
-            "Add_a_column1",
-            "regexColumn1"
+            "join1",
+            "Grouping1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -48211,6 +121241,5091 @@
             "exact": [],
             "inexact": []
         },
+        "supported_servers_matrix": {
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
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+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
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+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
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+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                {
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+                    "usegalaxy": false
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+                },
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+                    "url": "http://galaxy.inf.ethz.ch"
+                },
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+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
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+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.org",
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+                    "url": "https://usegalaxy.org.au",
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@@ -48276,7 +126391,7 @@
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@@ -48371,7 +126486,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GTN Tutorial: Data manipulation Olympics - all steps and exercises",
                 "outputs": [],
                 "parent_id": "data-science/data-manipulation-olympics",
@@ -48511,7 +126626,6 @@
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@@ -48545,7 +126659,7 @@
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@@ -48577,11 +126691,6 @@
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@@ -48621,6 +126730,305 @@
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+                },
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@@ -48750,6 +127158,10 @@
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@@ -48928,7 +127340,6 @@
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@@ -48973,7 +127384,7 @@
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@@ -49000,8 +127411,140 @@
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+                    "url": "https://www.immportgalaxy.org/"
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@@ -49042,8 +127720,8 @@
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@@ -49161,7 +127839,7 @@
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         "questions": [
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@@ -49218,6 +127896,10 @@
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@@ -49242,7 +127924,7 @@
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@@ -49406,6 +128088,10 @@
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@@ -49430,7 +128116,7 @@
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@@ -49531,7 +128217,7 @@
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@@ -49588,6 +128274,10 @@
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         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
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         "tags": [
             "game",
@@ -49616,7 +128306,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 32,
-        "visitors": 1636,
+        "visitors": 1640,
         "zenodo_link": ""
     },
     {
@@ -49720,7 +128410,7 @@
             "By exploring protein entries in UniProtKB, interpret protein function, taxonomy, structure, interactions, variants, and more.",
             "Use unique identifiers to connect databases, download gene and protein data, visualize and compare sequence features."
         ],
-        "pageviews": 97,
+        "pageviews": 99,
         "pub_date": "2023-09-07",
         "questions": [
             "How can you search for proteins using text, gene, or protein names?",
@@ -49779,6 +128469,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
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         "symlink": null,
         "tags": [
             "work-in-progress"
@@ -49806,7 +128500,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 90,
-        "visitors": 88,
+        "visitors": 89,
         "zenodo_link": ""
     },
     {
@@ -49912,7 +128606,7 @@
             "Trace the execution of a program that contains an SQL query.",
             "Explain why most database applications are written in a general-purpose language rather than in SQL."
         ],
-        "pageviews": 695,
+        "pageviews": 696,
         "pub_date": "2021-10-11",
         "questions": [
             "How can I access databases from programs written in R?"
@@ -49972,6 +128666,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
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         "symlink": null,
         "tags": [
             "SQL",
@@ -50000,7 +128698,7 @@
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         "video_view": 0,
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-        "visitors": 537,
+        "visitors": 538,
         "zenodo_link": null
     },
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@@ -50101,7 +128799,7 @@
             "Understand the fundamentals of object assignment and math in python and can write simple statements and execute calcualtions in order to be able to summarize the results of calculations and classify valid and invalid statements.",
             "Translate some known math functions (e.g. euclidean distance, root algorithm) into python to transfer concepts from mathematics lessons directly into Python."
         ],
-        "pageviews": 678,
+        "pageviews": 685,
         "priority": 1,
         "pub_date": "2022-04-25",
         "questions": [
@@ -50146,6 +128844,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
+        },
         "symlink": null,
         "time_estimation": "30M",
         "title": "Python - Math",
@@ -50169,8 +128871,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 54,
-        "visitors": 539
+        "visit_duration": 53,
+        "visitors": 545
     },
     {
         "admin_install": {
@@ -50305,7 +129007,7 @@
             "Explore SQL City and discover who committed the murder",
             "Reinforce your experiences with SQL such as querying, filtering, and joining data."
         ],
-        "pageviews": 588,
+        "pageviews": 591,
         "pub_date": "2021-10-11",
         "questions": [
             "Who did the crime?"
@@ -50358,6 +129060,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
+        },
         "symlink": null,
         "tags": [
             "game",
@@ -50386,7 +129092,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 19,
-        "visitors": 545,
+        "visitors": 547,
         "zenodo_link": ""
     },
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@@ -50505,7 +129211,6 @@
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
@@ -50539,7 +129244,7 @@
             "Compose an R script file containing comments, commands, objects, and functions.",
             "Be able to work with objects (i.e. applying mathematical and logical operators, subsetting, retrieving values, etc)."
         ],
-        "pageviews": 2990,
+        "pageviews": 3013,
         "priority": 1,
         "pub_date": "2019-10-08",
         "questions": [
@@ -50590,8 +129295,140 @@
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
                 {
@@ -50603,9 +129440,144 @@
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
                 }
             ],
-            "inexact": []
+            "tools": [
+                {
+                    "id": "interactive_tool_rstudio",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
         },
         "symlink": null,
         "tags": [
@@ -50636,8 +129608,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 132,
-        "visitors": 2134,
+        "visit_duration": 131,
+        "visitors": 2154,
         "zenodo_link": ""
     },
     {
@@ -50794,7 +129766,7 @@
             "Explain the three-valued logic databases use when manipulating missing information.",
             "Write queries that handle missing information correctly."
         ],
-        "pageviews": 521,
+        "pageviews": 527,
         "pub_date": "2021-10-11",
         "questions": [
             "How can I get data from a database?",
@@ -50854,6 +129826,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
+        },
         "symlink": null,
         "tags": [
             "SQL"
@@ -50880,8 +129856,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 98,
-        "visitors": 408,
+        "visit_duration": 96,
+        "visitors": 412,
         "zenodo_link": null
     },
     {
@@ -51114,261 +130090,269 @@
                 }
             ]
         },
-        "symlink": null,
-        "tags": [
-            "bash"
-        ],
-        "time_estimation": "2H",
-        "title": "Advanced CLI in Galaxy",
-        "tools": [],
-        "topic_name": "data-science",
-        "topic_name_human": "Foundations of Data Science",
-        "tours": false,
-        "translations": {
-            "slides": [],
-            "tutorial": [],
-            "video": false
-        },
-        "tutorial_name": "cli-advanced",
-        "type": "tutorial",
-        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/cli-advanced/tutorial.html",
-        "urls": {
-            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-advanced/tutorial.json",
-            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-advanced/tutorial.json"
-        },
-        "version": 10,
-        "video": false,
-        "video_versions": 0,
-        "video_view": 0,
-        "visit_duration": 131,
-        "visitors": 701,
-        "zenodo_link": ""
-    },
-    {
-        "admin_install": {
-            "install_repository_dependencies": true,
-            "install_resolver_dependencies": true,
-            "install_tool_dependencies": true,
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
+        },
+        "symlink": null,
+        "tags": [
+            "bash"
+        ],
+        "time_estimation": "2H",
+        "title": "Advanced CLI in Galaxy",
+        "tools": [],
+        "topic_name": "data-science",
+        "topic_name_human": "Foundations of Data Science",
+        "tours": false,
+        "translations": {
+            "slides": [],
+            "tutorial": [],
+            "video": false
+        },
+        "tutorial_name": "cli-advanced",
+        "type": "tutorial",
+        "url": "https://training.galaxyproject.org//topics/data-science/tutorials/cli-advanced/tutorial.html",
+        "urls": {
+            "hands_on": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-advanced/tutorial.json",
+            "slides": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-advanced/tutorial.json"
+        },
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+        "video": false,
+        "video_versions": 0,
+        "video_view": 0,
+        "visit_duration": 131,
+        "visitors": 701,
+        "zenodo_link": ""
+    },
+    {
+        "admin_install": {
+            "install_repository_dependencies": true,
+            "install_resolver_dependencies": true,
+            "install_tool_dependencies": true,
+            "tools": []
+        },
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools: []\n",
+        "api": "https://training.galaxyproject.org/training-material/api/topics/data-science/tutorials/cli-basics/tutorial.json",
+        "contributors": [
+            {
+                "id": "carpentries",
+                "joined": "2021-09",
+                "name": "The Carpentries",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/carpentries/",
+                "ror": "0356fgm10",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/carpentries.json"
+            },
+            {
+                "affiliations": [
+                    "gallantries",
+                    "by-covid",
+                    "erasmusmc",
+                    "elixir-europe",
+                    "elixir-converge"
+                ],
+                "contact_for_training": false,
+                "elixir_node": "nl",
+                "former_affiliations": [
+                    "deNBI",
+                    "avans-atgm",
+                    "uni-freiburg"
+                ],
+                "id": "hexylena",
+                "joined": "2017-09",
+                "location": {
+                    "country": "NL",
+                    "lat": 51.91,
+                    "lon": 4.46
+                },
+                "maintainer_contact": "gitter",
+                "matrix": "hexylena:matrix.org",
+                "name": "Helena Rasche",
+                "orcid": "0000-0001-9760-8992",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/hexylena.json"
+            },
+            {
+                "affiliations": [
+                    "avans-atgm"
+                ],
+                "id": "bazante1",
+                "joined": "2020-12",
+                "name": "Bazante Sanders",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/bazante1/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/bazante1.json"
+            },
+            {
+                "avatar": "https://gallantries.github.io/assets/images/gallantries-logo.png",
+                "end_date": "2023-09-30",
+                "funder": true,
+                "funder_name": "Erasmus+ Programme",
+                "funding_id": "2020-1-NL01-KA203-064717",
+                "funding_statement": "This project (<a href=\"https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717\"><code class=\"language-plaintext highlighter-rouge\">2020-1-NL01-KA203-064717</code></a>) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.\n<img src=\"https://gallantries.github.io/assets/images/logosbeneficaireserasmusright_en.jpg\" alt=\"eu flag with the text: with the support of the erasmus programme of the european union\" />\n<img src=\"https://www.erasmusplus.nl/assets/images/logo.png\" alt=\"erasmus plus logo\" />",
+                "funding_system": "erasmusplus",
+                "github": false,
+                "id": "gallantries",
+                "joined": "2020-09",
+                "members": [
+                    "abretaud",
+                    "bebatut",
+                    "colineroyaux",
+                    "fpsom",
+                    "hexylena",
+                    "shiltemann",
+                    "yvanlebras"
+                ],
+                "name": "Gallantries: Bridging Training Communities in Life Science, Environment and Health",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/gallantries/",
+                "short_name": "Gallantries",
+                "start_date": "2020-09-01",
+                "url": "https://training.galaxyproject.org/training-material/api/funders/gallantries.json"
+            },
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+                "former_members": [
+                    "dirowa",
+                    "hexylena"
+                ],
+                "id": "avans-atgm",
+                "joined": "2020-11",
+                "members": [
+                    "bazante1"
+                ],
+                "name": "Avans Hogeschool",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/avans-atgm/",
+                "ror": "015d5s513",
+                "url": "https://training.galaxyproject.org/training-material/api/organisations/avans-atgm.json"
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+        "follow_up_training": [
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+                "topic_name": "data-science",
+                "tutorials": [
+                    "cli-advanced",
+                    "cli-bashcrawl"
+                ],
+                "type": "internal"
+            }
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+        "hands_on": true,
+        "id": "data-science/cli-basics",
+        "inexact_supported_servers": [
+            "UseGalaxy.eu",
+            "UseGalaxy.org",
+            "UseGalaxy.org.au",
+            "UseGalaxy.fr"
+        ],
+        "js_requirements": {
+            "mathjax": null,
+            "mermaid": false
+        },
+        "key_points": [
+            "A shell is a program whose primary purpose is to read commands and run other programs.",
+            "This lesson uses Bash, the default shell in many implementations of Unix.",
+            "Programs can be run in Bash by entering commands at the command-line prompt.",
+            "The shell's main advantages are its high action-to-keystroke ratio, its support for automating repetitive tasks, and its capacity to access networked machines.",
+            "The shell's main disadvantages are its primarily textual nature and how cryptic its commands and operation can be.",
+            "The file system is responsible for managing information on the disk.",
+            "Information is stored in files, which are stored in directories (folders).",
+            "Directories can also store other directories, which then form a directory tree.",
+            "`cd [path]` changes the current working directory.",
+            "`ls [path]` prints a listing of a specific file or directory; `ls` on its own lists the current working directory.",
+            "`pwd` prints the user's current working directory.",
+            "`/` on its own is the root directory of the whole file system.",
+            "Most commands take options (flags) that begin with a `-`.",
+            "A relative path specifies a location starting from the current location.",
+            "An absolute path specifies a location from the root of the file system.",
+            "Directory names in a path are separated with `/` on Unix, but `\\` on Windows.",
+            "`..` means 'the directory above the current one'; `.` on its own means 'the current directory'.",
+            "`cp [old] [new]` copies a file.",
+            "`mkdir [path]` creates a new directory.",
+            "`mv [old] [new]` moves (renames) a file or directory.",
+            "`rm [path]` removes (deletes) a file.",
+            "`*` matches zero or more characters in a filename, so `*.txt` matches all files ending in `.txt`.",
+            "`?` matches any single character in a filename, so `?.txt` matches `a.txt` but not `any.txt`.",
+            "Use of the Control key may be described in many ways, including `Ctrl-X`, `Control-X`, and `^X`.",
+            "The shell does not have a trash bin: once something is deleted, it's really gone.",
+            "Most files' names are `something.extension`. The extension isn't required, and doesn't guarantee anything, but is normally used to indicate the type of data in the file.",
+            "Depending on the type of work you do, you may need a more powerful text editor than Nano."
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+            "Explain when and why command-line interfaces should be used instead of graphical interfaces.",
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+            "Translate an absolute path into a relative path and vice versa.",
+            "Construct absolute and relative paths that identify specific files and directories.",
+            "Use options and arguments to change the behaviour of a shell command.",
+            "Demonstrate the use of tab completion and explain its advantages.",
+            "Create a directory hierarchy that matches a given diagram.",
+            "Create files in that hierarchy using an editor or by copying and renaming existing files.",
+            "Delete, copy and move specified files and/or directories."
+        ],
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+            "How can I see what files and directories I have?",
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-            "A shell is a program whose primary purpose is to read commands and run other programs.",
-            "This lesson uses Bash, the default shell in many implementations of Unix.",
-            "Programs can be run in Bash by entering commands at the command-line prompt.",
-            "The shell's main advantages are its high action-to-keystroke ratio, its support for automating repetitive tasks, and its capacity to access networked machines.",
-            "The shell's main disadvantages are its primarily textual nature and how cryptic its commands and operation can be.",
-            "The file system is responsible for managing information on the disk.",
-            "Information is stored in files, which are stored in directories (folders).",
-            "Directories can also store other directories, which then form a directory tree.",
-            "`cd [path]` changes the current working directory.",
-            "`ls [path]` prints a listing of a specific file or directory; `ls` on its own lists the current working directory.",
-            "`pwd` prints the user's current working directory.",
-            "`/` on its own is the root directory of the whole file system.",
-            "Most commands take options (flags) that begin with a `-`.",
-            "A relative path specifies a location starting from the current location.",
-            "An absolute path specifies a location from the root of the file system.",
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-            "`cp [old] [new]` copies a file.",
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-            "`mv [old] [new]` moves (renames) a file or directory.",
-            "`rm [path]` removes (deletes) a file.",
-            "`*` matches zero or more characters in a filename, so `*.txt` matches all files ending in `.txt`.",
-            "`?` matches any single character in a filename, so `?.txt` matches `a.txt` but not `any.txt`.",
-            "Use of the Control key may be described in many ways, including `Ctrl-X`, `Control-X`, and `^X`.",
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-            "Explain the similarities and differences between a file and a directory.",
-            "Translate an absolute path into a relative path and vice versa.",
-            "Construct absolute and relative paths that identify specific files and directories.",
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-            "Demonstrate the use of tab completion and explain its advantages.",
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             "Use command line tools to perform variant calling."
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             "Explain why most database applications are written in a general-purpose language rather than in SQL."
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             "Use the log to view the diff",
             "Undo a bad change"
         ],
-        "pageviews": 354,
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         "pub_date": "2022-06-16",
         "questions": [
             "How can I start tracking my changes with git?",
@@ -52204,6 +131200,10 @@
                 }
             ]
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         "objectives": [
             "Understand the structure of a \"function\" in order to be able to construct their own functions and predict which functions will not work."
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@@ -52395,6 +131395,10 @@
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@@ -52419,7 +131423,7 @@
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         "time_estimation": "3H",
         "title": "Advanced Python",
@@ -52768,7 +131776,7 @@
             "Modify the aesthetics of an existing ggplot plot (including axis labels and color).",
             "Build complex and customized plots from data in a data frame."
         ],
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         "priority": 2,
         "pub_date": "2023-06-16",
         "questions": [
@@ -52814,6 +131822,10 @@
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-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)",
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@@ -52986,7 +131997,7 @@
             "Apply common `dplyr` functions to manipulate data in R.",
             "Employ the \u2018pipe\u2019 operator to link together a sequence of functions."
         ],
-        "pageviews": 2086,
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         "priority": 2,
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@@ -53044,8 +132055,140 @@
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+                        {
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+                        {
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+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
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+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.0.1"
+                }
+            ]
         },
         "symlink": null,
         "tags": [
@@ -61282,7 +141619,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSENTINEL2A_20230214-105638-781_L2A_T31UET_D.zip\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Preprocess sentinel 2 data\"];\n  0 -->|output| 1;\n  2[\"Compute spectral indices\"];\n  1 -->|output_refl| 2;\n  3[\"Compute biodiversity indices\"];\n  1 -->|output_refl| 3;\n  4[\"Map diversity\"];\n  1 -->|output_refl| 4;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Sentinel 2 example",
                 "outputs": [
                     {
@@ -61629,7 +141966,6 @@
         "exact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.no"
         ],
         "feedback_mean_note": null,
@@ -61652,7 +141988,7 @@
             "Visualize the data to understand them",
             "Clean GBIF dataset for further analyses"
         ],
-        "pageviews": 508,
+        "pageviews": 511,
         "pub_date": "2022-10-28",
         "questions": [
             "How can I get ecological data from GBIF?",
@@ -61661,11 +141997,11 @@
         ],
         "short_id": "T00129",
         "short_tools": [
-            "Summary_Statistics1",
             "Count1",
-            "Filter1",
             "gdal_ogr2ogr",
-            "spocc_occ"
+            "spocc_occ",
+            "Summary_Statistics1",
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -61683,17 +142019,811 @@
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ],
+            "inexact": []
+        },
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
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+                    "url": "http://gigagalaxy.net/"
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+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                    "url": "https://www.immportgalaxy.org/"
+                },
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+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
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+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
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+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
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+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
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@@ -61729,8 +142859,8 @@
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-        "visitors": 387,
+        "visit_duration": 60,
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@@ -61761,7 +142891,7 @@
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-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "GBIF data Quality check and filtering workflow Feb-2020",
                 "outputs": [],
                 "parent_id": "ecology/gbif_cleaning",
@@ -61977,6 +143107,278 @@
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+                            "state": "local"
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         "tags": [
             "Metadata",
@@ -62119,14 +143521,14 @@
         ],
         "dir": "topics/ecology/tutorials/phylogeny-data-prep",
         "edam_operation": [
-            "Genome annotation",
             "Genome assembly",
+            "Transcriptome assembly",
+            "Genetic variation analysis",
             "Sequence analysis",
-            "Multiple sequence alignment",
+            "Genome annotation",
             "Sequence assembly validation",
+            "Multiple sequence alignment",
             "Scaffolding",
-            "Transcriptome assembly",
-            "Genetic variation analysis",
             "Sequence clustering"
         ],
         "edam_topic": [],
@@ -62157,7 +143559,7 @@
             "Find a set of common proteins across the samples (orthologs)",
             "Align orthologs across samples"
         ],
-        "pageviews": 2073,
+        "pageviews": 2081,
         "pub_date": "2022-10-21",
         "questions": [
             "How do I find a set of common proteins (orthologs) across related species or strains?",
@@ -62174,19 +143576,19 @@
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-            "repeatmasker_wrapper",
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-            "Filter1",
-            "proteinortho",
-            "busco",
-            "proteinortho_grab_proteins",
             "tp_replace_in_line",
             "funannotate_predict",
-            "clipkit",
             "collapse_dataset",
+            "clipkit",
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             "clustalw",
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+            "glimmer_gbk_to_orf",
+            "repeatmasker_wrapper",
+            "proteinortho_grab_proteins",
+            "proteinortho",
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -62201,6 +143603,1954 @@
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@@ -62244,7 +145594,7 @@
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@@ -62314,7 +145664,7 @@
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                 "name": "preparing genomic data for phylogeny recostruction (GTN)",
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@@ -63351,7 +146701,7 @@
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         "questions": [
             "How to analyze RAD sequencing data for a genetic map study?"
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-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Genetic Map Rad Seq Workflow",
                 "outputs": [],
                 "parent_id": "ecology/genetic-map-rad-seq",
@@ -64176,14 +147938,14 @@
         "dir": "topics/ecology/tutorials/ref-based-rad-seq",
         "edam_operation": [
             "Data handling",
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
+            "Genome indexing",
+            "Sequence composition calculation",
             "Generation",
-            "Statistical calculation",
             "Validation",
-            "Sequence composition calculation",
-            "Genome indexing"
+            "Sequencing quality control",
+            "Read mapping",
+            "Sequence alignment",
+            "Statistical calculation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -64205,7 +147967,7 @@
             "SNP calling from RAD sequencing data",
             "Calculate population genomics statistics from RAD sequencing data"
         ],
-        "pageviews": 3808,
+        "pageviews": 3814,
         "pub_date": "2017-02-14",
         "questions": [
             "How to analyze RAD sequencing data using a reference genome for a population genomics study?"
@@ -64217,24 +147979,24 @@
         ],
         "short_id": "T00133",
         "short_tools": [
-            "stacks_procrad",
+            "Cut1",
+            "cat1",
             "Count1",
-            "Summary_Statistics1",
-            "Filter1",
+            "tp_replace_in_line",
+            "bwa",
             "Convert characters1",
+            "stacks_procrad",
+            "fastqc",
             "tp_sort_header_tool",
             "stacks_refmap",
-            "tp_replace_in_line",
-            "multiqc",
-            "bwa_wrapper",
+            "regex_replace",
             "Grep1",
-            "Cut1",
-            "bwa",
+            "Summary_Statistics1",
             "stacks_populations",
-            "regex_replace",
-            "fastqc",
-            "cat1",
-            "addValue"
+            "multiqc",
+            "bwa_wrapper",
+            "addValue",
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -64243,6 +148005,2643 @@
             "exact": [],
             "inexact": []
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@@ -64293,7 +150692,7 @@
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         "video_view": 0,
         "visit_duration": 104,
-        "visitors": 2275,
+        "visitors": 2280,
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@@ -64450,7 +150849,7 @@
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-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Workflow Constructed From History 'STACKS RAD: Population Genomics With Reference Genome'",
                 "outputs": [],
                 "parent_id": "ecology/ref-based-rad-seq",
@@ -64646,7 +151045,7 @@
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-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Ref Based Rad Seq",
                 "outputs": [],
                 "parent_id": "ecology/ref-based-rad-seq",
@@ -64762,7 +151161,7 @@
             "Learn about NetCDF xarray map plotting tool",
             "Learn about visualizing the climate data using NetCDF xarray map plotting using the different kinds of projections and colormap options"
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         "questions": [
             "What is xarray map plotting?",
@@ -64780,11 +151179,11 @@
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-            "xarray_metadata_info",
-            "xarray_mapplot",
             "graphicsmagick_image_montage",
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             "cdo_operations",
-            "xarray_coords_info"
+            "xarray_mapplot",
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@@ -64805,6 +151204,828 @@
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+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.46.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.46.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.46.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.46.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.46.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.46.0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "RAD-seq",
@@ -65531,7 +153471,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 129,
-        "visitors": 2343,
+        "visitors": 2350,
         "workflows": [
             {
                 "creators": [],
@@ -65688,7 +153628,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPopulation_map.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nBarcodes_SRR034310.tabular\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSRR034310.fastq\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nref_genome_chromFa.tar\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Stacks: process radtags\"];\n  1 -->|output| 4;\n  2 -->|output| 4;\n  5[\"Stacks: process radtags\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  6[\"Stacks: process radtags\"];\n  1 -->|output| 6;\n  2 -->|output| 6;\n  7[\"FastQC\"];\n  2 -->|output| 7;\n  8[\"Stacks: de novo map\"];\n  4 -->|demultiplexed| 8;\n  0 -->|output| 8;\n  9[\"Stacks: populations\"];\n  8 -->|all_output| 9;\n  0 -->|output| 9;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "de novo Rad Seq",
                 "outputs": [],
                 "parent_id": "ecology/de-novo-rad-seq",
@@ -65927,23 +153867,23 @@
         ],
         "short_id": "T00134",
         "short_tools": [
+            "regionalgam_ab_index",
             "Count1",
-            "mergeCols1",
-            "regionalgam_glmmpql",
-            "Filter1",
-            "tp_awk_tool",
-            "Paste1",
-            "regionalgam_plot_trend",
             "flight-curve",
-            "ggplot2_point",
-            "tab2csv_R",
-            "csv2tab_R",
-            "regionalgam_gls",
-            "regionalgam_flight_curve",
             "regexColumn1",
+            "regionalgam_flight_curve",
+            "tp_awk_tool",
+            "regionalgam_autocor_acf",
+            "regionalgam_glmmpql",
+            "regionalgam_gls",
+            "ggplot2_point",
             "Remove beginning1",
-            "regionalgam_ab_index",
-            "regionalgam_autocor_acf"
+            "csv2tab_R",
+            "tab2csv_R",
+            "regionalgam_plot_trend",
+            "mergeCols1",
+            "Paste1",
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -65952,6 +153892,2458 @@
             "exact": [],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "id": "Count1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "missing"
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+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
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+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Filter1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
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+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
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+                        },
+                        {
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+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
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+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Paste1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
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+                        {
+                            "server": "http://dintor.eurac.edu/",
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+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
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+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
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+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
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+                            "state": "exact",
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+                            "state": "missing"
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+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "Species populations EBV class",
@@ -66067,7 +156459,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAbundance index file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Filter\"];\n  0 -->|output| 1;\n  2[\"Filter\"];\n  0 -->|output| 2;\n  3[\"Filter\"];\n  0 -->|output| 3;\n  4[\"Filter\"];\n  0 -->|output| 4;\n  5[\"Filter\"];\n  0 -->|output| 5;\n  6[\"Paste\"];\n  1 -->|out_file1| 6;\n  2 -->|out_file1| 6;\n  7[\"Paste\"];\n  3 -->|out_file1| 7;\n  4 -->|out_file1| 7;\n  8[\"Paste\"];\n  6 -->|out_file1| 8;\n  7 -->|out_file1| 8;\n  9[\"Paste\"];\n  8 -->|out_file1| 9;\n  5 -->|out_file1| 9;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Abundance Index \"stacked\" Visualization Creation",
                 "outputs": [],
                 "parent_id": "ecology/regionalGAM",
@@ -66158,7 +156550,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nFlight curve dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Filter\"];\n  0 -->|output| 1;\n  2[\"Filter\"];\n  0 -->|output| 2;\n  3[\"Paste\"];\n  1 -->|out_file1| 3;\n  2 -->|out_file1| 3;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Phenology \"stacked\" Visualization Creation",
                 "outputs": [],
                 "parent_id": "ecology/regionalGAM",
@@ -66254,7 +156646,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"CSV to Tabular\"];\n  0 -->|output| 1;\n  10[\"Count\"];\n  8 -->|output| 10;\n  11[\"Column Regex Find And Replace\"];\n  8 -->|output| 11;\n  12[\"Count\"];\n  9 -->|output| 12;\n  13[\"Column Regex Find And Replace\"];\n  9 -->|output| 13;\n  14[\"Merge Columns\"];\n  11 -->|out_file1| 14;\n  15[\"Merge Columns\"];\n  13 -->|out_file1| 15;\n  16[\"Remove beginning\"];\n  14 -->|out_file1| 16;\n  17[\"Remove beginning\"];\n  15 -->|out_file1| 17;\n  18[\"Paste\"];\n  16 -->|out_file1| 18;\n  17 -->|out_file1| 18;\n  2[\"Column Regex Find And Replace\"];\n  1 -->|output| 2;\n  3[\"Count\"];\n  2 -->|out_file1| 3;\n  4[\"Filter\"];\n  2 -->|out_file1| 4;\n  5[\"Filter\"];\n  2 -->|out_file1| 5;\n  6[\"Tabular to CSV\"];\n  4 -->|out_file1| 6;\n  7[\"Tabular to CSV\"];\n  5 -->|out_file1| 7;\n  8[\"Flight curve\"];\n  6 -->|output| 8;\n  9[\"Flight curve\"];\n  7 -->|output| 9;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Tutorial regionalGAM Complete Multispecies",
                 "outputs": [],
                 "parent_id": "ecology/regionalGAM",
@@ -66364,7 +156756,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nregionalGAM.csv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Text reformatting\"];\n  0 -->|output| 1;\n  2[\"Count\"];\n  1 -->|outfile| 2;\n  3[\"Flight curve\"];\n  2 -->|out_file1| 3;\n  4[\"Abundance index\"];\n  2 -->|out_file1| 4;\n  3 -->|output| 4;\n  5[\"Scatterplot w ggplot2\"];\n  3 -->|output| 5;\n  6[\"Expected temporal trend\"];\n  4 -->|output| 6;\n  7[\"Model temporal trend\"];\n  4 -->|output| 7;\n  6 -->|output2| 7;\n  8[\"Autocorrelation test\"];\n  7 -->|output2| 8;\n  9[\"Plot abundance\"];\n  4 -->|output| 9;\n  7 -->|output2| 9;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Regional GAM Workflow",
                 "outputs": [
                     {
@@ -66857,8 +157249,8 @@
         "dir": "topics/ecology/tutorials/marine_omics_bgc",
         "edam_operation": [
             "Sequence motif recognition",
-            "Genome annotation",
-            "Protein feature detection"
+            "Protein feature detection",
+            "Genome annotation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -66884,7 +157276,7 @@
             "Discover SanntiS a tool for identifying BGCs in genomic & metagenomic data",
             "Manage fasta files"
         ],
-        "pageviews": 24,
+        "pageviews": 25,
         "pub_date": "2024-08-19",
         "questions": [
             "Which biological questions are addressed by the tutorial?",
@@ -66892,11 +157284,11 @@
         ],
         "short_id": "T00450",
         "short_tools": [
-            "SanntiS_marine",
-            "sanntis_marine",
             "interproscan",
             "prodigal",
-            "regex1"
+            "regex1",
+            "sanntis_marine",
+            "SanntiS_marine"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -66905,6 +157297,825 @@
             "exact": [],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
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+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
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+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
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+                    "url": "http://gigagalaxy.net/"
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+                },
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+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                    "usegalaxy": false
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+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
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+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
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                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nFasta nucelotide file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Prodigal Gene Predictor \"];\n  0 -->|output| 1;\n  351cf550-c05d-4bad-9394-fe9b45ef6298[\"Output\\nProtein fasta file\"];\n  1 --> 351cf550-c05d-4bad-9394-fe9b45ef6298;\n  style 351cf550-c05d-4bad-9394-fe9b45ef6298 stroke:#2c3143,stroke-width:4px;\n  2[\"Sanntis: Build Genbank \"];\n  0 -->|output| 2;\n  1 -->|output_faa| 2;\n  1b9f0275-191a-4e90-b4b4-7b10475f4602[\"Output\\nGenbank file\"];\n  2 --> 1b9f0275-191a-4e90-b4b4-7b10475f4602;\n  style 1b9f0275-191a-4e90-b4b4-7b10475f4602 stroke:#2c3143,stroke-width:4px;\n  3[\"Regex Find And Replace\"];\n  1 -->|output_faa| 3;\n  e41e8fb9-c5f6-425f-a351-f8fa92f7821d[\"Output\\nClean protein fasta file\"];\n  3 --> e41e8fb9-c5f6-425f-a351-f8fa92f7821d;\n  style e41e8fb9-c5f6-425f-a351-f8fa92f7821d stroke:#2c3143,stroke-width:4px;\n  4[\" InterProScan\"];\n  3 -->|out_file1| 4;\n  522b49db-7650-41e7-b888-01bb3cb1b451[\"Output\\nTabular file (.tsv)\"];\n  4 --> 522b49db-7650-41e7-b888-01bb3cb1b451;\n  style 522b49db-7650-41e7-b888-01bb3cb1b451 stroke:#2c3143,stroke-width:4px;\n  5[\"Sanntis: identify biosynthetic gene clusters\"];\n  2 -->|output_sanntis_gb| 5;\n  4 -->|outfile_tsv| 5;\n  c96c8c7e-0a50-4506-a144-9d941f50eb5e[\"Output\\n SMBGC Annotation\"];\n  5 --> c96c8c7e-0a50-4506-a144-9d941f50eb5e;\n  style c96c8c7e-0a50-4506-a144-9d941f50eb5e stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Marine Omics identifying biosynthetic gene clusters",
                 "outputs": [
                     {
@@ -67401,8 +158612,7 @@
         "edam_operation": [],
         "edam_topic": [],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -67427,7 +158637,7 @@
             "Partition occurrence data",
             "Model a theoretical ecological niche and predict species distribution in a future climate scenario by using SDM"
         ],
-        "pageviews": 4208,
+        "pageviews": 4213,
         "pub_date": "2019-07-04",
         "questions": [
             "How to build & evaluate a niche model, visualize and project it?"
@@ -67436,11 +158646,11 @@
         "short_id": "T00135",
         "short_tools": [
             "tabular_to_csv",
-            "Filter1",
             "interactive_tool_wallace",
-            "spocc_occ",
             "tp_find_and_replace",
-            "tp_cut_tool"
+            "spocc_occ",
+            "tp_cut_tool",
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -67451,14 +158661,982 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
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+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
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+                },
+                {
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+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
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+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
                 }
             ],
-            "inexact": []
+            "tools": [
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+                    "id": "Filter1",
+                    "servers": [
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+                            "state": "local"
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+                            "state": "local"
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+                            "state": "local"
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+                            "server": "http://pepsimili.e-nios.com:8080/",
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+                        {
+                            "server": "https://usegalaxy.org",
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+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
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+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
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+                        {
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+                            "state": "missing"
+                        },
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+                        }
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+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
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+                            "state": "inexact",
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+                                "9.3+galaxy2"
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+                            "state": "missing"
+                        },
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@@ -67497,7 +159675,7 @@
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         "video_view": 0,
         "visit_duration": 69,
-        "visitors": 2666,
+        "visitors": 2670,
         "workflows": [
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@@ -67542,7 +159720,7 @@
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-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Species Distribution Modeling With Wallace From GBIF - Training Material",
                 "outputs": [
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@@ -67786,7 +159964,7 @@
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             "Create an ecoregionalization map"
         ],
-        "pageviews": 64,
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@@ -67794,18 +159972,18 @@
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             "ecoregion_GeoNearestNeighbor",
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-            "ecoregion_cluster_estimate",
-            "tp_cut_tool",
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-            "regexColumn1"
+            "mergeCols1",
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@@ -67820,6 +159998,1783 @@
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                 "history": [
                     {
                         "hash": "106094184ea15924f444a0b076b0afecd065494a",
@@ -67978,8 +161933,8 @@
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                 ],
                 "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\noccurrence.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\npivot_wider_jupytool_notebook.ipynb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nceamarc_env.tsv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Advanced Cut\"];\n  0 -->|output| 3;\n  4[\"Column Regex Find And Replace\"];\n  3 -->|output| 4;\n  5[\"Column Regex Find And Replace\"];\n  4 -->|out_file1| 5;\n  6[\"Column Regex Find And Replace\"];\n  5 -->|out_file1| 6;\n  7[\"Column Regex Find And Replace\"];\n  6 -->|out_file1| 7;\n  8[\"Filter Tabular\"];\n  7 -->|out_file1| 8;\n  9[\"Column Regex Find And Replace\"];\n  8 -->|output| 9;\n  10[\"Column Regex Find And Replace\"];\n  9 -->|out_file1| 10;\n  11[\"Column Regex Find And Replace\"];\n  10 -->|out_file1| 11;\n  12[\"Column Regex Find And Replace\"];\n  11 -->|out_file1| 12;\n  13[\"Column Regex Find And Replace\"];\n  12 -->|out_file1| 13;\n  14[\"Merge Columns\"];\n  13 -->|out_file1| 14;\n  15[\"Advanced Cut\"];\n  14 -->|out_file1| 15;\n  16[\"Interactive JupyTool and notebook\"];\n  1 -->|output| 16;\n  15 -->|output| 16;\n  b3689891-b1e5-4af7-aa8a-a01cfdd249e6[\"Output\\nocc_out\"];\n  16 --> b3689891-b1e5-4af7-aa8a-a01cfdd249e6;\n  style b3689891-b1e5-4af7-aa8a-a01cfdd249e6 stroke:#2c3143,stroke-width:4px;\n  17[\"GeoNearestNeighbor\"];\n  2 -->|output| 17;\n  16 -->|output_dataset| 17;\n  3d871fdd-1ca8-4ca5-80dd-b50ec7193a09[\"Output\\nocc_env_out\"];\n  17 --> 3d871fdd-1ca8-4ca5-80dd-b50ec7193a09;\n  style 3d871fdd-1ca8-4ca5-80dd-b50ec7193a09 stroke:#2c3143,stroke-width:4px;\n  23ef2c88-6caa-4a4a-bf33-34e51ea63787[\"Output\\ninfo_out\"];\n  17 --> 23ef2c88-6caa-4a4a-bf33-34e51ea63787;\n  style 23ef2c88-6caa-4a4a-bf33-34e51ea63787 stroke:#2c3143,stroke-width:4px;\n  18[\"BRT tool prediction\"];\n  2 -->|output| 18;\n  17 -->|occ_env_out| 18;\n  5003067a-90e6-4b6f-bcb5-15c7f07a587b[\"Output\\ncoll_pred\"];\n  18 --> 5003067a-90e6-4b6f-bcb5-15c7f07a587b;\n  style 5003067a-90e6-4b6f-bcb5-15c7f07a587b stroke:#2c3143,stroke-width:4px;\n  2588bbcf-1064-43c1-9eb3-aaa9a699be61[\"Output\\ncoll_val\"];\n  18 --> 2588bbcf-1064-43c1-9eb3-aaa9a699be61;\n  style 2588bbcf-1064-43c1-9eb3-aaa9a699be61 stroke:#2c3143,stroke-width:4px;\n  7d4abdef-22d7-40e0-9d45-51a8151a6ab5[\"Output\\ncoll_distri\"];\n  18 --> 7d4abdef-22d7-40e0-9d45-51a8151a6ab5;\n  style 7d4abdef-22d7-40e0-9d45-51a8151a6ab5 stroke:#2c3143,stroke-width:4px;\n  d4f30afa-ddd7-4be3-827b-504c9b152e79[\"Output\\ncoll_plots\"];\n  18 --> d4f30afa-ddd7-4be3-827b-504c9b152e79;\n  style d4f30afa-ddd7-4be3-827b-504c9b152e79 stroke:#2c3143,stroke-width:4px;\n  19[\"TaxaSeeker\"];\n  2 -->|output| 19;\n  17 -->|occ_env_out| 19;\n  18 -->|outputpred| 19;\n  5109d040-6932-4a69-8a7a-01372852ec58[\"Output\\nsummary\"];\n  19 --> 5109d040-6932-4a69-8a7a-01372852ec58;\n  style 5109d040-6932-4a69-8a7a-01372852ec58 stroke:#2c3143,stroke-width:4px;\n  66fd292a-c542-4e7b-a8cb-124095e6e8ed[\"Output\\ntaxa\"];\n  19 --> 66fd292a-c542-4e7b-a8cb-124095e6e8ed;\n  style 66fd292a-c542-4e7b-a8cb-124095e6e8ed stroke:#2c3143,stroke-width:4px;\n  a4c7a093-d640-46ba-8681-5bd09c899215[\"Output\\ntaxa_clean\"];\n  19 --> a4c7a093-d640-46ba-8681-5bd09c899215;\n  style a4c7a093-d640-46ba-8681-5bd09c899215 stroke:#2c3143,stroke-width:4px;\n  20[\"ClusterEstimate\"];\n  2 -->|output| 20;\n  18 -->|outputpred| 20;\n  19 -->|output2| 20;\n  fd5e25b2-31b8-446b-bbde-33f4978cbbce[\"Output\\nSIH_index\"];\n  20 --> fd5e25b2-31b8-446b-bbde-33f4978cbbce;\n  style fd5e25b2-31b8-446b-bbde-33f4978cbbce stroke:#2c3143,stroke-width:4px;\n  ada14639-f7a0-454c-a0b9-a6efdf019186[\"Output\\ndata_to_clus\"];\n  20 --> ada14639-f7a0-454c-a0b9-a6efdf019186;\n  style ada14639-f7a0-454c-a0b9-a6efdf019186 stroke:#2c3143,stroke-width:4px;\n  7556cf4a-92f7-443f-a43f-cc011a4eea8f[\"Output\\ndatabio_table\"];\n  20 --> 7556cf4a-92f7-443f-a43f-cc011a4eea8f;\n  style 7556cf4a-92f7-443f-a43f-cc011a4eea8f stroke:#2c3143,stroke-width:4px;\n  21[\"ClaraClust\"];\n  2 -->|output| 21;\n  20 -->|output3| 21;\n  20 -->|output2| 21;\n  65123e97-b2fa-429d-bf32-5733ccb17fb5[\"Output\\nSIH_plot\"];\n  21 --> 65123e97-b2fa-429d-bf32-5733ccb17fb5;\n  style 65123e97-b2fa-429d-bf32-5733ccb17fb5 stroke:#2c3143,stroke-width:4px;\n  38a7227b-a1f5-4728-bdac-87d0764c3a29[\"Output\\ncluster_points\"];\n  21 --> 38a7227b-a1f5-4728-bdac-87d0764c3a29;\n  style 38a7227b-a1f5-4728-bdac-87d0764c3a29 stroke:#2c3143,stroke-width:4px;\n  592084ea-4cbe-477d-b826-e01ec4f52650[\"Output\\ncluster_info\"];\n  21 --> 592084ea-4cbe-477d-b826-e01ec4f52650;\n  style 592084ea-4cbe-477d-b826-e01ec4f52650 stroke:#2c3143,stroke-width:4px;\n  22[\"EcoMap\"];\n  21 -->|output2| 22;\n  2f8feb4c-ed0a-4bfc-89e8-e7befd040ada[\"Output\\neco_map\"];\n  22 --> 2f8feb4c-ed0a-4bfc-89e8-e7befd040ada;\n  style 2f8feb4c-ed0a-4bfc-89e8-e7befd040ada stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\noccurrence.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\npivot_wider_jupytool_notebook.ipynb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nceamarc_env.tsv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Advanced Cut\"];\n  0 -->|output| 3;\n  4[\"Column Regex Find And Replace\"];\n  3 -->|output| 4;\n  5[\"Column Regex Find And Replace\"];\n  4 -->|out_file1| 5;\n  6[\"Column Regex Find And Replace\"];\n  5 -->|out_file1| 6;\n  7[\"Column Regex Find And Replace\"];\n  6 -->|out_file1| 7;\n  8[\"Filter Tabular\"];\n  7 -->|out_file1| 8;\n  9[\"Column Regex Find And Replace\"];\n  8 -->|output| 9;\n  10[\"Column Regex Find And Replace\"];\n  9 -->|out_file1| 10;\n  11[\"Column Regex Find And Replace\"];\n  10 -->|out_file1| 11;\n  12[\"Column Regex Find And Replace\"];\n  11 -->|out_file1| 12;\n  13[\"Column Regex Find And Replace\"];\n  12 -->|out_file1| 13;\n  14[\"Merge Columns\"];\n  13 -->|out_file1| 14;\n  15[\"Advanced Cut\"];\n  14 -->|out_file1| 15;\n  16[\"Interactive JupyTool and notebook\"];\n  1 -->|output| 16;\n  15 -->|output| 16;\n  86d84a13-c4b0-46ff-9b7a-55e6a2445c38[\"Output\\nocc_out\"];\n  16 --> 86d84a13-c4b0-46ff-9b7a-55e6a2445c38;\n  style 86d84a13-c4b0-46ff-9b7a-55e6a2445c38 stroke:#2c3143,stroke-width:4px;\n  17[\"GeoNearestNeighbor\"];\n  2 -->|output| 17;\n  16 -->|output_dataset| 17;\n  c74e2b45-61ae-406c-b901-85743e8c53b0[\"Output\\nocc_env_out\"];\n  17 --> c74e2b45-61ae-406c-b901-85743e8c53b0;\n  style c74e2b45-61ae-406c-b901-85743e8c53b0 stroke:#2c3143,stroke-width:4px;\n  b180902b-c53d-42af-970d-e3a4fa724a83[\"Output\\ninfo_out\"];\n  17 --> b180902b-c53d-42af-970d-e3a4fa724a83;\n  style b180902b-c53d-42af-970d-e3a4fa724a83 stroke:#2c3143,stroke-width:4px;\n  18[\"BRT tool prediction\"];\n  2 -->|output| 18;\n  17 -->|occ_env_out| 18;\n  71486d3e-6976-4b66-a96e-0723bd6cf284[\"Output\\ncoll_pred\"];\n  18 --> 71486d3e-6976-4b66-a96e-0723bd6cf284;\n  style 71486d3e-6976-4b66-a96e-0723bd6cf284 stroke:#2c3143,stroke-width:4px;\n  e4dba3f1-3f8c-41dd-8561-d38a264a9397[\"Output\\ncoll_val\"];\n  18 --> e4dba3f1-3f8c-41dd-8561-d38a264a9397;\n  style e4dba3f1-3f8c-41dd-8561-d38a264a9397 stroke:#2c3143,stroke-width:4px;\n  4a9faa40-4ec8-4ae5-972a-ad75b7afe0fd[\"Output\\ncoll_distri\"];\n  18 --> 4a9faa40-4ec8-4ae5-972a-ad75b7afe0fd;\n  style 4a9faa40-4ec8-4ae5-972a-ad75b7afe0fd stroke:#2c3143,stroke-width:4px;\n  fcd1d43b-893c-4ff8-a536-3b1b16fe8ce9[\"Output\\ncoll_plots\"];\n  18 --> fcd1d43b-893c-4ff8-a536-3b1b16fe8ce9;\n  style fcd1d43b-893c-4ff8-a536-3b1b16fe8ce9 stroke:#2c3143,stroke-width:4px;\n  19[\"TaxaSeeker\"];\n  2 -->|output| 19;\n  17 -->|occ_env_out| 19;\n  18 -->|outputpred| 19;\n  d875a696-789b-4110-a7d2-1f2c55fc178a[\"Output\\nsummary\"];\n  19 --> d875a696-789b-4110-a7d2-1f2c55fc178a;\n  style d875a696-789b-4110-a7d2-1f2c55fc178a stroke:#2c3143,stroke-width:4px;\n  aba68832-0c76-4289-a205-f9fdd6330d47[\"Output\\ntaxa\"];\n  19 --> aba68832-0c76-4289-a205-f9fdd6330d47;\n  style aba68832-0c76-4289-a205-f9fdd6330d47 stroke:#2c3143,stroke-width:4px;\n  bb4e8a78-6856-43c0-a21f-32d8e81b840d[\"Output\\ntaxa_clean\"];\n  19 --> bb4e8a78-6856-43c0-a21f-32d8e81b840d;\n  style bb4e8a78-6856-43c0-a21f-32d8e81b840d stroke:#2c3143,stroke-width:4px;\n  20[\"ClusterEstimate\"];\n  2 -->|output| 20;\n  18 -->|outputpred| 20;\n  19 -->|output2| 20;\n  1bec460e-a930-4fe0-914b-20bea45ff1d0[\"Output\\nSIH_index\"];\n  20 --> 1bec460e-a930-4fe0-914b-20bea45ff1d0;\n  style 1bec460e-a930-4fe0-914b-20bea45ff1d0 stroke:#2c3143,stroke-width:4px;\n  b5244dcb-7c79-453e-92ca-c6cb3be2e784[\"Output\\ndata_to_clus\"];\n  20 --> b5244dcb-7c79-453e-92ca-c6cb3be2e784;\n  style b5244dcb-7c79-453e-92ca-c6cb3be2e784 stroke:#2c3143,stroke-width:4px;\n  76c42c90-409b-420b-bb98-bebc9c8f631d[\"Output\\ndatabio_table\"];\n  20 --> 76c42c90-409b-420b-bb98-bebc9c8f631d;\n  style 76c42c90-409b-420b-bb98-bebc9c8f631d stroke:#2c3143,stroke-width:4px;\n  21[\"ClaraClust\"];\n  2 -->|output| 21;\n  20 -->|output3| 21;\n  20 -->|output2| 21;\n  4e027e0c-2a34-41bd-b3b4-8ea4d7d6d1e8[\"Output\\nSIH_plot\"];\n  21 --> 4e027e0c-2a34-41bd-b3b4-8ea4d7d6d1e8;\n  style 4e027e0c-2a34-41bd-b3b4-8ea4d7d6d1e8 stroke:#2c3143,stroke-width:4px;\n  54bbb4be-ec07-4c15-ae85-2008a397ea4d[\"Output\\ncluster_points\"];\n  21 --> 54bbb4be-ec07-4c15-ae85-2008a397ea4d;\n  style 54bbb4be-ec07-4c15-ae85-2008a397ea4d stroke:#2c3143,stroke-width:4px;\n  bf9162bf-3dcd-4112-865d-b43a4107ed0c[\"Output\\ncluster_info\"];\n  21 --> bf9162bf-3dcd-4112-865d-b43a4107ed0c;\n  style bf9162bf-3dcd-4112-865d-b43a4107ed0c stroke:#2c3143,stroke-width:4px;\n  22[\"EcoMap\"];\n  21 -->|output2| 22;\n  5fe27614-a0d9-45c2-8a06-8ae90697ff9a[\"Output\\neco_map\"];\n  22 --> 5fe27614-a0d9-45c2-8a06-8ae90697ff9a;\n  style 5fe27614-a0d9-45c2-8a06-8ae90697ff9a stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-08 10:05:42 +0000",
                 "name": "Ecoregionalization workflow",
                 "outputs": [
                     {
@@ -68042,7 +161997,7 @@
                             {
                                 "label": "occ_out",
                                 "output_name": "output_dataset",
-                                "uuid": "b3689891-b1e5-4af7-aa8a-a01cfdd249e6"
+                                "uuid": "86d84a13-c4b0-46ff-9b7a-55e6a2445c38"
                             }
                         ]
                     },
@@ -68104,12 +162059,12 @@
                             {
                                 "label": "occ_env_out",
                                 "output_name": "occ_env_out",
-                                "uuid": "3d871fdd-1ca8-4ca5-80dd-b50ec7193a09"
+                                "uuid": "c74e2b45-61ae-406c-b901-85743e8c53b0"
                             },
                             {
                                 "label": "info_out",
                                 "output_name": "info_out",
-                                "uuid": "23ef2c88-6caa-4a4a-bf33-34e51ea63787"
+                                "uuid": "b180902b-c53d-42af-970d-e3a4fa724a83"
                             }
                         ]
                     },
@@ -68170,22 +162125,22 @@
                             {
                                 "label": "coll_pred",
                                 "output_name": "outputpred",
-                                "uuid": "5003067a-90e6-4b6f-bcb5-15c7f07a587b"
+                                "uuid": "71486d3e-6976-4b66-a96e-0723bd6cf284"
                             },
                             {
                                 "label": "coll_val",
                                 "output_name": "outputval",
-                                "uuid": "2588bbcf-1064-43c1-9eb3-aaa9a699be61"
+                                "uuid": "e4dba3f1-3f8c-41dd-8561-d38a264a9397"
                             },
                             {
                                 "label": "coll_distri",
                                 "output_name": "outputspdistri",
-                                "uuid": "7d4abdef-22d7-40e0-9d45-51a8151a6ab5"
+                                "uuid": "4a9faa40-4ec8-4ae5-972a-ad75b7afe0fd"
                             },
                             {
                                 "label": "coll_plots",
                                 "output_name": "outputplots",
-                                "uuid": "d4f30afa-ddd7-4be3-827b-504c9b152e79"
+                                "uuid": "fcd1d43b-893c-4ff8-a536-3b1b16fe8ce9"
                             }
                         ]
                     },
@@ -68246,17 +162201,17 @@
                             {
                                 "label": "summary",
                                 "output_name": "output1",
-                                "uuid": "5109d040-6932-4a69-8a7a-01372852ec58"
+                                "uuid": "d875a696-789b-4110-a7d2-1f2c55fc178a"
                             },
                             {
                                 "label": "taxa",
                                 "output_name": "output2",
-                                "uuid": "66fd292a-c542-4e7b-a8cb-124095e6e8ed"
+                                "uuid": "aba68832-0c76-4289-a205-f9fdd6330d47"
                             },
                             {
                                 "label": "taxa_clean",
                                 "output_name": "output3",
-                                "uuid": "a4c7a093-d640-46ba-8681-5bd09c899215"
+                                "uuid": "bb4e8a78-6856-43c0-a21f-32d8e81b840d"
                             }
                         ]
                     },
@@ -68317,17 +162272,17 @@
                             {
                                 "label": "SIH_index",
                                 "output_name": "output1",
-                                "uuid": "fd5e25b2-31b8-446b-bbde-33f4978cbbce"
+                                "uuid": "1bec460e-a930-4fe0-914b-20bea45ff1d0"
                             },
                             {
                                 "label": "data_to_clus",
                                 "output_name": "output2",
-                                "uuid": "ada14639-f7a0-454c-a0b9-a6efdf019186"
+                                "uuid": "b5244dcb-7c79-453e-92ca-c6cb3be2e784"
                             },
                             {
                                 "label": "databio_table",
                                 "output_name": "output3",
-                                "uuid": "7556cf4a-92f7-443f-a43f-cc011a4eea8f"
+                                "uuid": "76c42c90-409b-420b-bb98-bebc9c8f631d"
                             }
                         ]
                     },
@@ -68388,17 +162343,17 @@
                             {
                                 "label": "SIH_plot",
                                 "output_name": "output1",
-                                "uuid": "65123e97-b2fa-429d-bf32-5733ccb17fb5"
+                                "uuid": "4e027e0c-2a34-41bd-b3b4-8ea4d7d6d1e8"
                             },
                             {
                                 "label": "cluster_points",
                                 "output_name": "output2",
-                                "uuid": "38a7227b-a1f5-4728-bdac-87d0764c3a29"
+                                "uuid": "54bbb4be-ec07-4c15-ae85-2008a397ea4d"
                             },
                             {
                                 "label": "cluster_info",
                                 "output_name": "output3",
-                                "uuid": "592084ea-4cbe-477d-b826-e01ec4f52650"
+                                "uuid": "bf9162bf-3dcd-4112-865d-b43a4107ed0c"
                             }
                         ]
                     },
@@ -68443,7 +162398,7 @@
                             {
                                 "label": "eco_map",
                                 "output_name": "output",
-                                "uuid": "2f8feb4c-ed0a-4bfc-89e8-e7befd040ada"
+                                "uuid": "5fe27614-a0d9-45c2-8a06-8ae90697ff9a"
                             }
                         ]
                     }
@@ -68586,8 +162541,8 @@
         ],
         "short_id": "T00400",
         "short_tools": [
-            "interactive_tool_holoviz",
-            "interactive_tool_copernicus_notebook"
+            "interactive_tool_copernicus_notebook",
+            "interactive_tool_holoviz"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -68602,6 +162557,408 @@
             ],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
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+                    "url": "http://galaxy.inf.ethz.ch"
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+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                    "url": "https://usegalaxy.cz/",
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+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
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+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
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+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
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+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "interactive_tool_holoviz",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
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+                            "state": "missing"
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "earth-system",
@@ -68674,7 +163031,7 @@
                 "inputs": [],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"Copernicus Data Space Ecosystem\"];\n  1[\"Holoviz\"];\n  0 -->|output_collection| 1;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "NDVI with OpenEO",
                 "outputs": [],
                 "parent_id": "ecology/ndvi_openeo",
@@ -68762,7 +163119,7 @@
                 "inputs": [],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"Copernicus Data Space Ecosystem\"];\n  1[\"Holoviz\"];\n  0 -->|output_collection| 1;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "NDVI with OpenEO",
                 "outputs": [],
                 "parent_id": "ecology/ndvi_openeo",
@@ -69012,7 +163369,6 @@
         "id": "ecology/PAMPA-toolsuite-tutorial",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
@@ -69037,7 +163393,7 @@
             "Learning how to construct a Generalized Linear (Mixed) Model from a usual ecological question",
             "Learning how to interpret a Generalized Linear (Mixed) Model"
         ],
-        "pageviews": 1285,
+        "pageviews": 1289,
         "pub_date": "2020-11-19",
         "questions": [
             "How to evaluate properly populations and communities biological state with abundance data?",
@@ -69061,20 +163417,20 @@
         "short_id": "T00125",
         "short_tools": [
             "Count1",
-            "tp_easyjoin_tool",
-            "tp_cat",
-            "mergeCols1",
-            "Filter1",
+            "pampa_communitymetrics",
+            "pampa_presabs",
             "pampa_glmcomm",
-            "pampa_plotglm",
+            "regex1",
+            "tp_cat",
+            "tp_easyjoin_tool",
+            "regexColumn1",
             "tp_sort_header_tool",
-            "pampa_glmsp",
-            "pampa_presabs",
             "datamash_transpose",
-            "regexColumn1",
+            "pampa_plotglm",
+            "pampa_glmsp",
+            "mergeCols1",
             "tp_cut_tool",
-            "pampa_communitymetrics",
-            "regex1"
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -69094,14 +163450,2389 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
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+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
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+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
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+                {
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+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
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+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
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+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
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                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
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+                    "servers": [
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+                            "state": "local"
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+                            "state": "local"
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+                        {
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+                            "state": "local"
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+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
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+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
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+                        {
+                            "server": "https://galaxytrakr.org/",
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+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
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+                            "server": "http://pepsimili.e-nios.com:8080/",
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+                            "state": "exact",
+                            "version": "1.1.0"
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+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.1.0"
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             ]
         },
@@ -69153,7 +165884,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 109,
-        "visitors": 962,
+        "visitors": 966,
         "workflows": [
             {
                 "creators": [],
@@ -69284,7 +166015,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Column Regex Find And Replace\"];\n  0 -->|output| 3;\n  4[\"Column Regex Find And Replace\"];\n  1 -->|output| 4;\n  5[\"Concatenate datasets\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Column Regex Find And Replace\"];\n  2 -->|output| 6;\n  7[\"Merge Columns\"];\n  3 -->|out_file1| 7;\n  8[\"Merge Columns\"];\n  4 -->|out_file1| 8;\n  9[\"Count\"];\n  5 -->|out_file1| 9;\n  10[\"Filter\"];\n  5 -->|out_file1| 10;\n  11[\"Merge Columns\"];\n  6 -->|out_file1| 11;\n  12[\"Regex Find And Replace\"];\n  7 -->|out_file1| 12;\n  13[\"Regex Find And Replace\"];\n  8 -->|out_file1| 13;\n  14[\"Column Regex Find And Replace\"];\n  10 -->|out_file1| 14;\n  15[\"Regex Find And Replace\"];\n  11 -->|out_file1| 15;\n  16[\"Calculate presence absence table\"];\n  12 -->|out_file1| 16;\n  17[\"Calculate presence absence table\"];\n  13 -->|out_file1| 17;\n  18[\"Merge Columns\"];\n  14 -->|out_file1| 18;\n  19[\"Calculate presence absence table\"];\n  15 -->|out_file1| 19;\n  20[\"Regex Find And Replace\"];\n  18 -->|out_file1| 20;\n  21[\"Calculate community metrics\"];\n  20 -->|out_file1| 21;\n  22[\"Column Regex Find And Replace\"];\n  20 -->|out_file1| 22;\n  23[\"Merge Columns\"];\n  22 -->|out_file1| 23;\n  24[\"Column Regex Find And Replace\"];\n  23 -->|out_file1| 24;\n  25[\"Advanced Cut\"];\n  24 -->|out_file1| 25;\n  26[\"Sort\"];\n  25 -->|output| 26;\n  27[\"Regex Find And Replace\"];\n  26 -->|outfile| 27;\n  28[\"Compute GLM on community data\"];\n  21 -->|output_community| 28;\n  27 -->|out_file1| 28;\n  29[\"Compute GLM on population data\"];\n  16 -->|output_presabs| 29;\n  27 -->|out_file1| 29;\n  30[\"Compute GLM on population data\"];\n  17 -->|output_presabs| 30;\n  27 -->|out_file1| 30;\n  31[\"Compute GLM on population data\"];\n  19 -->|output_presabs| 31;\n  27 -->|out_file1| 31;\n  32[\"Transpose\"];\n  28 -->|output_summary| 32;\n  33[\"Create a plot from GLM data\"];\n  21 -->|output_community| 33;\n  28 -->|output_summary| 33;\n  27 -->|out_file1| 33;\n  34[\"Transpose\"];\n  29 -->|output_summary| 34;\n  35[\"Create a plot from GLM data\"];\n  16 -->|output_presabs| 35;\n  29 -->|output_summary| 35;\n  27 -->|out_file1| 35;\n  36[\"Transpose\"];\n  30 -->|output_summary| 36;\n  37[\"Create a plot from GLM data\"];\n  17 -->|output_presabs| 37;\n  30 -->|output_summary| 37;\n  27 -->|out_file1| 37;\n  38[\"Transpose\"];\n  31 -->|output_summary| 38;\n  39[\"Create a plot from GLM data\"];\n  19 -->|output_presabs| 39;\n  31 -->|output_summary| 39;\n  27 -->|out_file1| 39;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Compute and analyze biodiversity metrics with PAMPA toolsuite",
                 "outputs": [],
                 "parent_id": "ecology/PAMPA-toolsuite-tutorial",
@@ -69527,9 +166258,9 @@
         ],
         "short_id": "T00332",
         "short_tools": [
-            "tp_cut_tool",
             "obis_data",
-            "obisindicators"
+            "obisindicators",
+            "tp_cut_tool"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -69544,6 +166275,853 @@
             ],
             "inexact": []
         },
+        "supported_servers_matrix": {
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+                    "url": "http://apostl.moffitt.org/"
+                },
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
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+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
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+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
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+                            "state": "missing"
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+                        {
+                            "server": "https://neo.engr.uconn.edu/",
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+                        {
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+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.0.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.0.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.0.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
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+                    "version": "0.0.2"
+                }
+            ]
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         "symlink": null,
         "tags": [
             "earth-system",
@@ -69625,7 +167203,7 @@
                 "inputs": [],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"OBIS occurences\"];\n  1[\"Advanced Cut\"];\n  0 -->|output| 1;\n  2[\"Ocean biodiversity indicators\"];\n  1 -->|output| 2;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Marine Omics visualisation",
                 "outputs": [],
                 "parent_id": "ecology/obisindicators",
@@ -70543,8 +168121,8 @@
         "edam_operation": [
             "Statistical calculation",
             "Sequencing quality control",
-            "Sequence composition calculation",
-            "Sequence analysis"
+            "Sequence analysis",
+            "Sequence composition calculation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -70557,8 +168135,7 @@
         "hands_on": true,
         "id": "ecology/Obitools-metabarcoding",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr"
+            "UseGalaxy.cz"
         ],
         "js_requirements": {
             "mathjax": null,
@@ -70574,7 +168151,7 @@
             "Deal with paired-end data to create consensus sequences",
             "Clean, filter and anlayse data to obtain strong results"
         ],
-        "pageviews": 4327,
+        "pageviews": 4359,
         "pub_date": "2022-02-28",
         "questions": [
             "how to analyze DNA metabarcoding / eDNA data produced on Illumina sequencers using the OBITools?"
@@ -70595,23 +168172,23 @@
         ],
         "short_id": "T00124",
         "short_tools": [
-            "obi_ngsfilter",
-            "join1",
-            "fastq_groomer",
-            "Filter1",
-            "obi_grep",
-            "obi_illumina_pairend",
-            "unzip",
-            "obi_annotate",
-            "wc_gnu",
             "Cut1",
+            "obi_annotate",
+            "obi_tab",
+            "obi_grep",
+            "obi_uniq",
+            "fastqc",
             "obi_clean",
+            "join1",
             "seq_filter_by_id",
-            "fastqc",
-            "obi_uniq",
-            "obi_tab",
+            "unzip",
+            "wc_gnu",
+            "obi_stat",
             "ncbi_blastn_wrapper",
-            "obi_stat"
+            "obi_illumina_pairend",
+            "obi_ngsfilter",
+            "fastq_groomer",
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -70639,11 +168216,2495 @@
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
+                }
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
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+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
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+                },
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+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
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+                    "name": "CoralSNP",
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+                },
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+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
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+                    "url": "http://dintor.eurac.edu/"
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+                },
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+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
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+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
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+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
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+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
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+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
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+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
                     "usegalaxy": false
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+                    "name": "InteractoMIX",
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+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
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+                            "server": "http://gigagalaxy.net/",
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+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
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+                            "server": "https://neo.engr.uconn.edu/",
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+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
                 }
             ]
         },
@@ -70696,8 +170757,8 @@
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         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 118,
-        "visitors": 3031,
+        "visit_duration": 119,
+        "visitors": 3052,
         "workflows": [
             {
                 "creators": [],
@@ -70762,7 +170823,7 @@
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-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Workflow constructed from history 'Tuto Obitools'",
                 "outputs": [],
                 "parent_id": "ecology/Obitools-metabarcoding",
@@ -71029,8 +171090,7 @@
         "hands_on": true,
         "id": "ecology/biodiversity-data-exploration",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr"
+            "UseGalaxy.cz"
         ],
         "js_requirements": {
             "mathjax": null,
@@ -71046,7 +171106,7 @@
             "Explore Biodiversity data with taxonomic, temporal and geographical informations",
             "Have an idea about quality content of the data regarding statistical tests like normality or homoscedasticity and coverage like temporal or geographical coverage"
         ],
-        "pageviews": 1713,
+        "pageviews": 1716,
         "pub_date": "2022-03-01",
         "questions": [
             "How to explore biodiversity data?",
@@ -71069,15 +171129,15 @@
         ],
         "short_id": "T00126",
         "short_tools": [
+            "ecology_homogeneity_normality",
+            "regexColumn1",
+            "ecology_presence_abs_abund",
             "ecology_beta_diversity",
+            "Remove beginning1",
+            "ecology_link_between_var",
             "ecology_stat_presence_abs",
             "tool_anonymization",
-            "ecology_link_between_var",
-            "ecology_presence_abs_abund",
-            "tp_cut_tool",
-            "ecology_homogeneity_normality",
-            "Remove beginning1",
-            "regexColumn1"
+            "tp_cut_tool"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -71095,11 +171155,1366 @@
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
+                }
+            ]
+        },
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
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+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
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+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
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+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
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+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
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+                    "url": "http://gigagalaxy.net/"
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+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
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+                    "url": "https://www.immportgalaxy.org/"
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+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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@@ -71140,8 +172555,8 @@
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         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 168,
-        "visitors": 1170,
+        "visit_duration": 167,
+        "visitors": 1173,
         "workflows": [
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@@ -71204,7 +172619,7 @@
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-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Workflow 'Biodiversity data exploration tuto'",
                 "outputs": [
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@@ -71814,8 +173229,7 @@
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         "edam_topic": [],
         "exact_supported_servers": [
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-            "UseGalaxy.fr"
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@@ -71839,7 +173253,7 @@
             "Learn how to create rich metadata using Ecological Metadata Language (EML) standard",
             "Learn how to update EML metadata"
         ],
-        "pageviews": 90,
+        "pageviews": 95,
         "pub_date": "2024-03-04",
         "questions": [
             "How to generate detailled metadata easily from biodiversity datasets ?",
@@ -71859,14 +173273,281 @@
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@@ -71901,8 +173582,8 @@
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@@ -72009,10 +173690,10 @@
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@@ -72021,8 +173702,7 @@
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@@ -72051,16 +173731,16 @@
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@@ -72072,33 +173752,736 @@
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+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
                 }
             ]
         },
@@ -72135,8 +174518,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 212,
-        "visitors": 260,
+        "visit_duration": 202,
+        "visitors": 267,
         "workflows": [
             {
                 "creators": [
@@ -72243,7 +174626,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Kraken2\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  a408a644-58cd-4f5e-af25-15b5ea63aa76[\"Output\\nkraken_report_reads\"];\n  2 --> a408a644-58cd-4f5e-af25-15b5ea63aa76;\n  style a408a644-58cd-4f5e-af25-15b5ea63aa76 stroke:#2c3143,stroke-width:4px;\n  54b85a53-72ee-4b73-b186-7fd55e8aab9b[\"Output\\nkraken_report_tabular\"];\n  2 --> 54b85a53-72ee-4b73-b186-7fd55e8aab9b;\n  style 54b85a53-72ee-4b73-b186-7fd55e8aab9b stroke:#2c3143,stroke-width:4px;\n  3[\"Bracken\"];\n  2 -->|report_output| 3;\n  ae6c6464-f5f5-4e5b-b616-d38166fc0133[\"Output\\nbracken_report_tsv\"];\n  3 --> ae6c6464-f5f5-4e5b-b616-d38166fc0133;\n  style ae6c6464-f5f5-4e5b-b616-d38166fc0133 stroke:#2c3143,stroke-width:4px;\n  8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8[\"Output\\nbracken_kraken_report\"];\n  3 --> 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8;\n  style 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8 stroke:#2c3143,stroke-width:4px;\n  4[\"Recentrifuge\"];\n  2 -->|output| 4;\n  b5694f2d-c8cd-4460-bfff-74fd0792ecb3[\"Output\\nrecentrifuge_stats_tabular\"];\n  4 --> b5694f2d-c8cd-4460-bfff-74fd0792ecb3;\n  style b5694f2d-c8cd-4460-bfff-74fd0792ecb3 stroke:#2c3143,stroke-width:4px;\n  bd947a1d-0443-465f-8658-5d76d9ce69f8[\"Output\\nrecentrifuge_report_html\"];\n  4 --> bd947a1d-0443-465f-8658-5d76d9ce69f8;\n  style bd947a1d-0443-465f-8658-5d76d9ce69f8 stroke:#2c3143,stroke-width:4px;\n  c7457acb-41bc-4191-b3fb-6716e15fbe57[\"Output\\nrecentrifuge_data_tabular\"];\n  4 --> c7457acb-41bc-4191-b3fb-6716e15fbe57;\n  style c7457acb-41bc-4191-b3fb-6716e15fbe57 stroke:#2c3143,stroke-width:4px;\n  94f6ff07-0e06-47ad-88f8-a058d0808537[\"Output\\nrecentrifuge_logfile\"];\n  4 --> 94f6ff07-0e06-47ad-88f8-a058d0808537;\n  style 94f6ff07-0e06-47ad-88f8-a058d0808537 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Checking expected species and contamination in bacterial isolate",
                 "outputs": [
                     {
@@ -72623,11 +175006,11 @@
         ],
         "short_id": "T00127",
         "short_tools": [
-            "cb_eco",
             "cb_ivr",
-            "cb_div",
             "cb_dissim",
-            "cb_qecb"
+            "cb_eco",
+            "cb_qecb",
+            "cb_div"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -72636,6 +175019,934 @@
             "exact": [],
             "inexact": []
         },
+        "supported_servers_matrix": {
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
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+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
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+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
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+                    "version": "local"
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+                            "state": "missing"
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+                        {
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+                        {
+                            "server": "https://galaxytrakr.org/",
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+                            "state": "missing"
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+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
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+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
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+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
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+                        {
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+                            "server": "https://galaxy.pasteur.fr/",
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+                        {
+                            "server": "https://galaxytrakr.org/",
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+                        },
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+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
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+                        {
+                            "server": "http://gigagalaxy.net/",
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+                            "server": "https://galaxy.hyphy.org/",
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+                            "server": "https://galaxy-web.ipk-gatersleben.de",
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+                            "server": "https://www.immportgalaxy.org/",
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+                            "server": "https://neo.engr.uconn.edu/",
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+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.0.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.0.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.0.0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "Ecosystem EBV class",
@@ -72928,7 +176239,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nchampbloc_ivr_val.csv\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nchampbloc_ivr.csv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nficheterrain_val.csv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nficheterrain.csv\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nchampbloc_qecb_val.csv\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nchampbloc_qecb.csv\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"IVR\"];\n  3 -->|output| 6;\n  2 -->|output| 6;\n  0 -->|output| 6;\n  1 -->|output| 6;\n  7[\"QECB\"];\n  3 -->|output| 7;\n  2 -->|output| 7;\n  4 -->|output| 7;\n  5 -->|output| 7;\n  8[\"Champs blocs indicators\"];\n  7 -->|output_rds| 8;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Champs blocs indicators",
                 "outputs": [
                     {
@@ -73615,7 +176926,7 @@
             "Learn to use Panoply in Galaxy to visuallize EBV cube netCDF geo-referenced data",
             "Learn how Panoply plots are exported to Galaxy"
         ],
-        "pageviews": 220,
+        "pageviews": 222,
         "pub_date": "2022-10-28",
         "questions": [
             "How to start Panoply interactive environment in Galaxy?",
@@ -73647,6 +176958,278 @@
             ],
             "inexact": []
         },
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
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+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
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+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "interactive_tool_panoply",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
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+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
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+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
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+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
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+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
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+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
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+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "interactive-tools",
@@ -73677,8 +177260,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 103,
-        "visitors": 161
+        "visit_duration": 101,
+        "visitors": 163
     },
     {
         "admin_install": {
@@ -73832,7 +177415,7 @@
             "Deal with QGIS execution management",
             "Access, filter, and import GIS data using WFS webservice"
         ],
-        "pageviews": 166,
+        "pageviews": 167,
         "pub_date": "2023-10-11",
         "questions": [
             "How to use WFS webservice to access and import GIS data through Galaxy"
@@ -73854,6 +177437,278 @@
             ],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
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+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
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+                    "url": "http://gigagalaxy.net/"
+                },
+                {
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+                    "url": "https://galaxy.hyphy.org/",
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+                {
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                    "url": "https://www.immportgalaxy.org/"
+                },
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+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
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+                    "url": "http://galaxy.inf.ethz.ch"
+                },
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+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                },
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+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
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+                    "url": "https://viralvariant.anses.fr/"
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+                    "servers": [
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+                            "state": "missing"
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
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+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
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+                        {
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+                        {
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                }
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         "tags": [
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@@ -73888,8 +177743,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 74,
-        "visitors": 139
+        "visit_duration": 73,
+        "visitors": 140
     },
     {
         "admin_install": {
@@ -74084,22 +177939,21 @@
         ],
         "dir": "topics/epigenetics/tutorials/formation_of_super-structures_on_xi",
         "edam_operation": [
+            "Primer removal",
+            "Sequence composition calculation",
             "Peak calling",
-            "Sequence trimming",
-            "Read mapping",
-            "Sequencing quality control",
-            "Statistical calculation",
             "Gene regulatory network analysis",
-            "Sequence composition calculation",
-            "Mapping",
+            "Sequencing quality control",
+            "Read mapping",
             "Read pre-processing",
-            "Primer removal",
-            "Enrichment analysis"
+            "Sequence trimming",
+            "Enrichment analysis",
+            "Statistical calculation",
+            "Mapping"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
@@ -74133,7 +177987,7 @@
             "Extract coverage files",
             "Call enriched regions or peaks"
         ],
-        "pageviews": 5907301,
+        "pageviews": 5938958,
         "pub_date": "2018-09-17",
         "questions": [
             "Histone modification?",
@@ -74147,22 +178001,22 @@
         ],
         "short_id": "T00140",
         "short_tools": [
+            "cat1",
+            "trim_galore",
             "deeptools_plot_correlation",
+            "deeptools_plot_heatmap",
+            "fastqc",
+            "deeptools_compute_matrix",
             "deeptools_plot_fingerprint",
-            "macs2_callpeak",
-            "deeptools_bam_compare",
-            "Filter1",
             "bedtools_sortbed",
-            "fastqc",
-            "deeptools_plot_heatmap",
+            "deeptools_bam_compare",
             "deeptools_multi_bam_summary",
+            "deeptools_bam_coverage",
+            "bowtie2",
             "samtools_idxstats",
+            "macs2_callpeak",
             "bedtools_mergebed",
-            "bowtie2",
-            "deeptools_bam_coverage",
-            "deeptools_compute_matrix",
-            "cat1",
-            "trim_galore"
+            "Filter1"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -74173,11 +178027,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -74212,6 +178061,2551 @@
                 }
             ]
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+        "supported_servers_matrix": {
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
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+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
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+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
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+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
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+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
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+                },
+                {
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+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
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+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
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+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
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+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
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+                        {
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+                            "state": "local"
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "GTN - ChIP Seq - Formation Of Super Structures On Xi",
                 "outputs": [
                     {
@@ -75315,20 +181709,20 @@
         "dir": "topics/epigenetics/tutorials/atac-seq",
         "edam_operation": [
             "Data handling",
+            "Sequence alignment analysis",
+            "Primer removal",
+            "Formatting",
+            "Sequence composition calculation",
             "Peak calling",
+            "Gene regulatory network analysis",
+            "Sequencing quality control",
             "Visualisation",
-            "Sequence trimming",
             "Read mapping",
-            "Sequencing quality control",
-            "Sequence composition calculation",
-            "Sequence alignment analysis",
-            "Statistical calculation",
-            "Gene regulatory network analysis",
-            "Mapping",
             "Read pre-processing",
-            "Primer removal",
+            "Sequence trimming",
             "Enrichment analysis",
-            "Formatting"
+            "Statistical calculation",
+            "Mapping"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -75358,7 +181752,7 @@
             "Generate a heatmap of transcription start site accessibility",
             "Visualise peaks for specific regions"
         ],
-        "pageviews": 5998000,
+        "pageviews": 6029850,
         "pub_date": "2019-09-02",
         "questions": [
             "Which DNA regions are accessible in the human lymphoblastoid cell line GM12878?",
@@ -75380,24 +181774,24 @@
         ],
         "short_id": "T00137",
         "short_tools": [
-            "picard_MarkDuplicates",
+            "Cut1",
+            "bamFilter",
             "pygenomeTracks",
-            "Filter1",
-            "tp_sort_header_tool",
+            "bedtools_intersectbed",
+            "wig_to_bigWig",
             "cutadapt",
             "deeptools_plot_heatmap",
-            "bamFilter",
-            "samtools_idxstats",
-            "bedtools_intersectbed",
+            "fastqc",
+            "tp_sort_header_tool",
+            "deeptools_compute_matrix",
+            "pe_histogram",
             "Grep1",
-            "Cut1",
+            "picard_MarkDuplicates",
+            "bowtie2",
             "bedtools_bamtobed",
-            "pe_histogram",
+            "samtools_idxstats",
             "macs2_callpeak",
-            "fastqc",
-            "wig_to_bigWig",
-            "deeptools_compute_matrix",
-            "bowtie2"
+            "Filter1"
         ],
         "slides": true,
         "slides_recordings": [
@@ -75430,6 +181824,2765 @@
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             ]
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+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
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+                            "server": "https://vm-chemflow-francegrille.eu/",
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+                            "state": "local"
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+                            "state": "local"
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+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
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+                        {
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+                            "state": "local"
+                        },
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+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "3h",
         "title": "ATAC-Seq data analysis",
@@ -75473,7 +184626,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 264,
-        "visitors": 2186389,
+        "visitors": 2196989,
         "workflows": [
             {
                 "creators": [],
@@ -75759,7 +184912,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nbed file with genes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nctcf peaks\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nATAC R2 read in fastq.gz format\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nATAC R1 read in fastq.gz format\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Filter\"];\n  1 -->|output| 4;\n  5[\"FastQC\"];\n  2 -->|output| 5;\n  6[\"ATAC remove nextera adapters with cutadapt\"];\n  3 -->|output| 6;\n  2 -->|output| 6;\n  7[\"FastQC\"];\n  3 -->|output| 7;\n  8[\"bedtools Intersect intervals\"];\n  4 -->|out_file1| 8;\n  0 -->|output| 8;\n  9[\"FastQC\"];\n  6 -->|out2| 9;\n  10[\"Bowtie2\"];\n  6 -->|out1| 10;\n  6 -->|out2| 10;\n  11[\"FastQC\"];\n  6 -->|out1| 11;\n  12[\"Filter BAM ATAC\"];\n  10 -->|output| 12;\n  13[\"MarkDuplicates\"];\n  12 -->|out_file1| 13;\n  14[\"bedtools BAM to BED\"];\n  13 -->|outFile| 14;\n  15[\"Paired-end histogram\"];\n  13 -->|outFile| 15;\n  16[\"MACS2 callpeak\"];\n  14 -->|output| 16;\n  17[\"Wig/BedGraph-to-bigWig\"];\n  16 -->|output_treat_pileup| 17;\n  18[\"computeMatrix\"];\n  17 -->|out_file1| 18;\n  0 -->|output| 18;\n  19[\"pyGenomeTracks\"];\n  17 -->|out_file1| 19;\n  16 -->|output_narrowpeaks| 19;\n  0 -->|output| 19;\n  1 -->|output| 19;\n  20[\"computeMatrix\"];\n  17 -->|out_file1| 20;\n  8 -->|output| 20;\n  65159c9c-050b-4069-8704-8f66c0563a98[\"Output\\ncomputeMatrix on input dataset(s): Matrix\"];\n  20 --> 65159c9c-050b-4069-8704-8f66c0563a98;\n  style 65159c9c-050b-4069-8704-8f66c0563a98 stroke:#2c3143,stroke-width:4px;\n  21[\"plotHeatmap\"];\n  18 -->|outFileName| 21;\n  22[\"plotHeatmap\"];\n  20 -->|outFileName| 22;\n  74a36643-b88f-4378-8f9c-c1b20ee2651e[\"Output\\nplotHeatmap on input dataset(s): Image\"];\n  22 --> 74a36643-b88f-4378-8f9c-c1b20ee2651e;\n  style 74a36643-b88f-4378-8f9c-c1b20ee2651e stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "ATAC-seq GTM",
                 "outputs": [
                     {
@@ -77260,24 +186413,23 @@
             "topic_3169"
         ],
         "edam_operation": [
-            "Peak calling",
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
-            "Sequence composition calculation",
             "Genome indexing",
+            "Sequence composition calculation",
             "Generation",
-            "Statistical calculation",
+            "Peak calling",
             "Gene regulatory network analysis",
-            "Mapping",
-            "Enrichment analysis"
+            "Sequencing quality control",
+            "Read mapping",
+            "Enrichment analysis",
+            "Sequence alignment",
+            "Statistical calculation",
+            "Mapping"
         ],
         "edam_topic": [
             "ChIP-seq"
         ],
         "exact_supported_servers": [
             "UseGalaxy.be",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
@@ -77314,7 +186466,7 @@
             "Identify unique/common TAL1 peaks occupying gene promoters",
             "Visually inspect TAL1 peaks with Trackster"
         ],
-        "pageviews": 11314,
+        "pageviews": 11344,
         "pub_date": "2016-12-20",
         "questions": [
             "How is raw ChIP-seq data processed and analyzed?",
@@ -77335,20 +186487,20 @@
         ],
         "short_id": "T00143",
         "short_tools": [
+            "bwa",
             "deeptools_plot_correlation",
+            "bedtools_intersectbed",
+            "trimmomatic",
+            "deeptools_plot_heatmap",
+            "fastqc",
+            "deeptools_compute_matrix",
+            "deeptools_compute_gc_bias",
             "deeptools_plot_fingerprint",
             "deeptools_bam_compare",
-            "deeptools_compute_gc_bias",
-            "deeptools_plot_heatmap",
             "deeptools_correct_gc_bias",
             "deeptools_multi_bam_summary",
             "samtools_idxstats",
-            "bedtools_intersectbed",
-            "bwa",
-            "macs2_callpeak",
-            "fastqc",
-            "trimmomatic",
-            "deeptools_compute_matrix"
+            "macs2_callpeak"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -77359,11 +186511,6 @@
                     "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -77403,6 +186550,2268 @@
                 }
             ]
         },
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+                    "url": "http://apostl.moffitt.org/"
+                },
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+                },
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+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
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+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
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+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
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+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
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+                    "name": "Galaxy@AuBi",
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+                },
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+                    "usegalaxy": true
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                 "history": [
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                         "hash": "818f002190ef7fb261a841024556075ceff1df49",
@@ -77731,8 +189140,8 @@
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+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)",
                 "outputs": [
                     {
@@ -77779,7 +189188,7 @@
                             {
                                 "label": "output_overlapping_peaks",
                                 "output_name": "output",
-                                "uuid": "0b9a3e20-a9d6-4464-85f0-012664b895ff"
+                                "uuid": "a218190b-c2f9-4ab5-b763-27d911f4200b"
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@@ -77827,7 +189236,7 @@
                             {
                                 "label": "output_g1e_peaks",
                                 "output_name": "output",
-                                "uuid": "609ee90a-2c9e-4bde-82d6-5f59516c3bad"
+                                "uuid": "de848c17-5a1e-4076-bb37-2482bbb4f8a7"
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                         ]
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@@ -77875,7 +189284,7 @@
                             {
                                 "label": "output_megakaryocyte_peaks",
                                 "output_name": "output",
-                                "uuid": "0bb490b2-77e5-4b59-82eb-6a2b918c2788"
+                                "uuid": "70f39bcc-a61e-4600-894b-cd53ecab6436"
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@@ -78016,8 +189425,8 @@
             "topic_3173"
         ],
         "edam_operation": [
-            "Sequencing quality control",
             "Statistical calculation",
+            "Sequencing quality control",
             "Sequence composition calculation"
         ],
         "edam_topic": [
@@ -78054,7 +189463,7 @@
             "Learn how to analyse methylation data",
             "Get a first intuition what are common pitfalls."
         ],
-        "pageviews": 20136,
+        "pageviews": 20190,
         "pub_date": "2017-02-16",
         "questions": [
             "What is methylation and why it cannot be recognised by a normal NGS procedure?",
@@ -78063,15 +189472,15 @@
         ],
         "short_id": "T00142",
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-            "pileometh",
+            "metilene",
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             "bwameth",
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+            "pileometh",
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+            "tp_tail_tool",
+            "tp_awk_tool",
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         "slides": false,
         "slides_recordings": false,
@@ -78116,6 +189525,1513 @@
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+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "0.2.6.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.2.6.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.2.6.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "0.2.6.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.2.6.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.2.6.1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.2.6.1"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "3h",
         "title": "DNA Methylation data analysis",
@@ -78149,8 +191065,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 126,
-        "visitors": 11375,
+        "visit_duration": 127,
+        "visitors": 11413,
         "workflows": [
             {
                 "creators": [],
@@ -78161,7 +191077,7 @@
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-                "modified": "2024-10-02 12:08:08 +0000",
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+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Workflow Methylation Seq",
                 "outputs": [
                     {
@@ -78481,7 +191397,7 @@
                             {
                                 "label": "plot_profile_tabular",
                                 "output_name": "output_outFileNameData",
-                                "uuid": "2259f2ac-1538-44ce-8c84-e6de532838fc"
+                                "uuid": "2dfba29e-86a4-4d50-9d8d-bd90b0fc8914"
                             }
                         ]
                     }
@@ -78626,7 +191542,7 @@
             "Learn how to perform reproducible Infinium Human Methylation BeadChip analysis",
             "Visualise differentially methylated positions using UCSC browser"
         ],
-        "pageviews": 5900005,
+        "pageviews": 5931630,
         "pub_date": "2018-08-27",
         "questions": [
             "Which DNA regions and positions are diffrentialy methylated in pre MAPKi treatment and post MAPKi resistance Melanomas GSE65183?",
@@ -78634,12 +191550,12 @@
         ],
         "short_id": "T00139",
         "short_tools": [
-            "chipeakanno_annopeaks",
+            "Cut1",
             "clusterprofiler_go",
+            "chipeakanno_annopeaks",
+            "Remove beginning1",
             "clusterprofiler_bitr",
-            "Cut1",
-            "minfi_analysis",
-            "Remove beginning1"
+            "minfi_analysis"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -78663,6 +191579,940 @@
             ],
             "inexact": []
         },
+        "supported_servers_matrix": {
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
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+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
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+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
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+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
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+                    "usegalaxy": true
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+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
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+                    "servers": [
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+                            "state": "local"
+                        },
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+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
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+                        },
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+                            "state": "local"
+                        },
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+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
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+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
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+                        },
+                        {
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+                            "state": "local"
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+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
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+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
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+                            "server": "https://usegalaxy.no/",
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                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nR01C02_Red.idat\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nR02C02_Red.idat\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nR05C02_Red.idat\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nR06C02_Red.idat\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nR01C02_Green.idat\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nR02C02_Green.idat\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nR05C02_Green.idat\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nR06C02_Green.idat\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nphenotype Table txt file\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\nUCSC Main on Human\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"Infinium Human Methylation BeadChip\"];\n  4 -->|output| 10;\n  5 -->|output| 10;\n  6 -->|output| 10;\n  7 -->|output| 10;\n  0 -->|output| 10;\n  1 -->|output| 10;\n  2 -->|output| 10;\n  3 -->|output| 10;\n  8 -->|output| 10;\n  9 -->|output| 10;\n  2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a[\"Output\\nSNPInfo Table\"];\n  10 --> 2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a;\n  style 2ac7dd5d-ed74-4d58-b1cb-be7dcca9154a stroke:#2c3143,stroke-width:4px;\n  d1732a98-1861-4612-bdaa-f68861c22f56[\"Output\\nDifferentially Methylated Regions\"];\n  10 --> d1732a98-1861-4612-bdaa-f68861c22f56;\n  style d1732a98-1861-4612-bdaa-f68861c22f56 stroke:#2c3143,stroke-width:4px;\n  9aa8b4a9-611e-4a39-864f-400f17866a9e[\"Output\\nDifferentially Methylated Positions\"];\n  10 --> 9aa8b4a9-611e-4a39-864f-400f17866a9e;\n  style 9aa8b4a9-611e-4a39-864f-400f17866a9e stroke:#2c3143,stroke-width:4px;\n  14ddb6f7-637e-4193-bfb5-80aeae4fab64[\"Output\\nQuality Control Report\"];\n  10 --> 14ddb6f7-637e-4193-bfb5-80aeae4fab64;\n  style 14ddb6f7-637e-4193-bfb5-80aeae4fab64 stroke:#2c3143,stroke-width:4px;\n  c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d[\"Output\\nQuality Control Plot\"];\n  10 --> c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d;\n  style c8c37ff8-716d-4c23-a84f-7cebcb4b6c9d stroke:#2c3143,stroke-width:4px;\n  11[\"ChIPpeakAnno annoPeaks\"];\n  10 -->|dmp| 11;\n  bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5[\"Output\\nTable of Annotated Peaks\"];\n  11 --> bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5;\n  style bedf4346-da4d-4e1a-bf3c-a7d20f3ec3c5 stroke:#2c3143,stroke-width:4px;\n  12[\"Cut\"];\n  11 -->|tab| 12;\n  0b54dfe5-f84a-4288-b631-ae4dc2384a17[\"Output\\nCut on Table of Annotated Peaks\"];\n  12 --> 0b54dfe5-f84a-4288-b631-ae4dc2384a17;\n  style 0b54dfe5-f84a-4288-b631-ae4dc2384a17 stroke:#2c3143,stroke-width:4px;\n  13[\"Remove beginning\"];\n  12 -->|out_file1| 13;\n  8f65cf82-7427-4273-ba0b-a6673ee1ff2d[\"Output\\nRemove beginning on the cut output\"];\n  13 --> 8f65cf82-7427-4273-ba0b-a6673ee1ff2d;\n  style 8f65cf82-7427-4273-ba0b-a6673ee1ff2d stroke:#2c3143,stroke-width:4px;\n  14[\"Cluster Profiler Bitr\"];\n  13 -->|out_file1| 14;\n  7989f80a-3e79-4d2f-bbe4-e4d641eebd6a[\"Output\\nTable of Translated Gene ID's\"];\n  14 --> 7989f80a-3e79-4d2f-bbe4-e4d641eebd6a;\n  style 7989f80a-3e79-4d2f-bbe4-e4d641eebd6a stroke:#2c3143,stroke-width:4px;\n  15[\"Cluster Profiler GO\"];\n  14 -->|translation| 15;\n  ff6c7018-b821-4ade-9931-fa99aeb0a86c[\"Output\\nGO Enrichment Analysis of a Gene Set\"];\n  15 --> ff6c7018-b821-4ade-9931-fa99aeb0a86c;\n  style ff6c7018-b821-4ade-9931-fa99aeb0a86c stroke:#2c3143,stroke-width:4px;\n  03b88399-095b-4bd5-9693-528c60338407[\"Output\\nGO Enrichment Analysis Visualization\"];\n  15 --> 03b88399-095b-4bd5-9693-528c60338407;\n  style 03b88399-095b-4bd5-9693-528c60338407 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Infinium Human Methylation BeadChip",
                 "outputs": [
                     {
@@ -79586,10 +193436,10 @@
         ],
         "dir": "topics/epigenetics/tutorials/hicexplorer",
         "edam_operation": [
-            "Generation",
             "Sequence alignment",
             "Genome indexing",
-            "Read mapping"
+            "Read mapping",
+            "Generation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -79610,7 +193460,7 @@
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-09",
-        "pageviews": 10656,
+        "pageviews": 10681,
         "pub_date": "2018-02-23",
         "questions": [
             "Why is a Hi-C analysis useful?",
@@ -79619,14 +193469,14 @@
         ],
         "short_id": "T00141",
         "short_tools": [
+            "hicexplorer_hicbuildmatrix",
             "bwa_mem",
             "hicexplorer_hicmergematrixbins",
-            "hicexplorer_hicpca",
-            "hicexplorer_hicfindtads",
             "hicexplorer_hicplotmatrix",
-            "hicexplorer_hicplottads",
-            "hicexplorer_hicbuildmatrix",
-            "hicexplorer_hiccorrectmatrix"
+            "hicexplorer_hicfindtads",
+            "hicexplorer_hiccorrectmatrix",
+            "hicexplorer_hicpca",
+            "hicexplorer_hicplottads"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -79634,6 +193484,1346 @@
             "exact": [],
             "inexact": []
         },
+        "supported_servers_matrix": {
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+                },
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+                },
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+                    "name": "ChemFlow",
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+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.8.0"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "1h",
         "title": "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer",
@@ -79667,7 +194857,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 95,
-        "visitors": 5935,
+        "visitors": 5955,
         "workflows": [
             {
                 "creators": [],
@@ -79897,7 +195087,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nR1.fastq\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nR2.fastq\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nH3K27me3.bw\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nH3K36me3.bw\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nH4K16ac.bw\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\ndm3_genes.bed\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"Map with BWA-MEM\"];\n  0 -->|output| 6;\n  7[\"Map with BWA-MEM\"];\n  1 -->|output| 7;\n  8[\"hicBuildMatrix\"];\n  7 -->|output| 8;\n  6 -->|output| 8;\n  9[\"hicMergeMatrixBins\"];\n  8 -->|outFileName| 9;\n  10[\"hicCorrectMatrix\"];\n  8 -->|outFileName| 10;\n  11[\"hicCorrectMatrix\"];\n  8 -->|outFileName| 11;\n  12[\"hicPlotMatrix\"];\n  9 -->|outFileName| 12;\n  13[\"hicPlotMatrix\"];\n  11 -->|outFileName| 13;\n  14[\"hicFindTADs\"];\n  11 -->|outFileName| 14;\n  15[\"hicPCA\"];\n  14 -->|matrix_output| 15;\n  16[\"hicPlotTADs\"];\n  14 -->|domains| 16;\n  11 -->|outFileName| 16;\n  14 -->|tad_score| 16;\n  15 -->|pca1| 16;\n  15 -->|pca2| 16;\n  3 -->|output| 16;\n  2 -->|output| 16;\n  4 -->|output| 16;\n  5 -->|output| 16;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Galaxy Workflow Galaxy Hi C",
                 "outputs": [],
                 "parent_id": "epigenetics/hicexplorer",
@@ -80178,20 +195368,20 @@
         "draft": true,
         "edam_operation": [
             "Data handling",
+            "Sequence alignment analysis",
+            "Primer removal",
+            "Formatting",
+            "Sequence composition calculation",
             "Peak calling",
+            "Gene regulatory network analysis",
+            "Sequencing quality control",
             "Visualisation",
-            "Sequence trimming",
             "Read mapping",
-            "Sequencing quality control",
-            "Sequence composition calculation",
-            "Sequence alignment analysis",
-            "Statistical calculation",
             "Read pre-processing",
-            "Gene regulatory network analysis",
-            "Mapping",
-            "Formatting",
-            "Primer removal",
-            "Enrichment analysis"
+            "Sequence trimming",
+            "Enrichment analysis",
+            "Statistical calculation",
+            "Mapping"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -80218,7 +195408,7 @@
             "Apply an enrichment analysis and a robust peak detection",
             "Find protein binding motifs"
         ],
-        "pageviews": 2162,
+        "pageviews": 2207,
         "pub_date": "2024-03-06",
         "questions": [
             "Which binding motif has the transcription factor GATA1?",
@@ -80227,27 +195417,27 @@
         ],
         "short_id": "T00424",
         "short_tools": [
-            "picard_MarkDuplicates",
-            "pygenomeTracks",
-            "deeptools_plot_heatmap",
-            "bamFilter",
+            "__EXTRACT_DATASET__",
+            "trim_galore",
             "bedtools_intersectbed",
-            "macs2_callpeak",
-            "wig_to_bigWig",
-            "meme_chip",
-            "Extract genomic DNA 1",
-            "pe_histogram",
-            "fastqc",
+            "cutadapt",
             "deeptools_compute_matrix",
-            "bowtie2",
             "idr",
-            "__EXTRACT_DATASET__",
+            "meme_chip",
+            "bedtools_bamtobed",
             "Filter1",
-            "cutadapt",
+            "bamFilter",
+            "wig_to_bigWig",
+            "deeptools_plot_heatmap",
             "Grep1",
-            "bedtools_bamtobed",
+            "picard_MarkDuplicates",
+            "macs2_callpeak",
+            "pygenomeTracks",
             "__FLATTEN__",
-            "trim_galore"
+            "Extract genomic DNA 1",
+            "fastqc",
+            "pe_histogram",
+            "bowtie2"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -80255,6 +195445,4236 @@
             "exact": [],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
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+                    "usegalaxy": false
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+                },
+                {
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+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
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+                    "servers": [
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+                        },
+                        {
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+                        {
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+                            "server": "https://galaxytrakr.org/",
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
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+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
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+                        {
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+                        {
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+                        {
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+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
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+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "trim_galore/cd7e644cae1d"
+                },
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+                    "id": "Filter1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
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+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
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+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
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+                        {
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+                            "state": "local"
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+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
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+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
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+                    "id": "Grep1",
+                    "servers": [
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+                            "state": "local"
+                        },
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+                            "state": "local"
+                        },
+                        {
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+                        {
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+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
+                        },
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
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+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "missing"
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+                        {
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+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
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+                        {
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+                            "state": "missing"
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+                            "state": "local"
+                        },
+                        {
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+                        },
+                        {
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+                        {
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+                        {
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@@ -80310,8 +199730,8 @@
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-        "visitors": 1659,
+        "visit_duration": 85,
+        "visitors": 1700,
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@@ -80464,7 +199884,7 @@
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-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "ATAC-seq GTM",
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@@ -81973,16 +201393,16 @@
         "dir": "topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification",
         "draft": true,
         "edam_operation": [
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-            "Sequence trimming",
-            "Read mapping",
-            "Sequencing quality control",
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-            "Statistical calculation",
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             "Gene regulatory network analysis",
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-            "Primer removal",
-            "Enrichment analysis"
+            "Sequence trimming",
+            "Enrichment analysis",
+            "Statistical calculation"
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@@ -81995,7 +201415,6 @@
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@@ -82019,7 +201438,7 @@
             "Extract coverage files",
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         ],
-        "pageviews": 2415,
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         "questions": [
             "How is raw ChIP-seq data processed and analyzed?",
@@ -82032,20 +201451,20 @@
         ],
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-            "bam_to_sam",
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-            "macs2_callpeak",
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-            "deeptools_compute_matrix",
             "bowtie2",
-            "trim_galore"
+            "samtools_idxstats",
+            "macs2_callpeak"
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@@ -82069,10 +201488,141 @@
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@@ -82087,6 +201637,2244 @@
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-                "modified": "2024-10-02 12:08:07 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Identification Of The Binding Sites Of The Estrogen Receptor - Qc Mapping",
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@@ -82904,14 +204693,14 @@
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-            "Phylogenetic tree generation",
             "Multiple sequence alignment",
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             "Phylogenetic tree generation (from molecular sequences)",
-            "Phylogenetic tree reconstruction",
-            "Sequence analysis",
-            "Phylogenetic tree generation (maximum likelihood and Bayesian methods)"
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@@ -82946,7 +204735,7 @@
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             "Explore phylogenetic signal using phylogenetic networks"
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         "questions": [
@@ -82957,10 +204746,10 @@
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+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "7.489+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "7.520+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "7.221.3",
+                                "7.487+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "7.508+galaxy0",
+                                "7.489+galaxy0",
+                                "7.487+galaxy0",
+                                "7.505+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "7.508+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "7.221.3",
+                                "7.489+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "7.508+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "7.508+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "7.508+galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "phylogenetics",
@@ -83039,7 +205552,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 128,
-        "visitors": 1020,
+        "visitors": 1054,
         "workflows": [
             {
                 "creators": [
@@ -83116,7 +205629,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput FASTA Sequence File\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"MAFFT\"];\n  0 -->|output| 1;\n  e5d56101-daff-420b-82e9-dc6cc923f7ab[\"Output\\noutputAlignment\"];\n  1 --> e5d56101-daff-420b-82e9-dc6cc923f7ab;\n  style e5d56101-daff-420b-82e9-dc6cc923f7ab stroke:#2c3143,stroke-width:4px;\n  2[\"FASTTREE\"];\n  1 -->|outputAlignment| 2;\n  632ce28d-3086-490e-bd97-949eb2cb385a[\"Output\\noutput\"];\n  2 --> 632ce28d-3086-490e-bd97-949eb2cb385a;\n  style 632ce28d-3086-490e-bd97-949eb2cb385a stroke:#2c3143,stroke-width:4px;\n  3[\"IQ-TREE\"];\n  1 -->|outputAlignment| 3;\n  b8434b2b-2001-4b1a-bd06-faeab18519a4[\"Output\\ntreefile\"];\n  3 --> b8434b2b-2001-4b1a-bd06-faeab18519a4;\n  style b8434b2b-2001-4b1a-bd06-faeab18519a4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Tree Building (imported from uploaded file)",
                 "outputs": [
                     {
@@ -83415,7 +205928,6 @@
         "hands_on": true,
         "id": "evolution/mtb_phylogeny",
         "inexact_supported_servers": [
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
         ],
         "js_requirements": {
@@ -83430,7 +205942,7 @@
             "Understand the basic concepts behind phylogenetic trees, as applied to *Mycobacterium tuberculosis*",
             "Be able to read and interrogate a phylogeny encountered in the literature"
         ],
-        "pageviews": 2071,
+        "pageviews": 2078,
         "pub_date": "2022-03-16",
         "questions": [
             "What information can I get from a phylogenetic tree?",
@@ -83454,8 +205966,8 @@
         ],
         "short_id": "T00144",
         "short_tools": [
-            "upload1",
             "interactive_tool_rstudio",
+            "upload1",
             "raxml"
         ],
         "slides": false,
@@ -83470,14 +205982,693 @@
             ],
             "inexact": [
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "id": "interactive_tool_rstudio",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
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+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
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+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
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+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
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+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
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+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
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+                        {
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+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
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+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/raxml/raxml/8.2.12+galaxy0",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
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+                        },
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+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
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+                        {
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+                        },
+                        {
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+                        },
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+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
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+                        },
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+                        {
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+                        },
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+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "8.2.4+galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "8.2.12+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "8.2.12+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "8.2.4+galaxy2",
+                                "8.2.4+galaxy3"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "8.2.12+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "8.2.12+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
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+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
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+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
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+                            "state": "exact",
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+                        },
+                        {
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+                        {
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+                            "state": "missing"
+                        },
+                        {
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+                        {
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+                            "version": "8.2.4+galaxy2"
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+                        {
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+                            "state": "exact",
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+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
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+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "8.2.4+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "inexact",
+                            "versions": [
+                                "8.2.12+galaxy0",
+                                "8.2.12+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "8.2.4+galaxy2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
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+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
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+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
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+                    "version": "local"
                 }
             ]
         },
@@ -83515,8 +206706,8 @@
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         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 134,
-        "visitors": 1373,
+        "visit_duration": 135,
+        "visitors": 1378,
         "workflows": [
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                 "creators": [],
@@ -83587,7 +206778,7 @@
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Mtb phylogeny",
                 "outputs": [
                     {
@@ -83922,9 +207113,9 @@
             "topic_2885"
         ],
         "edam_operation": [
-            "Phylogenetic tree visualisation",
             "Variant calling",
             "Antimicrobial resistance prediction",
+            "Phylogenetic tree visualisation",
             "Phylogenetic tree generation"
         ],
         "edam_topic": [
@@ -83965,7 +207156,7 @@
             "Identify transmission clusters based on SNP distances",
             "Study the emergence and spread of drug resistance based on transmission analysis."
         ],
-        "pageviews": 2499,
+        "pageviews": 2504,
         "pub_date": "2022-03-16",
         "requirements": [
             {
@@ -83985,24 +207176,24 @@
         ],
         "short_id": "T00145",
         "short_tools": [
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+            "tp_replace_in_line",
             "tp_sed_tool",
-            "tp_easyjoin_tool",
-            "tp_cat",
             "bcftools_consensus",
-            "samtools_view",
-            "upload1",
             "snippy",
+            "snp_sites",
+            "collapse_dataset",
+            "trimmomatic",
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+            "tp_easyjoin_tool",
             "tp_grep_tool",
-            "tp_replace_in_line",
-            "snp_dists",
             "Grep1",
             "tb_variant_filter",
+            "addName",
             "tb_profiler_profile",
-            "collapse_dataset",
-            "snp_sites",
-            "trimmomatic",
+            "upload1",
             "__MERGE_COLLECTION__",
-            "addName"
+            "snp_dists"
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         "slides": false,
         "slides_recordings": false,
@@ -84032,6 +207223,3430 @@
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+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "1.8+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.1.0"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.3.5+galaxy0",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "2.2.1+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.2.1+galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "3.4.0+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.2.1+galaxy1",
+                                "2.2.1+galaxy2",
+                                "2.2.1+galaxy0",
+                                "2.2.1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "3.4.0+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "3.3.5+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "3.3.5+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "3.3.5+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "3.3.5+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "3.3.5+galaxy0"
+                },
+                {
+                    "id": "upload1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "workflows"
@@ -92217,8 +221261,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 180,
-        "visitors": 621,
+        "visit_duration": 179,
+        "visitors": 623,
         "workflows": [
             {
                 "creators": [],
@@ -92289,7 +221333,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIris Dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Convert CSV to tabular\"];\n  0 -->|output| 1;\n  2[\"Datamash\"];\n  1 -->|tabular| 2;\n  5fc8c705-b9e2-4008-aa85-e84504b8395f[\"Output\\ndatamash_output\"];\n  2 --> 5fc8c705-b9e2-4008-aa85-e84504b8395f;\n  style 5fc8c705-b9e2-4008-aa85-e84504b8395f stroke:#2c3143,stroke-width:4px;\n  3[\"Remove beginning\"];\n  1 -->|tabular| 3;\n  4[\"Cut\"];\n  3 -->|out_file1| 4;\n  5[\"Group\"];\n  3 -->|out_file1| 5;\n  7e07839c-e8ca-4692-8b8e-6eb3607066de[\"Output\\ngroup1\"];\n  5 --> 7e07839c-e8ca-4692-8b8e-6eb3607066de;\n  style 7e07839c-e8ca-4692-8b8e-6eb3607066de stroke:#2c3143,stroke-width:4px;\n  6[\"Group\"];\n  3 -->|out_file1| 6;\n  9cb98227-aa5b-4b77-933c-ffba1e98566e[\"Output\\ngroup2\"];\n  6 --> 9cb98227-aa5b-4b77-933c-ffba1e98566e;\n  style 9cb98227-aa5b-4b77-933c-ffba1e98566e stroke:#2c3143,stroke-width:4px;\n  7[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 7;\n  8[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 8;\n  9[\"Unique\"];\n  4 -->|out_file1| 9;\n  fc73409c-7878-4391-bc91-f99a5be0ba06[\"Output\\nunique_output\"];\n  9 --> fc73409c-7878-4391-bc91-f99a5be0ba06;\n  style fc73409c-7878-4391-bc91-f99a5be0ba06 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GTN Training: Workflow Reports - Galaxy 101 For Everyone",
                 "outputs": [
                     {
@@ -92696,7 +221740,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIris Dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Convert CSV to tabular\"];\n  0 -->|output| 1;\n  2[\"Datamash\"];\n  1 -->|tabular| 2;\n  5381f9b0-5170-484c-828e-4469ec27ab3e[\"Output\\ndatamash_output\"];\n  2 --> 5381f9b0-5170-484c-828e-4469ec27ab3e;\n  style 5381f9b0-5170-484c-828e-4469ec27ab3e stroke:#2c3143,stroke-width:4px;\n  3[\"Remove beginning\"];\n  1 -->|tabular| 3;\n  4[\"Cut\"];\n  3 -->|out_file1| 4;\n  5[\"Group\"];\n  3 -->|out_file1| 5;\n  836a57b3-3657-435b-b396-869af7e2f35e[\"Output\\ngroup1\"];\n  5 --> 836a57b3-3657-435b-b396-869af7e2f35e;\n  style 836a57b3-3657-435b-b396-869af7e2f35e stroke:#2c3143,stroke-width:4px;\n  6[\"Group\"];\n  3 -->|out_file1| 6;\n  82e163a4-8fc5-4b8e-8186-9fc66cd75b1d[\"Output\\ngroup2\"];\n  6 --> 82e163a4-8fc5-4b8e-8186-9fc66cd75b1d;\n  style 82e163a4-8fc5-4b8e-8186-9fc66cd75b1d stroke:#2c3143,stroke-width:4px;\n  7[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 7;\n  bbbac6ca-64fb-46ad-8798-6c7c5369ccaf[\"Output\\nSepal Plot (PNG)\"];\n  7 --> bbbac6ca-64fb-46ad-8798-6c7c5369ccaf;\n  style bbbac6ca-64fb-46ad-8798-6c7c5369ccaf stroke:#2c3143,stroke-width:4px;\n  8[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 8;\n  74ee0c3c-53c2-44cf-b0e8-2a10c24166c9[\"Output\\nPetal Plot (PNG)\"];\n  8 --> 74ee0c3c-53c2-44cf-b0e8-2a10c24166c9;\n  style 74ee0c3c-53c2-44cf-b0e8-2a10c24166c9 stroke:#2c3143,stroke-width:4px;\n  9[\"Unique\"];\n  4 -->|out_file1| 9;\n  6bcc2f96-255e-48f5-a37b-7d6a2c123493[\"Output\\nIris Species\"];\n  9 --> 6bcc2f96-255e-48f5-a37b-7d6a2c123493;\n  style 6bcc2f96-255e-48f5-a37b-7d6a2c123493 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GTN Training: Workflow Reports",
                 "outputs": [
                     {
@@ -93046,13 +222090,13 @@
                 {
                     "name": "intermine_galaxy_exchange",
                     "owner": "iuc",
-                    "revisions": "c24014d80001",
+                    "revisions": "faef2b1622a3",
                     "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: intermine_galaxy_exchange\n  owner: iuc\n  revisions: c24014d80001\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: intermine_galaxy_exchange\n  owner: iuc\n  revisions: faef2b1622a3\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
         "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/intermine/tutorial.json",
         "contributions": {
             "authorship": [
@@ -93111,8 +222155,8 @@
         ],
         "short_id": "T00152",
         "short_tools": [
-            "intermine",
-            "galaxy_intermine_exchange"
+            "galaxy_intermine_exchange",
+            "intermine"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -93152,6 +222196,414 @@
             ],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "intermine",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
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+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
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+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
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+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
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+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
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+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
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+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/intermine_galaxy_exchange/galaxy_intermine_exchange/0.0.1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.0.1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "gmod",
@@ -93242,7 +222694,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Create InterMine Interchange\"];\n  0 -->|output| 1;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Intermine import/export",
                 "outputs": [
                     {
@@ -93381,7 +222833,6 @@
             "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
@@ -93408,7 +222859,7 @@
             "Understand key aspects of workflows",
             "Create clean, non-repetitive workflows"
         ],
-        "pageviews": 5838,
+        "pageviews": 5867,
         "pub_date": "2020-07-17",
         "questions": [
             "How can you construct Galaxy workflows from scratch?",
@@ -93420,9 +222871,9 @@
         ],
         "short_id": "T00163",
         "short_tools": [
+            "Show beginning1",
             "Paste1",
-            "tp_tac",
-            "Show beginning1"
+            "tp_tac"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -93449,11 +222900,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -93478,6 +222924,550 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Paste1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Show beginning1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
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+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "missing"
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+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
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+                    "servers": [
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
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+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
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+                    "version": "1.1.0"
+                }
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         "symlink": null,
         "tags": [
             "workflows"
@@ -93508,8 +223498,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 179,
-        "visitors": 4590,
+        "visit_duration": 180,
+        "visitors": 4614,
         "workflows": [
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@@ -93581,7 +223571,7 @@
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Tutorial workflow",
                 "outputs": [
                     {
@@ -93763,7 +223753,7 @@
                 ],
                 "license": null,
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Subworkflow",
                 "outputs": [
                     {
@@ -94361,7 +224351,7 @@
             "Submit raw sequencing reads and metadata to ENA's test server",
             "Submit consensus sequence and metadata to ENA's test server"
         ],
-        "pageviews": 4806337,
+        "pageviews": 4837959,
         "pub_date": "2021-08-10",
         "questions": [
             "How do you submit raw sequence reads and assembled genomes to the European Nucleotide Archive?"
@@ -94393,6 +224383,597 @@
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+                            "state": "inexact",
+                            "versions": [
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+                                "0.3.1",
+                                "0.3",
+                                "0.7.1+galaxy1",
+                                "0.5.3",
+                                "0.6.1",
+                                "0.6.0",
+                                "0.4.1",
+                                "0.3.3",
+                                "0.3.2",
+                                "0.4.3",
+                                "0.6.3+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
+                                "0.7.3+galaxy1",
+                                "0.7.1+galaxy1",
+                                "0.5.3",
+                                "0.6.1",
+                                "0.6.0",
+                                "0.3.3",
+                                "0.4.3",
+                                "0.6.3+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.7.1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "covid19"
@@ -94424,7 +225005,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 236,
-        "visitors": 1810937,
+        "visitors": 1821325,
         "workflows": [
             {
                 "creators": [],
@@ -94448,7 +225029,7 @@
                 "inputs": [],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"ENA Upload tool\"];\n  1[\"ENA Upload tool\"];",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "GTN_ENA_upload_workflow",
                 "outputs": [
                     {
@@ -94636,8 +225217,8 @@
         ],
         "dir": "topics/galaxy-interface/tutorials/workflow-automation",
         "edam_operation": [
-            "Tree-based sequence alignment",
-            "Variant classification"
+            "Variant classification",
+            "Tree-based sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -94651,8 +225232,7 @@
         "hands_on": true,
         "id": "galaxy-interface/workflow-automation",
         "inexact_supported_servers": [
-            "MISSISSIPPI",
-            "UseGalaxy.fr"
+            "MISSISSIPPI"
         ],
         "js_requirements": {
             "mathjax": null,
@@ -94670,7 +225250,7 @@
             "Be able to write simple shell scripts for running multiple workflows concurrently or sequentially.",
             "Learn how to use Pangolin to assign annotated variants to lineages."
         ],
-        "pageviews": 2813,
+        "pageviews": 2825,
         "pub_date": "2021-06-08",
         "questions": [
             "How can I schedule and run tens or hundreds of Galaxy workflows easily?",
@@ -94702,11 +225282,11 @@
         ],
         "short_id": "T00162",
         "short_tools": [
-            "pangolin",
-            "bcftools_consensus",
-            "snpSift_filter",
             "compose_text_param",
-            "collapse_dataset"
+            "bcftools_consensus",
+            "collapse_dataset",
+            "pangolin",
+            "snpSift_filter"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -94739,11 +225319,874 @@
                     "name": "MISSISSIPPI",
                     "url": "https://mississippi.sorbonne-universite.fr",
                     "usegalaxy": false
+                }
+            ]
+        },
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+            "servers": [
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
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+                    "usegalaxy": false
+                },
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+                    "name": "Mandoiu Lab",
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+                },
+                {
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+                },
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+                    "url": "http://galaxy.inf.ethz.ch"
+                },
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+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
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+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
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+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
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+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
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+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
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+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "4.3+t.galaxy1"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
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+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "exact",
+                            "version": "4.3+t.galaxy1"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "exact",
+                            "version": "4.3+t.galaxy1"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "4.3+t.galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "4.3+t.galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "4.3+t.galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "4.3+t.galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "4.3+t.galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "4.3+t.galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "4.3+t.galaxy1"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "5.1.0"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "5.1.0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "5.1.0"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "5.1.0",
+                                "1.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "4.2"
                 }
             ]
         },
@@ -94782,7 +226225,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 120,
-        "visitors": 2277,
+        "visitors": 2288,
         "workflows": [
             {
                 "creators": [
@@ -94915,7 +226358,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nVariant calls\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nmin-AF for consensus variant\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Compose text parameter value\"];\n  1 -->|output| 3;\n  4[\"SnpSift Filter\"];\n  3 -->|out1| 4;\n  0 -->|output| 4;\n  ee67c5ed-ff7c-404b-ad20-19259edbc671[\"Output\\nconsensus_variants\"];\n  4 --> ee67c5ed-ff7c-404b-ad20-19259edbc671;\n  style ee67c5ed-ff7c-404b-ad20-19259edbc671 stroke:#2c3143,stroke-width:4px;\n  5[\"bcftools consensus\"];\n  4 -->|output| 5;\n  2 -->|output| 5;\n  9028f80e-4112-40d8-9a49-f671677d304f[\"Output\\nconsensus\"];\n  5 --> 9028f80e-4112-40d8-9a49-f671677d304f;\n  style 9028f80e-4112-40d8-9a49-f671677d304f stroke:#2c3143,stroke-width:4px;\n  6[\"Collapse Collection\"];\n  5 -->|output_file| 6;\n  1dd7978e-b907-42d6-8fc4-f6fadeefcad1[\"Output\\nmultisample_consensus_fasta\"];\n  6 --> 1dd7978e-b907-42d6-8fc4-f6fadeefcad1;\n  style 1dd7978e-b907-42d6-8fc4-f6fadeefcad1 stroke:#2c3143,stroke-width:4px;\n  7[\"Pangolin\"];\n  6 -->|output| 7;\n  e02d2cfb-9842-4069-957c-6cf4ec197056[\"Output\\npangolin_results\"];\n  7 --> e02d2cfb-9842-4069-957c-6cf4ec197056;\n  style e02d2cfb-9842-4069-957c-6cf4ec197056 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "vcf2lineage",
                 "outputs": [
                     {
@@ -95310,7 +226753,6 @@
             "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
@@ -95336,7 +226778,7 @@
         "objectives": [
             "Learn how to use Workflow Parameters to improve your Workflows"
         ],
-        "pageviews": 2067,
+        "pageviews": 2075,
         "pub_date": "2019-06-27",
         "questions": [
             "What are Workflow Parameters",
@@ -95400,11 +226842,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -95429,6 +226866,290 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "9.3+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.1.0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "workflows"
@@ -95458,7 +227179,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 135,
-        "visitors": 1594,
+        "visitors": 1600,
         "workflows": [
             {
                 "creators": [],
@@ -95510,7 +227231,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Select first\"];\n  0 -->|output| 1;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Select First N Lines",
                 "outputs": [
                     {
@@ -95687,7 +227408,7 @@
             "Getting started with Galaxy workflows on Dockstore",
             "Register your Galaxy workflow on Dockstore"
         ],
-        "pageviews": 4061190,
+        "pageviews": 4092802,
         "pub_date": "2022-01-14",
         "short_id": "S00061",
         "short_tools": [],
@@ -95727,6 +227448,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
+        },
         "symlink": null,
         "title": "Galaxy workflows in Dockstore",
         "tools": [],
@@ -95749,8 +227474,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 148,
-        "visitors": 1583144
+        "visit_duration": 149,
+        "visitors": 1593548
     },
     {
         "admin_install": {
@@ -95830,8 +227555,8 @@
         ],
         "dir": "topics/galaxy-interface/tutorials/ncbi-sarf",
         "edam_operation": [
-            "SNP detection",
-            "Data handling"
+            "Data handling",
+            "SNP detection"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -95863,7 +227588,7 @@
             "Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content",
             "Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format"
         ],
-        "pageviews": 5142217,
+        "pageviews": 5173835,
         "pub_date": "2021-05-31",
         "questions": [
             "How can I search SRA SARS-CoV-2 metadata from within Galaxy?",
@@ -95895,13 +227620,13 @@
         ],
         "short_id": "T00155",
         "short_tools": [
-            "query_tabular",
-            "tp_cat",
-            "jq",
-            "fastq_dump",
             "snpeff_sars_cov_2",
+            "tp_cat",
+            "query_tabular",
             "fastq_to_fasta_python",
-            "fasterq_dump"
+            "fasterq_dump",
+            "fastq_dump",
+            "jq"
         ],
         "slides": true,
         "slides_recordings": [
@@ -95955,6 +227680,1182 @@
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             ]
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@@ -96130,6 +229031,10 @@
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@@ -96253,6 +229158,10 @@
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@@ -96440,6 +229349,10 @@
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@@ -96571,6 +229484,10 @@
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@@ -96691,7 +229607,7 @@
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@@ -96724,17 +229640,284 @@
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@@ -96912,6 +230095,10 @@
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-            "collapse_dataset"
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+                            "versions": [
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+                                "5.1.0",
+                                "4.1"
+                            ]
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+                            "server": "https://viralvariant.anses.fr/",
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@@ -97166,8 +231085,8 @@
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@@ -97239,7 +231158,7 @@
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             "What are name tags or hash tags?",
@@ -97288,6 +231207,10 @@
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         "time_estimation": "20m",
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@@ -97312,7 +231235,7 @@
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@@ -97441,7 +231363,7 @@
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@@ -97466,8 +231388,140 @@
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-                    "url": "https://usegalaxy.fr/",
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+                    "usegalaxy": true
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@@ -97479,9 +231533,144 @@
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+                            "state": "local"
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+                        {
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+                        {
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+                            "state": "local"
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+                        {
+                            "server": "https://viralvariant.anses.fr/",
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@@ -97511,8 +231700,8 @@
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@@ -97596,7 +231785,7 @@
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         "questions": [
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@@ -97645,6 +231834,10 @@
                 }
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@@ -97669,7 +231862,7 @@
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@@ -97718,7 +231911,7 @@
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@@ -97767,6 +231960,10 @@
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@@ -97791,7 +231988,7 @@
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@@ -97871,7 +232068,7 @@
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         "pub_date": "2020-07-15",
         "questions": [
             "How can you find your datasets?",
@@ -97916,6 +232113,10 @@
                 }
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@@ -97940,7 +232141,7 @@
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@@ -98183,7 +232384,7 @@
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         "questions": [
             "How do Galaxy histories work?"
@@ -98258,6 +232459,10 @@
                 }
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         "time_estimation": "30m",
         "title": "Understanding Galaxy history system",
@@ -98281,8 +232486,8 @@
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-        "visitors": 4031,
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@@ -98386,7 +232591,7 @@
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         "questions": [
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@@ -98432,6 +232637,292 @@
                 }
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
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+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
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+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
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+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
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+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
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+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
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+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
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         "tags": [
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@@ -98460,8 +232951,8 @@
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         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 157,
-        "visitors": 75
+        "visit_duration": 154,
+        "visitors": 78
     },
     {
         "admin_install": {
@@ -98562,6 +233053,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
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         "time_estimation": "30m",
         "title": "Use Jupyter notebooks in Galaxy",
@@ -98660,10 +233155,10 @@
             "topic_0080"
         ],
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-            "Genome visualisation",
+            "Coding region prediction",
             "Gene prediction",
-            "Genome annotation",
-            "Coding region prediction"
+            "Genome visualisation",
+            "Genome annotation"
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             "Genomics",
@@ -98694,7 +233189,6 @@
             "MISSISSIPPI",
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             "UseGalaxy.cz",
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         ],
@@ -98715,7 +233209,7 @@
             "Annotate genome with Prokka",
             "View annotations in JBrowse"
         ],
-        "pageviews": 5925124,
+        "pageviews": 5956792,
         "pub_date": "2018-03-06",
         "questions": [
             "How can we annotate a bacterial genome?",
@@ -98737,8 +233231,8 @@
         ],
         "short_id": "T00168",
         "short_tools": [
-            "jbrowse",
-            "prokka"
+            "prokka",
+            "jbrowse"
         ],
         "slides": true,
         "slides_recordings": [
@@ -98796,19 +233290,629 @@
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                 },
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-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
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+                },
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+                },
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+                        {
+                            "server": "https://galaxytrakr.org/",
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+                            "state": "missing"
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+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
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+                        },
+                        {
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+                            "state": "inexact",
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+                                "1.16.10+galaxy0",
+                                "1.12.5+galaxy1",
+                                "1.12.5+galaxy2",
+                                "1.16.5+galaxy4",
+                                "1.12.5+galaxy0",
+                                "0.1",
+                                "1.16.4+galaxy3",
+                                "1.16.5+galaxy7",
+                                "1.16.5+galaxy6",
+                                "1.16.8+galaxy0",
+                                "1.12.5+galaxy3",
+                                "1.16.5+galaxy3",
+                                "0.5.2.1",
+                                "1.16.1+galaxy0",
+                                "0.7.0.3",
+                                "1.16.8+galaxy1",
+                                "1.16.5+galaxy5",
+                                "1.16.4+galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.16.11+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.16.11+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.16.11+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.16.11+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.16.11+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.16.11+galaxy1"
                 }
             ]
         },
@@ -98846,7 +233950,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 259,
-        "visitors": 2149523,
+        "visitors": 2160036,
         "workflows": [
             {
                 "creators": [
@@ -98977,7 +234081,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs.fasta\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Prokka\"];\n  0 -->|output| 1;\n  a336c364-e69e-47eb-ace6-a7fe46d285fe[\"Output\\ngff_output\"];\n  1 --> a336c364-e69e-47eb-ace6-a7fe46d285fe;\n  style a336c364-e69e-47eb-ace6-a7fe46d285fe stroke:#2c3143,stroke-width:4px;\n  2[\"JBrowse\"];\n  1 -->|out_fna| 2;\n  1 -->|out_gff| 2;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Genome Annotation with Prokka ",
                 "outputs": [
                     {
@@ -99198,10 +234302,10 @@
         "dir": "topics/genome-annotation/tutorials/secondary-metabolite-discovery",
         "draft": true,
         "edam_operation": [
-            "Gene prediction",
             "Data handling",
-            "Service invocation",
             "Differential gene expression analysis",
+            "Gene prediction",
+            "Service invocation",
             "Sequence clustering"
         ],
         "edam_topic": [],
@@ -99230,7 +234334,7 @@
             "Extraction of gene cluster products using a custom script.",
             "Query of the products in compound libraries using cheminformatic tools."
         ],
-        "pageviews": 285,
+        "pageviews": 304,
         "pub_date": "2024-02-21",
         "questions": [
             "How to discover secondary metabolites produced by microorganisms ?",
@@ -99239,19 +234343,19 @@
         ],
         "short_id": "T00420",
         "short_tools": [
+            "collapse_dataset",
+            "edu.tamu.cpt.gff3.customGbkToGff",
             "ctb_np-likeness-calculator",
-            "interactive_tool_jupyter_notebook",
-            "antismash",
-            "ctb_simsearch",
-            "tp_awk_tool",
             "bp_genbank2gff3",
+            "ctb_silicos_qed",
+            "ncbi_acc_download",
+            "tp_awk_tool",
+            "interactive_tool_jupyter_notebook",
             "ctb_chemfp_mol2fps",
+            "Remove beginning1",
+            "ctb_simsearch",
             "openbabel_remDuplicates",
-            "ncbi_acc_download",
-            "collapse_dataset",
-            "ctb_silicos_qed",
-            "edu.tamu.cpt.gff3.customGbkToGff",
-            "Remove beginning1"
+            "antismash"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -99265,6 +234369,1928 @@
             ],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
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+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
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+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
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+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
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+                            "state": "local"
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+                        },
+                        {
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+                    "version": "local"
+                },
+                {
+                    "id": "interactive_tool_jupyter_notebook",
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@@ -99412,7 +236438,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nQuery Genomes\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nJupyter Notebook Genbank2Features\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTarget Molecules Natural Compound Library\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"NCBI Accession Download\"];\n  0 -->|output| 3;\n  faecdec3-711d-43ba-bb91-38a4b4b3932d[\"Output\\nNCBI Accession Download on input dataset(s): Log\"];\n  3 --> faecdec3-711d-43ba-bb91-38a4b4b3932d;\n  style faecdec3-711d-43ba-bb91-38a4b4b3932d stroke:#2c3143,stroke-width:4px;\n  c8857c6f-ec99-4d29-8c98-be7a63a9f029[\"Output\\nNCBI Accession Download on input dataset(s): Downloaded Files\"];\n  3 --> c8857c6f-ec99-4d29-8c98-be7a63a9f029;\n  style c8857c6f-ec99-4d29-8c98-be7a63a9f029 stroke:#2c3143,stroke-width:4px;\n  4[\"Molecule to fingerprint\"];\n  2 -->|output| 4;\n  5[\"Antismash\"];\n  3 -->|output| 5;\n  cc813ad7-f423-4cb8-ba79-8201abab206a[\"Output\\nAntismash on input dataset(s): HTML report\"];\n  5 --> cc813ad7-f423-4cb8-ba79-8201abab206a;\n  style cc813ad7-f423-4cb8-ba79-8201abab206a stroke:#2c3143,stroke-width:4px;\n  6[\"Collapse clusters in one Genbank entry\"];\n  5 -->|genbank| 6;\n  7[\"Extract SMILES qualifiers\"];\n  1 -->|output| 7;\n  6 -->|output| 7;\n  8[\"Convert table to smi format\"];\n  7 -->|output_collection| 8;\n  9[\"Remove beginning\"];\n  8 -->|outfile| 9;\n  10[\"Remove duplicated molecules\"];\n  9 -->|out_file1| 10;\n  11[\"Molecule to fingerprint\"];\n  10 -->|outfile| 11;\n  12[\"Natural Product\"];\n  10 -->|outfile| 12;\n  13[\"Drug-likeness\"];\n  10 -->|outfile| 13;\n  14[\"Similarity Search\"];\n  11 -->|outfile| 14;\n  4 -->|outfile| 14;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Gene Cluster Product Similarity Search ",
                 "outputs": [
                     {
@@ -99864,8 +236890,8 @@
         ],
         "edam_operation": [
             "Genome visualisation",
-            "Genome annotation",
-            "Read mapping"
+            "Read mapping",
+            "Genome annotation"
         ],
         "edam_topic": [
             "Whole genome sequencing",
@@ -99878,8 +236904,7 @@
         ],
         "exact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -99922,7 +236947,7 @@
             "Get information about ARGs",
             "Visualize the ARGs and plasmid genes in their genomic context"
         ],
-        "pageviews": 1576,
+        "pageviews": 1633,
         "pub_date": "2024-01-23",
         "questions": [
             "Which resistance genes are on a bacterial genome?",
@@ -99946,12 +236971,12 @@
         "short_id": "T00401",
         "short_tools": [
             "jbrowse",
-            "tbl2gff3",
-            "upload1",
             "Grep1",
-            "staramr_search",
+            "tbl2gff3",
             "bakta",
-            "bowtie2"
+            "upload1",
+            "bowtie2",
+            "staramr_search"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -99967,11 +236992,6 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
                 }
             ],
             "inexact": [
@@ -99987,6 +237007,1163 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
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+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
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+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
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+                {
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+                    "url": "https://galaxy.pasteur.fr/",
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+                    "url": "https://galaxytrakr.org/",
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+                },
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+                },
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+                },
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+                },
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
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+                },
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+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                    "usegalaxy": true
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+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
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-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"staramr\"];\n  0 -->|output| 3;\n  000e2ab9-92db-45bb-a0ef-ecccf06da616[\"Output\\nstararm_detailed_summary\"];\n  3 --> 000e2ab9-92db-45bb-a0ef-ecccf06da616;\n  style 000e2ab9-92db-45bb-a0ef-ecccf06da616 stroke:#2c3143,stroke-width:4px;\n  4[\"Bakta\"];\n  0 -->|output| 4;\n  c848b1eb-7262-4627-b7a7-05a13b968935[\"Output\\nbakta_annotation_summary\"];\n  4 --> c848b1eb-7262-4627-b7a7-05a13b968935;\n  style c848b1eb-7262-4627-b7a7-05a13b968935 stroke:#2c3143,stroke-width:4px;\n  5[\"Bowtie2\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  0 -->|output| 5;\n  352e63d3-8aca-4dff-878c-10497f65bb74[\"Output\\nbowtie_mapping_stats\"];\n  5 --> 352e63d3-8aca-4dff-878c-10497f65bb74;\n  style 352e63d3-8aca-4dff-878c-10497f65bb74 stroke:#2c3143,stroke-width:4px;\n  6[\"Select\"];\n  3 -->|detailed_summary| 6;\n  7[\"Table to GFF3\"];\n  6 -->|out_file1| 7;\n  8[\"JBrowse\"];\n  4 -->|annotation_gff3| 8;\n  7 -->|output| 8;\n  5 -->|output| 8;\n  3c3bd5fd-419c-45b2-afcd-c6d02af82695[\"Output\\njbrowse_output\"];\n  8 --> 3c3bd5fd-419c-45b2-afcd-c6d02af82695;\n  style 3c3bd5fd-419c-45b2-afcd-c6d02af82695 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nforward_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nreverse_reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"staramr\"];\n  0 -->|output| 3;\n  455bde1a-6195-4ea2-9577-35eea97a546a[\"Output\\nstararm_detailed_summary\"];\n  3 --> 455bde1a-6195-4ea2-9577-35eea97a546a;\n  style 455bde1a-6195-4ea2-9577-35eea97a546a stroke:#2c3143,stroke-width:4px;\n  4[\"Bakta\"];\n  0 -->|output| 4;\n  065a7e6a-7ce3-4763-8698-959f019c6c76[\"Output\\nbakta_annotation_summary\"];\n  4 --> 065a7e6a-7ce3-4763-8698-959f019c6c76;\n  style 065a7e6a-7ce3-4763-8698-959f019c6c76 stroke:#2c3143,stroke-width:4px;\n  5[\"Bowtie2\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  0 -->|output| 5;\n  57f88358-7a42-45c7-a538-55476519e3ec[\"Output\\nbowtie_mapping_stats\"];\n  5 --> 57f88358-7a42-45c7-a538-55476519e3ec;\n  style 57f88358-7a42-45c7-a538-55476519e3ec stroke:#2c3143,stroke-width:4px;\n  6[\"Select\"];\n  3 -->|detailed_summary| 6;\n  7[\"Table to GFF3\"];\n  6 -->|out_file1| 7;\n  8[\"JBrowse\"];\n  4 -->|annotation_gff3| 8;\n  7 -->|output| 8;\n  5 -->|output| 8;\n  bac18ad5-2731-45bc-8b53-5cfaca1e06c5[\"Output\\njbrowse_output\"];\n  8 --> bac18ad5-2731-45bc-8b53-5cfaca1e06c5;\n  style bac18ad5-2731-45bc-8b53-5cfaca1e06c5 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "mrsa AMR gene detection",
                 "outputs": [
                     {
@@ -100237,7 +238414,7 @@
                             {
                                 "label": "stararm_detailed_summary",
                                 "output_name": "detailed_summary",
-                                "uuid": "000e2ab9-92db-45bb-a0ef-ecccf06da616"
+                                "uuid": "455bde1a-6195-4ea2-9577-35eea97a546a"
                             }
                         ]
                     },
@@ -100311,7 +238488,7 @@
                             {
                                 "label": "bakta_annotation_summary",
                                 "output_name": "annotation_tsv",
-                                "uuid": "c848b1eb-7262-4627-b7a7-05a13b968935"
+                                "uuid": "065a7e6a-7ce3-4763-8698-959f019c6c76"
                             }
                         ]
                     },
@@ -100368,7 +238545,7 @@
                             {
                                 "label": "bowtie_mapping_stats",
                                 "output_name": "mapping_stats",
-                                "uuid": "352e63d3-8aca-4dff-878c-10497f65bb74"
+                                "uuid": "57f88358-7a42-45c7-a538-55476519e3ec"
                             }
                         ]
                     },
@@ -100421,7 +238598,7 @@
                             {
                                 "label": "jbrowse_output",
                                 "output_name": "output",
-                                "uuid": "3c3bd5fd-419c-45b2-afcd-c6d02af82695"
+                                "uuid": "bac18ad5-2731-45bc-8b53-5cfaca1e06c5"
                             }
                         ]
                     }
@@ -100541,7 +238718,7 @@
             "Learn how to run different tools in Galaxy to perform sequence comparison at fine and coarse-grained levels",
             "Learn how to post-process your sequence comparisons"
         ],
-        "pageviews": 5735585,
+        "pageviews": 5767220,
         "pub_date": "2021-02-08",
         "questions": [
             "How can we run pairwise genome comparisons using Galaxy?",
@@ -100597,6 +238774,704 @@
                 }
             ]
         },
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+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
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+                },
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+                },
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+                },
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+                },
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+                    "url": "http://gigagalaxy.net/"
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+                    "usegalaxy": true
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+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
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+                    "name": "Viral Variant Visualizer (VVV)",
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+                            "state": "exact",
+                            "version": "1.5.a"
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+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.5.a"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.5.a"
+                },
+                {
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+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
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+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "1.2"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.2"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "plants",
@@ -100630,7 +239505,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 283,
-        "visitors": 2085776,
+        "visitors": 2096155,
         "workflows": [
             {
                 "creators": [],
@@ -100731,7 +239606,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery chromosome\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference chromosome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Chromeister\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  58cf0c0c-9200-4ba4-9727-6d908ccdfa9a[\"Output\\nChromeister on input dataset(s): Detected events\"];\n  2 --> 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a;\n  style 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a stroke:#2c3143,stroke-width:4px;\n  2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c[\"Output\\nChromeister on input dataset(s): Comparison metainformation\"];\n  2 --> 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c;\n  style 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c stroke:#2c3143,stroke-width:4px;\n  c248576c-1c39-416c-99d0-40c520e3da67[\"Output\\nChromeister on input dataset(s): Comparison dotplot\"];\n  2 --> c248576c-1c39-416c-99d0-40c520e3da67;\n  style c248576c-1c39-416c-99d0-40c520e3da67 stroke:#2c3143,stroke-width:4px;\n  5f9aad77-f9ee-4932-ab22-bb5fd83f416c[\"Output\\nChromeister on input dataset(s): Comparison matrix\"];\n  2 --> 5f9aad77-f9ee-4932-ab22-bb5fd83f416c;\n  style 5f9aad77-f9ee-4932-ab22-bb5fd83f416c stroke:#2c3143,stroke-width:4px;\n  dea450c2-7126-43dc-af7a-9f2b704c76dd[\"Output\\nChromeister on input dataset(s): Comparison score\"];\n  2 --> dea450c2-7126-43dc-af7a-9f2b704c76dd;\n  style dea450c2-7126-43dc-af7a-9f2b704c76dd stroke:#2c3143,stroke-width:4px;\n  9a03f722-5588-4a3f-b70e-0ec9979c16dd[\"Output\\nChromeister on input dataset(s): Detected events plot\"];\n  2 --> 9a03f722-5588-4a3f-b70e-0ec9979c16dd;\n  style 9a03f722-5588-4a3f-b70e-0ec9979c16dd stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "CHROMEISTER chromosome comparison",
                 "outputs": [
                     {
@@ -101047,7 +239922,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery sequence\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference sequence\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Gecko\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  6275abc1-d74e-45a7-b8ab-3c88426cc488[\"Output\\nGecko on input dataset(s): CSV\"];\n  2 --> 6275abc1-d74e-45a7-b8ab-3c88426cc488;\n  style 6275abc1-d74e-45a7-b8ab-3c88426cc488 stroke:#2c3143,stroke-width:4px;\n  3[\"Text reformatting\"];\n  2 -->|alignments2| 3;\n  4[\"ClustalW\"];\n  3 -->|outfile| 4;\n  d63c1172-a591-4bf6-b307-052ca19e7098[\"Output\\nClustalW on input dataset(s): clustal\"];\n  4 --> d63c1172-a591-4bf6-b307-052ca19e7098;\n  style d63c1172-a591-4bf6-b307-052ca19e7098 stroke:#2c3143,stroke-width:4px;\n  d7758e3a-522d-4439-8c9a-03f784284ebd[\"Output\\nClustalW on input dataset(s): dnd\"];\n  4 --> d7758e3a-522d-4439-8c9a-03f784284ebd;\n  style d7758e3a-522d-4439-8c9a-03f784284ebd stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GECKO pairwise comparison",
                 "outputs": [
                     {
@@ -101566,7 +240441,7 @@
             "Learn how to manually refine genome annotations within Apollo",
             "Export refined genome annotations"
         ],
-        "pageviews": 5119567,
+        "pageviews": 5151189,
         "pub_date": "2021-06-04",
         "questions": [
             "How to visualize your genome after automated annotations have been performed?",
@@ -101608,9 +240483,9 @@
         "short_tools": [
             "jbrowse",
             "create_or_update",
+            "create_account",
             "iframe",
-            "list_organism",
-            "create_account"
+            "list_organism"
         ],
         "slides": true,
         "slides_recordings": [
@@ -101648,6 +240523,854 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
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+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
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+                    "name": "MISSISSIPPI",
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+                    "usegalaxy": false
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+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
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+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                {
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+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
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+                {
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+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
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+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
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+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
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+            ],
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+                            ]
+                        },
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+                        },
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+                            "state": "exact",
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+                            "state": "exact",
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         "tags": [
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@@ -101684,8 +241407,8 @@
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         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 299,
-        "visitors": 1906178,
+        "visit_duration": 300,
+        "visitors": 1916586,
         "workflows": [
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@@ -101876,7 +241599,7 @@
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Apollo Load Test",
                 "outputs": [
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@@ -102508,17 +242231,16 @@
         ],
         "dir": "topics/genome-annotation/tutorials/repeatmasker",
         "edam_operation": [
-            "Genome annotation",
             "Editing",
-            "Repeat sequence detection",
             "RNA-Seq analysis",
-            "Mapping"
+            "Repeat sequence detection",
+            "Mapping",
+            "Genome annotation"
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@@ -102551,7 +242273,7 @@
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         ],
-        "pageviews": 9655,
+        "pageviews": 9726,
         "priority": 1,
         "pub_date": "2021-11-29",
         "questions": [
@@ -102586,10 +242308,10 @@
         ],
         "short_id": "T00178",
         "short_tools": [
-            "bedtools_maskfastabed",
+            "repeatmasker_wrapper",
             "repeatmodeler",
-            "red",
-            "repeatmasker_wrapper"
+            "bedtools_maskfastabed",
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@@ -102607,8 +242329,140 @@
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                 },
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-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
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+                },
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+                },
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+                    "url": "https://www.immportgalaxy.org/"
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+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
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+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
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+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
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+                    "usegalaxy": true
+                },
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+                    "url": "https://usegalaxy.no/",
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@@ -102620,9 +242474,574 @@
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
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+                    "url": "https://viralvariant.anses.fr/"
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@@ -102655,8 +243074,8 @@
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-        "visit_duration": 82,
-        "visitors": 7397,
+        "visit_duration": 84,
+        "visitors": 7448,
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@@ -102713,7 +243132,7 @@
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
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@@ -103009,15 +243428,15 @@
             "topic_0362"
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-            "Genome annotation",
-            "Genome visualisation",
             "Genome assembly",
+            "Transcriptome assembly",
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             "Sequence assembly validation",
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-            "Sequence annotation",
-            "Transcriptome assembly"
+            "Gene prediction",
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@@ -103044,7 +243463,7 @@
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             "View annotations in JBrowse"
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         "pub_date": "2024-08-21",
         "questions": [
             "How to annotate an eukaryotic genome with Helixer?",
@@ -103061,12 +243480,12 @@
         ],
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             "jbrowse",
             "compleasm",
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-            "jcvi_gff_stats",
-            "gffread",
-            "helixer"
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@@ -103075,6 +243494,1161 @@
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+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
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+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
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+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
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+                        {
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+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
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+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
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+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
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+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.8.4"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "eukaryota",
@@ -103111,8 +244685,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 157,
-        "visitors": 86,
+        "visit_duration": 127,
+        "visitors": 106,
         "workflows": [
             {
                 "creators": [
@@ -103177,7 +244751,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGenome\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Helixer\"];\n  0 -->|output| 1;\n  9ebeb90d-1528-494c-a88d-50f28836d7c7[\"Output\\nHelixer\"];\n  1 --> 9ebeb90d-1528-494c-a88d-50f28836d7c7;\n  style 9ebeb90d-1528-494c-a88d-50f28836d7c7 stroke:#2c3143,stroke-width:4px;\n  2[\"compleasm\"];\n  0 -->|output| 2;\n  e0d3aa0b-d18b-41af-a6fc-28a8688fe9a5[\"Output\\ncompleasm miniprot\"];\n  2 --> e0d3aa0b-d18b-41af-a6fc-28a8688fe9a5;\n  style e0d3aa0b-d18b-41af-a6fc-28a8688fe9a5 stroke:#2c3143,stroke-width:4px;\n  93b908a5-e39f-4cfb-84c3-edf4ab8b71cf[\"Output\\ncompleasm full table\"];\n  2 --> 93b908a5-e39f-4cfb-84c3-edf4ab8b71cf;\n  style 93b908a5-e39f-4cfb-84c3-edf4ab8b71cf stroke:#2c3143,stroke-width:4px;\n  7c9cb7e2-dfac-4aa1-b87d-f6a2eb7e21a5[\"Output\\ncompleasm full table busco\"];\n  2 --> 7c9cb7e2-dfac-4aa1-b87d-f6a2eb7e21a5;\n  style 7c9cb7e2-dfac-4aa1-b87d-f6a2eb7e21a5 stroke:#2c3143,stroke-width:4px;\n  9215afe6-4aad-4d43-a3a1-c2c5ab0ea1e2[\"Output\\ncompleasm translated protein\"];\n  2 --> 9215afe6-4aad-4d43-a3a1-c2c5ab0ea1e2;\n  style 9215afe6-4aad-4d43-a3a1-c2c5ab0ea1e2 stroke:#2c3143,stroke-width:4px;\n  3[\"BUSCO\"];\n  0 -->|output| 3;\n  703a797f-428b-4c41-984f-1283bb8eecaa[\"Output\\nBUSCO sum\"];\n  3 --> 703a797f-428b-4c41-984f-1283bb8eecaa;\n  style 703a797f-428b-4c41-984f-1283bb8eecaa stroke:#2c3143,stroke-width:4px;\n  e3879637-613a-45cf-90a0-3eecab2e0981[\"Output\\nBUSCO miniprot\"];\n  3 --> e3879637-613a-45cf-90a0-3eecab2e0981;\n  style e3879637-613a-45cf-90a0-3eecab2e0981 stroke:#2c3143,stroke-width:4px;\n  acbfdee0-cafd-46e8-81e9-8a1fd22ee758[\"Output\\nBUSCO gff3\"];\n  3 --> acbfdee0-cafd-46e8-81e9-8a1fd22ee758;\n  style acbfdee0-cafd-46e8-81e9-8a1fd22ee758 stroke:#2c3143,stroke-width:4px;\n  5574f029-f31d-4d20-a847-4d1818f95707[\"Output\\nBUSCO summary image\"];\n  3 --> 5574f029-f31d-4d20-a847-4d1818f95707;\n  style 5574f029-f31d-4d20-a847-4d1818f95707 stroke:#2c3143,stroke-width:4px;\n  b19bfb5f-901f-4568-a461-53bfc980bdcc[\"Output\\nBUSCO missing\"];\n  3 --> b19bfb5f-901f-4568-a461-53bfc980bdcc;\n  style b19bfb5f-901f-4568-a461-53bfc980bdcc stroke:#2c3143,stroke-width:4px;\n  0ba757ff-6c1b-496b-a288-335369058923[\"Output\\nBUSCO table\"];\n  3 --> 0ba757ff-6c1b-496b-a288-335369058923;\n  style 0ba757ff-6c1b-496b-a288-335369058923 stroke:#2c3143,stroke-width:4px;\n  4[\"Genome annotation statistics Helixer\"];\n  1 -->|output| 4;\n  0 -->|output| 4;\n  a445f12b-685d-47af-b407-90fa7ea935b1[\"Output\\ngraphs helixer\"];\n  4 --> a445f12b-685d-47af-b407-90fa7ea935b1;\n  style a445f12b-685d-47af-b407-90fa7ea935b1 stroke:#2c3143,stroke-width:4px;\n  8eae8a88-c73d-42dc-ad0d-62d2f1d29c6a[\"Output\\nsummary helixer\"];\n  4 --> 8eae8a88-c73d-42dc-ad0d-62d2f1d29c6a;\n  style 8eae8a88-c73d-42dc-ad0d-62d2f1d29c6a stroke:#2c3143,stroke-width:4px;\n  5[\"JBrowse\"];\n  0 -->|output| 5;\n  1 -->|output| 5;\n  2bac35a7-8379-4269-9769-e0e0c541f4a3[\"Output\\nJBrowse output\"];\n  5 --> 2bac35a7-8379-4269-9769-e0e0c541f4a3;\n  style 2bac35a7-8379-4269-9769-e0e0c541f4a3 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Training - Helixer",
                 "outputs": [
                     {
@@ -103669,15 +245243,15 @@
             "topic_0798"
         ],
         "edam_operation": [
+            "Sequence motif recognition",
+            "Genome assembly",
+            "Genome visualisation",
+            "Protein feature detection",
             "Genome annotation",
-            "Nucleic acid feature detection",
             "Multilocus sequence typing",
-            "Genome visualisation",
-            "Genome assembly",
-            "Sequence motif recognition",
-            "Structural variation detection",
+            "Nucleic acid feature detection",
             "Scaffolding",
-            "Protein feature detection"
+            "Structural variation detection"
         ],
         "edam_topic": [
             "Genomics",
@@ -103689,8 +245263,7 @@
             "Mobile genetic elements"
         ],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -103743,7 +245316,7 @@
             "Process the outputs to formate them for visualization needs",
             "Visualize a draft bacterial genome and its annotations"
         ],
-        "pageviews": 2969,
+        "pageviews": 3039,
         "pub_date": "2024-02-01",
         "questions": [
             "Which genes are on a draft bacterial genome?",
@@ -103766,16 +245339,16 @@
         ],
         "short_id": "T00403",
         "short_tools": [
-            "jbrowse",
-            "tbl2gff3",
-            "plasmidfinder",
             "integron_finder",
-            "upload1",
-            "isescan",
+            "jbrowse",
             "tp_tail_tool",
             "bakta",
+            "tbl2gff3",
+            "upload1",
             "tp_replace_in_column",
-            "Grouping1"
+            "Grouping1",
+            "isescan",
+            "plasmidfinder"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -103786,28 +245359,1604 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
-            ],
-            "inexact": [
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
                 {
                     "name": "Galaxy@AuBi",
                     "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Grouping1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
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@@ -103923,7 +247072,7 @@
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@@ -105342,7 +250691,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGenome assembly\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nRNASeq reads forward\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nRNASeq reads reverse\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nProtein evidence sequences\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nNCBI submission template\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gbk\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gff3\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"RNA STAR\"];\n  0 -->|output| 7;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  79cf59ea-3aef-4cb8-9c70-5b42e03a5da9[\"Output\\nMapped RNASeq\"];\n  7 --> 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9;\n  style 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9 stroke:#2c3143,stroke-width:4px;\n  8[\"Funannotate predict annotation\"];\n  3 -->|output| 8;\n  7 -->|mapped_reads| 8;\n  0 -->|output| 8;\n  9[\"eggNOG Mapper\"];\n  8 -->|fasta_proteins| 9;\n  10[\"InterProScan\"];\n  8 -->|fasta_proteins| 10;\n  11[\"Funannotate functional\"];\n  9 -->|annotations| 11;\n  8 -->|annot_gbk| 11;\n  10 -->|outfile_xml| 11;\n  4 -->|output| 11;\n  d0694cd1-6d81-4d72-83b9-94cb57dc1502[\"Output\\nFinal annotation (genbank)\"];\n  11 --> d0694cd1-6d81-4d72-83b9-94cb57dc1502;\n  style d0694cd1-6d81-4d72-83b9-94cb57dc1502 stroke:#2c3143,stroke-width:4px;\n  9a1e7b70-1090-41ed-8637-65b7372a9f6c[\"Output\\nFinal annotation (CDS sequences)\"];\n  11 --> 9a1e7b70-1090-41ed-8637-65b7372a9f6c;\n  style 9a1e7b70-1090-41ed-8637-65b7372a9f6c stroke:#2c3143,stroke-width:4px;\n  99fffa40-2196-491d-9a66-559ebf2d9561[\"Output\\nFinal annotation (mRNA sequences)\"];\n  11 --> 99fffa40-2196-491d-9a66-559ebf2d9561;\n  style 99fffa40-2196-491d-9a66-559ebf2d9561 stroke:#2c3143,stroke-width:4px;\n  17b03b77-0485-4176-b2b3-03bfa2d3bcb0[\"Output\\nFinal annotation (protein sequences)\"];\n  11 --> 17b03b77-0485-4176-b2b3-03bfa2d3bcb0;\n  style 17b03b77-0485-4176-b2b3-03bfa2d3bcb0 stroke:#2c3143,stroke-width:4px;\n  4a0602fc-e6d2-43fc-9957-344707c22c05[\"Output\\nFinal annotation (GFF3)\"];\n  11 --> 4a0602fc-e6d2-43fc-9957-344707c22c05;\n  style 4a0602fc-e6d2-43fc-9957-344707c22c05 stroke:#2c3143,stroke-width:4px;\n  12[\"JBrowse\"];\n  0 -->|output| 12;\n  11 -->|gff3| 12;\n  7 -->|mapped_reads| 12;\n  ac4d8805-f123-44d2-b30f-8ac906cc471f[\"Output\\nJBrowse\"];\n  12 --> ac4d8805-f123-44d2-b30f-8ac906cc471f;\n  style ac4d8805-f123-44d2-b30f-8ac906cc471f stroke:#2c3143,stroke-width:4px;\n  13[\"Funannotate compare\"];\n  5 -->|output| 13;\n  11 -->|gbk| 13;\n  e531c81f-f6b7-4c82-a712-c562873ff714[\"Output\\nFunannotate compare report\"];\n  13 --> e531c81f-f6b7-4c82-a712-c562873ff714;\n  style e531c81f-f6b7-4c82-a712-c562873ff714 stroke:#2c3143,stroke-width:4px;\n  14[\"AEGeAn ParsEval\"];\n  6 -->|output| 14;\n  11 -->|gff3| 14;\n  0d776b46-2c1c-4083-9f9d-a213fa62eb81[\"Output\\nAEGeAN report\"];\n  14 --> 0d776b46-2c1c-4083-9f9d-a213fa62eb81;\n  style 0d776b46-2c1c-4083-9f9d-a213fa62eb81 stroke:#2c3143,stroke-width:4px;\n  15[\"Busco\"];\n  11 -->|fa_proteins| 15;\n  57a619f5-b331-4ca6-8e6e-72eb61860032[\"Output\\nBusco summary\"];\n  15 --> 57a619f5-b331-4ca6-8e6e-72eb61860032;\n  style 57a619f5-b331-4ca6-8e6e-72eb61860032 stroke:#2c3143,stroke-width:4px;\n  97d23764-ad4a-4d69-948c-c81afb76fbaf[\"Output\\nBusco image\"];\n  15 --> 97d23764-ad4a-4d69-948c-c81afb76fbaf;\n  style 97d23764-ad4a-4d69-948c-c81afb76fbaf stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Funannotate",
                 "outputs": [
                     {
@@ -106347,13 +251696,13 @@
             "topic_0084"
         ],
         "edam_operation": [
-            "Database search",
+            "Multiple sequence alignment",
+            "Sequence alignment analysis",
             "Transcriptome assembly",
-            "Phylogenetic tree generation",
+            "Coding region prediction",
+            "Database search",
             "De-novo assembly",
-            "Sequence alignment analysis",
-            "Multiple sequence alignment",
-            "Coding region prediction"
+            "Phylogenetic tree generation"
         ],
         "edam_topic": [
             "Genomics",
@@ -106385,7 +251734,7 @@
         "objectives": [
             "Provide a quick method for identifying genes of interest in unannotated or newly assembled genomes"
         ],
-        "pageviews": 1602,
+        "pageviews": 1608,
         "priority": 2,
         "pub_date": "2022-09-08",
         "questions": [
@@ -106411,22 +251760,22 @@
         ],
         "short_id": "T00174",
         "short_tools": [
-            "orfipy",
-            "rapidnj",
-            "join1",
-            "bg_diamond_makedb",
-            "Filter1",
+            "Cut1",
+            "cat1",
+            "bg_diamond_view",
             "tp_split_on_column",
-            "tab2fasta",
             "collapse_dataset",
             "rbc_mafft",
-            "bg_diamond_view",
-            "Cut1",
-            "Add_a_column1",
-            "bg_diamond",
+            "tab2fasta",
             "regexColumn1",
             "gops_intersect_1",
-            "cat1"
+            "join1",
+            "rapidnj",
+            "bg_diamond",
+            "orfipy",
+            "Add_a_column1",
+            "bg_diamond_makedb",
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -106451,6 +251800,2526 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Cut1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Filter1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "cat1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
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+                            "state": "exact",
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+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "7.489+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "7.489+galaxy0"
+                        },
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+                            "state": "exact",
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+                        },
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         "symlink": null,
         "tags": [
             "evolution",
@@ -106501,8 +254370,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 215,
-        "visitors": 1045,
+        "visit_duration": 213,
+        "visitors": 1051,
         "workflows": [
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                 "creators": [
@@ -106611,7 +254480,7 @@
                 ],
                 "license": null,
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Comparative gene analysis",
                 "outputs": [
                     {
@@ -106849,12 +254718,12 @@
         "dir": "topics/genome-annotation/tutorials/annotation-with-maker-short",
         "edam_operation": [
             "Sequence assembly validation",
-            "Genome annotation",
+            "Genome assembly",
+            "Transcriptome assembly",
             "Scaffolding",
+            "Genome visualisation",
             "Sequence annotation",
-            "Transcriptome assembly",
-            "Genome assembly",
-            "Genome visualisation"
+            "Genome annotation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -106883,7 +254752,7 @@
             "Evaluate annotation quality with BUSCO",
             "View annotations in JBrowse"
         ],
-        "pageviews": 4148,
+        "pageviews": 4243,
         "priority": 3,
         "pub_date": "2021-01-12",
         "questions": [
@@ -106892,13 +254761,13 @@
         ],
         "short_id": "T00167",
         "short_tools": [
+            "jcvi_gff_stats",
             "jbrowse",
-            "busco",
             "fasta-stats",
+            "busco",
+            "maker",
             "maker_map_ids",
-            "jcvi_gff_stats",
-            "gffread",
-            "maker"
+            "gffread"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -106913,6 +254782,1196 @@
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             ]
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+                },
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+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
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+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
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+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
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+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
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+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
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+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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@@ -106950,8 +256009,8 @@
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-        "visit_duration": 189,
-        "visitors": 2836,
+        "visit_duration": 198,
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@@ -107173,7 +256232,7 @@
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                 "name": "Genome annotation with Maker (short)",
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@@ -107973,10 +257032,10 @@
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-            "Sequence trimming",
-            "Transposon prediction",
             "Read pre-processing",
-            "Primer removal"
+            "Sequence trimming",
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@@ -108015,7 +257074,7 @@
             "Predict Essential genes with Transit",
             "Compare gene essentiality in control sample and an different experimental condition"
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@@ -108025,18 +257084,18 @@
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-            "tp_easyjoin_tool",
-            "Filter1",
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-            "cutadapt",
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-            "deeptools_bam_coverage"
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@@ -108072,6 +257131,1854 @@
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+                                "3.4+galaxy2",
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+                                "3.4+galaxy1",
+                                "4.6+galaxy1",
+                                "1.1.a",
+                                "3.5+galaxy1",
+                                "4.9+galaxy0",
+                                "3.5+galaxy0",
+                                "4.8+galaxy0",
+                                "4.6+galaxy0",
+                                "1.16",
+                                "3.5+galaxy2"
+                            ]
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+                        },
+                        {
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+                            "state": "exact",
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+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.16.5"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "bacteria",
@@ -108115,7 +259022,7 @@
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         "video_view": 0,
         "visit_duration": 256,
-        "visitors": 2140389,
+        "visitors": 2150876,
         "workflows": [
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                 "creators": [],
@@ -108314,7 +259221,7 @@
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Essential genes detection with Transposon insertion sequencing",
                 "outputs": [
                     {
@@ -110130,17 +261037,17 @@
         ],
         "dir": "topics/genome-annotation/tutorials/annotation-with-maker",
         "edam_operation": [
-            "Genome annotation",
-            "Ab-initio gene prediction",
-            "Genome visualisation",
             "Genome assembly",
+            "Transcriptome assembly",
+            "Genome visualisation",
+            "Genome annotation",
             "Sequence assembly validation",
-            "Gene prediction",
-            "Homology-based gene prediction",
             "Scaffolding",
-            "Sequence annotation",
+            "Gene prediction",
+            "Ab-initio gene prediction",
             "Operation",
-            "Transcriptome assembly"
+            "Sequence annotation",
+            "Homology-based gene prediction"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -110175,7 +261082,7 @@
             "Evaluate annotation quality with BUSCO",
             "View annotations in JBrowse"
         ],
-        "pageviews": 21813,
+        "pageviews": 21856,
         "priority": 4,
         "pub_date": "2018-09-24",
         "questions": [
@@ -110184,15 +261091,15 @@
         ],
         "short_id": "T00166",
         "short_tools": [
+            "jcvi_gff_stats",
             "jbrowse",
-            "augustus_training",
-            "busco",
             "fasta-stats",
-            "maker_map_ids",
-            "jcvi_gff_stats",
+            "busco",
             "snap_training",
-            "gffread",
-            "maker"
+            "augustus_training",
+            "maker",
+            "maker_map_ids",
+            "gffread"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -110233,6 +261140,1418 @@
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             ]
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+                },
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+                            "version": "2.31.11"
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+                            "version": "2.31.11"
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+                            "server": "https://usegalaxy.org",
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+                            "version": "2.31.11"
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+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
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+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "2013_11_29+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "2013_11_29+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2013_11_29+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "2013_11_29+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2013_11_29+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2013_11_29+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2013_11_29+galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "gmod",
@@ -110273,7 +262592,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 113,
-        "visitors": 11759,
+        "visitors": 11791,
         "workflows": [
             {
                 "creators": [
@@ -110481,7 +262800,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nEST and/or cDNA\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nProtein sequences\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGenome sequence\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Maker\"];\n  0 -->|output| 3;\n  2 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Fasta Statistics\"];\n  2 -->|output| 4;\n  2d3829e6-f5b9-46d1-83e3-17efff814e09[\"Output\\nFasta Statistics on input dataset(s): Fasta summary stats\"];\n  4 --> 2d3829e6-f5b9-46d1-83e3-17efff814e09;\n  style 2d3829e6-f5b9-46d1-83e3-17efff814e09 stroke:#2c3143,stroke-width:4px;\n  5[\"Busco\"];\n  2 -->|output| 5;\n  a15e1214-23a2-484b-9c75-1635fcd61fe3[\"Output\\nBUSCO: short summary\"];\n  5 --> a15e1214-23a2-484b-9c75-1635fcd61fe3;\n  style a15e1214-23a2-484b-9c75-1635fcd61fe3 stroke:#2c3143,stroke-width:4px;\n  7806088d-f657-4389-9d54-6a3bdfa233b2[\"Output\\nBUSCO: list of missing ortholog genes\"];\n  5 --> 7806088d-f657-4389-9d54-6a3bdfa233b2;\n  style 7806088d-f657-4389-9d54-6a3bdfa233b2 stroke:#2c3143,stroke-width:4px;\n  6a27d0f6-d83c-42b1-a7af-5f99ba5debe2[\"Output\\nBUSCO: full table\"];\n  5 --> 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2;\n  style 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2 stroke:#2c3143,stroke-width:4px;\n  6[\"Train Augustus\"];\n  2 -->|output| 6;\n  3 -->|output_gff| 6;\n  7[\"Genome annotation statistics\"];\n  3 -->|output_gff| 7;\n  2 -->|output| 7;\n  2bed9aa6-5f22-494d-9caa-f0ece8464f15[\"Output\\nGenome annotation statistics: graphs (first round)\"];\n  7 --> 2bed9aa6-5f22-494d-9caa-f0ece8464f15;\n  style 2bed9aa6-5f22-494d-9caa-f0ece8464f15 stroke:#2c3143,stroke-width:4px;\n  71d41ce2-e90d-435b-9b64-ab4320524770[\"Output\\nGenome annotation statistics: summary (first round)\"];\n  7 --> 71d41ce2-e90d-435b-9b64-ab4320524770;\n  style 71d41ce2-e90d-435b-9b64-ab4320524770 stroke:#2c3143,stroke-width:4px;\n  8[\"gffread\"];\n  3 -->|output_gff| 8;\n  2 -->|output| 8;\n  9[\"Train SNAP\"];\n  2 -->|output| 9;\n  3 -->|output_gff| 9;\n  10[\"Busco\"];\n  8 -->|output_exons| 10;\n  a79ab19d-9802-42ca-8ffa-8c197a16c8b8[\"Output\\nBusco summary first round\"];\n  10 --> a79ab19d-9802-42ca-8ffa-8c197a16c8b8;\n  style a79ab19d-9802-42ca-8ffa-8c197a16c8b8 stroke:#2c3143,stroke-width:4px;\n  11[\"Maker\"];\n  6 -->|output_tar| 11;\n  9 -->|output| 11;\n  2 -->|output| 11;\n  3 -->|output_full| 11;\n  12[\"gffread\"];\n  11 -->|output_gff| 12;\n  2 -->|output| 12;\n  13[\"Train Augustus\"];\n  2 -->|output| 13;\n  11 -->|output_gff| 13;\n  42d5aadd-3a8c-441d-913f-ee8745a99b0b[\"Output\\nAugus: trained model\"];\n  13 --> 42d5aadd-3a8c-441d-913f-ee8745a99b0b;\n  style 42d5aadd-3a8c-441d-913f-ee8745a99b0b stroke:#2c3143,stroke-width:4px;\n  14[\"Genome annotation statistics\"];\n  11 -->|output_gff| 14;\n  2 -->|output| 14;\n  9def2c6e-fd3c-4969-b5d4-d13c187c1144[\"Output\\nGenome annotation statistics: graphs (second round)\"];\n  14 --> 9def2c6e-fd3c-4969-b5d4-d13c187c1144;\n  style 9def2c6e-fd3c-4969-b5d4-d13c187c1144 stroke:#2c3143,stroke-width:4px;\n  61f7a150-a4a2-46b1-89f5-2170d466656e[\"Output\\nGenome annotation statistics: summary (second round)\"];\n  14 --> 61f7a150-a4a2-46b1-89f5-2170d466656e;\n  style 61f7a150-a4a2-46b1-89f5-2170d466656e stroke:#2c3143,stroke-width:4px;\n  15[\"Train SNAP\"];\n  2 -->|output| 15;\n  11 -->|output_gff| 15;\n  458887f7-0661-4bde-ab1a-875aac6caed8[\"Output\\nSNAP: trained model\"];\n  15 --> 458887f7-0661-4bde-ab1a-875aac6caed8;\n  style 458887f7-0661-4bde-ab1a-875aac6caed8 stroke:#2c3143,stroke-width:4px;\n  16[\"Busco\"];\n  12 -->|output_exons| 16;\n  f52b1b41-0ea5-4384-bd43-4927273c909c[\"Output\\nBusco summary second round\"];\n  16 --> f52b1b41-0ea5-4384-bd43-4927273c909c;\n  style f52b1b41-0ea5-4384-bd43-4927273c909c stroke:#2c3143,stroke-width:4px;\n  17[\"Maker\"];\n  13 -->|output_tar| 17;\n  15 -->|output| 17;\n  2 -->|output| 17;\n  11 -->|output_full| 17;\n  18[\"Map annotation ids\"];\n  17 -->|output_gff| 18;\n  63575dcf-54d1-4cb1-b5fb-a2810b4da807[\"Output\\nMap annotation ids: renamed GFF\"];\n  18 --> 63575dcf-54d1-4cb1-b5fb-a2810b4da807;\n  style 63575dcf-54d1-4cb1-b5fb-a2810b4da807 stroke:#2c3143,stroke-width:4px;\n  19[\"JBrowse\"];\n  2 -->|output| 19;\n  3 -->|output_gff| 19;\n  18 -->|renamed| 19;\n  11 -->|output_gff| 19;\n  3 -->|output_evidences| 19;\n  11 -->|output_evidences| 19;\n  17 -->|output_evidences| 19;\n  5a38ae83-e177-45f3-aa9f-4c1844584fa5[\"Output\\nJBrowse: report\"];\n  19 --> 5a38ae83-e177-45f3-aa9f-4c1844584fa5;\n  style 5a38ae83-e177-45f3-aa9f-4c1844584fa5 stroke:#2c3143,stroke-width:4px;\n  20[\"gffread\"];\n  18 -->|renamed| 20;\n  2 -->|output| 20;\n  52fcac23-b612-4377-a19a-2e3b667a23e3[\"Output\\nGffread: exons\"];\n  20 --> 52fcac23-b612-4377-a19a-2e3b667a23e3;\n  style 52fcac23-b612-4377-a19a-2e3b667a23e3 stroke:#2c3143,stroke-width:4px;\n  5c47c25e-0ddb-4ade-a5d0-873ff4add28c[\"Output\\nGffread: translation of cds\"];\n  20 --> 5c47c25e-0ddb-4ade-a5d0-873ff4add28c;\n  style 5c47c25e-0ddb-4ade-a5d0-873ff4add28c stroke:#2c3143,stroke-width:4px;\n  84d9183b-9589-464b-9f82-4dae7f87133e[\"Output\\nGffread: cds\"];\n  20 --> 84d9183b-9589-464b-9f82-4dae7f87133e;\n  style 84d9183b-9589-464b-9f82-4dae7f87133e stroke:#2c3143,stroke-width:4px;\n  21[\"Genome annotation statistics\"];\n  18 -->|renamed| 21;\n  2 -->|output| 21;\n  f5d4a6bf-1ff8-435a-8084-7921e25bff3a[\"Output\\nGenome annotation statistics: graphs (third round)\"];\n  21 --> f5d4a6bf-1ff8-435a-8084-7921e25bff3a;\n  style f5d4a6bf-1ff8-435a-8084-7921e25bff3a stroke:#2c3143,stroke-width:4px;\n  5a863bd4-10f2-4ac8-81b6-ce8b7f663e42[\"Output\\nGenome annotation statistics: summary (third round)\"];\n  21 --> 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42;\n  style 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42 stroke:#2c3143,stroke-width:4px;\n  22[\"Busco\"];\n  20 -->|output_exons| 22;\n  0bc78676-eecc-4168-894d-34c4ca07cdf3[\"Output\\nBusco summary final round\"];\n  22 --> 0bc78676-eecc-4168-894d-34c4ca07cdf3;\n  style 0bc78676-eecc-4168-894d-34c4ca07cdf3 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Genome annotation with Maker ",
                 "outputs": [
                     {
@@ -111485,20 +263804,19 @@
         ],
         "dir": "topics/genome-annotation/tutorials/functional",
         "edam_operation": [
-            "Fold recognition",
+            "Sequence alignment analysis",
             "Homology-based gene prediction",
-            "Genome annotation",
-            "Information extraction",
-            "Protein feature detection",
             "Sequence motif recognition",
-            "Sequence alignment analysis",
-            "Query and retrieval"
+            "Query and retrieval",
+            "Protein feature detection",
+            "Fold recognition",
+            "Information extraction",
+            "Genome annotation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
@@ -111524,7 +263842,7 @@
         "objectives": [
             "Perform functional annotation using EggNOG-mapper and InterProScan"
         ],
-        "pageviews": 3511,
+        "pageviews": 3537,
         "priority": 6,
         "pub_date": "2022-07-20",
         "questions": [
@@ -111532,10 +263850,10 @@
         ],
         "short_id": "T00173",
         "short_tools": [
-            "ncbi_blastp_wrapper",
+            "bg_diamond",
             "eggnog_mapper",
             "interproscan",
-            "bg_diamond"
+            "ncbi_blastp_wrapper"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -111552,11 +263870,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -111576,6 +263889,731 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
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@@ -111671,7 +264709,7 @@
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@@ -111999,7 +265037,7 @@
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@@ -112026,9 +265064,9 @@
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@@ -112054,6 +265092,580 @@
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+                                "1.16.5+galaxy7",
+                                "1.16.5+galaxy6",
+                                "1.16.8+galaxy0",
+                                "1.12.5+galaxy3",
+                                "1.16.5+galaxy3",
+                                "0.5.2.1",
+                                "1.16.1+galaxy0",
+                                "0.7.0.3",
+                                "1.16.8+galaxy1",
+                                "1.16.5+galaxy5",
+                                "1.16.4+galaxy2"
+                            ]
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+                        },
+                        {
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+                            "state": "exact",
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+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.16.11+galaxy1"
+                }
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         "tags": [
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@@ -112088,8 +265700,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 156,
-        "visitors": 900,
+        "visit_duration": 155,
+        "visitors": 906,
         "zenodo_link": "https://zenodo.org/record/3270822"
     },
     {
@@ -112189,10 +265801,10 @@
         ],
         "dir": "topics/genome-annotation/tutorials/lncrna",
         "edam_operation": [
-            "Sequence annotation",
-            "Classification",
             "Transcriptome assembly",
+            "Classification",
             "Annotation",
+            "Sequence annotation",
             "RNA-Seq analysis"
         ],
         "edam_topic": [],
@@ -112205,7 +265817,6 @@
             "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
@@ -112232,7 +265843,7 @@
             "Classify lncRNAs according to their location",
             "Update genome annotation with lncRNAs"
         ],
-        "pageviews": 1367,
+        "pageviews": 1383,
         "priority": 7,
         "pub_date": "2022-09-23",
         "questions": [
@@ -112295,10 +265906,141 @@
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
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+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
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+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
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+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
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+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
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+                {
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+                    "url": "http://hyperbrowser.uio.no/hb/"
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+                    "url": "http://gigagalaxy.net/"
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+                    "url": "https://galaxy.hyphy.org/",
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+                },
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+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
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+                    "url": "http://galaxy.interactomix.com/"
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+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
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+                    "url": "https://neo.engr.uconn.edu/"
+                },
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+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
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+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.be/",
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+                    "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
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+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
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                 {
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                     "url": "https://usegalaxy.no/",
@@ -112313,6 +266055,1395 @@
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
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+                                "1.0.3",
+                                "2.2.1+galaxy0",
+                                "2.2.3+galaxy0",
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+                                "1.2.3",
+                                "1.3.3.1",
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+                                "2.2.1+galaxy0",
+                                "2.2.3+galaxy0",
+                                "2.1.7",
+                                "1.3.3.1",
+                                "2.1.7+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
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+                    ],
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                 }
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         },
@@ -112353,7 +267484,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 122,
-        "visitors": 1008,
+        "visitors": 1023,
         "workflows": [
             {
                 "creators": [
@@ -112480,7 +267611,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmapped_RNASeq.bam\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ngenome_annotation.gff3\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ngenome_assembly.fasta\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"StringTie\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"gffread\"];\n  1 -->|output| 4;\n  5[\"FEELnc\"];\n  3 -->|output_gtf| 5;\n  2 -->|output| 5;\n  4 -->|output_gtf| 5;\n  4055b259-173c-492d-86a4-5e662b663421[\"Output\\nmRNAs\"];\n  5 --> 4055b259-173c-492d-86a4-5e662b663421;\n  style 4055b259-173c-492d-86a4-5e662b663421 stroke:#2c3143,stroke-width:4px;\n  abc029ba-b7ba-4586-88b4-5e5d758c2f39[\"Output\\nlncRNAs\"];\n  5 --> abc029ba-b7ba-4586-88b4-5e5d758c2f39;\n  style abc029ba-b7ba-4586-88b4-5e5d758c2f39 stroke:#2c3143,stroke-width:4px;\n  93ff3464-d1bb-4059-86af-3e703da3e542[\"Output\\nClassifier output\"];\n  5 --> 93ff3464-d1bb-4059-86af-3e703da3e542;\n  style 93ff3464-d1bb-4059-86af-3e703da3e542 stroke:#2c3143,stroke-width:4px;\n  6[\"Concatenate datasets\"];\n  4 -->|output_gtf| 6;\n  5 -->|candidate_lncRNA| 6;\n  7b91b6a4-ef67-4359-9c93-eabcc021b0fc[\"Output\\nfinal_annotation\"];\n  6 --> 7b91b6a4-ef67-4359-9c93-eabcc021b0fc;\n  style 7b91b6a4-ef67-4359-9c93-eabcc021b0fc stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Long non-coding RNAs (lncRNAs) annotation with FEELnc",
                 "outputs": [
                     {
@@ -112787,18 +267918,17 @@
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-            "Sequence trimming",
-            "Sequencing quality control",
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-            "Validation",
-            "Sequence composition calculation",
             "Genetic variation analysis",
+            "Primer removal",
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@@ -112827,7 +267957,7 @@
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             "Generate volcano plot to visualise results"
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-        "pageviews": 4524944,
+        "pageviews": 4556668,
         "priority": 8,
         "pub_date": "2021-10-15",
         "questions": [
@@ -112872,14 +268002,14 @@
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-            "mageck_test",
-            "mageck_mle",
-            "tp_awk_tool",
             "volcanoplot",
             "cutadapt",
+            "fastqc",
+            "tp_awk_tool",
+            "mageck_mle",
             "multiqc",
             "mageck_count",
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@@ -112899,11 +268029,6 @@
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@@ -112938,6 +268063,1827 @@
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+                                "1.6",
+                                "1.16.1",
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+                            "state": "inexact",
+                            "versions": [
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+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "3.5+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
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+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "3.5+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "3.5+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
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         "tags": [
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@@ -112980,7 +269926,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 274,
-        "visitors": 1730919,
+        "visitors": 1741405,
         "workflows": [
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@@ -113090,7 +270036,7 @@
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow constructed from history 'CRISPR tutorial Kenji'",
                 "outputs": [],
                 "parent_id": "genome-annotation/crispr-screen",
@@ -113193,10 +270139,10 @@
             "topic_0080"
         ],
         "edam_operation": [
-            "Genome visualisation",
+            "Coding region prediction",
             "Gene prediction",
-            "Genome annotation",
-            "Coding region prediction"
+            "Genome visualisation",
+            "Genome annotation"
         ],
         "edam_topic": [
             "Genomics",
@@ -113227,7 +270173,6 @@
             "MISSISSIPPI",
             "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
@@ -113248,7 +270193,7 @@
             "Annotate genome with Prokka",
             "View annotations in JBrowse"
         ],
-        "pageviews": 5925127,
+        "pageviews": 5956800,
         "pub_date": "2018-03-06",
         "questions": [
             "How can we annotate a bacterial genome?",
@@ -113270,8 +270215,8 @@
         ],
         "short_id": "T00168",
         "short_tools": [
-            "jbrowse",
-            "prokka"
+            "prokka",
+            "jbrowse"
         ],
         "slides": true,
         "slides_recordings": [
@@ -113329,19 +270274,629 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
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+                    "url": "http://apostl.moffitt.org/"
+                },
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
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+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
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+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
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+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
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+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
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+                    "name": "Genomic Hyperbrowser",
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+                },
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+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                    "url": "https://www.immportgalaxy.org/"
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+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                                "1.12.5+galaxy1",
+                                "1.12.5+galaxy2",
+                                "1.16.5+galaxy4",
+                                "1.12.5+galaxy0",
+                                "0.1",
+                                "1.16.4+galaxy3",
+                                "1.16.5+galaxy7",
+                                "1.16.5+galaxy6",
+                                "1.16.8+galaxy0",
+                                "1.12.5+galaxy3",
+                                "1.16.5+galaxy3",
+                                "0.5.2.1",
+                                "1.16.1+galaxy0",
+                                "0.7.0.3",
+                                "1.16.8+galaxy1",
+                                "1.16.5+galaxy5",
+                                "1.16.4+galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.16.11+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.16.11+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.16.11+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.16.11+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.16.11+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.16.11+galaxy1"
                 }
             ]
         },
@@ -113379,7 +270934,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 259,
-        "visitors": 2149523,
+        "visitors": 2160036,
         "workflows": [
             {
                 "creators": [
@@ -113510,7 +271065,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Genome Annotation with Prokka ",
                 "outputs": [
                     {
@@ -113841,8 +271396,8 @@
         ],
         "edam_operation": [
             "Genome visualisation",
-            "Genome annotation",
-            "Read mapping"
+            "Read mapping",
+            "Genome annotation"
         ],
         "edam_topic": [
             "Whole genome sequencing",
@@ -113855,8 +271410,7 @@
         ],
         "exact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -113899,7 +271453,7 @@
             "Get information about ARGs",
             "Visualize the ARGs and plasmid genes in their genomic context"
         ],
-        "pageviews": 1576,
+        "pageviews": 1633,
         "pub_date": "2024-01-23",
         "questions": [
             "Which resistance genes are on a bacterial genome?",
@@ -113923,12 +271477,12 @@
         "short_id": "T00401",
         "short_tools": [
             "jbrowse",
-            "tbl2gff3",
-            "upload1",
             "Grep1",
-            "staramr_search",
+            "tbl2gff3",
             "bakta",
-            "bowtie2"
+            "upload1",
+            "bowtie2",
+            "staramr_search"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -113944,11 +271498,6 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
                 }
             ],
             "inexact": [
@@ -113964,6 +271513,1163 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
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+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
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+                    "url": "https://usegalaxy.be/",
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+                },
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+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
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+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
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+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
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+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
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+                            "state": "local"
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+                            "state": "local"
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+                        {
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+                            "state": "local"
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+                        {
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+                            "state": "local"
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+                        {
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+                        },
+                        {
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+                            "state": "local"
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+                        {
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+                            "state": "local"
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+                        {
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+                            "state": "local"
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+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
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+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
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+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.5.1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.10.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.10.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.7.2+galaxy0",
+                                "0.8.0+galaxy0",
+                                "0.7.1+galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.10.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.10.0+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.10.0+galaxy1"
+                },
+                {
+                    "id": "upload1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "gmod",
@@ -114003,8 +272709,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 165,
-        "visitors": 1138,
+        "visit_duration": 178,
+        "visitors": 1181,
         "workflows": [
             {
                 "creators": [
@@ -114026,7 +272732,7 @@
                     "report": null,
                     "subworkflows": false
                 },
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                 ],
                 "license": "MIT",
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-                "modified": "2024-10-02 12:08:08 +0000",
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+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "mrsa AMR gene detection",
                 "outputs": [
                     {
@@ -114214,7 +272920,7 @@
                             {
                                 "label": "stararm_detailed_summary",
                                 "output_name": "detailed_summary",
-                                "uuid": "000e2ab9-92db-45bb-a0ef-ecccf06da616"
+                                "uuid": "455bde1a-6195-4ea2-9577-35eea97a546a"
                             }
                         ]
                     },
@@ -114288,7 +272994,7 @@
                             {
                                 "label": "bakta_annotation_summary",
                                 "output_name": "annotation_tsv",
-                                "uuid": "c848b1eb-7262-4627-b7a7-05a13b968935"
+                                "uuid": "065a7e6a-7ce3-4763-8698-959f019c6c76"
                             }
                         ]
                     },
@@ -114345,7 +273051,7 @@
                             {
                                 "label": "bowtie_mapping_stats",
                                 "output_name": "mapping_stats",
-                                "uuid": "352e63d3-8aca-4dff-878c-10497f65bb74"
+                                "uuid": "57f88358-7a42-45c7-a538-55476519e3ec"
                             }
                         ]
                     },
@@ -114398,7 +273104,7 @@
                             {
                                 "label": "jbrowse_output",
                                 "output_name": "output",
-                                "uuid": "3c3bd5fd-419c-45b2-afcd-c6d02af82695"
+                                "uuid": "bac18ad5-2731-45bc-8b53-5cfaca1e06c5"
                             }
                         ]
                     }
@@ -114666,7 +273372,7 @@
             "Learn how to manually refine genome annotations within Apollo",
             "Export refined genome annotations"
         ],
-        "pageviews": 5119570,
+        "pageviews": 5151198,
         "pub_date": "2021-06-04",
         "questions": [
             "How to visualize your genome after automated annotations have been performed?",
@@ -114708,9 +273414,9 @@
         "short_tools": [
             "jbrowse",
             "create_or_update",
+            "create_account",
             "iframe",
-            "list_organism",
-            "create_account"
+            "list_organism"
         ],
         "slides": true,
         "slides_recordings": [
@@ -114748,6 +273454,854 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/gga/apollo_create_account/create_account/3.1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
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         "tags": [
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@@ -114784,8 +274338,8 @@
         "video": true,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 299,
-        "visitors": 1906178,
+        "visit_duration": 300,
+        "visitors": 1916586,
         "workflows": [
             {
                 "creators": [],
@@ -114976,7 +274530,7 @@
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Apollo Load Test",
                 "outputs": [
                     {
@@ -115551,15 +275105,15 @@
             "topic_0798"
         ],
         "edam_operation": [
+            "Sequence motif recognition",
+            "Genome assembly",
+            "Genome visualisation",
+            "Protein feature detection",
             "Genome annotation",
-            "Nucleic acid feature detection",
             "Multilocus sequence typing",
-            "Genome visualisation",
-            "Genome assembly",
-            "Sequence motif recognition",
-            "Structural variation detection",
+            "Nucleic acid feature detection",
             "Scaffolding",
-            "Protein feature detection"
+            "Structural variation detection"
         ],
         "edam_topic": [
             "Genomics",
@@ -115571,8 +275125,7 @@
             "Mobile genetic elements"
         ],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -115625,7 +275178,7 @@
             "Process the outputs to formate them for visualization needs",
             "Visualize a draft bacterial genome and its annotations"
         ],
-        "pageviews": 2969,
+        "pageviews": 3039,
         "pub_date": "2024-02-01",
         "questions": [
             "Which genes are on a draft bacterial genome?",
@@ -115648,16 +275201,16 @@
         ],
         "short_id": "T00403",
         "short_tools": [
-            "jbrowse",
-            "tbl2gff3",
-            "plasmidfinder",
             "integron_finder",
-            "upload1",
-            "isescan",
+            "jbrowse",
             "tp_tail_tool",
             "bakta",
+            "tbl2gff3",
+            "upload1",
             "tp_replace_in_column",
-            "Grouping1"
+            "Grouping1",
+            "isescan",
+            "plasmidfinder"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -115668,28 +275221,1604 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                }
+            ],
+            "inexact": [
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+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
-            ],
-            "inexact": [
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+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
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+                },
+                {
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+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
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+                },
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                 {
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                     "url": "https://galaxy.mesocentre.uca.fr",
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+                },
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+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
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+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
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+                    "url": "http://galaxy.inf.ethz.ch"
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+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.2"
+                },
+                {
+                    "id": "upload1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
                 }
             ]
         },
@@ -115734,8 +276863,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 140,
-        "visitors": 2243,
+        "visit_duration": 138,
+        "visitors": 2301,
         "workflows": [
             {
                 "creators": [
@@ -115805,7 +276934,7 @@
                 ],
                 "license": "AGPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ncontigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"ISEScan\"];\n  0 -->|output| 1;\n  2bb672cb-4536-46b0-8a22-8590a0ca36c7[\"Output\\nisescan_results\"];\n  1 --> 2bb672cb-4536-46b0-8a22-8590a0ca36c7;\n  style 2bb672cb-4536-46b0-8a22-8590a0ca36c7 stroke:#2c3143,stroke-width:4px;\n  2[\"PlasmidFinder\"];\n  0 -->|output| 2;\n  614064e6-4b0f-4e38-b04e-e3f61ba41b46[\"Output\\nplasmidfinder_results\"];\n  2 --> 614064e6-4b0f-4e38-b04e-e3f61ba41b46;\n  style 614064e6-4b0f-4e38-b04e-e3f61ba41b46 stroke:#2c3143,stroke-width:4px;\n  3[\"Integron Finder\"];\n  0 -->|output| 3;\n  d26788cf-2441-4f29-ac39-b6be96f192eb[\"Output\\nintegronfinder_summary\"];\n  3 --> d26788cf-2441-4f29-ac39-b6be96f192eb;\n  style d26788cf-2441-4f29-ac39-b6be96f192eb stroke:#2c3143,stroke-width:4px;\n  4[\"Bakta\"];\n  0 -->|output| 4;\n  d3a40a8b-1bd1-42b6-a91e-756379b86d94[\"Output\\nbakta_summary\"];\n  4 --> d3a40a8b-1bd1-42b6-a91e-756379b86d94;\n  style d3a40a8b-1bd1-42b6-a91e-756379b86d94 stroke:#2c3143,stroke-width:4px;\n  5[\"Group\"];\n  1 -->|all_results| 5;\n  6[\"Group\"];\n  1 -->|all_results| 6;\n  7[\"Replace Text\"];\n  2 -->|result_file| 7;\n  8[\"Select last\"];\n  7 -->|outfile| 8;\n  9[\"Table to GFF3\"];\n  8 -->|outfile| 9;\n  10[\"JBrowse\"];\n  0 -->|output| 10;\n  4 -->|annotation_gff3| 10;\n  9 -->|output| 10;\n  1 -->|annotation| 10;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Bacterial Genome Annotation",
                 "outputs": [
                     {
@@ -116091,13 +277220,13 @@
                 {
                     "name": "intermine_galaxy_exchange",
                     "owner": "iuc",
-                    "revisions": "c24014d80001",
+                    "revisions": "faef2b1622a3",
                     "tool_panel_section_label": "Convert Formats",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: intermine_galaxy_exchange\n  owner: iuc\n  revisions: c24014d80001\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: intermine_galaxy_exchange\n  owner: iuc\n  revisions: faef2b1622a3\n  tool_panel_section_label: Convert Formats\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
         "api": "https://training.galaxyproject.org/training-material/api/topics/galaxy-interface/tutorials/intermine/tutorial.json",
         "contributions": {
             "authorship": [
@@ -116156,8 +277285,8 @@
         ],
         "short_id": "T00152",
         "short_tools": [
-            "intermine",
-            "galaxy_intermine_exchange"
+            "galaxy_intermine_exchange",
+            "intermine"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -116197,6 +277326,414 @@
             ],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "intermine",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/intermine_galaxy_exchange/galaxy_intermine_exchange/0.0.1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.0.1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.0.1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "gmod",
@@ -116287,7 +277824,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Create InterMine Interchange\"];\n  0 -->|output| 1;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Intermine import/export",
                 "outputs": [
                     {
@@ -116458,9 +277995,9 @@
             "topic_0199"
         ],
         "edam_operation": [
-            "Genome visualisation",
             "Variant calling",
             "Phylogenetic tree visualisation",
+            "Genome visualisation",
             "Phylogenetic tree generation"
         ],
         "edam_topic": [
@@ -116483,7 +278020,6 @@
         "inexact_supported_servers": [
             "GalaxyTrakr",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
@@ -116505,7 +278041,7 @@
             "Determine the effect of those variants on genomic features",
             "Understand if the SNP is potentially affecting the phenotype"
         ],
-        "pageviews": 20692,
+        "pageviews": 20722,
         "pub_date": "2018-02-26",
         "questions": [
             "How do we detect differences between a set of reads from a microorganism and a reference genome"
@@ -116548,19 +278084,459 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
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+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
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+                        {
+                            "server": "https://usegalaxy.no/",
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+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.7.0.3"
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+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.7.0.3"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
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+                            "state": "missing"
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+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
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+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "3.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "4.6.0+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "3.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "3.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "3.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
+                                "4.6.0+galaxy0",
+                                "4.5.0+galaxy1",
+                                "4.5.0"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "3.2"
                 }
             ]
         },
@@ -116597,7 +278573,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 119,
-        "visitors": 12475,
+        "visitors": 12499,
         "workflows": [
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@@ -116608,7 +278584,7 @@
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                 "name": "Microbial Variant Calling",
                 "outputs": [
                     {
@@ -116867,12 +278843,12 @@
                             {
                                 "label": "snippy_fasta",
                                 "output_name": "snpconsensus",
-                                "uuid": "419ad933-d100-406b-bd61-a70885eec0f8"
+                                "uuid": "f432cfbd-c6cc-49ad-9409-0495d7415813"
                             },
                             {
                                 "label": "snippy_tabular",
                                 "output_name": "snpsum",
-                                "uuid": "47781ae9-a682-40a9-aa61-b972e5e5c9af"
+                                "uuid": "5916043f-7be5-4efc-a4d4-ca603d18046a"
                             }
                         ]
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@@ -116928,7 +278904,7 @@
                             {
                                 "label": "jbrowse_html",
                                 "output_name": "output",
-                                "uuid": "6d6b3661-34ed-417a-b7b6-394afe7a0edd"
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                             }
                         ]
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@@ -117217,23 +279193,23 @@
             "topic_4013"
         ],
         "edam_operation": [
-            "Scatter plot plotting",
+            "Genome assembly",
             "Sequencing error detection",
-            "Sequence alignment",
+            "Sequence assembly visualisation",
+            "De-novo assembly",
+            "Filtering",
+            "Mapping assembly",
+            "Scatter plot plotting",
+            "Sequence assembly validation",
             "Visualisation",
             "Cross-assembly",
-            "Read mapping",
-            "Sequencing quality control",
-            "Genome assembly",
-            "De-novo assembly",
+            "Sequence alignment",
+            "Sequence composition calculation",
             "Box-Whisker plot plotting",
+            "Sequencing quality control",
+            "Read mapping",
             "Sequence contamination filtering",
-            "Sequence assembly validation",
-            "Mapping assembly",
-            "Statistical calculation",
-            "Sequence assembly visualisation",
-            "Filtering",
-            "Sequence composition calculation"
+            "Statistical calculation"
         ],
         "edam_topic": [
             "Sequence assembly",
@@ -117289,7 +279265,7 @@
             "Run tools to assess the quality of an assembly",
             "Understand the outputs of tools to assess the quality of an assembly"
         ],
-        "pageviews": 10977,
+        "pageviews": 11067,
         "pub_date": "2021-03-24",
         "questions": [
             "How to check the quality of the MinION data (together with Illumina data)?",
@@ -117298,18 +279274,18 @@
         ],
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-            "fastp",
-            "filtlong",
             "bandage_image",
-            "porechop",
-            "upload1",
-            "quast",
-            "flye",
+            "polypolish",
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             "bwa_mem2",
-            "polypolish",
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+            "fastp",
+            "porechop",
+            "CONVERTER_bz2_to_uncompressed",
+            "quast",
+            "flye"
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         "slides": false,
         "slides_recordings": false,
@@ -117329,6 +279305,2040 @@
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@@ -117492,7 +281502,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNanopore raw reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina forward raw reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nIllumina reverse raw reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Convert compressed file to uncompressed.\"];\n  0 -->|output| 3;\n  4[\"FastQC\"];\n  0 -->|output| 4;\n  5[\"fastp\"];\n  1 -->|output| 5;\n  2 -->|output| 5;\n  6[\"NanoPlot\"];\n  3 -->|output1| 6;\n  a97e6f33-8182-4a33-86dd-6cfbb83a842d[\"Output\\nnanoplot_before_filtering\"];\n  6 --> a97e6f33-8182-4a33-86dd-6cfbb83a842d;\n  style a97e6f33-8182-4a33-86dd-6cfbb83a842d stroke:#2c3143,stroke-width:4px;\n  7[\"filtlong\"];\n  5 -->|out1| 7;\n  5 -->|out2| 7;\n  0 -->|output| 7;\n  8[\"Flye\"];\n  7 -->|outfile| 8;\n  f12e718f-1bd5-490d-bd41-f0747aaa41a6[\"Output\\nflye_assembly_info\"];\n  8 --> f12e718f-1bd5-490d-bd41-f0747aaa41a6;\n  style f12e718f-1bd5-490d-bd41-f0747aaa41a6 stroke:#2c3143,stroke-width:4px;\n  9[\"NanoPlot\"];\n  7 -->|outfile| 9;\n  89524090-f590-434d-89e2-66f0b1a23c7c[\"Output\\nnanoplot_after_filtering\"];\n  9 --> 89524090-f590-434d-89e2-66f0b1a23c7c;\n  style 89524090-f590-434d-89e2-66f0b1a23c7c stroke:#2c3143,stroke-width:4px;\n  10[\"Bandage Image\"];\n  8 -->|assembly_gfa| 10;\n  11[\"BWA-MEM2\"];\n  5 -->|out2| 11;\n  8 -->|consensus| 11;\n  12[\"Quast\"];\n  8 -->|consensus| 12;\n  dabfb8fd-8791-4959-a9dc-9b3c1e57a69c[\"Output\\nquast_report_before_polishing\"];\n  12 --> dabfb8fd-8791-4959-a9dc-9b3c1e57a69c;\n  style dabfb8fd-8791-4959-a9dc-9b3c1e57a69c stroke:#2c3143,stroke-width:4px;\n  13[\"BWA-MEM2\"];\n  5 -->|out1| 13;\n  8 -->|consensus| 13;\n  14[\"Polypolish\"];\n  8 -->|consensus| 14;\n  13 -->|bam_output| 14;\n  11 -->|bam_output| 14;\n  15[\"Quast\"];\n  14 -->|polished_fasta| 15;\n  8 -->|consensus| 15;\n  4e465b51-68bf-4203-9a7c-897f46c70277[\"Output\\nquast_report_after_polishing\"];\n  15 --> 4e465b51-68bf-4203-9a7c-897f46c70277;\n  style 4e465b51-68bf-4203-9a7c-897f46c70277 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)",
                 "outputs": [
                     {
@@ -118017,9 +282027,9 @@
             "topic_3301"
         ],
         "edam_operation": [
+            "Read mapping",
             "Sequence alignment",
             "Sequence visualisation",
-            "Read mapping",
             "Genome visualisation",
             "Mapping"
         ],
@@ -118052,7 +282062,7 @@
             "Perform sequence comparison to locate rearrangements",
             "Identify genes located in deletions"
         ],
-        "pageviews": 12166,
+        "pageviews": 12192,
         "pub_date": "2018-06-14",
         "questions": [
             "I just assembled a genome. How does it compare with already sequenced genomes?",
@@ -118069,33 +282079,33 @@
         ],
         "short_id": "T00032",
         "short_tools": [
-            "join1",
+            "cat1",
             "tp_sed_tool",
             "lastz_wrapper_2",
-            "upload1",
-            "fasta_filter_by_length",
-            "bedtools_intersectbed",
-            "datamash_ops",
-            "circos_interval_to_tiles",
             "jbrowse",
-            "tp_cat",
-            "mergeCols1",
-            "Filter1",
-            "bedtools_sortbed",
-            "tp_sort_header_tool",
-            "Grep1",
-            "Cut1",
+            "circos_interval_to_tiles",
+            "tp_grep_tool",
+            "circos",
+            "bedtools_complementbed",
             "collapse_dataset",
-            "cat1",
+            "bedtools_intersectbed",
+            "upload1",
+            "datamash_ops",
             "tp_replace_in_column",
             "addValue",
-            "circos_aln_to_links",
-            "fasta_compute_length",
-            "circos",
-            "tp_grep_tool",
+            "Filter1",
             "tp_replace_in_line",
             "random_lines1",
-            "bedtools_complementbed"
+            "tp_sort_header_tool",
+            "Grep1",
+            "fasta_compute_length",
+            "mergeCols1",
+            "Cut1",
+            "fasta_filter_by_length",
+            "tp_cat",
+            "join1",
+            "bedtools_sortbed",
+            "circos_aln_to_links"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -118103,6 +282113,4276 @@
             "exact": [],
             "inexact": []
         },
+        "supported_servers_matrix": {
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
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+                    "name": "MISSISSIPPI",
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+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
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+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
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+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "servers": [
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+                        },
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+                        {
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+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
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+                            "server": "http://hyperbrowser.uio.no/hb/",
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
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+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                            "state": "local"
+                        },
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+                            "server": "https://palfinder.ls.manchester.ac.uk/",
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+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
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+                        {
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+                        },
+                        {
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+                        },
+                        {
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+                            "state": "local"
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+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
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+                    "id": "Filter1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
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+                        },
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+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
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+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
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+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
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+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
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+                            "server": "https://galaxy-web.ipk-gatersleben.de",
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+                        {
+                            "server": "https://www.immportgalaxy.org/",
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+                        {
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+                            "state": "local"
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+                    ],
+                    "version": "local"
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+                    "servers": [
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+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
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+                        },
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+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
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+                        {
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+                            "state": "local"
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+                        {
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+                            "state": "local"
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+                        {
+                            "server": "https://galaxytrakr.org/",
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+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
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+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
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+                        },
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
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+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                        {
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+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
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+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
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+                        },
+                        {
+                            "server": "https://usegalaxy.org",
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+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
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+                        {
+                            "server": "https://viralvariant.anses.fr/",
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+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "cat1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
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+                        {
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+                        {
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+                        {
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+                        },
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+                        },
+                        {
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+        "visitors": 6047,
         "workflows": [
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                 "creators": [],
@@ -118353,7 +286633,7 @@
                 ],
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Ecoli Comparison",
                 "outputs": [],
                 "parent_id": "assembly/ecoli_comparison",
@@ -118513,7 +286793,6 @@
             "Galaxy@AuBi",
             "UseGalaxy.be",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
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             "UseGalaxy.org.au"
@@ -118545,7 +286824,7 @@
             "Build several visualisations in JBrowse",
             "Have basic familiarity with moving around JBrowse, and loading several data tracks"
         ],
-        "pageviews": 5902528,
+        "pageviews": 5934160,
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             "How can I visualise features or blast data?",
@@ -118574,11 +286853,6 @@
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                     "usegalaxy": true
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@@ -118618,6 +286892,297 @@
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+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.16.9+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
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+                            "versions": [
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+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.16.9+galaxy0"
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+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.16.9+galaxy0"
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+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.16.9+galaxy0"
+                        },
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+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.16.9+galaxy0"
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+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
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+                    ],
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+                }
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@@ -118648,7 +287213,7 @@
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         "video_view": 0,
         "visit_duration": 287,
-        "visitors": 2137509,
+        "visitors": 2147987,
         "zenodo_link": "https://doi.org/10.5281/zenodo.3591856"
     },
     {
@@ -118749,7 +287314,7 @@
         "objectives": [
             "Validate your genes and create an official gene set from them."
         ],
-        "pageviews": 12,
+        "pageviews": 13,
         "pub_date": "2023-11-02",
         "questions": [
             "I have several genomes assemblies that are not annotated (or I do not trust annotations)",
@@ -118793,6 +287358,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
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+            "tools": []
+        },
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@@ -118822,7 +287391,7 @@
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         "video_view": 0,
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-        "visitors": 10,
+        "visitors": 11,
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     },
     {
@@ -118986,19 +287555,18 @@
         ],
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         "edam_operation": [
-            "Generation",
-            "Statistical calculation",
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
             "Sequence composition calculation",
+            "Sequencing quality control",
+            "Genome indexing",
+            "Read mapping",
             "Genome visualisation",
-            "Genome indexing"
+            "Statistical calculation",
+            "Sequence alignment",
+            "Generation"
         ],
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         "exact_supported_servers": [
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-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
@@ -119032,7 +287600,7 @@
             "Critique large data sets and use bioinformatics to assess genetics data",
             "Tap into the interdisciplinary nature of science"
         ],
-        "pageviews": 956,
+        "pageviews": 961,
         "pub_date": "2023-07-10",
         "questions": [
             "How do I check my data quality?",
@@ -119042,8 +287610,8 @@
         "short_id": "T00356",
         "short_tools": [
             "bwa_mem",
-            "fastqc",
-            "jbrowse"
+            "jbrowse",
+            "fastqc"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -119054,11 +287622,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
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-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -119108,6 +287671,620 @@
                 }
             ]
         },
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+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
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+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
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+                },
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+                },
+                {
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+                    "url": "http://dintor.eurac.edu/"
+                },
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+                },
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+                    "usegalaxy": false
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+                {
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+                },
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+                    "url": "http://gigagalaxy.net/"
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+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
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+                {
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
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+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
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+                    "url": "http://galaxy.interactomix.com/"
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+                    "url": "https://neo.engr.uconn.edu/"
+                },
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+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
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+                    "url": "https://usegalaxy.no/",
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+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
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@@ -119385,26 +288562,25 @@
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-            "Genome assembly",
             "Sequence motif recognition",
-            "Query and retrieval",
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@@ -119446,7 +288622,7 @@
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@@ -119492,16 +288668,16 @@
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-            "interproscan",
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+            "picard_MergeSamFiles",
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@@ -119513,11 +288689,6 @@
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@@ -119542,6 +288713,2200 @@
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+                        {
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+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
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+                            ]
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+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
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+                        {
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+                            "state": "missing"
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+                            "server": "https://galaxy.hyphy.org/",
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+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
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+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
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+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
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+                            ]
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+                        {
+                            "server": "https://neo.engr.uconn.edu/",
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+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.7.2b",
+                                "2.7.11a+galaxy0",
+                                "2.7.8a",
+                                "2.5.2b-0",
+                                "2.7.7a",
+                                "2.6.0b-1",
+                                "2.7.5b",
+                                "2.5.2b-2",
+                                "2.6.0b-2",
+                                "2.7.2a"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.7.10b+galaxy4",
+                                "2.7.10b+galaxy3"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.7.8a+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "2.7.8a+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2.7.8a+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.7.8a+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.7.8a+galaxy0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "gmod",
@@ -119586,7 +290951,7 @@
         "video_versions": 2,
         "video_view": 0,
         "visit_duration": 127,
-        "visitors": 7195,
+        "visitors": 7264,
         "workflows": [
             {
                 "creators": [
@@ -119799,7 +291164,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGenome assembly\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nRNASeq reads forward\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nRNASeq reads reverse\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nProtein evidence sequences\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nNCBI submission template\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gbk\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nAlternate annotation gff3\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"RNA STAR\"];\n  0 -->|output| 7;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  79cf59ea-3aef-4cb8-9c70-5b42e03a5da9[\"Output\\nMapped RNASeq\"];\n  7 --> 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9;\n  style 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9 stroke:#2c3143,stroke-width:4px;\n  8[\"Funannotate predict annotation\"];\n  3 -->|output| 8;\n  7 -->|mapped_reads| 8;\n  0 -->|output| 8;\n  9[\"eggNOG Mapper\"];\n  8 -->|fasta_proteins| 9;\n  10[\"InterProScan\"];\n  8 -->|fasta_proteins| 10;\n  11[\"Funannotate functional\"];\n  9 -->|annotations| 11;\n  8 -->|annot_gbk| 11;\n  10 -->|outfile_xml| 11;\n  4 -->|output| 11;\n  d0694cd1-6d81-4d72-83b9-94cb57dc1502[\"Output\\nFinal annotation (genbank)\"];\n  11 --> d0694cd1-6d81-4d72-83b9-94cb57dc1502;\n  style d0694cd1-6d81-4d72-83b9-94cb57dc1502 stroke:#2c3143,stroke-width:4px;\n  9a1e7b70-1090-41ed-8637-65b7372a9f6c[\"Output\\nFinal annotation (CDS sequences)\"];\n  11 --> 9a1e7b70-1090-41ed-8637-65b7372a9f6c;\n  style 9a1e7b70-1090-41ed-8637-65b7372a9f6c stroke:#2c3143,stroke-width:4px;\n  99fffa40-2196-491d-9a66-559ebf2d9561[\"Output\\nFinal annotation (mRNA sequences)\"];\n  11 --> 99fffa40-2196-491d-9a66-559ebf2d9561;\n  style 99fffa40-2196-491d-9a66-559ebf2d9561 stroke:#2c3143,stroke-width:4px;\n  17b03b77-0485-4176-b2b3-03bfa2d3bcb0[\"Output\\nFinal annotation (protein sequences)\"];\n  11 --> 17b03b77-0485-4176-b2b3-03bfa2d3bcb0;\n  style 17b03b77-0485-4176-b2b3-03bfa2d3bcb0 stroke:#2c3143,stroke-width:4px;\n  4a0602fc-e6d2-43fc-9957-344707c22c05[\"Output\\nFinal annotation (GFF3)\"];\n  11 --> 4a0602fc-e6d2-43fc-9957-344707c22c05;\n  style 4a0602fc-e6d2-43fc-9957-344707c22c05 stroke:#2c3143,stroke-width:4px;\n  12[\"JBrowse\"];\n  0 -->|output| 12;\n  11 -->|gff3| 12;\n  7 -->|mapped_reads| 12;\n  ac4d8805-f123-44d2-b30f-8ac906cc471f[\"Output\\nJBrowse\"];\n  12 --> ac4d8805-f123-44d2-b30f-8ac906cc471f;\n  style ac4d8805-f123-44d2-b30f-8ac906cc471f stroke:#2c3143,stroke-width:4px;\n  13[\"Funannotate compare\"];\n  5 -->|output| 13;\n  11 -->|gbk| 13;\n  e531c81f-f6b7-4c82-a712-c562873ff714[\"Output\\nFunannotate compare report\"];\n  13 --> e531c81f-f6b7-4c82-a712-c562873ff714;\n  style e531c81f-f6b7-4c82-a712-c562873ff714 stroke:#2c3143,stroke-width:4px;\n  14[\"AEGeAn ParsEval\"];\n  6 -->|output| 14;\n  11 -->|gff3| 14;\n  0d776b46-2c1c-4083-9f9d-a213fa62eb81[\"Output\\nAEGeAN report\"];\n  14 --> 0d776b46-2c1c-4083-9f9d-a213fa62eb81;\n  style 0d776b46-2c1c-4083-9f9d-a213fa62eb81 stroke:#2c3143,stroke-width:4px;\n  15[\"Busco\"];\n  11 -->|fa_proteins| 15;\n  57a619f5-b331-4ca6-8e6e-72eb61860032[\"Output\\nBusco summary\"];\n  15 --> 57a619f5-b331-4ca6-8e6e-72eb61860032;\n  style 57a619f5-b331-4ca6-8e6e-72eb61860032 stroke:#2c3143,stroke-width:4px;\n  97d23764-ad4a-4d69-948c-c81afb76fbaf[\"Output\\nBusco image\"];\n  15 --> 97d23764-ad4a-4d69-948c-c81afb76fbaf;\n  style 97d23764-ad4a-4d69-948c-c81afb76fbaf stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Funannotate",
                 "outputs": [
                     {
@@ -120771,12 +292136,12 @@
         "dir": "topics/genome-annotation/tutorials/annotation-with-maker-short",
         "edam_operation": [
             "Sequence assembly validation",
-            "Genome annotation",
+            "Genome assembly",
+            "Transcriptome assembly",
             "Scaffolding",
+            "Genome visualisation",
             "Sequence annotation",
-            "Transcriptome assembly",
-            "Genome assembly",
-            "Genome visualisation"
+            "Genome annotation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -120805,7 +292170,7 @@
             "Evaluate annotation quality with BUSCO",
             "View annotations in JBrowse"
         ],
-        "pageviews": 4148,
+        "pageviews": 4243,
         "priority": 3,
         "pub_date": "2021-01-12",
         "questions": [
@@ -120814,13 +292179,13 @@
         ],
         "short_id": "T00167",
         "short_tools": [
+            "jcvi_gff_stats",
             "jbrowse",
-            "busco",
             "fasta-stats",
+            "busco",
+            "maker",
             "maker_map_ids",
-            "jcvi_gff_stats",
-            "gffread",
-            "maker"
+            "gffread"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -120835,6 +292200,1196 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
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+                    "url": "https://galaxy.pasteur.fr/",
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+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
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+                {
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+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
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+                    "url": "http://gigagalaxy.net/"
+                },
+                {
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+                    "usegalaxy": false
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+                {
+                    "name": "IPK Galaxy Blast Suite",
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+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                    "usegalaxy": false
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+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
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+                },
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+                    "usegalaxy": true
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+                    "usegalaxy": true
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+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
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@@ -121095,7 +293650,7 @@
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@@ -121879,17 +294434,17 @@
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-            "Genome annotation",
-            "Ab-initio gene prediction",
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@@ -121924,7 +294479,7 @@
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@@ -121933,15 +294488,15 @@
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+            "augustus_training",
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@@ -121982,6 +294537,1418 @@
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@@ -122022,7 +295989,7 @@
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@@ -122230,7 +296197,7 @@
                 ],
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7806088d-f657-4389-9d54-6a3bdfa233b2[\"Output\\nBUSCO: list of missing ortholog genes\"];\n  5 --> 7806088d-f657-4389-9d54-6a3bdfa233b2;\n  style 7806088d-f657-4389-9d54-6a3bdfa233b2 stroke:#2c3143,stroke-width:4px;\n  6a27d0f6-d83c-42b1-a7af-5f99ba5debe2[\"Output\\nBUSCO: full table\"];\n  5 --> 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2;\n  style 6a27d0f6-d83c-42b1-a7af-5f99ba5debe2 stroke:#2c3143,stroke-width:4px;\n  6[\"Train Augustus\"];\n  2 -->|output| 6;\n  3 -->|output_gff| 6;\n  7[\"Genome annotation statistics\"];\n  3 -->|output_gff| 7;\n  2 -->|output| 7;\n  2bed9aa6-5f22-494d-9caa-f0ece8464f15[\"Output\\nGenome annotation statistics: graphs (first round)\"];\n  7 --> 2bed9aa6-5f22-494d-9caa-f0ece8464f15;\n  style 2bed9aa6-5f22-494d-9caa-f0ece8464f15 stroke:#2c3143,stroke-width:4px;\n  71d41ce2-e90d-435b-9b64-ab4320524770[\"Output\\nGenome annotation statistics: summary (first round)\"];\n  7 --> 71d41ce2-e90d-435b-9b64-ab4320524770;\n  style 71d41ce2-e90d-435b-9b64-ab4320524770 stroke:#2c3143,stroke-width:4px;\n  8[\"gffread\"];\n  3 -->|output_gff| 8;\n  2 -->|output| 8;\n  9[\"Train SNAP\"];\n  2 -->|output| 9;\n  3 -->|output_gff| 9;\n  10[\"Busco\"];\n  8 -->|output_exons| 10;\n  a79ab19d-9802-42ca-8ffa-8c197a16c8b8[\"Output\\nBusco summary first round\"];\n  10 --> a79ab19d-9802-42ca-8ffa-8c197a16c8b8;\n  style a79ab19d-9802-42ca-8ffa-8c197a16c8b8 stroke:#2c3143,stroke-width:4px;\n  11[\"Maker\"];\n  6 -->|output_tar| 11;\n  9 -->|output| 11;\n  2 -->|output| 11;\n  3 -->|output_full| 11;\n  12[\"gffread\"];\n  11 -->|output_gff| 12;\n  2 -->|output| 12;\n  13[\"Train Augustus\"];\n  2 -->|output| 13;\n  11 -->|output_gff| 13;\n  42d5aadd-3a8c-441d-913f-ee8745a99b0b[\"Output\\nAugus: trained model\"];\n  13 --> 42d5aadd-3a8c-441d-913f-ee8745a99b0b;\n  style 42d5aadd-3a8c-441d-913f-ee8745a99b0b stroke:#2c3143,stroke-width:4px;\n  14[\"Genome annotation statistics\"];\n  11 -->|output_gff| 14;\n  2 -->|output| 14;\n  9def2c6e-fd3c-4969-b5d4-d13c187c1144[\"Output\\nGenome annotation statistics: graphs (second round)\"];\n  14 --> 9def2c6e-fd3c-4969-b5d4-d13c187c1144;\n  style 9def2c6e-fd3c-4969-b5d4-d13c187c1144 stroke:#2c3143,stroke-width:4px;\n  61f7a150-a4a2-46b1-89f5-2170d466656e[\"Output\\nGenome annotation statistics: summary (second round)\"];\n  14 --> 61f7a150-a4a2-46b1-89f5-2170d466656e;\n  style 61f7a150-a4a2-46b1-89f5-2170d466656e stroke:#2c3143,stroke-width:4px;\n  15[\"Train SNAP\"];\n  2 -->|output| 15;\n  11 -->|output_gff| 15;\n  458887f7-0661-4bde-ab1a-875aac6caed8[\"Output\\nSNAP: trained model\"];\n  15 --> 458887f7-0661-4bde-ab1a-875aac6caed8;\n  style 458887f7-0661-4bde-ab1a-875aac6caed8 stroke:#2c3143,stroke-width:4px;\n  16[\"Busco\"];\n  12 -->|output_exons| 16;\n  f52b1b41-0ea5-4384-bd43-4927273c909c[\"Output\\nBusco summary second round\"];\n  16 --> f52b1b41-0ea5-4384-bd43-4927273c909c;\n  style f52b1b41-0ea5-4384-bd43-4927273c909c stroke:#2c3143,stroke-width:4px;\n  17[\"Maker\"];\n  13 -->|output_tar| 17;\n  15 -->|output| 17;\n  2 -->|output| 17;\n  11 -->|output_full| 17;\n  18[\"Map annotation ids\"];\n  17 -->|output_gff| 18;\n  63575dcf-54d1-4cb1-b5fb-a2810b4da807[\"Output\\nMap annotation ids: renamed GFF\"];\n  18 --> 63575dcf-54d1-4cb1-b5fb-a2810b4da807;\n  style 63575dcf-54d1-4cb1-b5fb-a2810b4da807 stroke:#2c3143,stroke-width:4px;\n  19[\"JBrowse\"];\n  2 -->|output| 19;\n  3 -->|output_gff| 19;\n  18 -->|renamed| 19;\n  11 -->|output_gff| 19;\n  3 -->|output_evidences| 19;\n  11 -->|output_evidences| 19;\n  17 -->|output_evidences| 19;\n  5a38ae83-e177-45f3-aa9f-4c1844584fa5[\"Output\\nJBrowse: report\"];\n  19 --> 5a38ae83-e177-45f3-aa9f-4c1844584fa5;\n  style 5a38ae83-e177-45f3-aa9f-4c1844584fa5 stroke:#2c3143,stroke-width:4px;\n  20[\"gffread\"];\n  18 -->|renamed| 20;\n  2 -->|output| 20;\n  52fcac23-b612-4377-a19a-2e3b667a23e3[\"Output\\nGffread: exons\"];\n  20 --> 52fcac23-b612-4377-a19a-2e3b667a23e3;\n  style 52fcac23-b612-4377-a19a-2e3b667a23e3 stroke:#2c3143,stroke-width:4px;\n  5c47c25e-0ddb-4ade-a5d0-873ff4add28c[\"Output\\nGffread: translation of cds\"];\n  20 --> 5c47c25e-0ddb-4ade-a5d0-873ff4add28c;\n  style 5c47c25e-0ddb-4ade-a5d0-873ff4add28c stroke:#2c3143,stroke-width:4px;\n  84d9183b-9589-464b-9f82-4dae7f87133e[\"Output\\nGffread: cds\"];\n  20 --> 84d9183b-9589-464b-9f82-4dae7f87133e;\n  style 84d9183b-9589-464b-9f82-4dae7f87133e stroke:#2c3143,stroke-width:4px;\n  21[\"Genome annotation statistics\"];\n  18 -->|renamed| 21;\n  2 -->|output| 21;\n  f5d4a6bf-1ff8-435a-8084-7921e25bff3a[\"Output\\nGenome annotation statistics: graphs (third round)\"];\n  21 --> f5d4a6bf-1ff8-435a-8084-7921e25bff3a;\n  style f5d4a6bf-1ff8-435a-8084-7921e25bff3a stroke:#2c3143,stroke-width:4px;\n  5a863bd4-10f2-4ac8-81b6-ce8b7f663e42[\"Output\\nGenome annotation statistics: summary (third round)\"];\n  21 --> 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42;\n  style 5a863bd4-10f2-4ac8-81b6-ce8b7f663e42 stroke:#2c3143,stroke-width:4px;\n  22[\"Busco\"];\n  20 -->|output_exons| 22;\n  0bc78676-eecc-4168-894d-34c4ca07cdf3[\"Output\\nBusco summary final round\"];\n  22 --> 0bc78676-eecc-4168-894d-34c4ca07cdf3;\n  style 0bc78676-eecc-4168-894d-34c4ca07cdf3 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Genome annotation with Maker ",
                 "outputs": [
                     {
@@ -123265,7 +297232,7 @@
             "Learn how to manually refine genome annotations within Apollo",
             "Export refined genome annotations"
         ],
-        "pageviews": 1584,
+        "pageviews": 1591,
         "priority": 6,
         "pub_date": "2022-08-22",
         "questions": [
@@ -123292,9 +297259,9 @@
         ],
         "short_id": "T00170",
         "short_tools": [
+            "iframe",
             "jbrowse",
-            "create_or_update",
-            "iframe"
+            "create_or_update"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -123320,6 +297287,580 @@
                 }
             ]
         },
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+                    "url": "http://apostl.moffitt.org/"
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+                },
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+                },
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+                            "state": "missing"
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+                        {
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+                            "state": "exact",
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+                        {
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+                            "state": "exact",
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         "tags": [
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@@ -123354,8 +297895,8 @@
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         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 156,
-        "visitors": 900,
+        "visit_duration": 155,
+        "visitors": 906,
         "zenodo_link": "https://zenodo.org/record/3270822"
     },
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@@ -123513,7 +298054,7 @@
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             "Track objects over multiple frames using CellProfiler in Galaxy"
         ],
-        "pageviews": 2318,
+        "pageviews": 2331,
         "pub_date": "2021-03-17",
         "questions": [
             "How to segment and track objects in fluorescence time-lapse microscopy images?"
@@ -123529,17 +298070,17 @@
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         "short_id": "T00182",
         "short_tools": [
-            "cp_overlay_outlines",
-            "cp_common",
-            "cp_save_images",
+            "cp_color_to_gray",
+            "cp_measure_object_intensity",
+            "cp_measure_object_size_shape",
+            "cp_export_to_spreadsheet",
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-            "cp_export_to_spreadsheet",
-            "cp_color_to_gray",
-            "cp_measure_object_size_shape",
+            "cp_overlay_outlines",
+            "cp_common",
+            "cp_save_images",
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         ],
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@@ -123565,6 +298106,1777 @@
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+                            "state": "inexact",
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+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.2"
+                        },
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+                            "state": "exact",
+                            "version": "0.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
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+                    ],
+                    "version": "0.2"
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+        },
         "symlink": null,
         "time_estimation": "1H",
         "title": "Object tracking using CellProfiler",
@@ -123602,7 +299914,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 62,
-        "visitors": 1841,
+        "visitors": 1853,
         "workflows": [
             {
                 "creators": [],
@@ -123681,7 +299993,7 @@
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "CP_object_tracking_example",
                 "outputs": [
                     {
@@ -124594,7 +300906,7 @@
             "How to handle images in Galaxy.",
             "How to perform basic image processing in Galaxy."
         ],
-        "pageviews": 2945,
+        "pageviews": 2947,
         "pub_date": "2019-08-13",
         "questions": [
             "How do I use Galaxy with imaging data?",
@@ -124605,15 +300917,15 @@
         ],
         "short_id": "T00181",
         "short_tools": [
-            "ip_threshold",
-            "ip_overlay_images",
             "ip_histogram_equalization",
-            "ip_binary_to_labelimage",
-            "unzip",
-            "ip_imageinfo",
             "ip_filter_standard",
             "ip_count_objects",
-            "ip_convertimage"
+            "ip_binary_to_labelimage",
+            "ip_imageinfo",
+            "ip_convertimage",
+            "ip_overlay_images",
+            "unzip",
+            "ip_threshold"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -124637,6 +300949,2529 @@
                 }
             ]
         },
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+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
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+                    "url": "https://galaxytrakr.org/",
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@@ -124682,7 +303517,7 @@
         "video_versions": 0,
         "video_view": 0,
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-        "visitors": 2029,
+        "visitors": 2031,
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@@ -124790,7 +303625,7 @@
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow constructed from Tutorial 'Introduction to image analysis using Galaxy'",
                 "outputs": [
                     {
@@ -125048,7 +303883,7 @@
             "Understand the tools available in Galaxy for multiplex tissue imaging analysis",
             "Analyze and visualize publicly available TMA data using Galaxy"
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-        "pageviews": 1069,
+        "pageviews": 1106,
         "pub_date": "2023-02-14",
         "questions": [
             "What tools are available for pre-processing multiplex tissue images in Galaxy?",
@@ -125059,16 +303894,16 @@
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@@ -125087,6 +303922,1508 @@
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+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "2.2.8+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "2.2.8+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.2.8+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "2.2.8+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.2.8+galaxy1"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.5.3+galaxy1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.5.3+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.5.1+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "inexact",
+                            "versions": [
+                                "1.5.1+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.5.1+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.5.3+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.5.3+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.5.3+galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "3H",
         "title": "End-to-End Tissue Microarray Image Analysis with Galaxy-ME",
@@ -125121,8 +305458,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 115,
-        "visitors": 774,
+        "visit_duration": 118,
+        "visitors": 794,
         "workflows": [
             {
                 "creators": [],
@@ -125257,7 +305594,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nmarkers.csv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nPhenotypeWorkflow\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"BaSiC Illumination\"];\n  0 -->|output| 3;\n  4[\"ASHLAR\"];\n  3 -->|output_dfp| 4;\n  3 -->|output_ffp| 4;\n  0 -->|output| 4;\n  1 -->|output| 4;\n  5[\"UNetCoreograph\"];\n  4 -->|output| 5;\n  6[\"Mesmer\"];\n  5 -->|tma_sections| 6;\n  ee73bee3-59e7-4e1c-87fd-197b8eac7e15[\"Output\\nMesmer on input dataset(s): Mask\"];\n  6 --> ee73bee3-59e7-4e1c-87fd-197b8eac7e15;\n  style ee73bee3-59e7-4e1c-87fd-197b8eac7e15 stroke:#2c3143,stroke-width:4px;\n  7[\"Convert image\"];\n  5 -->|tma_sections| 7;\n  8[\"MCQUANT\"];\n  1 -->|output| 8;\n  5 -->|tma_sections| 8;\n  6 -->|mask| 8;\n  fe28534a-2b3f-4ecc-8ba9-a106b2d1425c[\"Output\\nPrimary Mask Quantification\"];\n  8 --> fe28534a-2b3f-4ecc-8ba9-a106b2d1425c;\n  style fe28534a-2b3f-4ecc-8ba9-a106b2d1425c stroke:#2c3143,stroke-width:4px;\n  9[\"Rename OME-TIFF Channels\"];\n  1 -->|output| 9;\n  7 -->|output| 9;\n  10[\"Convert McMicro Output to Anndata\"];\n  8 -->|cellmask| 10;\n  11[\"Single Cell Phenotyping\"];\n  10 -->|outfile| 11;\n  2 -->|output| 11;\n  12[\"Vitessce Visualization\"];\n  11 -->|output| 12;\n  9 -->|renamed_image| 12;\n  6 -->|mask| 12;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GTN_Exemplar_002_TMA_workflow",
                 "outputs": [
                     {
@@ -126160,7 +306497,6 @@
         "id": "imaging/tutorial-CP",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
@@ -126182,7 +306518,7 @@
             "How to segment cell nucleoli using CellProfiler in Galaxy.",
             "How to extract features for images, nuclei and nucleoli."
         ],
-        "pageviews": 5902177,
+        "pageviews": 5933805,
         "pub_date": "2020-07-01",
         "questions": [
             "How do I run an image analysis pipeline on public data using CellProfiler?",
@@ -126199,25 +306535,25 @@
         "short_id": "T00183",
         "short_tools": [
             "cp_convert_objects_to_image",
+            "cp_measure_image_intensity",
+            "idr_download_by_ids",
+            "cp_relate_objects",
             "cp_common",
             "cp_save_images",
-            "cp_identify_primary_objects",
             "cp_mask_image",
-            "cp_export_to_spreadsheet",
-            "cp_display_data_on_image",
-            "cp_gray_to_color",
-            "cp_measure_image_intensity",
-            "cp_measure_texture",
+            "cp_identify_primary_objects",
+            "cp_measure_image_area_occupied",
+            "cp_measure_image_quality",
             "cp_cellprofiler",
-            "cp_measure_object_intensity",
+            "cp_display_data_on_image",
             "cp_measure_granularity",
-            "cp_measure_image_quality",
-            "cp_measure_object_size_shape",
-            "cp_image_math",
-            "idr_download_by_ids",
             "cp_enhance_or_suppress_features",
-            "cp_measure_image_area_occupied",
-            "cp_relate_objects"
+            "cp_gray_to_color",
+            "cp_image_math",
+            "cp_measure_object_size_shape",
+            "cp_measure_texture",
+            "cp_export_to_spreadsheet",
+            "cp_measure_object_intensity"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -126241,19 +306577,2902 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "3.1.9"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "3.1.9+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "3.1.9"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "3.1.9"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "3.1.9"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "3.1.9"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
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+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "0.41"
+                        },
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+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.44"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.41"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.42",
+                                "0.43",
+                                "0.44"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
+                                "0.44.1"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.41"
                 }
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         },
@@ -126301,8 +309520,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 229,
-        "visitors": 2136907,
+        "visit_duration": 228,
+        "visitors": 2147384,
         "workflows": [
             {
                 "creators": [],
@@ -126368,7 +309587,7 @@
                 "inputs": [],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"Starting modules\"];\n  1[\"Download images\"];\n  2[\"Segment complete nuclei\"];\n  0 -->|output_pipeline| 2;\n  3[\"Segmentation mask complete nuclei\"];\n  2 -->|output_pipeline| 3;\n  4[\"Label nuclei\"];\n  3 -->|output_pipeline| 4;\n  5[\"Save labelled nuclei\"];\n  4 -->|output_pipeline| 5;\n  6[\"Detect dark holes in nuclei\"];\n  5 -->|output_pipeline| 6;\n  7[\"Segment nucleoli that fall inside nuclei\"];\n  6 -->|output_pipeline| 7;\n  8[\"Segment nucleoli\"];\n  7 -->|output_pipeline| 8;\n  9[\"Convert the segmented nucleoli into an image\"];\n  8 -->|output_pipeline| 9;\n  10[\"Combine masks nuclei + nucleoli\"];\n  9 -->|output_pipeline| 10;\n  11[\"Save combined segmentation masks\"];\n  10 -->|output_pipeline| 11;\n  12[\"Segment all nuclei\"];\n  11 -->|output_pipeline| 12;\n  13[\"Segmentation mask nucleoli including cells touching borders\"];\n  12 -->|output_pipeline| 13;\n  14[\"Extract background\"];\n  13 -->|output_pipeline| 14;\n  15[\"Measure the image granularity\"];\n  14 -->|output_pipeline| 15;\n  16[\"Measure the nuclei texture\"];\n  15 -->|output_pipeline| 16;\n  17[\"Measure the nuclei intensity\"];\n  16 -->|output_pipeline| 17;\n  18[\"Measure size and shape of nuclei and nucleoli\"];\n  17 -->|output_pipeline| 18;\n  19[\"Relate nucleoli with their parent nuclei\"];\n  18 -->|output_pipeline| 19;\n  20[\"Measure the image quality\"];\n  19 -->|output_pipeline| 20;\n  21[\"Measure the area occupied by nuclei and nucleoli\"];\n  20 -->|output_pipeline| 21;\n  22[\"Measure the image intensity\"];\n  21 -->|output_pipeline| 22;\n  23[\"Export measurements\"];\n  22 -->|output_pipeline| 23;\n  24[\"Run CellProfiler\"];\n  1 -->|output_tar| 24;\n  23 -->|output_pipeline| 24;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "CP_pipeline_IDR_training",
                 "outputs": [
                     {
@@ -127596,13 +310815,6 @@
                     "tool_panel_section_label": "Imaging",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
-                {
-                    "name": "2d_split_binaryimage_by_watershed",
-                    "owner": "imgteam",
-                    "revisions": "f8f7987586b7",
-                    "tool_panel_section_label": "Imaging",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
                 {
                     "name": "unzip",
                     "owner": "imgteam",
@@ -127619,7 +310831,7 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: 2d_auto_threshold\n  owner: imgteam\n  revisions: 0c777d708acc\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_auto_threshold\n  owner: imgteam\n  revisions: 3df9f0a4bf34\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_feature_extraction\n  owner: imgteam\n  revisions: 5791a7f65275\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_feature_extraction\n  owner: imgteam\n  revisions: 0a53256b48c6\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_filter_segmentation_by_features\n  owner: imgteam\n  revisions: e576b73a2e2f\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_simple_filter\n  owner: imgteam\n  revisions: dba87c4b32d3\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_simple_filter\n  owner: imgteam\n  revisions: f70b215d155c\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_split_binaryimage_by_watershed\n  owner: imgteam\n  revisions: f8f7987586b7\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unzip\n  owner: imgteam\n  revisions: 57f0914ddb7b\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: 2d_auto_threshold\n  owner: imgteam\n  revisions: 0c777d708acc\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_auto_threshold\n  owner: imgteam\n  revisions: 3df9f0a4bf34\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_feature_extraction\n  owner: imgteam\n  revisions: 5791a7f65275\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_feature_extraction\n  owner: imgteam\n  revisions: 0a53256b48c6\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_filter_segmentation_by_features\n  owner: imgteam\n  revisions: e576b73a2e2f\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_simple_filter\n  owner: imgteam\n  revisions: dba87c4b32d3\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: 2d_simple_filter\n  owner: imgteam\n  revisions: f70b215d155c\n  tool_panel_section_label: Imaging\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: unzip\n  owner: imgteam\n  revisions: 57f0914ddb7b\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
         "api": "https://training.galaxyproject.org/training-material/api/topics/imaging/tutorials/hela-screen-analysis/tutorial.json",
         "contributors": [
             {
@@ -127699,7 +310911,7 @@
             "How to extract features from an imaging screen in Galaxy.",
             "How to analyse extracted features from an imaging screen in Galaxy."
         ],
-        "pageviews": 736,
+        "pageviews": 737,
         "pub_date": "2019-08-13",
         "questions": [
             "How do I analyze a HeLa fluorescence siRNA screen?",
@@ -127720,13 +310932,13 @@
         ],
         "short_id": "T00180",
         "short_tools": [
+            "collapse_dataset",
             "ip_2d_split_binaryimage_by_watershed",
+            "ip_filter_standard",
             "ip_2d_feature_extraction",
-            "ip_threshold",
             "unzip",
-            "ip_filter_standard",
             "ip_2d_filter_segmentation_by_features",
-            "collapse_dataset"
+            "ip_threshold"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -127755,6 +310967,1680 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
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+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "5.1.0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "HeLa"
@@ -127794,7 +312680,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 163,
-        "visitors": 565,
+        "visitors": 566,
         "workflows": [
             {
                 "creators": [
@@ -127922,7 +312808,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\ninput images\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nrules\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\ud83d\udee0\ufe0f Subworkflow\\nfeature_extraction\"];\n  style 2 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"merge_table\"];\n  2 -->|output| 3;\n  3fc2324d-233b-4785-9fb7-9c30b2daaef4[\"Output\\noutput\"];\n  3 --> 3fc2324d-233b-4785-9fb7-9c30b2daaef4;\n  style 3fc2324d-233b-4785-9fb7-9c30b2daaef4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "analyze_screen",
                 "outputs": [
                     {
@@ -128127,7 +313013,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ninput image\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nrules\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Filter Image\"];\n  0 -->|output| 2;\n  3[\"Auto Threshold\"];\n  2 -->|output| 3;\n  4[\"Split objects\"];\n  3 -->|output| 4;\n  5[\"2D Feature Extraction\"];\n  4 -->|output| 5;\n  6[\"Filter segmentation\"];\n  5 -->|output| 6;\n  4 -->|output| 6;\n  1 -->|output| 6;\n  b90cbc94-33fd-4600-96b5-8cf0bcaf2e94[\"Output\\noutput\"];\n  6 --> b90cbc94-33fd-4600-96b5-8cf0bcaf2e94;\n  style b90cbc94-33fd-4600-96b5-8cf0bcaf2e94 stroke:#2c3143,stroke-width:4px;\n  7[\"2D Feature Extraction\"];\n  6 -->|output| 7;\n  0 -->|output| 7;\n  3d3c037a-50ef-443b-a6f8-8a37db6bfb36[\"Output\\noutput\"];\n  7 --> 3d3c037a-50ef-443b-a6f8-8a37db6bfb36;\n  style 3d3c037a-50ef-443b-a6f8-8a37db6bfb36 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "feature_extraction",
                 "outputs": [
                     {
@@ -128377,7 +313263,7 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-10-02",
+        "mod_date": "2024-10-08",
         "objectives": [
             "Locate bioimage data repositories",
             "Compare repositories to find which are suitable for your data",
@@ -128385,7 +313271,7 @@
         ],
         "pageviews": 0,
         "priority": 4,
-        "pub_date": "2024-10-02",
+        "pub_date": "2024-10-08",
         "questions": [
             "What are the commonly used repositories for bioimaging data?",
             "Which repositories are suitable for my data?",
@@ -128439,6 +313325,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
+        },
         "symlink": true,
         "tags": [
             "fair",
@@ -128579,7 +313469,7 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-10-02",
+        "mod_date": "2024-10-08",
         "objectives": [
             "Organise bioimage metadata",
             "Find out what REMBI is and why it is useful",
@@ -128588,7 +313478,7 @@
         ],
         "pageviews": 0,
         "priority": 5,
-        "pub_date": "2024-10-02",
+        "pub_date": "2024-10-08",
         "questions": [
             "What is REMBI and why should I use it?",
             "What information should be included when collecting bioimage data?"
@@ -128652,6 +313542,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
+        },
         "symlink": true,
         "tags": [
             "fair",
@@ -128918,7 +313812,6 @@
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
@@ -128953,7 +313846,7 @@
             "Learn how to create a workflow",
             "Learn how to share your work"
         ],
-        "pageviews": 30397,
+        "pageviews": 30440,
         "pub_date": "2016-03-29",
         "questions": [
             "How to use Galaxy?",
@@ -128961,16 +313854,16 @@
         ],
         "short_id": "T00189",
         "short_tools": [
-            "CONVERTER_interval_to_bed_0",
-            "upload1",
-            "tp_sort_header_tool",
             "Cut1",
-            "Add_a_column1",
-            "get_flanks1",
+            "tp_sort_header_tool",
             "gops_intersect_1",
             "tp_tail_tool",
+            "upload1",
+            "get_flanks1",
             "tp_replace_in_column",
-            "Grouping1"
+            "Grouping1",
+            "Add_a_column1",
+            "CONVERTER_interval_to_bed_0"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -128982,11 +313875,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -129011,6 +313899,1671 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "CONVERTER_interval_to_bed_0",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Cut1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Grouping1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
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+                            "server": "https://galaxytrakr.org/",
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+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
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+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
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+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "3H",
         "title": "From peaks to genes",
@@ -129047,7 +315600,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 201,
-        "visitors": 18132,
+        "visitors": 18167,
         "workflows": [
             {
                 "creators": [],
@@ -129058,7 +315611,7 @@
                     "report": null,
                     "subworkflows": false
                 },
-                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPeaks\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenes\"]\n  2[label=\"Select last\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Replace Text\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Get flanks\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Replace Text\"]\n  3 -> 5 [label=\"outfile\"]\n  6[label=\"Replace Text\"]\n  5 -> 6 [label=\"outfile\"]\n  7[label=\"Convert Genomic Intervals To BED\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"Intersect\"]\n  4 -> 8 [label=\"out_file1\"]\n  7 -> 8 [label=\"output1\"]\n  9[label=\"Group\"]\n  8 -> 9 [label=\"output\"]\n  kc5516cb081d74425b0b580c1cf1e8255[color=lightseagreen,label=\"Output\\nchr_count\"]\n  9 -> kc5516cb081d74425b0b580c1cf1e8255\n}",
+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nPeaks\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nGenes\"]\n  2[label=\"Select last\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Replace Text\"]\n  0 -> 3 [label=\"output\"]\n  4[label=\"Get flanks\"]\n  1 -> 4 [label=\"output\"]\n  5[label=\"Replace Text\"]\n  3 -> 5 [label=\"outfile\"]\n  6[label=\"Replace Text\"]\n  5 -> 6 [label=\"outfile\"]\n  7[label=\"Convert Genomic Intervals To BED\"]\n  6 -> 7 [label=\"outfile\"]\n  8[label=\"Intersect\"]\n  4 -> 8 [label=\"out_file1\"]\n  7 -> 8 [label=\"output1\"]\n  9[label=\"Group\"]\n  8 -> 9 [label=\"output\"]\n  kc1704d6987d24cf48fdd2ce2360ef6d1[color=lightseagreen,label=\"Output\\nchr_count\"]\n  9 -> kc1704d6987d24cf48fdd2ce2360ef6d1\n}",
                 "history": [
                     {
                         "hash": "48c2e99e6ac6b3f944b81c5725182a61c3a85d81",
@@ -129123,8 +315676,8 @@
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPeaks\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGenes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Select last\"];\n  0 -->|output| 2;\n  3[\"Replace Text\"];\n  0 -->|output| 3;\n  4[\"Get flanks\"];\n  1 -->|output| 4;\n  5[\"Replace Text\"];\n  3 -->|outfile| 5;\n  6[\"Replace Text\"];\n  5 -->|outfile| 6;\n  7[\"Convert Genomic Intervals To BED\"];\n  6 -->|outfile| 7;\n  8[\"Intersect\"];\n  4 -->|out_file1| 8;\n  7 -->|output1| 8;\n  9[\"Group\"];\n  8 -->|output| 9;\n  c5516cb0-81d7-4425-b0b5-80c1cf1e8255[\"Output\\nchr_count\"];\n  9 --> c5516cb0-81d7-4425-b0b5-80c1cf1e8255;\n  style c5516cb0-81d7-4425-b0b5-80c1cf1e8255 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPeaks\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGenes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Select last\"];\n  0 -->|output| 2;\n  3[\"Replace Text\"];\n  0 -->|output| 3;\n  4[\"Get flanks\"];\n  1 -->|output| 4;\n  5[\"Replace Text\"];\n  3 -->|outfile| 5;\n  6[\"Replace Text\"];\n  5 -->|outfile| 6;\n  7[\"Convert Genomic Intervals To BED\"];\n  6 -->|outfile| 7;\n  8[\"Intersect\"];\n  4 -->|out_file1| 8;\n  7 -->|output1| 8;\n  9[\"Group\"];\n  8 -->|output| 9;\n  c1704d69-87d2-4cf4-8fdd-2ce2360ef6d1[\"Output\\nchr_count\"];\n  9 --> c1704d69-87d2-4cf4-8fdd-2ce2360ef6d1;\n  style c1704d69-87d2-4cf4-8fdd-2ce2360ef6d1 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Galaxy Introduction Peaks2Genes - Part 1",
                 "outputs": [
                     {
@@ -129161,7 +315714,7 @@
                             {
                                 "label": "chr_count",
                                 "output_name": "out_file1",
-                                "uuid": "c5516cb0-81d7-4425-b0b5-80c1cf1e8255"
+                                "uuid": "c1704d69-87d2-4cf4-8fdd-2ce2360ef6d1"
                             }
                         ]
                     }
@@ -129271,7 +315824,6 @@
         "inexact_supported_servers": [
             "MISSISSIPPI",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no"
         ],
         "js_requirements": {
@@ -129293,21 +315845,21 @@
             "Learn how to run a published Galaxy workflow",
             "Learn how histories can be inspected and re-used."
         ],
-        "pageviews": 2395,
+        "pageviews": 2406,
         "pub_date": "2021-08-25",
         "questions": [
             "How to reproduce published Galaxy results (workflows and histories)"
         ],
         "short_id": "T00192",
         "short_tools": [
+            "Cut1",
             "tp_sorted_uniq",
-            "csv_to_tabular",
-            "upload1",
             "ggplot2_point",
-            "Cut1",
+            "upload1",
             "Remove beginning1",
             "datamash_ops",
-            "Grouping1"
+            "Grouping1",
+            "csv_to_tabular"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -129335,26 +315887,1257 @@
                     "usegalaxy": true
                 }
             ],
-            "inexact": [
+            "inexact": [
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
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+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "1.1.0"
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+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.8+galaxy0"
+                            ]
+                        },
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+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
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+                            "server": "http://gigagalaxy.net/",
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+                            "state": "inexact",
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+                                "1.1.0+galaxy2"
+                            ]
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+                            "server": "https://galaxy-web.ipk-gatersleben.de",
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+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "1.8+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.1.0"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "2.2.1+galaxy1"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.2.1+galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "3.4.0+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "2.2.1+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "3.4.0+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.2.1+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.2.1+galaxy2",
+                                "3.3.5+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2.2.1+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
+                                "2.2.1+galaxy2",
+                                "3.4.0+galaxy1",
+                                "3.3.5+galaxy2",
+                                "3.3.5+galaxy0",
+                                "3.4.0+galaxy0",
+                                "3.3.5+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.2.1+galaxy1"
+                },
+                {
+                    "id": "upload1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
                 }
             ]
         },
@@ -129390,8 +317173,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 263,
-        "visitors": 1748,
+        "visit_duration": 262,
+        "visitors": 1756,
         "workflows": [
             {
                 "creators": [],
@@ -129402,7 +317185,7 @@
                     "report": null,
                     "subworkflows": false
                 },
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+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\niris\"]\n  1[label=\"Convert CSV to tabular\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Datamash\"]\n  1 -> 2 [label=\"tabular\"]\n  k60dc8637ad014cb6bab04b118656552f[color=lightseagreen,label=\"Output\\ndatamash_output\"]\n  2 -> k60dc8637ad014cb6bab04b118656552f\n  3[label=\"Remove beginning\"]\n  1 -> 3 [label=\"tabular\"]\n  4[label=\"Cut\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"Group\"]\n  3 -> 5 [label=\"out_file1\"]\n  ke7de7df5e49d4a818a5bde5adda038e6[color=lightseagreen,label=\"Output\\ngroup1\"]\n  5 -> ke7de7df5e49d4a818a5bde5adda038e6\n  6[label=\"Group\"]\n  3 -> 6 [label=\"out_file1\"]\n  k034862374aa04a2f9456a3bddfbe0da9[color=lightseagreen,label=\"Output\\ngroup2\"]\n  6 -> k034862374aa04a2f9456a3bddfbe0da9\n  7[label=\"Scatterplot w ggplot2\"]\n  3 -> 7 [label=\"out_file1\"]\n  8[label=\"Scatterplot w ggplot2\"]\n  3 -> 8 [label=\"out_file1\"]\n  9[label=\"Unique\"]\n  4 -> 9 [label=\"out_file1\"]\n  kec39c0adeb2647d6b9a7c2e5ffa043c6[color=lightseagreen,label=\"Output\\nunique_output\"]\n  9 -> kec39c0adeb2647d6b9a7c2e5ffa043c6\n}",
                 "history": [
                     {
                         "hash": "03bdb9f97f1f07b25cb24c182fce72381d420781",
@@ -129441,8 +317224,8 @@
                     }
                 ],
                 "license": null,
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\niris\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Convert CSV to tabular\"];\n  0 -->|output| 1;\n  2[\"Datamash\"];\n  1 -->|tabular| 2;\n  3c20f940-c1be-4766-ba5c-4c12b2dcbf74[\"Output\\ndatamash_output\"];\n  2 --> 3c20f940-c1be-4766-ba5c-4c12b2dcbf74;\n  style 3c20f940-c1be-4766-ba5c-4c12b2dcbf74 stroke:#2c3143,stroke-width:4px;\n  3[\"Remove beginning\"];\n  1 -->|tabular| 3;\n  4[\"Cut\"];\n  3 -->|out_file1| 4;\n  5[\"Group\"];\n  3 -->|out_file1| 5;\n  ff6ea340-8562-4177-b5d0-01c7ac754d76[\"Output\\ngroup1\"];\n  5 --> ff6ea340-8562-4177-b5d0-01c7ac754d76;\n  style ff6ea340-8562-4177-b5d0-01c7ac754d76 stroke:#2c3143,stroke-width:4px;\n  6[\"Group\"];\n  3 -->|out_file1| 6;\n  a5b275c7-5fb6-4bb4-b102-6e7c586badb9[\"Output\\ngroup2\"];\n  6 --> a5b275c7-5fb6-4bb4-b102-6e7c586badb9;\n  style a5b275c7-5fb6-4bb4-b102-6e7c586badb9 stroke:#2c3143,stroke-width:4px;\n  7[\"Scatterplot w ggplot2\"];\n  3 -->|out_file1| 7;\n  8[\"Scatterplot w ggplot2\"];\n  3 -->|out_file1| 8;\n  9[\"Unique\"];\n  4 -->|out_file1| 9;\n  ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6[\"Output\\nunique_output\"];\n  9 --> ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6;\n  style ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\niris\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Convert CSV to tabular\"];\n  0 -->|output| 1;\n  2[\"Datamash\"];\n  1 -->|tabular| 2;\n  60dc8637-ad01-4cb6-bab0-4b118656552f[\"Output\\ndatamash_output\"];\n  2 --> 60dc8637-ad01-4cb6-bab0-4b118656552f;\n  style 60dc8637-ad01-4cb6-bab0-4b118656552f stroke:#2c3143,stroke-width:4px;\n  3[\"Remove beginning\"];\n  1 -->|tabular| 3;\n  4[\"Cut\"];\n  3 -->|out_file1| 4;\n  5[\"Group\"];\n  3 -->|out_file1| 5;\n  e7de7df5-e49d-4a81-8a5b-de5adda038e6[\"Output\\ngroup1\"];\n  5 --> e7de7df5-e49d-4a81-8a5b-de5adda038e6;\n  style e7de7df5-e49d-4a81-8a5b-de5adda038e6 stroke:#2c3143,stroke-width:4px;\n  6[\"Group\"];\n  3 -->|out_file1| 6;\n  03486237-4aa0-4a2f-9456-a3bddfbe0da9[\"Output\\ngroup2\"];\n  6 --> 03486237-4aa0-4a2f-9456-a3bddfbe0da9;\n  style 03486237-4aa0-4a2f-9456-a3bddfbe0da9 stroke:#2c3143,stroke-width:4px;\n  7[\"Scatterplot w ggplot2\"];\n  3 -->|out_file1| 7;\n  8[\"Scatterplot w ggplot2\"];\n  3 -->|out_file1| 8;\n  9[\"Unique\"];\n  4 -->|out_file1| 9;\n  ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6[\"Output\\nunique_output\"];\n  9 --> ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6;\n  style ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GTN Training: Galaxy 101 For Everyone",
                 "outputs": [
                     {
@@ -129491,7 +317274,7 @@
                             {
                                 "label": "datamash_output",
                                 "output_name": "out_file",
-                                "uuid": "3c20f940-c1be-4766-ba5c-4c12b2dcbf74"
+                                "uuid": "60dc8637-ad01-4cb6-bab0-4b118656552f"
                             }
                         ]
                     },
@@ -129535,7 +317318,7 @@
                             {
                                 "label": "group1",
                                 "output_name": "out_file1",
-                                "uuid": "ff6ea340-8562-4177-b5d0-01c7ac754d76"
+                                "uuid": "e7de7df5-e49d-4a81-8a5b-de5adda038e6"
                             }
                         ]
                     },
@@ -129579,7 +317362,7 @@
                             {
                                 "label": "group2",
                                 "output_name": "out_file1",
-                                "uuid": "a5b275c7-5fb6-4bb4-b102-6e7c586badb9"
+                                "uuid": "03486237-4aa0-4a2f-9456-a3bddfbe0da9"
                             }
                         ]
                     },
@@ -129980,7 +317763,7 @@
             "Become comfortable converting text-based files in a variety of ways.",
             "Reason about the expected outcome of tools"
         ],
-        "pageviews": 5158,
+        "pageviews": 5367,
         "pub_date": "2022-07-20",
         "questions": [
             "How can I do basic data manipulation in Galaxy?",
@@ -129988,25 +317771,25 @@
         ],
         "short_id": "T00184",
         "short_tools": [
+            "cat1",
             "",
-            "join1",
-            "Count1",
-            "upload1",
+            "regexColumn1",
             "wc_gnu",
-            "datamash_ops",
-            "Grouping1",
+            "Remove beginning1",
             "tp_sorted_uniq",
-            "tabular_to_csv",
-            "tp_cat",
+            "upload1",
+            "datamash_ops",
             "Filter1",
+            "Count1",
             "tp_sort_header_tool",
-            "tp_split_on_column",
+            "Add_a_column1",
             "Cut1",
-            "Remove beginning1",
-            "cat1",
+            "tp_split_on_column",
+            "tabular_to_csv",
+            "tp_cat",
             "Show beginning1",
-            "Add_a_column1",
-            "regexColumn1"
+            "join1",
+            "Grouping1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -130015,6 +317798,5091 @@
             "exact": [],
             "inexact": []
         },
+        "supported_servers_matrix": {
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         "symlink": null,
         "tags": [
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@@ -130079,8 +322947,8 @@
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-        "visitors": 3366,
+        "visit_duration": 216,
+        "visitors": 3515,
         "workflows": [
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@@ -130197,7 +323065,7 @@
                 ],
                 "license": null,
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GTN Tutorial: Data manipulation Olympics - all steps and exercises",
                 "outputs": [],
                 "parent_id": "introduction/data-manipulation-olympics",
@@ -130295,7 +323163,6 @@
             "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
@@ -130326,7 +323193,7 @@
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             "Familiarize yourself with the basics of Galaxy"
         ],
-        "pageviews": 28209,
+        "pageviews": 28264,
         "pub_date": "2017-10-18",
         "questions": [
             "Do genes on opposite strands ever overlap?  If so, how often?"
@@ -130359,11 +323226,11 @@
         ],
         "short_id": "T00191",
         "short_tools": [
+            "cat1",
             "tp_cat",
-            "Filter1",
-            "gene2exon1",
             "gops_intersect_1",
-            "cat1"
+            "gene2exon1",
+            "Filter1"
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         "slides": false,
         "slides_recordings": false,
@@ -130385,11 +323252,6 @@
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                     "usegalaxy": true
                 },
-                {
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-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -130414,6 +323276,819 @@
                 }
             ]
         },
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+                    "url": "http://apostl.moffitt.org/"
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+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
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         "time_estimation": "2H30M",
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@@ -130444,7 +324119,7 @@
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@@ -130516,7 +324191,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
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@@ -130614,7 +324289,7 @@
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-            "Sequence alignment",
-            "Read mapping",
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@@ -130827,7 +324502,6 @@
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@@ -130851,7 +324525,7 @@
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@@ -130872,21 +324546,21 @@
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@@ -131075,7 +327378,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "NGS_tutorial",
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@@ -132070,7 +328373,7 @@
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@@ -132116,6 +328419,10 @@
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@@ -132139,7 +328446,7 @@
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@@ -132241,7 +328548,7 @@
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         "questions": [
             "Which Galaxy instance should I use?"
@@ -132284,6 +328591,10 @@
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@@ -132308,7 +328619,7 @@
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+                            "state": "missing"
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+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "0.72+galaxy1",
+                                "0.72",
+                                "0.73+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "inexact",
+                            "versions": [
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+                            ]
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.72+galaxy1",
+                                "0.73+galaxy0",
+                                "0.69"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.73+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "0.74+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.72+galaxy1",
+                                "0.72",
+                                "0.65",
+                                "0.71"
+                            ]
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.74+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "0.74+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.74+galaxy0",
+                                "0.69",
+                                "0.65",
+                                "0.68",
+                                "0.52",
+                                "0.67",
+                                "0.63",
+                                "0.62",
+                                "0.64"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.74+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.72+galaxy1",
+                                "0.73+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.74+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.74+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.74+galaxy1"
                 }
             ]
         },
@@ -132855,7 +329960,7 @@
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         "video_view": 0,
         "visit_duration": 421,
-        "visitors": 2172617,
+        "visitors": 2183385,
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@@ -132866,7 +329971,7 @@
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@@ -132933,8 +330038,8 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
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@@ -132977,7 +330082,7 @@
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                                 "output_name": "output",
-                                "uuid": "4706cfda-1f28-494e-85f0-1d797d3dbacc"
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@@ -133021,7 +330126,7 @@
                             {
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-                                "uuid": "8191d6ec-149a-4eda-bd00-c277f56474a8"
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@@ -133253,7 +330358,6 @@
             "UseGalaxy.be",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)"
         ],
@@ -133280,7 +330384,7 @@
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             "Learn how to share your work"
         ],
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         "questions": [
@@ -133314,12 +330418,12 @@
         ],
         "short_id": "T00186",
         "short_tools": [
+            "bedtools_intersectbed",
+            "tp_sort_header_tool",
             "comp1",
             "upload1",
-            "tp_sort_header_tool",
-            "tp_head_tool",
-            "bedtools_intersectbed",
-            "datamash_ops"
+            "datamash_ops",
+            "tp_head_tool"
         ],
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         "slides_recordings": false,
@@ -133358,10 +330462,136 @@
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -133371,6 +330601,1197 @@
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "id": "comp1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
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+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
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+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
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+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
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+                        {
+                            "server": "http://gigagalaxy.net/",
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+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
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+                            "server": "https://galaxy-web.ipk-gatersleben.de",
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+                            "server": "https://www.immportgalaxy.org/",
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+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
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+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
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+                            "state": "missing"
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+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
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+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
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+                    "version": "local"
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+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "exact",
+                            "version": "1.8+galaxy0"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.1.0",
+                                "1.0.6"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.8+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.8+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.1.0",
+                                "1.1.0+galaxy2",
+                                "1.0.6",
+                                "1.1.0+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.8+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.8+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.8+galaxy0"
+                },
+                {
+                    "id": "upload1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
                 }
             ]
         },
@@ -133406,8 +331827,8 @@
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 201,
-        "visitors": 32513,
+        "visit_duration": 203,
+        "visitors": 33181,
         "workflows": [
             {
                 "creators": [
@@ -133546,7 +331967,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nExons\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nFeatures\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"bedtools Intersect intervals\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"Datamash\"];\n  2 -->|output| 3;\n  4[\"Sort\"];\n  3 -->|out_file| 4;\n  5[\"Select first\"];\n  4 -->|outfile| 5;\n  6[\"Compare two Datasets\"];\n  0 -->|output| 6;\n  5 -->|outfile| 6;\n  565e3d76-0230-4a5e-87c1-9c36ce0b7df8[\"Output\\ntop_5_exons\"];\n  6 --> 565e3d76-0230-4a5e-87c1-9c36ce0b7df8;\n  style 565e3d76-0230-4a5e-87c1-9c36ce0b7df8 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Find exons with the highest number of features",
                 "outputs": [
                     {
@@ -134761,7 +333182,6 @@
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)"
         ],
@@ -134799,7 +333219,7 @@
             "Learn how to create a workflow",
             "Learn how to share your work"
         ],
-        "pageviews": 25425,
+        "pageviews": 25553,
         "priority": 2,
         "pub_date": "2019-11-14",
         "questions": [
@@ -134834,14 +333254,14 @@
         ],
         "short_id": "T00187",
         "short_tools": [
+            "Cut1",
             "tp_sorted_uniq",
-            "csv_to_tabular",
-            "upload1",
             "ggplot2_point",
-            "Cut1",
+            "upload1",
             "Remove beginning1",
             "datamash_ops",
-            "Grouping1"
+            "Grouping1",
+            "csv_to_tabular"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -134853,11 +333273,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -134892,6 +333307,1239 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Cut1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Grouping1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Remove beginning1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
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+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "1H30M",
         "title": "Galaxy Basics for everyone",
@@ -134924,8 +334572,8 @@
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 251,
-        "visitors": 15289,
+        "visit_duration": 250,
+        "visitors": 15387,
         "workflows": [
             {
                 "creators": [],
@@ -135073,7 +334721,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\niris\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Convert CSV to tabular\"];\n  0 -->|output| 1;\n  2[\"Datamash\"];\n  1 -->|tabular| 2;\n  254f1b4b-d466-4f0e-8c46-0e97bbedae4d[\"Output\\ndatamash_output\"];\n  2 --> 254f1b4b-d466-4f0e-8c46-0e97bbedae4d;\n  style 254f1b4b-d466-4f0e-8c46-0e97bbedae4d stroke:#2c3143,stroke-width:4px;\n  3[\"Remove beginning\"];\n  1 -->|tabular| 3;\n  4[\"Cut\"];\n  3 -->|out_file1| 4;\n  5[\"Group\"];\n  3 -->|out_file1| 5;\n  a689bddf-14d0-4a72-b1f9-c34d8f50d2b3[\"Output\\ngroup1\"];\n  5 --> a689bddf-14d0-4a72-b1f9-c34d8f50d2b3;\n  style a689bddf-14d0-4a72-b1f9-c34d8f50d2b3 stroke:#2c3143,stroke-width:4px;\n  6[\"Group\"];\n  3 -->|out_file1| 6;\n  ac7c73b2-58dd-4c6e-85ce-ddf49323b206[\"Output\\ngroup2\"];\n  6 --> ac7c73b2-58dd-4c6e-85ce-ddf49323b206;\n  style ac7c73b2-58dd-4c6e-85ce-ddf49323b206 stroke:#2c3143,stroke-width:4px;\n  7[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 7;\n  8[\"Scatterplot with ggplot2\"];\n  3 -->|out_file1| 8;\n  9[\"Unique\"];\n  4 -->|out_file1| 9;\n  8a2b5e30-d42a-4019-9674-4b4af00c820a[\"Output\\nunique_output\"];\n  9 --> 8a2b5e30-d42a-4019-9674-4b4af00c820a;\n  style 8a2b5e30-d42a-4019-9674-4b4af00c820a stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GTN Training: Galaxy 101 For Everyone",
                 "outputs": [
                     {
@@ -135453,9 +335101,9 @@
         "dir": "topics/introduction/tutorials/vsi_qc",
         "draft": true,
         "edam_operation": [
-            "Sequencing quality control",
             "Validation",
-            "Sequence contamination filtering"
+            "Sequence contamination filtering",
+            "Sequencing quality control"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -135464,7 +335112,6 @@
             "HyPhy HIV NGS Tools",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
@@ -135492,7 +335139,7 @@
             "Learn about fastp",
             "Learn about multiqc"
         ],
-        "pageviews": 170,
+        "pageviews": 174,
         "priority": 10,
         "pub_date": "2024-03-26",
         "questions": [
@@ -135533,11 +335180,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -135567,6 +335209,452 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "0.23.2+galaxy0"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "exact",
+                            "version": "0.23.2+galaxy0"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "0.23.2+galaxy0"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "exact",
+                            "version": "0.23.2+galaxy0"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "0.23.4+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
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+                                "0.19.5+galaxy1",
+                                "0.19.3.2",
+                                "0.18.0.0",
+                                "0.19.3.3",
+                                "0.19.5",
+                                "0.12.4.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.23.2+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.23.2+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "0.23.2+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.23.2+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.23.2+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "exact",
+                            "version": "0.23.2+galaxy0"
+                        }
+                    ],
+                    "version": "0.23.2+galaxy0"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "1.11+galaxy1"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "1.11+galaxy1"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "exact",
+                            "version": "1.11+galaxy1"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "exact",
+                            "version": "1.11+galaxy1"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.8+galaxy0",
+                                "1.9"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.11+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.11+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.7",
+                                "1.11+galaxy0",
+                                "1.9+galaxy1",
+                                "1.8+galaxy0",
+                                "1.9",
+                                "1.8+galaxy2",
+                                "1.7.1",
+                                "1.8+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.11+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.11+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.11+galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "work-in-progress"
@@ -135596,8 +335684,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 237,
-        "visitors": 123,
+        "visit_duration": 229,
+        "visitors": 127,
         "zenodo_link": "https://zenodo.org/records/10870107"
     },
     {
@@ -135729,7 +335817,7 @@
             "Use pymuon-suite in Galaxy to find stopping sites",
             "Understand the limitations of these tools and techniques"
         ],
-        "pageviews": 179,
+        "pageviews": 180,
         "priority": 2,
         "pub_date": "2024-01-22",
         "questions": [
@@ -135752,8 +335840,8 @@
         ],
         "short_id": "T00402",
         "short_tools": [
-            "pm_uep_opt",
-            "pm_muairss_read"
+            "pm_muairss_read",
+            "pm_uep_opt"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -135773,6 +335861,412 @@
             ],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
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+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
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+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
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+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
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+                    "url": "https://usegalaxy.no/",
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+                    "url": "https://usegalaxy.org",
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+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
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+                            "state": "missing"
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
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+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
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+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.3.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.3.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.3.0+galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "1H",
         "title": "Finding the muon stopping site with pymuon-suite in Galaxy",
@@ -135800,7 +336294,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 135,
-        "visitors": 120,
+        "visitors": 121,
         "workflows": [
             {
                 "creators": [
@@ -135926,7 +336420,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nCopper-out.cell\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCopper.den_fmt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nCopper.castep\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"PyMuonSuite AIRSS UEP Optimise\"];\n  2 -->|output| 3;\n  1 -->|output| 3;\n  0 -->|output| 3;\n  f3be7cd2-3974-49f2-aa0e-96c79b4ab34c[\"Output\\nAll muons in host material\"];\n  3 --> f3be7cd2-3974-49f2-aa0e-96c79b4ab34c;\n  style f3be7cd2-3974-49f2-aa0e-96c79b4ab34c stroke:#2c3143,stroke-width:4px;\n  4[\"PyMuonSuite AIRSS Cluster\"];\n  3 -->|uep_results| 4;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Finding the Muon Stopping Site: pymuon-suite in Galaxy",
                 "outputs": [
                     {
@@ -136197,20 +336691,20 @@
         ],
         "dir": "topics/metabolomics/tutorials/gc_ms_with_xcms",
         "edam_operation": [
-            "Peak detection",
-            "Format validation",
-            "Standardisation and normalisation",
+            "Chromatogram visualisation",
+            "Clustering",
+            "Filtering",
             "Mass spectrum visualisation",
+            "Spectral library search",
             "Validation",
+            "Imputation",
+            "Label-free quantification",
+            "Format validation",
             "Formatting",
             "Chromatographic alignment",
-            "Clustering",
-            "Label-free quantification",
-            "Imputation",
-            "Correlation",
-            "Filtering",
-            "Chromatogram visualisation",
-            "Spectral library search"
+            "Standardisation and normalisation",
+            "Peak detection",
+            "Correlation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -136222,7 +336716,6 @@
         "id": "metabolomics/gc_ms_with_xcms",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
@@ -136242,7 +336735,7 @@
             "To explore what open-source alternative tools can be used in the analysis of GC-MS data, learn about their possible parametrisations.",
             "To analyse authentic data samples and compare them with a data library of human metabolome, composed from a collection of mostly endogenous compounds."
         ],
-        "pageviews": 2011,
+        "pageviews": 2031,
         "pub_date": "2023-05-08",
         "questions": [
             "What are the main steps of gas chromatography-mass spectrometry (GC-MS) data processing for metabolomic analysis?",
@@ -136260,20 +336753,20 @@
         ],
         "short_id": "T00344",
         "short_tools": [
-            "msnbase_readmsdata",
-            "riassigner",
+            "matchms_formatter",
             "ramclustr",
-            "waveica",
-            "abims_xcms_fillPeaks",
             "abims_xcms_xcmsSet",
+            "abims_xcms_group",
             "matchms_similarity",
-            "msconvert",
-            "xcms_merge",
+            "abims_xcms_retcor",
             "matchms_filtering",
+            "msnbase_readmsdata",
             "ramclustr_define_experiment",
-            "abims_xcms_group",
-            "matchms_formatter",
-            "abims_xcms_retcor"
+            "abims_xcms_fillPeaks",
+            "msconvert",
+            "riassigner",
+            "xcms_merge",
+            "waveica"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -136292,14 +336785,2250 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                            "state": "missing"
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+                        {
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+                            "state": "missing"
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+                        {
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+                            "state": "missing"
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
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+                        {
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+                            "state": "missing"
+                        },
+                        {
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+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
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+                        },
+                        {
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+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "3.0.19052.0",
+                                "3.0.19052.1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "3.0.20287.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "3.0.20287.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "3.0.19052.1",
+                                "0.3.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "3.0.20287.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "3.0.20287.2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
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+                    ],
+                    "version": "3.0.20287.2"
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+                            ]
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+                            "server": "http://apostl.moffitt.org/",
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+                            "state": "missing"
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+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
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+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
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+                            "server": "https://usegalaxy.org",
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+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
+                                "0.4.1+galaxy0"
+                            ]
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+                            "state": "missing"
+                        }
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+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
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+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
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+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
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+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.2.0+galaxy4"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.2.0+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.2.0+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
+                                "0.2.0+galaxy8"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.2.0+galaxy2"
                 }
             ]
         },
@@ -136342,8 +339071,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 97,
-        "visitors": 1498,
+        "visit_duration": 96,
+        "visitors": 1510,
         "workflows": [
             {
                 "creators": [
@@ -136530,7 +339259,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nReference compound list alkanes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference spectra\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nsample_metadata.tsv\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"msconvert\"];\n  3 -->|output| 4;\n  5[\"MSnbase readMSData\"];\n  4 -->|output| 5;\n  6[\"xcms findChromPeaks xcmsSet\"];\n  5 -->|xsetRData| 6;\n  7[\"xcms findChromPeaks Merger\"];\n  6 -->|xsetRData| 7;\n  2 -->|output| 7;\n  8[\"xcms groupChromPeaks group\"];\n  7 -->|xsetRData| 8;\n  9[\"xcms adjustRtime retcor\"];\n  8 -->|xsetRData| 9;\n  10[\"xcms groupChromPeaks group\"];\n  9 -->|xsetRData| 10;\n  11[\"xcms fillChromPeaks fillPeaks\"];\n  10 -->|xsetRData| 11;\n  940c7549-1bae-4ddd-9e92-75fc7d2c8eef[\"Output\\nFeature (peak) intensities\"];\n  11 --> 940c7549-1bae-4ddd-9e92-75fc7d2c8eef;\n  style 940c7549-1bae-4ddd-9e92-75fc7d2c8eef stroke:#2c3143,stroke-width:4px;\n  9f910e82-e7a5-4201-b944-1845ba6aa2e9[\"Output\\nFeature (peak) metadata (mz, rt, ...)\"];\n  11 --> 9f910e82-e7a5-4201-b944-1845ba6aa2e9;\n  style 9f910e82-e7a5-4201-b944-1845ba6aa2e9 stroke:#2c3143,stroke-width:4px;\n  5bab8f28-4df1-4397-af04-168546bd0e52[\"Output\\nxcmsObj (XCMSnExp)\"];\n  11 --> 5bab8f28-4df1-4397-af04-168546bd0e52;\n  style 5bab8f28-4df1-4397-af04-168546bd0e52 stroke:#2c3143,stroke-width:4px;\n  12[\"RAMClustR\"];\n  11 -->|xsetRData| 12;\n  92fac5e6-1578-4e52-ac9d-2982e19a5b88[\"Output\\nDeconvoluted spectra\"];\n  12 --> 92fac5e6-1578-4e52-ac9d-2982e19a5b88;\n  style 92fac5e6-1578-4e52-ac9d-2982e19a5b88 stroke:#2c3143,stroke-width:4px;\n  f7657c17-6293-4fbb-b014-28009d495de7[\"Output\\nFeature (spectra) intensities\"];\n  12 --> f7657c17-6293-4fbb-b014-28009d495de7;\n  style f7657c17-6293-4fbb-b014-28009d495de7 stroke:#2c3143,stroke-width:4px;\n  13[\"RIAssigner\"];\n  12 -->|mass_spectra_merged| 13;\n  0 -->|output| 13;\n  7ec6ce02-5d83-48ab-ba0a-94976db297e5[\"Output\\nRetention indexed spectra\"];\n  13 --> 7ec6ce02-5d83-48ab-ba0a-94976db297e5;\n  style 7ec6ce02-5d83-48ab-ba0a-94976db297e5 stroke:#2c3143,stroke-width:4px;\n  14[\"matchms similarity\"];\n  13 -->|output| 14;\n  1 -->|output| 14;\n  024327f7-13b8-4ce9-8708-9f430d7ceedf[\"Output\\nCosineGreedy scores of input dataset(s)\"];\n  14 --> 024327f7-13b8-4ce9-8708-9f430d7ceedf;\n  style 024327f7-13b8-4ce9-8708-9f430d7ceedf stroke:#2c3143,stroke-width:4px;\n  15[\"matchms scores formatter\"];\n  14 -->|similarity_scores| 15;\n  8a767006-4b3c-41ba-bea5-18fd100ce930[\"Output\\nmatchms_scores\"];\n  15 --> 8a767006-4b3c-41ba-bea5-18fd100ce930;\n  style 8a767006-4b3c-41ba-bea5-18fd100ce930 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GC MS using XCMS",
                 "outputs": [
                     {
@@ -136977,7 +339706,6 @@
         "id": "metabolomics/msi-finding-nglycans",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
@@ -137002,7 +339730,7 @@
             "Preprocessing raw MSI data.",
             "Performing supervised and unsupervised statistical analysis."
         ],
-        "pageviews": 2446,
+        "pageviews": 2449,
         "pub_date": "2019-04-13",
         "questions": [
             "Can N-linked glycans from FFPE tissues be detected by MALDI imaging?",
@@ -137020,18 +339748,18 @@
         ],
         "short_id": "T00199",
         "short_tools": [
+            "maldi_quant_preprocessing",
+            "cardinal_mz_images",
+            "cardinal_quality_report",
             "cardinal_combine",
-            "cardinal_segmentations",
-            "Summary_Statistics1",
             "cardinal_classification",
-            "Filter1",
             "maldi_quant_peak_detection",
-            "maldi_quant_preprocessing",
-            "cardinal_preprocessing",
             "Grep1",
-            "cardinal_mz_images",
+            "Summary_Statistics1",
             "join_files_on_column_fuzzy",
-            "cardinal_quality_report"
+            "cardinal_segmentations",
+            "cardinal_preprocessing",
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -137055,19 +339783,1827 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
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@@ -137107,8 +341643,8 @@
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-        "visitors": 1667,
+        "visit_duration": 113,
+        "visitors": 1669,
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@@ -137267,7 +341803,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "MSI Finding Diff Analytes",
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@@ -138152,13 +342688,13 @@
         ],
         "dir": "topics/metabolomics/tutorials/lcms",
         "edam_operation": [
-            "Peak detection",
-            "Label-free quantification",
+            "Chromatogram visualisation",
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             "Mass spectrum visualisation",
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             "Validation",
-            "Filtering",
-            "Chromatogram visualisation",
-            "Chromatographic alignment"
+            "Chromatographic alignment",
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@@ -138169,7 +342705,6 @@
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             "UseGalaxy.eu",
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@@ -138190,7 +342725,7 @@
             "To get familiar with the main steps constituting a metabolomic workflow for untargeted LC-MS analysis.",
             "To evaluate the potential of a workflow approach when dealing with LC-MS metabolomic data."
         ],
-        "pageviews": 18252,
+        "pageviews": 18274,
         "pub_date": "2019-07-02",
         "questions": [
             "What are the main steps of untargeted LC-MS data processing for metabolomic analysis?",
@@ -138198,19 +342733,19 @@
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-            "xcms_plot_chromatogram",
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@@ -138228,19 +342763,1963 @@
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+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2017.06"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
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+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
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@@ -138282,7 +344761,7 @@
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         "video_view": 0,
         "visit_duration": 95,
-        "visitors": 10803,
+        "visitors": 10823,
         "workflows": [
             {
                 "creators": [],
@@ -138380,7 +344859,7 @@
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                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHU_neg_048.mzML\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nInput dataset collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"xcms fillChromPeaks fillPeaks\"];\n  9 -->|xsetRData| 10;\n  11[\"CAMERA.annotate\"];\n  10 -->|xsetRData| 11;\n  12[\"Batch_correction\"];\n  10 -->|dataMatrix| 12;\n  0 -->|output| 12;\n  11 -->|variableMetadata| 12;\n  13[\"Quality Metrics\"];\n  10 -->|dataMatrix| 13;\n  0 -->|output| 13;\n  11 -->|variableMetadata| 13;\n  14[\"Quality Metrics\"];\n  12 -->|dataMatrix_out| 14;\n  0 -->|output| 14;\n  12 -->|variableMetadata_out| 14;\n  15[\"Generic_Filter\"];\n  12 -->|dataMatrix_out| 15;\n  14 -->|sampleMetadata_out| 15;\n  14 -->|variableMetadata_out| 15;\n  16[\"Univariate\"];\n  15 -->|dataMatrix_out| 16;\n  15 -->|sampleMetadata_out| 16;\n  15 -->|variableMetadata_out| 16;\n  17[\"Generic_Filter\"];\n  15 -->|dataMatrix_out| 17;\n  15 -->|sampleMetadata_out| 17;\n  16 -->|variableMetadata_out| 17;\n  18[\"HMDB MS search\"];\n  17 -->|variableMetadata_out| 18;\n  2[\"MSnbase readMSData\"];\n  1 -->|output| 2;\n  3[\"xcms findChromPeaks xcmsSet\"];\n  2 -->|xsetRData| 3;\n  4[\"xcms plot chromatogram\"];\n  3 -->|xsetRData| 4;\n  5[\"xcms findChromPeaks Merger\"];\n  3 -->|xsetRData| 5;\n  6[\"xcms groupChromPeaks group\"];\n  5 -->|xsetRData| 6;\n  7[\"xcms adjustRtime retcor\"];\n  6 -->|xsetRData| 7;\n  8[\"xcms plot chromatogram\"];\n  7 -->|xsetRData| 8;\n  9[\"xcms groupChromPeaks group\"];\n  7 -->|xsetRData| 9;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow Constructed From History 'imported: testpourGCC'",
                 "outputs": [],
                 "parent_id": "metabolomics/lcms",
@@ -138545,7 +345024,9 @@
         "feedback_number": 0,
         "hands_on": true,
         "id": "metabolomics/qcxms-predictions",
-        "inexact_supported_servers": [],
+        "inexact_supported_servers": [
+            "UseGalaxy.org.au"
+        ],
         "js_requirements": {
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             "mermaid": false
@@ -138565,7 +345046,7 @@
             "To generate 3D conformers and optimise them using semi-empirical quantum mechanical (SQM) methods.",
             "To produce simulated mass spectra for a given molecule in MSP (text based) format."
         ],
-        "pageviews": 7612,
+        "pageviews": 39240,
         "pub_date": "2024-10-01",
         "questions": [
             "Can I predict QC-based mass spectra starting from SMILES?",
@@ -138582,19 +345063,19 @@
                 "type": "internal"
             }
         ],
-        "short_id": null,
+        "short_id": "T00458",
         "short_tools": [
-            "openbabel_compound_convert",
-            "qcxms_production_run",
-            "__FILTER_FAILED_DATASETS__",
-            "ctb_im_conformers",
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-            "param_value_from_file",
             "xtb_molecular_optimization",
-            "tp_cut_tool",
-            "qcxms_neutral_run"
+            "tp_cat",
+            "param_value_from_file",
+            "ctb_im_conformers",
+            "qcxms_production_run",
+            "openbabel_compound_convert",
+            "qcxms_neutral_run",
+            "split_file_to_collection",
+            "__FILTER_FAILED_DATASETS__",
+            "tp_cut_tool"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -138606,7 +345087,1949 @@
                     "usegalaxy": true
                 }
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+            "inexact": [
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+                    "url": "https://usegalaxy.org.au",
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+                            "state": "missing"
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+                            "state": "missing"
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+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
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+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
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+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "6.6.1+galaxy3"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "6.6.1+galaxy3"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "6.6.1+galaxy3"
+                }
+            ]
         },
         "symlink": null,
         "time_estimation": "1H",
@@ -138645,8 +347068,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 149,
-        "visitors": 3260,
+        "visit_duration": 208,
+        "visitors": 14082,
         "workflows": [
             {
                 "creators": [
@@ -138787,7 +347210,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput Molecules with SMILES and NAME without a header.\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nNumber of conformers to generate\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nOptimization Levels\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nQC Method\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"Cut SMILES column\"];\n  0 -->|output| 4;\n  5[\"Cut NAME column\"];\n  0 -->|output| 5;\n  6[\"Split file\"];\n  4 -->|output| 6;\n  7[\"Split file\"];\n  5 -->|output| 7;\n  8[\"Parse parameter value\"];\n  7 -->|list_output_tab| 8;\n  9[\"Convert compounds from SMILES to SDF and add the name as title.\"];\n  8 -->|text_param| 9;\n  6 -->|list_output_tab| 9;\n  10[\"Merge the individual SDF files\"];\n  9 -->|outfile| 10;\n  11[\"Generate conformers\"];\n  10 -->|out_file1| 11;\n  1 -->|output| 11;\n  f4f8881e-cd64-42ae-8435-1288e4e473b5[\"Output\\nconformer_output\"];\n  11 --> f4f8881e-cd64-42ae-8435-1288e4e473b5;\n  style f4f8881e-cd64-42ae-8435-1288e4e473b5 stroke:#2c3143,stroke-width:4px;\n  12[\"Molecular format conversion \"];\n  11 -->|outfile| 12;\n  5dcb6f02-62c9-4f43-9810-a10052b59b41[\"Output\\nXYZ output\"];\n  12 --> 5dcb6f02-62c9-4f43-9810-a10052b59b41;\n  style 5dcb6f02-62c9-4f43-9810-a10052b59b41 stroke:#2c3143,stroke-width:4px;\n  13[\"xTB molecular optimization\"];\n  12 -->|file_outputs| 13;\n  2 -->|output| 13;\n  01a9a1af-e225-4613-94f9-dfdad37c93a2[\"Output\\noptimized output\"];\n  13 --> 01a9a1af-e225-4613-94f9-dfdad37c93a2;\n  style 01a9a1af-e225-4613-94f9-dfdad37c93a2 stroke:#2c3143,stroke-width:4px;\n  14[\"QCxMS neutral run\"];\n  3 -->|output| 14;\n  13 -->|output| 14;\n  e6e6a07b-d478-4a87-b491-42abee9094b1[\"Output\\n[.in] output\"];\n  14 --> e6e6a07b-d478-4a87-b491-42abee9094b1;\n  style e6e6a07b-d478-4a87-b491-42abee9094b1 stroke:#2c3143,stroke-width:4px;\n  969b3e2f-fbee-48f9-829a-c0032580e6f8[\"Output\\n[.xyz] output\"];\n  14 --> 969b3e2f-fbee-48f9-829a-c0032580e6f8;\n  style 969b3e2f-fbee-48f9-829a-c0032580e6f8 stroke:#2c3143,stroke-width:4px;\n  dc4811ad-6cff-42cc-a2f8-52ab585f47fe[\"Output\\n[.start] output\"];\n  14 --> dc4811ad-6cff-42cc-a2f8-52ab585f47fe;\n  style dc4811ad-6cff-42cc-a2f8-52ab585f47fe stroke:#2c3143,stroke-width:4px;\n  15[\"QCxMS production run\"];\n  14 -->|coords1| 15;\n  14 -->|coords2| 15;\n  14 -->|coords3| 15;\n  fc53168a-99f8-441c-9325-2d812bf03100[\"Output\\nres output\"];\n  15 --> fc53168a-99f8-441c-9325-2d812bf03100;\n  style fc53168a-99f8-441c-9325-2d812bf03100 stroke:#2c3143,stroke-width:4px;\n  16[\"Filter failed datasets\"];\n  15 -->|res_files| 16;\n  17[\"QCxMS get results\"];\n  12 -->|file_outputs| 17;\n  16 -->|output| 17;\n  d81bf92a-604c-46b9-86a9-bf3c2281ebcb[\"Output\\nMSP output\"];\n  17 --> d81bf92a-604c-46b9-86a9-bf3c2281ebcb;\n  style d81bf92a-604c-46b9-86a9-bf3c2281ebcb stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "End-to-end EI+ mass spectra prediction workflow using QCxMS",
                 "outputs": [
                     {
@@ -139146,7 +347569,7 @@
                     "toolshed.g2.bx.psu.edu/repos/recetox/qcxms_production_run/qcxms_production_run/5.2.1+galaxy3",
                     "toolshed.g2.bx.psu.edu/repos/recetox/xtb_molecular_optimization/xtb_molecular_optimization/6.6.1+galaxy3"
                 ],
-                "workflowhub_id": null
+                "workflowhub_id": "1367"
             }
         ],
         "zenodo_link": "https://zenodo.org/record/13327051"
@@ -139250,7 +347673,6 @@
             "HyPhy HIV NGS Tools",
             "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
@@ -139274,7 +347696,7 @@
             "Automatic generation of many m/z images.",
             "Overlay the distribution of several m/z in one image."
         ],
-        "pageviews": 3682,
+        "pageviews": 3683,
         "pub_date": "2019-02-21",
         "questions": [
             "What is the typical mass range of VOCs?",
@@ -139283,12 +347705,12 @@
         ],
         "short_id": "T00198",
         "short_tools": [
-            "Filter1",
-            "cardinal_data_exporter",
             "cardinal_filtering",
             "cardinal_mz_images",
-            "cardinal_quality_report",
-            "cardinal_spectra_plots"
+            "cardinal_spectra_plots",
+            "cardinal_data_exporter",
+            "Filter1",
+            "cardinal_quality_report"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -139317,19 +347739,1304 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
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+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
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+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
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+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
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+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
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+                    "name": "HyPhy HIV NGS Tools",
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+                    "usegalaxy": false
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
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+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
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+                },
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+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
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+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
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+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                    "url": "http://pepsimili.e-nios.com:8080/",
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+                                "2.6.0.1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.10.0.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.6.0.3"
+                        },
+                        {
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+                            "state": "inexact",
+                            "versions": [
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+                        {
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+                            "state": "missing"
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+                        {
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+                            "state": "exact",
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+                        },
+                        {
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+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.6.0.3"
                 }
             ]
         },
@@ -139366,7 +349073,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 105,
-        "visitors": 2533,
+        "visitors": 2534,
         "workflows": [
             {
                 "creators": [],
@@ -139505,7 +349212,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "MSI Workflow: spatial distribution",
                 "outputs": [
                     {
@@ -140253,17 +349960,16 @@
         ],
         "dir": "topics/metabolomics/tutorials/lcms-preprocessing",
         "edam_operation": [
-            "Peak detection",
-            "Label-free quantification",
+            "Chromatogram visualisation",
+            "Filtering",
             "Mass spectrum visualisation",
+            "Peak detection",
             "Validation",
-            "Filtering",
-            "Chromatogram visualisation",
-            "Chromatographic alignment"
+            "Chromatographic alignment",
+            "Label-free quantification"
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-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
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         "feedback_mean_note": null,
@@ -140293,7 +349999,7 @@
             "To get familiar with the way to use XCMS-based Galaxy modules dedicated to LC-MS data preprocessing.",
             "To evaluate the potential of a workflow approach when dealing with LC-MS preprocessing."
         ],
-        "pageviews": 5905248,
+        "pageviews": 5936896,
         "pub_date": "2020-02-04",
         "questions": [
             "What are the main steps of untargeted LC-MS data preprocessing for metabolomic analyses?",
@@ -140301,28 +350007,23 @@
         ],
         "short_id": "T00197",
         "short_tools": [
-            "msnbase_readmsdata",
+            "intens_check",
+            "abims_xcms_xcmsSet",
+            "abims_xcms_group",
+            "xcms_plot_chromatogram",
+            "xcms_export_samplemetadata",
+            "abims_xcms_retcor",
             "idchoice",
+            "msnbase_readmsdata",
             "abims_xcms_fillPeaks",
-            "abims_xcms_xcmsSet",
-            "abims_CAMERA_annotateDiffreport",
             "xcms_merge",
-            "xcms_plot_chromatogram",
-            "intens_check",
             "abims_xcms_summary",
-            "xcms_export_samplemetadata",
-            "abims_xcms_group",
-            "abims_xcms_retcor"
+            "abims_CAMERA_annotateDiffreport"
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                     "url": "https://usegalaxy.org",
@@ -140347,6 +350048,1852 @@
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+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
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+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
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+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
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+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                },
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+                    "usegalaxy": false
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                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
@@ -140650,6 +352319,861 @@
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
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+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
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+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
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@@ -140683,8 +353207,8 @@
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         "video_view": 0,
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-        "visitors": 1987,
+        "visit_duration": 112,
+        "visitors": 1994,
         "zenodo_link": "https://zenodo.org/record/5179809"
     },
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@@ -140744,19 +353268,18 @@
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         "draft": true,
         "edam_operation": [
-            "Peak detection",
-            "Label-free quantification",
+            "Chromatogram visualisation",
+            "Filtering",
             "Mass spectrum visualisation",
+            "Peak detection",
             "Validation",
-            "Filtering",
-            "Chromatogram visualisation",
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+            "Chromatographic alignment",
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@@ -140802,11 +353325,11 @@
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         "short_id": "T00194",
         "short_tools": [
-            "msnbase_readmsdata",
+            "abims_xcms_xcmsSet",
             "abims_xcms_group",
+            "msnbase_readmsdata",
             "abims_xcms_fillPeaks",
-            "xcms_merge",
-            "abims_xcms_xcmsSet"
+            "xcms_merge"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -140822,11 +353345,6 @@
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                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -140846,6 +353364,855 @@
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@@ -141060,6 +354427,10 @@
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@@ -141083,7 +354454,7 @@
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@@ -141309,12 +354680,12 @@
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@@ -141331,7 +354702,6 @@
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@@ -141353,7 +354723,7 @@
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@@ -141369,27 +354739,27 @@
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@@ -141404,19 +354774,3193 @@
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@@ -141480,7 +358024,7 @@
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                 "history": [
                     {
                         "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
@@ -141623,8 +358167,8 @@
                     }
                 ],
                 "license": null,
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSILVA Reference\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nAnguil Soil Sample\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nPampa Soil Sample\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nTrainset PDS alignment\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nTrainset PDS taxonomy\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Merge.files\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  6[\"Make.group\"];\n  1 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Unique.seqs\"];\n  5 -->|output| 7;\n  8[\"Count.seqs\"];\n  6 -->|output| 8;\n  7 -->|out_names| 8;\n  9[\"Summary.seqs\"];\n  8 -->|seq_count| 9;\n  7 -->|out_fasta| 9;\n  10[\"Screen.seqs\"];\n  7 -->|out_fasta| 10;\n  8 -->|seq_count| 10;\n  11[\"Align.seqs\"];\n  0 -->|output| 11;\n  10 -->|fasta_out| 11;\n  12[\"Summary.seqs\"];\n  10 -->|count_out| 12;\n  11 -->|out_file| 12;\n  13[\"Screen.seqs\"];\n  11 -->|out_file| 13;\n  10 -->|count_out| 13;\n  14[\"Filter.seqs\"];\n  13 -->|fasta_out| 14;\n  15[\"Pre.cluster\"];\n  14 -->|filteredfasta| 15;\n  13 -->|count_out| 15;\n  16[\"Classify.seqs\"];\n  15 -->|count_out| 16;\n  3 -->|output| 16;\n  15 -->|fasta_out| 16;\n  4 -->|output| 16;\n  17[\"Cluster.split\"];\n  16 -->|taxonomy_out| 17;\n  15 -->|fasta_out| 17;\n  15 -->|count_out| 17;\n  18[\"Make.shared\"];\n  15 -->|count_out| 18;\n  17 -->|otulist| 18;\n  2112be1d-8b08-408b-a525-1daed190d68c[\"Output\\nmothur_make_shared_shared\"];\n  18 --> 2112be1d-8b08-408b-a525-1daed190d68c;\n  style 2112be1d-8b08-408b-a525-1daed190d68c stroke:#2c3143,stroke-width:4px;\n  19[\"Classify.otu\"];\n  15 -->|count_out| 19;\n  16 -->|taxonomy_out| 19;\n  17 -->|otulist| 19;\n  20[\"Make.biom\"];\n  18 -->|shared| 20;\n  19 -->|taxonomies| 20;\n  21[\"Visualize  with Krona\"];\n  19 -->|taxonomies| 21;",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Amplicon Tutorial",
                 "outputs": [
                     {
@@ -141692,7 +358236,7 @@
                             {
                                 "label": "mothur_make_shared_shared",
                                 "output_name": "shared",
-                                "uuid": "62dd9aef-795b-44ba-bfa2-e63ed96c9d09"
+                                "uuid": "2112be1d-8b08-408b-a525-1daed190d68c"
                             }
                         ]
                     }
@@ -141782,7 +358326,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"MetaPhlAn2\"];\n  0 -->|output| 1;\n  2[\"Format MetaPhlAn2\"];\n  1 -->|output_file| 2;\n  3[\"HUMAnN2\"];\n  0 -->|output| 3;\n  1 -->|output_file| 3;\n  4[\"Krona pie chart\"];\n  2 -->|krona| 4;\n  5[\"Renormalize\"];\n  3 -->|gene_families_tsv| 5;\n  6[\"Regroup\"];\n  3 -->|gene_families_tsv| 6;\n  7[\"Renormalize\"];\n  6 -->|output_table| 7;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "WGS Part In \"Analyses Of Metagenomics Data - The Global Picture\"",
                 "outputs": [],
                 "parent_id": "microbiome/general-tutorial",
@@ -141969,13 +358513,13 @@
             "topic_0080"
         ],
         "edam_operation": [
-            "Taxonomic classification",
-            "Statistical calculation",
-            "Aggregation",
-            "Visualisation",
-            "Sequencing quality control",
             "Sequence composition calculation",
-            "Sequence contamination filtering"
+            "Sequence contamination filtering",
+            "Sequencing quality control",
+            "Visualisation",
+            "Aggregation",
+            "Statistical calculation",
+            "Taxonomic classification"
         ],
         "edam_topic": [
             "Metagenomics",
@@ -142016,7 +358560,7 @@
             "Identify yeast species contained in a sequenced beer sample using DNA",
             "Visualize the microbiome community of a beer sample"
         ],
-        "pageviews": 1942,
+        "pageviews": 1962,
         "pub_date": "2022-09-29",
         "questions": [
             "How can yeast strains in a beer sample be identified?",
@@ -142044,13 +358588,13 @@
         ],
         "short_id": "T00384",
         "short_tools": [
-            "porechop",
+            "krakentools_kreport2krona",
+            "fastqc",
             "fastp",
-            "Filter1",
-            "taxonomy_krona_chart",
+            "porechop",
             "kraken2",
-            "krakentools_kreport2krona",
-            "fastqc"
+            "taxonomy_krona_chart",
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -142086,6 +358630,1178 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Filter1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
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+                        {
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+                            "state": "missing"
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
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+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.2.4+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.2.4+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "0.2.4+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.2.4+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.2.4+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.2.4+galaxy0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "nanopore",
@@ -142124,8 +359840,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 178,
-        "visitors": 1239,
+        "visit_duration": 177,
+        "visitors": 1249,
         "workflows": [
             {
                 "creators": [
@@ -142152,7 +359868,7 @@
                     "report": null,
                     "subworkflows": false
                 },
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+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\ninput\"]\n  1[label=\"FastQC\"]\n  0 -> 1 [label=\"output\"]\n  2[label=\"Porechop\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"fastp\"]\n  2 -> 3 [label=\"outfile\"]\n  4[label=\"Kraken2\"]\n  3 -> 4 [label=\"out1\"]\n  k94b72e3144484eba90358ffb46ce3522[color=lightseagreen,label=\"Output\\nkraken_report\"]\n  4 -> k94b72e3144484eba90358ffb46ce3522\n  5[label=\"Filter\"]\n  4 -> 5 [label=\"report_output\"]\n  6[label=\"Filter\"]\n  4 -> 6 [label=\"report_output\"]\n  7[label=\"Krakentools: Convert kraken report file\"]\n  4 -> 7 [label=\"report_output\"]\n  k3df7f8cca7184768b80cb8ad55017014[color=lightseagreen,label=\"Output\\nkrakentool_report\"]\n  7 -> k3df7f8cca7184768b80cb8ad55017014\n  8[label=\"Krona pie chart\"]\n  7 -> 8 [label=\"output\"]\n}",
                 "history": [
                     {
                         "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
@@ -142192,8 +359908,8 @@
                     }
                 ],
                 "license": "MIT",
-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ninput\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"FastQC\"];\n  0 -->|output| 1;\n  2[\"Porechop\"];\n  0 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|outfile| 3;\n  4[\"Kraken2\"];\n  3 -->|out1| 4;\n  3a8bad46-ce3e-4b23-8415-7a539ee68ebb[\"Output\\nkraken_report\"];\n  4 --> 3a8bad46-ce3e-4b23-8415-7a539ee68ebb;\n  style 3a8bad46-ce3e-4b23-8415-7a539ee68ebb stroke:#2c3143,stroke-width:4px;\n  5[\"Filter\"];\n  4 -->|report_output| 5;\n  6[\"Filter\"];\n  4 -->|report_output| 6;\n  7[\"Krakentools: Convert kraken report file\"];\n  4 -->|report_output| 7;\n  e24a4cb0-9184-44a0-9b4c-0c554f059ace[\"Output\\nkrakentool_report\"];\n  7 --> e24a4cb0-9184-44a0-9b4c-0c554f059ace;\n  style e24a4cb0-9184-44a0-9b4c-0c554f059ace stroke:#2c3143,stroke-width:4px;\n  8[\"Krona pie chart\"];\n  7 -->|output| 8;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\ninput\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"FastQC\"];\n  0 -->|output| 1;\n  2[\"Porechop\"];\n  0 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|outfile| 3;\n  4[\"Kraken2\"];\n  3 -->|out1| 4;\n  94b72e31-4448-4eba-9035-8ffb46ce3522[\"Output\\nkraken_report\"];\n  4 --> 94b72e31-4448-4eba-9035-8ffb46ce3522;\n  style 94b72e31-4448-4eba-9035-8ffb46ce3522 stroke:#2c3143,stroke-width:4px;\n  5[\"Filter\"];\n  4 -->|report_output| 5;\n  6[\"Filter\"];\n  4 -->|report_output| 6;\n  7[\"Krakentools: Convert kraken report file\"];\n  4 -->|report_output| 7;\n  3df7f8cc-a718-4768-b80c-b8ad55017014[\"Output\\nkrakentool_report\"];\n  7 --> 3df7f8cc-a718-4768-b80c-b8ad55017014;\n  style 3df7f8cc-a718-4768-b80c-b8ad55017014 stroke:#2c3143,stroke-width:4px;\n  8[\"Krona pie chart\"];\n  7 -->|output| 8;",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Identification of the micro-organisms in a beer using Nanopore sequencing",
                 "outputs": [
                     {
@@ -142241,7 +359957,7 @@
                             {
                                 "label": "kraken_report",
                                 "output_name": "report_output",
-                                "uuid": "3a8bad46-ce3e-4b23-8415-7a539ee68ebb"
+                                "uuid": "94b72e31-4448-4eba-9035-8ffb46ce3522"
                             }
                         ]
                     },
@@ -142286,7 +360002,7 @@
                             {
                                 "label": "krakentool_report",
                                 "output_name": "output",
-                                "uuid": "e24a4cb0-9184-44a0-9b4c-0c554f059ace"
+                                "uuid": "3df7f8cc-a718-4768-b80c-b8ad55017014"
                             }
                         ]
                     }
@@ -142573,13 +360289,6 @@
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
-                {
-                    "name": "fasttree",
-                    "owner": "iuc",
-                    "revisions": "e005e659ae21",
-                    "tool_panel_section_label": "Genome Diversity",
-                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
-                },
                 {
                     "name": "ggplot2_heatmap",
                     "owner": "iuc",
@@ -142736,7 +360445,7 @@
                 }
             ]
         },
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text_processing\n  owner: bgruening\n  revisions: fbf99087e067\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: 86755160afbf\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: 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https://toolshed.g2.bx.psu.edu/\n- name: table_compute\n  owner: iuc\n  revisions: 3bf5661c0280\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
         "api": "https://training.galaxyproject.org/training-material/api/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.json",
         "contributions": {
             "authorship": [
@@ -142902,36 +360611,36 @@
             "topic_0080"
         ],
         "edam_operation": [
+            "Variant calling",
+            "Genome assembly",
+            "Sequence assembly visualisation",
+            "Base-calling",
+            "De-novo assembly",
+            "Antimicrobial resistance prediction",
+            "Mapping assembly",
+            "Taxonomic classification",
+            "Multilocus sequence typing",
+            "Multiple sequence alignment",
+            "Validation",
             "Scatter plot plotting",
             "Visualisation",
             "Cross-assembly",
-            "Phylogenetic tree generation",
-            "Genome assembly",
-            "Sequencing quality control",
-            "Box-Whisker plot plotting",
-            "Multiple sequence alignment",
-            "Mapping assembly",
-            "Base-calling",
             "Aggregation",
-            "Statistical calculation",
             "Pairwise sequence alignment",
-            "Validation",
-            "Taxonomic classification",
-            "Sequence composition calculation",
-            "Mapping",
-            "Antimicrobial resistance prediction",
-            "Phylogenetic tree analysis",
             "Data handling",
-            "Multilocus sequence typing",
-            "De-novo assembly",
             "Sequence alignment analysis",
+            "Phylogenetic tree generation (maximum likelihood and Bayesian methods)",
+            "Phylogenetic tree analysis",
+            "Phylogenetic tree generation (from molecular sequences)",
+            "Phylogenetic tree generation",
+            "Sequence composition calculation",
+            "Box-Whisker plot plotting",
+            "Sequence assembly",
+            "Sequencing quality control",
             "Phylogenetic tree reconstruction",
             "Sequence contamination filtering",
-            "Sequence assembly",
-            "Variant calling",
-            "Sequence assembly visualisation",
-            "Phylogenetic tree generation (from molecular sequences)",
-            "Phylogenetic tree generation (maximum likelihood and Bayesian methods)"
+            "Statistical calculation",
+            "Mapping"
         ],
         "edam_topic": [
             "Metagenomics",
@@ -142967,7 +360676,7 @@
             "Identify pathogens via SNP calling and build the consensus gemone of the samples",
             "Relate all samples' pathogenic genes for tracking pathogens via phylogenetic trees and heatmaps"
         ],
-        "pageviews": 2918,
+        "pageviews": 2968,
         "pub_date": "2023-01-26",
         "questions": [
             "What are the preprocessing steps to prepare ONT sequencing data for further analysis?",
@@ -143009,67 +360718,67 @@
         ],
         "short_id": "T00393",
         "short_tools": [
+            "regex1",
+            "regexColumn1",
+            "CONVERTER_gz_to_uncompressed",
+            "mlst",
+            "__BUILD_LIST__",
+            "Remove beginning1",
+            "fasta2tab",
+            "fastp",
+            "abricate",
+            "collapse_dataset",
+            "__FILTER_EMPTY_DATASETS__",
+            "samtools_depth",
+            "tab2fasta",
+            "tp_sorted_uniq",
+            "snpSift_filter",
+            "samtools_fastx",
+            "tp_replace_in_column",
+            "clair3",
+            "porechop",
             "__FILTER_FAILED_DATASETS__",
+            "Paste1",
+            "ggplot2_heatmap",
+            "bandage_image",
+            "bcftools_norm",
             "Count1",
-            "minimap2",
-            "snpSift_filter",
             "compose_text_param",
-            "tab2fasta",
-            "tp_find_and_replace",
-            "tp_head_tool",
-            "tp_multijoin_tool",
-            "param_value_from_file",
-            "collection_column_join",
-            "collection_element_identifiers",
-            "bcftools_norm",
-            "krakentools_kreport2krona",
             "krakentools_extract_kraken_reads",
-            "ggplot2_heatmap",
-            "bamtools_split_mapped",
-            "fasta_merge_files_and_filter_unique_sequences",
-            "barchart_gnuplot",
-            "samtools_fastx",
-            "flye",
+            "krakentools_kreport2krona",
             "medaka_consensus_pipeline",
-            "tp_cut_tool",
-            "fastqc",
+            "minimap2",
+            "newick_display",
+            "clustalw",
+            "collection_element_identifiers",
+            "barchart_gnuplot",
+            "tp_find_and_replace",
+            "fasta_merge_files_and_filter_unique_sequences",
+            "collection_column_join",
             "snpSift_extractFields",
-            "regex1",
-            "Grouping1",
-            "tp_sorted_uniq",
-            "porechop",
-            "table_compute",
-            "bcftools_consensus",
-            "split_file_to_collection",
-            "bandage_image",
-            "abricate",
-            "Paste1",
+            "Grep1",
             "add_line_to_file",
-            "tp_split_on_column",
+            "bamtools_split_mapped",
             "multiqc",
-            "Grep1",
+            "kraken2",
+            "Add_a_column1",
+            "tp_cut_tool",
             "Cut1",
-            "collapse_dataset",
-            "Remove beginning1",
-            "clustalw",
+            "tp_split_on_column",
+            "bcftools_consensus",
+            "tp_multijoin_tool",
+            "samtools_coverage",
             "bedtools_getfastabed",
-            "tp_replace_in_column",
+            "param_value_from_file",
+            "fastqc",
+            "nanoplot",
+            "table_compute",
+            "split_file_to_collection",
             "fasttree",
-            "newick_display",
-            "fastp",
-            "samtools_coverage",
-            "samtools_depth",
-            "clair3",
+            "Grouping1",
             "taxonomy_krona_chart",
-            "__FILTER_EMPTY_DATASETS__",
-            "kraken2",
-            "__BUILD_LIST__",
-            "Add_a_column1",
-            "mlst",
-            "nanoplot",
-            "regexColumn1",
-            "CONVERTER_gz_to_uncompressed",
-            "fasta2tab"
+            "flye",
+            "tp_head_tool"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -143090,6 +360799,10266 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
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@@ -143319,7 +371288,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nsamples_profile\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nreference_genome_of_tested_strain\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Convert compressed file to uncompressed.\"];\n  2 -->|output| 3;\n  9d6bde4a-7180-4097-9ffd-6992111a617c[\"Output\\ndecompressed_rg_file\"];\n  3 --> 9d6bde4a-7180-4097-9ffd-6992111a617c;\n  style 9d6bde4a-7180-4097-9ffd-6992111a617c stroke:#2c3143,stroke-width:4px;\n  4[\"Map with minimap2\"];\n  1 -->|output| 4;\n  0 -->|output| 4;\n  3 -->|output1| 4;\n  31779c23-4f26-418e-9418-2551e883dbe7[\"Output\\nmap_with_minimap2\"];\n  4 --> 31779c23-4f26-418e-9418-2551e883dbe7;\n  style 31779c23-4f26-418e-9418-2551e883dbe7 stroke:#2c3143,stroke-width:4px;\n  5[\"Clair3\"];\n  4 -->|alignment_output| 5;\n  3 -->|output1| 5;\n  1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53[\"Output\\nclair3_pileup_vcf\"];\n  5 --> 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53;\n  style 1cf1ee6c-4cb7-45e3-9c7b-88a1b678dd53 stroke:#2c3143,stroke-width:4px;\n  987f9145-83ab-44f1-801a-b0d527ecbce8[\"Output\\nclair3_full_alignment_vcf\"];\n  5 --> 987f9145-83ab-44f1-801a-b0d527ecbce8;\n  style 987f9145-83ab-44f1-801a-b0d527ecbce8 stroke:#2c3143,stroke-width:4px;\n  fab82215-f59a-43b1-92d7-37629a1fdb65[\"Output\\nclair3_merged_output\"];\n  5 --> fab82215-f59a-43b1-92d7-37629a1fdb65;\n  style fab82215-f59a-43b1-92d7-37629a1fdb65 stroke:#2c3143,stroke-width:4px;\n  6[\"Samtools depth\"];\n  4 -->|alignment_output| 6;\n  7[\"Samtools coverage\"];\n  4 -->|alignment_output| 7;\n  8[\"bcftools norm\"];\n  5 -->|merge_output| 8;\n  3 -->|output1| 8;\n  22553aa1-f5db-4d37-87c4-1164dbb3d2d5[\"Output\\nnormalized_vcf_output\"];\n  8 --> 22553aa1-f5db-4d37-87c4-1164dbb3d2d5;\n  style 22553aa1-f5db-4d37-87c4-1164dbb3d2d5 stroke:#2c3143,stroke-width:4px;\n  9[\"Advanced Cut\"];\n  6 -->|output| 9;\n  10[\"Remove beginning\"];\n  7 -->|output| 10;\n  11[\"SnpSift Filter\"];\n  8 -->|output_file| 11;\n  3e7981ec-2205-4571-93eb-10c0dd14b288[\"Output\\nquality_filtered_vcf_output\"];\n  11 --> 3e7981ec-2205-4571-93eb-10c0dd14b288;\n  style 3e7981ec-2205-4571-93eb-10c0dd14b288 stroke:#2c3143,stroke-width:4px;\n  12[\"Table Compute\"];\n  9 -->|output| 12;\n  13[\"Cut\"];\n  10 -->|out_file1| 13;\n  14[\"SnpSift Extract Fields\"];\n  11 -->|output| 14;\n  1b0f4f2c-4717-45be-b580-fe10cba78c35[\"Output\\nextracted_fields_from_the_vcf_output\"];\n  14 --> 1b0f4f2c-4717-45be-b580-fe10cba78c35;\n  style 1b0f4f2c-4717-45be-b580-fe10cba78c35 stroke:#2c3143,stroke-width:4px;\n  15[\"bcftools consensus\"];\n  11 -->|output| 15;\n  3 -->|output1| 15;\n  49497f3c-9332-4924-bcfd-cb71788ad2c2[\"Output\\nbcftools_consensus\"];\n  15 --> 49497f3c-9332-4924-bcfd-cb71788ad2c2;\n  style 49497f3c-9332-4924-bcfd-cb71788ad2c2 stroke:#2c3143,stroke-width:4px;\n  16[\"Select first\"];\n  13 -->|out_file1| 16;\n  17[\"Remove beginning\"];\n  14 -->|output| 17;\n  18[\"Collapse Collection\"];\n  16 -->|outfile| 18;\n  5ee1c158-1a85-45ca-9abd-b30632b3092c[\"Output\\nmapping_coverage_percentage_per_sample\"];\n  18 --> 5ee1c158-1a85-45ca-9abd-b30632b3092c;\n  style 5ee1c158-1a85-45ca-9abd-b30632b3092c stroke:#2c3143,stroke-width:4px;\n  19[\"Count\"];\n  17 -->|out_file1| 19;\n  20[\"Advanced Cut\"];\n  18 -->|output| 20;\n  21[\"Cut\"];\n  19 -->|out_file1| 21;\n  22[\"Paste\"];\n  20 -->|output| 22;\n  12 -->|table| 22;\n  25b7b87b-5ef1-487f-90cc-81351a2f81ce[\"Output\\nmapping_mean_depth_per_sample\"];\n  22 --> 25b7b87b-5ef1-487f-90cc-81351a2f81ce;\n  style 25b7b87b-5ef1-487f-90cc-81351a2f81ce stroke:#2c3143,stroke-width:4px;\n  23[\"Select first\"];\n  21 -->|out_file1| 23;\n  24[\"Collapse Collection\"];\n  23 -->|outfile| 24;\n  25[\"Column Regex Find And Replace\"];\n  24 -->|output| 25;\n  2852c4ee-24ea-4df7-b59e-54eb6e2f470b[\"Output\\nnumber_of_variants_per_sample\"];\n  25 --> 2852c4ee-24ea-4df7-b59e-54eb6e2f470b;\n  style 2852c4ee-24ea-4df7-b59e-54eb6e2f470b stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Allele-based Pathogen Identification",
                 "outputs": [
                     {
@@ -144083,7 +372052,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Extract element identifiers\"];\n  0 -->|output| 1;\n  d82a93c6-23a9-4f85-879c-ecd759a31087[\"Output\\nextracted_samples_IDs\"];\n  1 --> d82a93c6-23a9-4f85-879c-ecd759a31087;\n  style d82a93c6-23a9-4f85-879c-ecd759a31087 stroke:#2c3143,stroke-width:4px;\n  2[\"Build list\"];\n  0 -->|output| 2;\n  f5b5b256-8ddf-4da8-8111-b1f6d3025a0d[\"Output\\nlist_of_lists_of_preprocessed_samples\"];\n  2 --> f5b5b256-8ddf-4da8-8111-b1f6d3025a0d;\n  style f5b5b256-8ddf-4da8-8111-b1f6d3025a0d stroke:#2c3143,stroke-width:4px;\n  3[\"Split file\"];\n  1 -->|output| 3;\n  eb5317bd-4bad-4cad-9219-3ac379221d6e[\"Output\\nsplitted_extracted_samples_IDs\"];\n  3 --> eb5317bd-4bad-4cad-9219-3ac379221d6e;\n  style eb5317bd-4bad-4cad-9219-3ac379221d6e stroke:#2c3143,stroke-width:4px;\n  4[\"Flye\"];\n  2 -->|output| 4;\n  ff0d8c7b-2ac7-4c6d-a110-f71418dad938[\"Output\\nflye_consensus_fasta\"];\n  4 --> ff0d8c7b-2ac7-4c6d-a110-f71418dad938;\n  style ff0d8c7b-2ac7-4c6d-a110-f71418dad938 stroke:#2c3143,stroke-width:4px;\n  2385436f-fbe8-4d77-a40b-27a097d02941[\"Output\\nflye_assembly_graph\"];\n  4 --> 2385436f-fbe8-4d77-a40b-27a097d02941;\n  style 2385436f-fbe8-4d77-a40b-27a097d02941 stroke:#2c3143,stroke-width:4px;\n  0e42ce51-c46b-45d8-baa4-45c0e98ac712[\"Output\\nflye_assembly_gfa\"];\n  4 --> 0e42ce51-c46b-45d8-baa4-45c0e98ac712;\n  style 0e42ce51-c46b-45d8-baa4-45c0e98ac712 stroke:#2c3143,stroke-width:4px;\n  3f297aed-7cee-4999-bbf4-69d84de6b64f[\"Output\\nflye_assembly_info_tabular\"];\n  4 --> 3f297aed-7cee-4999-bbf4-69d84de6b64f;\n  style 3f297aed-7cee-4999-bbf4-69d84de6b64f stroke:#2c3143,stroke-width:4px;\n  5[\"Parse parameter value\"];\n  3 -->|list_output_txt| 5;\n  3608e170-c462-42a2-8003-f3f65baa3834[\"Output\\nparsed_extracted_samples_IDs_to_text\"];\n  5 --> 3608e170-c462-42a2-8003-f3f65baa3834;\n  style 3608e170-c462-42a2-8003-f3f65baa3834 stroke:#2c3143,stroke-width:4px;\n  6[\"medaka consensus pipeline\"];\n  4 -->|consensus| 6;\n  0 -->|output| 6;\n  9e5ad6ec-b408-4132-ba07-dec9fa626923[\"Output\\nmedaka_gaps_in_draft_bed_file\"];\n  6 --> 9e5ad6ec-b408-4132-ba07-dec9fa626923;\n  style 9e5ad6ec-b408-4132-ba07-dec9fa626923 stroke:#2c3143,stroke-width:4px;\n  fcbd3e3f-2e93-4798-b696-dad7db9f2efd[\"Output\\nmedaka_log_file\"];\n  6 --> fcbd3e3f-2e93-4798-b696-dad7db9f2efd;\n  style fcbd3e3f-2e93-4798-b696-dad7db9f2efd stroke:#2c3143,stroke-width:4px;\n  60656aac-ad2a-4c9b-9a68-b9fb18ae5595[\"Output\\nmedaka_propability_h5_file\"];\n  6 --> 60656aac-ad2a-4c9b-9a68-b9fb18ae5595;\n  style 60656aac-ad2a-4c9b-9a68-b9fb18ae5595 stroke:#2c3143,stroke-width:4px;\n  c790d434-8e78-4df0-a0d4-8f9da0692158[\"Output\\nmedaka_calls_of_draft_bam_file\"];\n  6 --> c790d434-8e78-4df0-a0d4-8f9da0692158;\n  style c790d434-8e78-4df0-a0d4-8f9da0692158 stroke:#2c3143,stroke-width:4px;\n  df361e19-b6d1-405b-96cc-b48c1ab7c604[\"Output\\nsample_all_contigs\"];\n  6 --> df361e19-b6d1-405b-96cc-b48c1ab7c604;\n  style df361e19-b6d1-405b-96cc-b48c1ab7c604 stroke:#2c3143,stroke-width:4px;\n  7[\"Bandage Image\"];\n  4 -->|assembly_gfa| 7;\n  9612a851-1f94-4d54-b001-5d082bcc9055[\"Output\\nbandage_assembly_graph_image\"];\n  7 --> 9612a851-1f94-4d54-b001-5d082bcc9055;\n  style 9612a851-1f94-4d54-b001-5d082bcc9055 stroke:#2c3143,stroke-width:4px;\n  8[\"Compose text parameter value\"];\n  5 -->|text_param| 8;\n  9[\"FASTA-to-Tabular\"];\n  6 -->|out_consensus| 9;\n  de06c362-5b0a-4c29-956e-fbf02539789a[\"Output\\nsample_specific_contigs_tabular_file_preparation\"];\n  9 --> de06c362-5b0a-4c29-956e-fbf02539789a;\n  style de06c362-5b0a-4c29-956e-fbf02539789a stroke:#2c3143,stroke-width:4px;\n  10[\"ABRicate\"];\n  6 -->|out_consensus| 10;\n  8f227fc7-2d92-4c6f-af64-e841c1315b4f[\"Output\\nabricate_with_vfdb_to_identify_genes_with_VFs\"];\n  10 --> 8f227fc7-2d92-4c6f-af64-e841c1315b4f;\n  style 8f227fc7-2d92-4c6f-af64-e841c1315b4f stroke:#2c3143,stroke-width:4px;\n  11[\"ABRicate\"];\n  6 -->|out_consensus| 11;\n  fa021d98-d885-4834-ac62-f30d5792260e[\"Output\\nabricate_report_using_ncbi_database_to_indentify_amr\"];\n  11 --> fa021d98-d885-4834-ac62-f30d5792260e;\n  style fa021d98-d885-4834-ac62-f30d5792260e stroke:#2c3143,stroke-width:4px;\n  12[\"Replace\"];\n  8 -->|out1| 12;\n  9 -->|output| 12;\n  174cb2c3-ed28-453c-8afb-85150e0b51ad[\"Output\\nsample_specific_contigs_tabular_file\"];\n  12 --> 174cb2c3-ed28-453c-8afb-85150e0b51ad;\n  style 174cb2c3-ed28-453c-8afb-85150e0b51ad stroke:#2c3143,stroke-width:4px;\n  13[\"Replace\"];\n  8 -->|out1| 13;\n  10 -->|report| 13;\n  19e56e00-6eef-4a4e-9cc6-d93dbf9420ad[\"Output\\nvfs\"];\n  13 --> 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad;\n  style 19e56e00-6eef-4a4e-9cc6-d93dbf9420ad stroke:#2c3143,stroke-width:4px;\n  14[\"Replace\"];\n  8 -->|out1| 14;\n  11 -->|report| 14;\n  a8eb74a5-362b-4f0f-a944-672e27981a41[\"Output\\namrs\"];\n  14 --> a8eb74a5-362b-4f0f-a944-672e27981a41;\n  style a8eb74a5-362b-4f0f-a944-672e27981a41 stroke:#2c3143,stroke-width:4px;\n  15[\"Tabular-to-FASTA\"];\n  12 -->|outfile| 15;\n  a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe[\"Output\\ncontigs\"];\n  15 --> a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe;\n  style a5bb1cbe-1bde-49a1-ad86-6d57b1319fbe stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Gene-based Pathogen Identification",
                 "outputs": [
                     {
@@ -145153,7 +373122,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nsamples_profile\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\ncollection_of_all_samples\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Porechop\"];\n  1 -->|output| 2;\n  34ea26db-11cb-41ee-85c3-75af8a53a2c0[\"Output\\nporechop_output_trimmed_reads\"];\n  2 --> 34ea26db-11cb-41ee-85c3-75af8a53a2c0;\n  style 34ea26db-11cb-41ee-85c3-75af8a53a2c0 stroke:#2c3143,stroke-width:4px;\n  3[\"NanoPlot\"];\n  1 -->|output| 3;\n  15ecf5b1-e0eb-405a-ac3a-359feb66d4cd[\"Output\\nnanoplot_qc_on_reads_before_preprocessing_nanostats\"];\n  3 --> 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd;\n  style 15ecf5b1-e0eb-405a-ac3a-359feb66d4cd stroke:#2c3143,stroke-width:4px;\n  304110f9-60d0-4ba2-8b3b-fae0e2a49554[\"Output\\nnanoplot_on_reads_before_preprocessing_nanostats_post_filtering\"];\n  3 --> 304110f9-60d0-4ba2-8b3b-fae0e2a49554;\n  style 304110f9-60d0-4ba2-8b3b-fae0e2a49554 stroke:#2c3143,stroke-width:4px;\n  f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e[\"Output\\nnanoplot_qc_on_reads_before_preprocessing_html_report\"];\n  3 --> f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e;\n  style f2bd0a1f-cd60-4a36-a7d0-8025cc19ea2e stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC\"];\n  1 -->|output| 4;\n  d0a64624-05d0-4068-835b-a025fc011760[\"Output\\nfastqc_quality_check_before_preprocessing_html_file\"];\n  4 --> d0a64624-05d0-4068-835b-a025fc011760;\n  style d0a64624-05d0-4068-835b-a025fc011760 stroke:#2c3143,stroke-width:4px;\n  e61fef5d-1bc8-4c8e-be6a-f74e210e9920[\"Output\\nfastqc_quality_check_before_preprocessing_text_file\"];\n  4 --> e61fef5d-1bc8-4c8e-be6a-f74e210e9920;\n  style e61fef5d-1bc8-4c8e-be6a-f74e210e9920 stroke:#2c3143,stroke-width:4px;\n  5[\"fastp\"];\n  2 -->|outfile| 5;\n  a2219483-50b7-4aed-98dd-333ad2e12eb8[\"Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal\"];\n  5 --> a2219483-50b7-4aed-98dd-333ad2e12eb8;\n  style a2219483-50b7-4aed-98dd-333ad2e12eb8 stroke:#2c3143,stroke-width:4px;\n  2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4[\"Output\\nnanopore_sequenced_reads_processed_with_fastp_after_host_removal_html_report\"];\n  5 --> 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4;\n  style 2a9a8b4d-458b-40e7-9a21-fb7108d5bbe4 stroke:#2c3143,stroke-width:4px;\n  6[\"MultiQC\"];\n  4 -->|text_file| 6;\n  ebffe782-a56c-431f-8af4-c0cb8d7a02fc[\"Output\\nmultiQC_stats_before_preprocessing\"];\n  6 --> ebffe782-a56c-431f-8af4-c0cb8d7a02fc;\n  style ebffe782-a56c-431f-8af4-c0cb8d7a02fc stroke:#2c3143,stroke-width:4px;\n  0f92196d-047d-4918-819d-c0ff7cd3ae85[\"Output\\nmultiQC_html_report_before_preprocessing\"];\n  6 --> 0f92196d-047d-4918-819d-c0ff7cd3ae85;\n  style 0f92196d-047d-4918-819d-c0ff7cd3ae85 stroke:#2c3143,stroke-width:4px;\n  7[\"Map with minimap2\"];\n  0 -->|output| 7;\n  5 -->|out1| 7;\n  9d7bb3b7-09a1-401f-a132-bb35a53375ea[\"Output\\nbam_map_to_host\"];\n  7 --> 9d7bb3b7-09a1-401f-a132-bb35a53375ea;\n  style 9d7bb3b7-09a1-401f-a132-bb35a53375ea stroke:#2c3143,stroke-width:4px;\n  8[\"NanoPlot\"];\n  5 -->|out1| 8;\n  b5899290-4c57-4662-ad22-860654652ade[\"Output\\nnanoplot_qc_on_reads_after_preprocessing_html_report\"];\n  8 --> b5899290-4c57-4662-ad22-860654652ade;\n  style b5899290-4c57-4662-ad22-860654652ade stroke:#2c3143,stroke-width:4px;\n  949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf[\"Output\\nnanoplot_on_reads_after_preprocessing_nanostats_post_filtering\"];\n  8 --> 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf;\n  style 949bfdf5-3d79-4dad-bdd8-c3a25e6af4cf stroke:#2c3143,stroke-width:4px;\n  42db7f93-919e-4bbb-81a1-06411a9da410[\"Output\\nnanoplot_qc_on_reads_after_preprocessing_nanostats\"];\n  8 --> 42db7f93-919e-4bbb-81a1-06411a9da410;\n  style 42db7f93-919e-4bbb-81a1-06411a9da410 stroke:#2c3143,stroke-width:4px;\n  9[\"FastQC\"];\n  5 -->|out1| 9;\n  09306471-afa0-4106-9cc7-259b93dfc862[\"Output\\nfastqc_quality_check_after_preprocessing_text_file\"];\n  9 --> 09306471-afa0-4106-9cc7-259b93dfc862;\n  style 09306471-afa0-4106-9cc7-259b93dfc862 stroke:#2c3143,stroke-width:4px;\n  084f982f-20f1-457e-8012-91ebbb85633d[\"Output\\nfastqc_quality_check_after_preprocessing_html_file\"];\n  9 --> 084f982f-20f1-457e-8012-91ebbb85633d;\n  style 084f982f-20f1-457e-8012-91ebbb85633d stroke:#2c3143,stroke-width:4px;\n  10[\"Split BAM by reads mapping status\"];\n  7 -->|alignment_output| 10;\n  14a53fe2-f296-43aa-86b7-243278c1050c[\"Output\\nnon_host_sequences_bam\"];\n  10 --> 14a53fe2-f296-43aa-86b7-243278c1050c;\n  style 14a53fe2-f296-43aa-86b7-243278c1050c stroke:#2c3143,stroke-width:4px;\n  3b1e626f-6bc1-484c-be01-366534361b73[\"Output\\nhost_sequences_bam\"];\n  10 --> 3b1e626f-6bc1-484c-be01-366534361b73;\n  style 3b1e626f-6bc1-484c-be01-366534361b73 stroke:#2c3143,stroke-width:4px;\n  11[\"Select\"];\n  9 -->|text_file| 11;\n  a809853b-119f-44d2-986b-8d2006439fbe[\"Output\\ntotal_sequences_before_hosts_sequences_removal\"];\n  11 --> a809853b-119f-44d2-986b-8d2006439fbe;\n  style a809853b-119f-44d2-986b-8d2006439fbe stroke:#2c3143,stroke-width:4px;\n  12[\"Samtools fastx\"];\n  10 -->|mapped| 12;\n  10d4eaec-81d8-444e-8075-7b77a1fb6870[\"Output\\nhost_sequences_fastq\"];\n  12 --> 10d4eaec-81d8-444e-8075-7b77a1fb6870;\n  style 10d4eaec-81d8-444e-8075-7b77a1fb6870 stroke:#2c3143,stroke-width:4px;\n  13[\"Samtools fastx\"];\n  10 -->|unmapped| 13;\n  0c2dd74d-ac4f-45cf-839c-50386a7ece28[\"Output\\nnon_host_sequences_fastq\"];\n  13 --> 0c2dd74d-ac4f-45cf-839c-50386a7ece28;\n  style 0c2dd74d-ac4f-45cf-839c-50386a7ece28 stroke:#2c3143,stroke-width:4px;\n  14[\"Collapse Collection\"];\n  11 -->|out_file1| 14;\n  15[\"Filter failed datasets\"];\n  12 -->|output| 15;\n  16[\"Kraken2\"];\n  13 -->|output| 16;\n  203d303e-8f3a-4242-971f-b345842ebdb8[\"Output\\nkraken2_with_kalamri_database_output\"];\n  16 --> 203d303e-8f3a-4242-971f-b345842ebdb8;\n  style 203d303e-8f3a-4242-971f-b345842ebdb8 stroke:#2c3143,stroke-width:4px;\n  843afd4d-23a8-46e7-b945-8b67dd7ae341[\"Output\\nkraken2_with_kalamri_database_report\"];\n  16 --> 843afd4d-23a8-46e7-b945-8b67dd7ae341;\n  style 843afd4d-23a8-46e7-b945-8b67dd7ae341 stroke:#2c3143,stroke-width:4px;\n  17[\"Cut\"];\n  14 -->|output| 17;\n  d07be9f1-d250-4008-91ee-59a68521eb56[\"Output\\nquality_retained_all_reads\"];\n  17 --> d07be9f1-d250-4008-91ee-59a68521eb56;\n  style d07be9f1-d250-4008-91ee-59a68521eb56 stroke:#2c3143,stroke-width:4px;\n  18[\"FastQC\"];\n  15 -->|output| 18;\n  b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7[\"Output\\nhosts_qc_text_file\"];\n  18 --> b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7;\n  style b0ee6e31-0eb1-437d-8c04-fc3640b9a0b7 stroke:#2c3143,stroke-width:4px;\n  b72ff57b-0921-43bf-a817-6cd444c8f3cb[\"Output\\nhosts_qc_html\"];\n  18 --> b72ff57b-0921-43bf-a817-6cd444c8f3cb;\n  style b72ff57b-0921-43bf-a817-6cd444c8f3cb stroke:#2c3143,stroke-width:4px;\n  19[\"Krakentools: Extract Kraken Reads By ID\"];\n  5 -->|out1| 19;\n  16 -->|report_output| 19;\n  16 -->|output| 19;\n  57e3b725-8e13-40b2-9acc-31fd56ebc80a[\"Output\\ncollection_of_preprocessed_samples\"];\n  19 --> 57e3b725-8e13-40b2-9acc-31fd56ebc80a;\n  style 57e3b725-8e13-40b2-9acc-31fd56ebc80a stroke:#2c3143,stroke-width:4px;\n  20[\"Select\"];\n  18 -->|text_file| 20;\n  3ba35c71-32f0-4741-98d4-ea8522e27500[\"Output\\ntotal_sequences_after_hosts_sequences_removal\"];\n  20 --> 3ba35c71-32f0-4741-98d4-ea8522e27500;\n  style 3ba35c71-32f0-4741-98d4-ea8522e27500 stroke:#2c3143,stroke-width:4px;\n  21[\"Collapse Collection\"];\n  20 -->|out_file1| 21;\n  22[\"Cut\"];\n  21 -->|output| 22;\n  cef36c68-4549-4fd6-b7c8-71fb21df012f[\"Output\\nquality_retained_hosts_reads\"];\n  22 --> cef36c68-4549-4fd6-b7c8-71fb21df012f;\n  style cef36c68-4549-4fd6-b7c8-71fb21df012f stroke:#2c3143,stroke-width:4px;\n  23[\"Column join\"];\n  17 -->|out_file1| 23;\n  22 -->|out_file1| 23;\n  24[\"Compute\"];\n  23 -->|tabular_output| 24;\n  25[\"Column Regex Find And Replace\"];\n  24 -->|out_file1| 25;\n  470892ee-dab9-48d7-ad97-45dbd52afaa7[\"Output\\nremoved_hosts_percentage_tabular\"];\n  25 --> 470892ee-dab9-48d7-ad97-45dbd52afaa7;\n  style 470892ee-dab9-48d7-ad97-45dbd52afaa7 stroke:#2c3143,stroke-width:4px;\n  26[\"MultiQC\"];\n  9 -->|text_file| 26;\n  25 -->|out_file1| 26;\n  0b1b5a73-36ee-42a2-a220-1ced6ec7378b[\"Output\\nmultiQC_html_report_after_preprocessing\"];\n  26 --> 0b1b5a73-36ee-42a2-a220-1ced6ec7378b;\n  style 0b1b5a73-36ee-42a2-a220-1ced6ec7378b stroke:#2c3143,stroke-width:4px;\n  13cbf6c7-6954-4458-aa66-a5b020c63822[\"Output\\nmultiQC_stats_after_preprocessing\"];\n  26 --> 13cbf6c7-6954-4458-aa66-a5b020c63822;\n  style 13cbf6c7-6954-4458-aa66-a5b020c63822 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Nanopore Preprocessing",
                 "outputs": [
                     {
@@ -146924,7 +374893,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\namr_identified_by_ncbi\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nvfs_of_genes_identified_by_vfdb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nmetadata\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nremoved_hosts_percentage_tabular\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nmapping_mean_depth_per_sample\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Collection\\namrs\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nmapping_coverage_percentage_per_sample\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nnumber_of_variants_per_sample\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Collection\\ncontigs\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Collection\\nvfs\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"Filter failed datasets\"];\n  0 -->|output| 10;\n  11[\"Filter failed datasets\"];\n  1 -->|output| 11;\n  12[\"Bar chart\"];\n  3 -->|output| 12;\n  0961166e-38b6-44e3-93db-100d821b0070[\"Output\\nnumber_of_reads_before_host_removal_and_number_of_host_reads_found_per_sample_fig\"];\n  12 --> 0961166e-38b6-44e3-93db-100d821b0070;\n  style 0961166e-38b6-44e3-93db-100d821b0070 stroke:#2c3143,stroke-width:4px;\n  13[\"Bar chart\"];\n  3 -->|output| 13;\n  548975e5-4619-49fc-9e95-4d7f4d761dfd[\"Output\\nremoved_host_percentage_fig\"];\n  13 --> 548975e5-4619-49fc-9e95-4d7f4d761dfd;\n  style 548975e5-4619-49fc-9e95-4d7f4d761dfd stroke:#2c3143,stroke-width:4px;\n  14[\"Bar chart\"];\n  4 -->|output| 14;\n  a71ebb67-1154-4f25-a62d-e8fa2b839e2e[\"Output\\nmapping_mean_depth_per_sample_fig\"];\n  14 --> a71ebb67-1154-4f25-a62d-e8fa2b839e2e;\n  style a71ebb67-1154-4f25-a62d-e8fa2b839e2e stroke:#2c3143,stroke-width:4px;\n  15[\"Filter failed datasets\"];\n  5 -->|output| 15;\n  16[\"Bar chart\"];\n  6 -->|output| 16;\n  2567360e-d39f-4316-84f5-77aaf8e8198c[\"Output\\nmapping_coverage_percentage_per_sample_fig\"];\n  16 --> 2567360e-d39f-4316-84f5-77aaf8e8198c;\n  style 2567360e-d39f-4316-84f5-77aaf8e8198c stroke:#2c3143,stroke-width:4px;\n  17[\"Bar chart\"];\n  7 -->|output| 17;\n  68c76f06-d2ea-4280-9e6f-a7b4f1568389[\"Output\\nnumber_of_Variants_and_SNPs_indentified_fig\"];\n  17 --> 68c76f06-d2ea-4280-9e6f-a7b4f1568389;\n  style 68c76f06-d2ea-4280-9e6f-a7b4f1568389 stroke:#2c3143,stroke-width:4px;\n  18[\"Filter failed datasets\"];\n  8 -->|output| 18;\n  19[\"Filter failed datasets\"];\n  9 -->|output| 19;\n  20[\"Remove beginning\"];\n  10 -->|output| 20;\n  21[\"Remove beginning\"];\n  11 -->|output| 21;\n  22[\"Remove beginning\"];\n  15 -->|output| 22;\n  23[\"Collapse Collection\"];\n  18 -->|output| 23;\n  86910e39-57bf-4a76-ac4c-739340fd2387[\"Output\\nall_samples_contigs_in_one_fasta_file\"];\n  23 --> 86910e39-57bf-4a76-ac4c-739340fd2387;\n  style 86910e39-57bf-4a76-ac4c-739340fd2387 stroke:#2c3143,stroke-width:4px;\n  24[\"Collapse Collection\"];\n  19 -->|output| 24;\n  02b996c6-a912-4e4e-b3ec-49601faaa452[\"Output\\nall_vfs_in_one_tabular\"];\n  24 --> 02b996c6-a912-4e4e-b3ec-49601faaa452;\n  style 02b996c6-a912-4e4e-b3ec-49601faaa452 stroke:#2c3143,stroke-width:4px;\n  25[\"Remove beginning\"];\n  19 -->|output| 25;\n  26[\"Count\"];\n  20 -->|out_file1| 26;\n  27[\"Count\"];\n  21 -->|out_file1| 27;\n  28[\"Group\"];\n  21 -->|out_file1| 28;\n  29[\"Unique\"];\n  22 -->|out_file1| 29;\n  30[\"Split by group\"];\n  24 -->|output| 30;\n  59f8cb09-424b-47b1-b94b-a612c2610cab[\"Output\\nsplit_by_group_collection\"];\n  30 --> 59f8cb09-424b-47b1-b94b-a612c2610cab;\n  style 59f8cb09-424b-47b1-b94b-a612c2610cab stroke:#2c3143,stroke-width:4px;\n  31[\"Unique\"];\n  25 -->|out_file1| 31;\n  32[\"Cut\"];\n  26 -->|out_file1| 32;\n  33[\"Cut\"];\n  27 -->|out_file1| 33;\n  34[\"Filter empty datasets\"];\n  28 -->|out_file1| 34;\n  35[\"Cut\"];\n  29 -->|outfile| 35;\n  36[\"Cut\"];\n  30 -->|split_output| 36;\n  eeb25a51-ea21-4a19-a196-55d5bd919b10[\"Output\\nadjusted_abricate_vfs_tabular_part1\"];\n  36 --> eeb25a51-ea21-4a19-a196-55d5bd919b10;\n  style eeb25a51-ea21-4a19-a196-55d5bd919b10 stroke:#2c3143,stroke-width:4px;\n  37[\"Cut\"];\n  31 -->|outfile| 37;\n  38[\"Collapse Collection\"];\n  32 -->|out_file1| 38;\n  39[\"Collapse Collection\"];\n  33 -->|out_file1| 39;\n  40[\"Column join\"];\n  34 -->|output| 40;\n  41[\"bedtools getfasta\"];\n  23 -->|output| 41;\n  35 -->|out_file1| 41;\n  42[\"Remove beginning\"];\n  36 -->|out_file1| 42;\n  aaaa4446-0817-4e5c-aa1b-9ec384f2a363[\"Output\\nadjusted_abricate_vfs_tabular_part2\"];\n  42 --> aaaa4446-0817-4e5c-aa1b-9ec384f2a363;\n  style aaaa4446-0817-4e5c-aa1b-9ec384f2a363 stroke:#2c3143,stroke-width:4px;\n  43[\"bedtools getfasta\"];\n  23 -->|output| 43;\n  37 -->|out_file1| 43;\n  44[\"Column Regex Find And Replace\"];\n  38 -->|output| 44;\n  4809c36b-31ef-4664-8e4e-47f0f72152de[\"Output\\namrs_count\"];\n  44 --> 4809c36b-31ef-4664-8e4e-47f0f72152de;\n  style 4809c36b-31ef-4664-8e4e-47f0f72152de stroke:#2c3143,stroke-width:4px;\n  45[\"Column Regex Find And Replace\"];\n  39 -->|output| 45;\n  87efc81d-4d84-4af3-831f-dfe033c59f78[\"Output\\nvfs_count\"];\n  45 --> 87efc81d-4d84-4af3-831f-dfe033c59f78;\n  style 87efc81d-4d84-4af3-831f-dfe033c59f78 stroke:#2c3143,stroke-width:4px;\n  46[\"Column Regex Find And Replace\"];\n  40 -->|tabular_output| 46;\n  f5c221e3-00ef-4834-9a5f-a94c97fd6764[\"Output\\nheatmap_table\"];\n  46 --> f5c221e3-00ef-4834-9a5f-a94c97fd6764;\n  style f5c221e3-00ef-4834-9a5f-a94c97fd6764 stroke:#2c3143,stroke-width:4px;\n  47[\"Regex Find And Replace\"];\n  41 -->|output| 47;\n  48[\"bedtools getfasta\"];\n  23 -->|output| 48;\n  42 -->|out_file1| 48;\n  82ce2107-89a3-438c-95bb-dc871b5258b7[\"Output\\nfiltered_sequences_with_vfs_fasta\"];\n  48 --> 82ce2107-89a3-438c-95bb-dc871b5258b7;\n  style 82ce2107-89a3-438c-95bb-dc871b5258b7 stroke:#2c3143,stroke-width:4px;\n  49[\"Regex Find And Replace\"];\n  43 -->|output| 49;\n  50[\"Multi-Join\"];\n  45 -->|out_file1| 50;\n  44 -->|out_file1| 50;\n  51[\"Heatmap w ggplot\"];\n  46 -->|out_file1| 51;\n  c0417c91-a513-4c6a-9a62-3aac2f1f8e85[\"Output\\nheatmap_pdf\"];\n  51 --> c0417c91-a513-4c6a-9a62-3aac2f1f8e85;\n  style c0417c91-a513-4c6a-9a62-3aac2f1f8e85 stroke:#2c3143,stroke-width:4px;\n  97816bc2-fd0c-4077-a721-8dd1470879d1[\"Output\\nheatmap_png\"];\n  51 --> 97816bc2-fd0c-4077-a721-8dd1470879d1;\n  style 97816bc2-fd0c-4077-a721-8dd1470879d1 stroke:#2c3143,stroke-width:4px;\n  52[\"Filter empty datasets\"];\n  47 -->|out_file1| 52;\n  53[\"ClustalW\"];\n  48 -->|output| 53;\n  9b7bd78c-f112-480b-a7df-c10711af254c[\"Output\\nclustalw_on_input_dnd\"];\n  53 --> 9b7bd78c-f112-480b-a7df-c10711af254c;\n  style 9b7bd78c-f112-480b-a7df-c10711af254c stroke:#2c3143,stroke-width:4px;\n  6af20322-24da-4036-80de-37bed2d25848[\"Output\\nclustalw_on_input_clustal\"];\n  53 --> 6af20322-24da-4036-80de-37bed2d25848;\n  style 6af20322-24da-4036-80de-37bed2d25848 stroke:#2c3143,stroke-width:4px;\n  54[\"Filter empty datasets\"];\n  49 -->|out_file1| 54;\n  55[\"Replace Text\"];\n  50 -->|outfile| 55;\n  91745da0-0b8d-4a7a-b927-b36107f17ec5[\"Output\\nvfs_amrs_count_table\"];\n  55 --> 91745da0-0b8d-4a7a-b927-b36107f17ec5;\n  style 91745da0-0b8d-4a7a-b927-b36107f17ec5 stroke:#2c3143,stroke-width:4px;\n  56[\"FASTA-to-Tabular\"];\n  52 -->|output| 56;\n  57[\"Filter empty datasets\"];\n  53 -->|output| 57;\n  32d00c1d-68c4-4069-8d5d-023aabdfadbe[\"Output\\nfiltered_empty_datasets\"];\n  57 --> 32d00c1d-68c4-4069-8d5d-023aabdfadbe;\n  style 32d00c1d-68c4-4069-8d5d-023aabdfadbe stroke:#2c3143,stroke-width:4px;\n  58[\"FASTA-to-Tabular\"];\n  54 -->|output| 58;\n  59[\"Cut\"];\n  56 -->|output| 59;\n  60[\"FASTTREE\"];\n  57 -->|output| 60;\n  aacdfe45-eb0c-4f6e-a479-eeb170774757[\"Output\\nfasttree_nhx\"];\n  60 --> aacdfe45-eb0c-4f6e-a479-eeb170774757;\n  style aacdfe45-eb0c-4f6e-a479-eeb170774757 stroke:#2c3143,stroke-width:4px;\n  61[\"Cut\"];\n  58 -->|output| 61;\n  62[\"Group\"];\n  59 -->|out_file1| 62;\n  63[\"Newick Display\"];\n  60 -->|output| 63;\n  0c22178c-dc85-4137-80e2-f3040b92bd20[\"Output\\nnewick_genes_tree_graphs_collection\"];\n  63 --> 0c22178c-dc85-4137-80e2-f3040b92bd20;\n  style 0c22178c-dc85-4137-80e2-f3040b92bd20 stroke:#2c3143,stroke-width:4px;\n  64[\"Group\"];\n  61 -->|out_file1| 64;\n  65[\"Tabular-to-FASTA\"];\n  62 -->|out_file1| 65;\n  66[\"Tabular-to-FASTA\"];\n  64 -->|out_file1| 66;\n  67[\"FASTA Merge Files and Filter Unique Sequences\"];\n  65 -->|output| 67;\n  68[\"FASTA Merge Files and Filter Unique Sequences\"];\n  66 -->|output| 68;\n  69[\"ClustalW\"];\n  67 -->|output| 69;\n  70[\"ClustalW\"];\n  68 -->|output| 70;\n  71[\"FASTTREE\"];\n  69 -->|output| 71;\n  72[\"FASTTREE\"];\n  70 -->|output| 72;\n  73[\"Newick Display\"];\n  71 -->|output| 73;\n  1f9cb2cf-219f-48de-8058-d6d45f3b3158[\"Output\\nall_samples_phylogenetic_tree_based_amrs\"];\n  73 --> 1f9cb2cf-219f-48de-8058-d6d45f3b3158;\n  style 1f9cb2cf-219f-48de-8058-d6d45f3b3158 stroke:#2c3143,stroke-width:4px;\n  74[\"Newick Display\"];\n  72 -->|output| 74;\n  6bb4b32b-7cca-4e04-8120-be9f64ccba39[\"Output\\nall_samples_phylogenetic_tree_based_vfs\"];\n  74 --> 6bb4b32b-7cca-4e04-8120-be9f64ccba39;\n  style 6bb4b32b-7cca-4e04-8120-be9f64ccba39 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation",
                 "outputs": [
                     {
@@ -148327,7 +376296,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\ncollection_of_preprocessed_samples\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nkraken_database\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"Kraken2\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  26f9041f-d8a4-4f64-8a53-404d5c7e2f61[\"Output\\nkraken2_with_pluspf_database_output\"];\n  2 --> 26f9041f-d8a4-4f64-8a53-404d5c7e2f61;\n  style 26f9041f-d8a4-4f64-8a53-404d5c7e2f61 stroke:#2c3143,stroke-width:4px;\n  f2ddd05b-66a0-4cea-9da6-ed107eecbe1b[\"Output\\nkraken2_with_pluspf_database_output_report\"];\n  2 --> f2ddd05b-66a0-4cea-9da6-ed107eecbe1b;\n  style f2ddd05b-66a0-4cea-9da6-ed107eecbe1b stroke:#2c3143,stroke-width:4px;\n  3[\"Krakentools: Convert kraken report file\"];\n  2 -->|report_output| 3;\n  c490ab8d-1b1d-4914-aa51-a62a967a4018[\"Output\\nconverted_kraken_report\"];\n  3 --> c490ab8d-1b1d-4914-aa51-a62a967a4018;\n  style c490ab8d-1b1d-4914-aa51-a62a967a4018 stroke:#2c3143,stroke-width:4px;\n  4[\"Krona pie chart\"];\n  3 -->|output| 4;\n  dcc857c6-f579-4c74-84ec-bb6ce3794a56[\"Output\\nkrona_pie_chart\"];\n  4 --> dcc857c6-f579-4c74-84ec-bb6ce3794a56;\n  style dcc857c6-f579-4c74-84ec-bb6ce3794a56 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Taxonomy Profiling and Visualization with Krona",
                 "outputs": [
                     {
@@ -148833,26 +376802,26 @@
             "topic_0080"
         ],
         "edam_operation": [
-            "Visualisation",
-            "Sequencing quality control",
-            "Phylogenetic inference",
-            "Phylogenetic tree editing",
-            "Statistical calculation",
+            "Sequence comparison",
             "Taxonomic classification",
             "Validation",
-            "Sequence composition calculation",
-            "Sequence comparison",
-            "Sequence similarity search",
-            "Phylogenetic tree analysis",
+            "Conversion",
+            "Visualisation",
             "Sequence trimming",
             "Phylogenetic analysis",
             "Phylogenetic tree visualisation",
+            "Phylogenetic inference",
+            "Nucleic acid sequence analysis",
             "Sequence alignment analysis",
             "Species frequency estimation",
-            "Conversion",
-            "Nucleic acid sequence analysis",
+            "Phylogenetic tree analysis",
+            "Primer removal",
+            "Sequence composition calculation",
+            "Phylogenetic tree editing",
+            "Sequencing quality control",
+            "Sequence similarity search",
             "Read pre-processing",
-            "Primer removal"
+            "Statistical calculation"
         ],
         "edam_topic": [
             "Metatranscriptomics",
@@ -148893,7 +376862,7 @@
             "Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes",
             "Visualise a community structure"
         ],
-        "pageviews": 5901051,
+        "pageviews": 5933139,
         "pub_date": "2019-11-21",
         "questions": [
             "How to analyze metatranscriptomics data?",
@@ -148938,25 +376907,25 @@
         ],
         "short_id": "T00388",
         "short_tools": [
-            "fastq_paired_end_interlacer",
-            "tp_find_and_replace",
-            "metaphlan",
-            "fastqc",
             "humann",
-            "graphlan_annotate",
-            "graphlan",
-            "humann_split_stratified_table",
+            "bg_sortmerna",
+            "combine_metaphlan2_humann2",
+            "metaphlan",
+            "cutadapt",
             "humann_renorm_table",
+            "graphlan_annotate",
+            "fastq_paired_end_interlacer",
+            "humann_unpack_pathways",
+            "export2graphlan",
             "humann_regroup_table",
-            "humann_rename_table",
-            "cutadapt",
-            "combine_metaphlan2_humann2",
-            "multiqc",
-            "bg_sortmerna",
+            "tp_find_and_replace",
             "Grep1",
+            "multiqc",
             "Cut1",
-            "export2graphlan",
-            "humann_unpack_pathways",
+            "humann_split_stratified_table",
+            "fastqc",
+            "humann_rename_table",
+            "graphlan",
             "taxonomy_krona_chart"
         ],
         "slides": true,
@@ -148988,6 +376957,3004 @@
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             ]
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+                            "state": "exact",
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+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
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+                            "state": "exact",
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+                            "server": "https://usegalaxy.org",
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+                            "state": "exact",
+                            "version": "2.1b.6"
+                        },
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+                    ],
+                    "version": "2.1b.6"
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         "symlink": null,
         "tags": [
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@@ -149037,7 +380004,7 @@
         "video_versions": 2,
         "video_view": 0,
         "visit_duration": 256,
-        "visitors": 2136358,
+        "visitors": 2147260,
         "workflows": [
             {
                 "creators": [
@@ -149154,7 +380121,7 @@
                 ],
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Main Metatranscriptomics Analysis",
                 "outputs": [],
                 "parent_id": "microbiome/metatranscriptomics",
@@ -149350,11 +380317,11 @@
             "topic_0080"
         ],
         "edam_operation": [
-            "Phylogenetic tree analysis",
-            "Statistical calculation",
             "Taxonomic classification",
-            "Aggregation",
             "Visualisation",
+            "Phylogenetic tree analysis",
+            "Aggregation",
+            "Statistical calculation",
             "Nucleic acid sequence analysis"
         ],
         "edam_topic": [
@@ -149371,7 +380338,6 @@
         "hands_on": true,
         "id": "microbiome/taxonomic-profiling",
         "inexact_supported_servers": [
-            "UseGalaxy.fr",
             "UseGalaxy.org.au"
         ],
         "js_requirements": {
@@ -149395,7 +380361,7 @@
             "Apply Krona and Pavian to visualize results of assignment and understand the output",
             "Identify taxonomic classification tool that fits best depending on their data"
         ],
-        "pageviews": 6096,
+        "pageviews": 6233,
         "pub_date": "2023-05-03",
         "questions": [
             "Which species (or genera, families, ...) are present in my sample?",
@@ -149424,15 +380390,15 @@
         ],
         "short_id": "T00395",
         "short_tools": [
+            "krakentools_kreport2krona",
+            "metaphlan",
             "interactive_tool_phinch",
-            "est_abundance",
-            "taxonomy_krona_chart",
             "interactive_tool_pavian",
-            "kraken2",
+            "est_abundance",
             "kraken_biom",
             "__UNZIP_COLLECTION__",
-            "krakentools_kreport2krona",
-            "metaphlan"
+            "taxonomy_krona_chart",
+            "kraken2"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -149447,14 +380413,1564 @@
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             "inexact": [
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-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
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+                },
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                     "usegalaxy": false
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+                    "url": "https://galaxy.pasteur.fr/",
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
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+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "4.0.6+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "4.0.3+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "4.0.6+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
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+                        {
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+                            "state": "missing"
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+                    ],
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@@ -149498,7 +382014,7 @@
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         "video_view": 0,
         "visit_duration": 118,
-        "visitors": 4443,
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@@ -149515,7 +382031,7 @@
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                         "hash": "0e0a2f2ccb650b0aab1ffc13838045164bdb5d30",
@@ -149582,8 +382098,8 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nraw-reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nmetadata\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Unzip collection\"];\n  0 -->|output| 2;\n  3[\"Kraken2\"];\n  0 -->|output| 3;\n  87c5ba05-7716-4741-9cb2-3931c24b9725[\"Output\\nkraken_report\"];\n  3 --> 87c5ba05-7716-4741-9cb2-3931c24b9725;\n  style 87c5ba05-7716-4741-9cb2-3931c24b9725 stroke:#2c3143,stroke-width:4px;\n  4[\"MetaPhlAn\"];\n  2 -->|forward| 4;\n  2 -->|reverse| 4;\n  cbf5e3ef-6672-4099-b9c0-f5d7a24ad4c0[\"Output\\nmetaphlan_output\"];\n  4 --> cbf5e3ef-6672-4099-b9c0-f5d7a24ad4c0;\n  style cbf5e3ef-6672-4099-b9c0-f5d7a24ad4c0 stroke:#2c3143,stroke-width:4px;\n  5[\"Krakentools: Convert kraken report file\"];\n  3 -->|report_output| 5;\n  aa51743d-1e76-44e7-ae8d-4e1ed3cc265a[\"Output\\nkrakentool_report\"];\n  5 --> aa51743d-1e76-44e7-ae8d-4e1ed3cc265a;\n  style aa51743d-1e76-44e7-ae8d-4e1ed3cc265a stroke:#2c3143,stroke-width:4px;\n  6[\"Kraken-biom\"];\n  3 -->|report_output| 6;\n  1 -->|output| 6;\n  7[\"Pavian\"];\n  3 -->|report_output| 7;\n  8[\"Estimate Abundance at Taxonomic Level\"];\n  3 -->|report_output| 8;\n  9[\"Krona pie chart\"];\n  4 -->|krona_output_file| 9;\n  10[\"Krona pie chart\"];\n  5 -->|output| 10;\n  11[\"Phinch Visualisation\"];\n  6 -->|biomOutput| 11;",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Taxonomic Profiling and Visualization of Metagenomic Data",
                 "outputs": [
                     {
@@ -149631,7 +382147,7 @@
                             {
                                 "label": "kraken_report",
                                 "output_name": "report_output",
-                                "uuid": "51c22a6e-0743-4510-b4e1-26afc897534a"
+                                "uuid": "87c5ba05-7716-4741-9cb2-3931c24b9725"
                             }
                         ]
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@@ -149701,7 +382217,7 @@
                             {
                                 "label": "metaphlan_output",
                                 "output_name": "output_file",
-                                "uuid": "6bcdc5a7-ddf9-4cdf-9729-b359d60490fb"
+                                "uuid": "cbf5e3ef-6672-4099-b9c0-f5d7a24ad4c0"
                             }
                         ]
                     },
@@ -149746,7 +382262,7 @@
                             {
                                 "label": "krakentool_report",
                                 "output_name": "output",
-                                "uuid": "2cc442f8-40ac-4c58-a82e-f4018ab8a0a5"
+                                "uuid": "aa51743d-1e76-44e7-ae8d-4e1ed3cc265a"
                             }
                         ]
                     }
@@ -150095,26 +382611,26 @@
             "topic_0080"
         ],
         "edam_operation": [
-            "Visualisation",
-            "Sequencing quality control",
-            "Phylogenetic inference",
-            "Phylogenetic tree editing",
-            "Statistical calculation",
+            "Sequence comparison",
             "Taxonomic classification",
             "Validation",
-            "Sequence composition calculation",
-            "Sequence comparison",
-            "Sequence similarity search",
-            "Phylogenetic tree analysis",
+            "Conversion",
+            "Visualisation",
             "Sequence trimming",
             "Phylogenetic analysis",
             "Phylogenetic tree visualisation",
+            "Phylogenetic inference",
+            "Nucleic acid sequence analysis",
             "Sequence alignment analysis",
             "Species frequency estimation",
-            "Conversion",
-            "Nucleic acid sequence analysis",
+            "Phylogenetic tree analysis",
+            "Primer removal",
+            "Sequence composition calculation",
+            "Phylogenetic tree editing",
+            "Sequencing quality control",
+            "Sequence similarity search",
             "Read pre-processing",
-            "Primer removal"
+            "Statistical calculation"
         ],
         "edam_topic": [
             "Metatranscriptomics",
@@ -150155,7 +382671,7 @@
             "Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes",
             "Visualise a community structure"
         ],
-        "pageviews": 351,
+        "pageviews": 357,
         "pub_date": "2020-02-13",
         "questions": [
             "How to analyze metatranscriptomics data?\"",
@@ -150200,25 +382716,25 @@
         ],
         "short_id": "T00389",
         "short_tools": [
-            "fastq_paired_end_interlacer",
-            "tp_find_and_replace",
-            "metaphlan",
-            "fastqc",
             "humann",
-            "graphlan_annotate",
-            "graphlan",
-            "humann_split_stratified_table",
+            "bg_sortmerna",
+            "combine_metaphlan2_humann2",
+            "metaphlan",
+            "cutadapt",
             "humann_renorm_table",
+            "graphlan_annotate",
+            "fastq_paired_end_interlacer",
+            "humann_unpack_pathways",
+            "export2graphlan",
             "humann_regroup_table",
-            "humann_rename_table",
-            "cutadapt",
-            "combine_metaphlan2_humann2",
-            "multiqc",
-            "bg_sortmerna",
+            "tp_find_and_replace",
             "Grep1",
+            "multiqc",
             "Cut1",
-            "export2graphlan",
-            "humann_unpack_pathways",
+            "humann_split_stratified_table",
+            "fastqc",
+            "humann_rename_table",
+            "graphlan",
             "taxonomy_krona_chart"
         ],
         "slides": false,
@@ -150250,6 +382766,3690 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
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+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "2.1b.6"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2.1b.6"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.1b.6"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.1b.6"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "metatranscriptomics",
@@ -150303,8 +386503,8 @@
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 86,
-        "visitors": 274,
+        "visit_duration": 84,
+        "visitors": 280,
         "workflows": [
             {
                 "creators": [
@@ -150421,7 +386621,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nT1A_forward\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nT1A_reverse\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Quality control Forward\"];\n  0 -->|output| 2;\n  025f2766-0802-461e-afbd-a716e6f81ba8[\"Output\\nFastQC on input dataset(s): RawData\"];\n  2 --> 025f2766-0802-461e-afbd-a716e6f81ba8;\n  style 025f2766-0802-461e-afbd-a716e6f81ba8 stroke:#2c3143,stroke-width:4px;\n  a54ee2fd-7bce-439a-9f1f-f9ec9bf00efd[\"Output\\nFastQC on input dataset(s): Webpage\"];\n  2 --> a54ee2fd-7bce-439a-9f1f-f9ec9bf00efd;\n  style a54ee2fd-7bce-439a-9f1f-f9ec9bf00efd stroke:#2c3143,stroke-width:4px;\n  3[\"Quality control Reverse\"];\n  1 -->|output| 3;\n  4[\"Cutadapt\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  4bc7c8a4-b985-41dd-b67f-a3dfecd38a67[\"Output\\nCutadapt on input dataset(s): Read 1 Output\"];\n  4 --> 4bc7c8a4-b985-41dd-b67f-a3dfecd38a67;\n  style 4bc7c8a4-b985-41dd-b67f-a3dfecd38a67 stroke:#2c3143,stroke-width:4px;\n  36ec0bba-e49a-47e2-b916-afec9b35cc3e[\"Output\\nCutadapt on input dataset(s): Read 2 Output\"];\n  4 --> 36ec0bba-e49a-47e2-b916-afec9b35cc3e;\n  style 36ec0bba-e49a-47e2-b916-afec9b35cc3e stroke:#2c3143,stroke-width:4px;\n  5[\"MultiQC\"];\n  2 -->|text_file| 5;\n  3 -->|text_file| 5;\n  b9ca2123-0ee0-40a0-b2ec-cfc94fa35849[\"Output\\nMultiQC on input dataset(s): Stats\"];\n  5 --> b9ca2123-0ee0-40a0-b2ec-cfc94fa35849;\n  style b9ca2123-0ee0-40a0-b2ec-cfc94fa35849 stroke:#2c3143,stroke-width:4px;\n  e94ceb7a-0d6b-41c8-b79d-035b315e0a06[\"Output\\nMultiQC on input dataset(s): Webpage\"];\n  5 --> e94ceb7a-0d6b-41c8-b79d-035b315e0a06;\n  style e94ceb7a-0d6b-41c8-b79d-035b315e0a06 stroke:#2c3143,stroke-width:4px;\n  6[\"rRNA/rDNA selection\"];\n  4 -->|out1| 6;\n  4 -->|out2| 6;\n  7[\"FASTQ interlacer\"];\n  6 -->|unaligned_forward| 7;\n  6 -->|unaligned_reverse| 7;\n  b060eebc-cd14-486e-806e-aae983bdf52d[\"Output\\nFASTQ interlacer singles from input dataset(s)\"];\n  7 --> b060eebc-cd14-486e-806e-aae983bdf52d;\n  style b060eebc-cd14-486e-806e-aae983bdf52d stroke:#2c3143,stroke-width:4px;\n  70b738db-5451-4eaa-91c0-eb445be297fb[\"Output\\nFASTQ interlacer pairs from input dataset(s)\"];\n  7 --> 70b738db-5451-4eaa-91c0-eb445be297fb;\n  style 70b738db-5451-4eaa-91c0-eb445be297fb stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow 1: Preprocessing",
                 "outputs": [
                     {
@@ -150985,7 +387185,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQC controlled forward reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nQC controlled reverse reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Taxonomic assignation\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  b3e3198d-394e-4aeb-ba6c-9e73bfe8d049[\"Output\\nMetaPhlAn on input dataset(s): SAM file\"];\n  2 --> b3e3198d-394e-4aeb-ba6c-9e73bfe8d049;\n  style b3e3198d-394e-4aeb-ba6c-9e73bfe8d049 stroke:#2c3143,stroke-width:4px;\n  a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b[\"Output\\nMetaPhlAn on input dataset(s): Predicted taxon relative abundances\"];\n  2 --> a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b;\n  style a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b stroke:#2c3143,stroke-width:4px;\n  30a9e692-8d31-45bd-9246-81ddead3ba03[\"Output\\nMetaPhlAn on input dataset(s): Bowtie2 output\"];\n  2 --> 30a9e692-8d31-45bd-9246-81ddead3ba03;\n  style 30a9e692-8d31-45bd-9246-81ddead3ba03 stroke:#2c3143,stroke-width:4px;\n  2465a9ab-a28e-4c58-b647-b6792f77ddf2[\"Output\\nMetaPhlAn on input dataset(s): BIOM file\"];\n  2 --> 2465a9ab-a28e-4c58-b647-b6792f77ddf2;\n  style 2465a9ab-a28e-4c58-b647-b6792f77ddf2 stroke:#2c3143,stroke-width:4px;\n  3[\"Cut\"];\n  2 -->|output_file| 3;\n  4[\"Krona pie chart\"];\n  2 -->|krona_output_file| 4;\n  5[\"Export to GraPhlAn\"];\n  3 -->|out_file1| 5;\n  f578de2e-6edd-4ee0-9bc4-9371d6fd957f[\"Output\\nExport to GraPhlAn on input dataset(s): Annotation\"];\n  5 --> f578de2e-6edd-4ee0-9bc4-9371d6fd957f;\n  style f578de2e-6edd-4ee0-9bc4-9371d6fd957f stroke:#2c3143,stroke-width:4px;\n  4e9cfae0-ee7b-4347-84db-5a3e24688e50[\"Output\\nExport to GraPhlAn on input dataset(s): Tree\"];\n  5 --> 4e9cfae0-ee7b-4347-84db-5a3e24688e50;\n  style 4e9cfae0-ee7b-4347-84db-5a3e24688e50 stroke:#2c3143,stroke-width:4px;\n  6[\"Generation, personalization and annotation of tree\"];\n  5 -->|annotation| 6;\n  5 -->|tree| 6;\n  edf4ecaf-dddd-43a3-ba4a-d683671c1815[\"Output\\nGeneration, personalization and annotation of tree on input dataset(s): Tree in PhyloXML\"];\n  6 --> edf4ecaf-dddd-43a3-ba4a-d683671c1815;\n  style edf4ecaf-dddd-43a3-ba4a-d683671c1815 stroke:#2c3143,stroke-width:4px;\n  7[\"Visualisation GraPhlAn\"];\n  6 -->|output_tree| 7;\n  b304fe87-de7e-48d2-8774-9c52d2395fa4[\"Output\\nGraPhlAn on input dataset(s): PNG\"];\n  7 --> b304fe87-de7e-48d2-8774-9c52d2395fa4;\n  style b304fe87-de7e-48d2-8774-9c52d2395fa4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow 2: Community Profile",
                 "outputs": [
                     {
@@ -151468,7 +387668,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInterlaced non-rRNA reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nPredicted taxon relative abundances\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Cut\"];\n  1 -->|output| 2;\n  3[\"Metabolic assignation\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  65797303-6f12-4ae8-9511-1af40f52e71d[\"Output\\nHUMAnN on input dataset(s): Pathways and their abundance\"];\n  3 --> 65797303-6f12-4ae8-9511-1af40f52e71d;\n  style 65797303-6f12-4ae8-9511-1af40f52e71d stroke:#2c3143,stroke-width:4px;\n  5cae6935-448b-4af9-ad78-7b17490e4d4a[\"Output\\nHUMAnN on input dataset(s): Pathways and their coverage\"];\n  3 --> 5cae6935-448b-4af9-ad78-7b17490e4d4a;\n  style 5cae6935-448b-4af9-ad78-7b17490e4d4a stroke:#2c3143,stroke-width:4px;\n  60492d72-7b3c-45c9-b32b-b6374ab08228[\"Output\\nHUMAnN on input dataset(s): Log\"];\n  3 --> 60492d72-7b3c-45c9-b32b-b6374ab08228;\n  style 60492d72-7b3c-45c9-b32b-b6374ab08228 stroke:#2c3143,stroke-width:4px;\n  ba124b0f-cbd5-4b65-b87a-84cfa578a927[\"Output\\nHUMAnN on input dataset(s): Gene families and their abundance\"];\n  3 --> ba124b0f-cbd5-4b65-b87a-84cfa578a927;\n  style ba124b0f-cbd5-4b65-b87a-84cfa578a927 stroke:#2c3143,stroke-width:4px;\n  4[\"Renormalize\"];\n  3 -->|gene_families_tsv| 4;\n  5[\"Renormalize\"];\n  3 -->|pathabundance_tsv| 5;\n  6[\"Regroup\"];\n  3 -->|gene_families_tsv| 6;\n  7[\"Replace\"];\n  4 -->|output| 7;\n  8[\"Unpack pathway abundances\"];\n  4 -->|output| 8;\n  5 -->|output| 8;\n  9[\"Rename features\"];\n  6 -->|output| 9;\n  10[\"Split a HUMAnN table\"];\n  6 -->|output| 10;\n  1ff60d0a-4a64-44c0-8b6f-bbdfa8566a0c[\"Output\\nSplit a HUMAnN table on input dataset(s): Unstratified table\"];\n  10 --> 1ff60d0a-4a64-44c0-8b6f-bbdfa8566a0c;\n  style 1ff60d0a-4a64-44c0-8b6f-bbdfa8566a0c stroke:#2c3143,stroke-width:4px;\n  6a65ee93-3a2e-4a81-94ff-35917396bdfa[\"Output\\nSplit a HUMAnN table on input dataset(s): Stratified table\"];\n  10 --> 6a65ee93-3a2e-4a81-94ff-35917396bdfa;\n  style 6a65ee93-3a2e-4a81-94ff-35917396bdfa stroke:#2c3143,stroke-width:4px;\n  11[\"Combination of taxonomic and metabolic assignations for gene families\"];\n  7 -->|outfile| 11;\n  2 -->|out_file1| 11;\n  b34cf972-ec0c-4ecc-ab77-bd0e61d8a0e2[\"Output\\nCombine MetaPhlAn2 and HUMAnN2 outputs on input dataset(s): Gene family abundances related to genus/species abundances\"];\n  11 --> b34cf972-ec0c-4ecc-ab77-bd0e61d8a0e2;\n  style b34cf972-ec0c-4ecc-ab77-bd0e61d8a0e2 stroke:#2c3143,stroke-width:4px;\n  12[\"Select\"];\n  9 -->|output| 12;\n  13[\"Select\"];\n  9 -->|output| 13;\n  14[\"Select\"];\n  9 -->|output| 14;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow 3: Functional Information",
                 "outputs": [
                     {
@@ -152229,7 +388429,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPredicted taxon relative abundances\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGene Family abundance\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nPathway abundance\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Cut\"];\n  0 -->|output| 3;\n  4[\"Renormalize\"];\n  1 -->|output| 4;\n  5[\"Regroup\"];\n  1 -->|output| 5;\n  6[\"Renormalize\"];\n  2 -->|output| 6;\n  7[\"Replace\"];\n  4 -->|output| 7;\n  8[\"Rename features\"];\n  5 -->|output| 8;\n  9[\"Split a HUMAnN table\"];\n  5 -->|output| 9;\n  7aba96f3-1648-4126-8e58-ca10cbd2e46d[\"Output\\nSplit a HUMAnN table on input dataset(s): Stratified table\"];\n  9 --> 7aba96f3-1648-4126-8e58-ca10cbd2e46d;\n  style 7aba96f3-1648-4126-8e58-ca10cbd2e46d stroke:#2c3143,stroke-width:4px;\n  2c36dc33-5981-4b2c-b615-a1677002e007[\"Output\\nSplit a HUMAnN table on input dataset(s): Unstratified table\"];\n  9 --> 2c36dc33-5981-4b2c-b615-a1677002e007;\n  style 2c36dc33-5981-4b2c-b615-a1677002e007 stroke:#2c3143,stroke-width:4px;\n  10[\"Unpack pathway abundances\"];\n  4 -->|output| 10;\n  6 -->|output| 10;\n  11[\"Combination of taxonomic and metabolic assignations for gene families\"];\n  7 -->|outfile| 11;\n  3 -->|out_file1| 11;\n  46161015-b2db-4241-846e-27dd803b0fb3[\"Output\\nCombine MetaPhlAn2 and HUMAnN2 outputs on input dataset(s): Gene family abundances related to genus/species abundances\"];\n  11 --> 46161015-b2db-4241-846e-27dd803b0fb3;\n  style 46161015-b2db-4241-846e-27dd803b0fb3 stroke:#2c3143,stroke-width:4px;\n  12[\"Select\"];\n  8 -->|output| 12;\n  13[\"Select\"];\n  8 -->|output| 13;\n  14[\"Select\"];\n  8 -->|output| 14;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow 3: Functional Information (quick)",
                 "outputs": [
                     {
@@ -152916,14 +389116,14 @@
             "topic_4013"
         ],
         "edam_operation": [
-            "Scatter plot plotting",
             "Genome assembly",
-            "Box-Whisker plot plotting",
+            "Sequence assembly visualisation",
             "De-novo assembly",
-            "Sequence analysis",
             "Mapping assembly",
+            "Sequence analysis",
+            "Box-Whisker plot plotting",
+            "Scatter plot plotting",
             "Aggregation",
-            "Sequence assembly visualisation",
             "Pairwise sequence alignment"
         ],
         "edam_topic": [
@@ -152969,7 +389169,7 @@
             "Determine the structure of the genome(s)",
             "Scan for antimicrobial resistance genes with Staramr"
         ],
-        "pageviews": 1950,
+        "pageviews": 1976,
         "pub_date": "2019-06-25",
         "questions": [
             "How do I assemble a genome with Nanopore data?",
@@ -152998,15 +389198,15 @@
         ],
         "short_id": "T00394",
         "short_tools": [
-            "unicycler",
-            "minimap2",
             "bandage_image",
-            "PlasFlow",
-            "racon",
+            "minimap2",
+            "unicycler",
             "nanoplot",
+            "PlasFlow",
             "gfa_to_fa",
-            "staramr_search",
-            "miniasm"
+            "miniasm",
+            "racon",
+            "staramr_search"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -153014,12 +389214,143 @@
         "supported_servers": {
             "exact": [
                 {
-                    "name": "UseGalaxy.eu",
-                    "url": "https://usegalaxy.eu",
-                    "usegalaxy": true
-                }
-            ],
-            "inexact": [
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.be",
                     "url": "https://usegalaxy.be/",
@@ -153030,6 +389361,11 @@
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -153044,6 +389380,2544 @@
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1.1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
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+                            "state": "exact",
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+                            "server": "https://usegalaxy.org.au",
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+                        },
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@@ -153095,8 +391969,8 @@
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         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 242,
-        "visitors": 1281,
+        "visit_duration": 243,
+        "visitors": 1301,
         "workflows": [
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@@ -153142,7 +392016,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Copy Of GTN Training - Antibiotic Resistance Detection",
                 "outputs": [],
                 "parent_id": "microbiome/plasmid-metagenomics-nanopore",
@@ -153267,13 +392141,13 @@
             "topic_4038"
         ],
         "edam_operation": [
-            "Taxonomic classification",
-            "Statistical calculation",
-            "Visualisation",
+            "Sequence contamination filtering",
             "Validation",
             "Sequencing quality control",
+            "Visualisation",
             "Sequence composition calculation",
-            "Sequence contamination filtering"
+            "Statistical calculation",
+            "Taxonomic classification"
         ],
         "edam_topic": [
             "Microbial ecology",
@@ -153311,7 +392185,7 @@
             "Analyze and preprocess Nanopore reads",
             "Use Kraken2 to assign a taxonomic labels"
         ],
-        "pageviews": 3844,
+        "pageviews": 3894,
         "pub_date": "2020-11-24",
         "questions": [
             "How can we analyse the health status of the soil?",
@@ -153325,15 +392199,15 @@
         ],
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-            "porechop",
-            "fastp",
             "tp_replace_in_line",
-            "taxonomy_krona_chart",
-            "multiqc",
-            "kraken2",
             "datamash_reverse",
+            "multiqc",
             "fastqc",
-            "Remove beginning1"
+            "Remove beginning1",
+            "fastp",
+            "porechop",
+            "kraken2",
+            "taxonomy_krona_chart"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -153379,6 +392253,1484 @@
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@@ -153419,8 +393771,8 @@
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-        "visitors": 2758,
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+        "visitors": 2802,
         "workflows": [
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@@ -153471,7 +393823,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Training: 16S rRNA Analysis with Nanopore Sequencing Reads",
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@@ -153764,8 +394116,8 @@
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             "DNA barcoding",
             "Visualisation",
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-            "Deposition"
+            "Deposition",
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         "edam_topic": [
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@@ -153799,7 +394151,7 @@
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             "Assess the effectiveness of using phyloseq for exploring and visualizing ASV data to gain ecological and evolutionary insights"
         ],
-        "pageviews": 1460,
+        "pageviews": 1566,
         "pub_date": "2024-06-05",
         "questions": [
             "What are the primary steps involved in generating an ASV table using DADA2 from 16S rRNA gene sequencing data?",
@@ -153826,26 +394178,26 @@
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-            "phyloseq_from_dada2"
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+            "dada2_dada",
+            "Add_a_column1",
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@@ -153860,6 +394212,4604 @@
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@@ -153920,7 +398870,7 @@
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-        "visitors": 1089,
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@@ -154017,7 +398967,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Building an amplicon sequence variant (ASV) table from 16S data using DADA2",
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                     {
@@ -154343,8 +399293,8 @@
         ],
         "dir": "topics/microbiome/tutorials/lotus2-identifying-fungi",
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-            "DNA barcoding",
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@@ -154378,7 +399328,7 @@
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             "What is the fungal community composition in a given soil sample?"
@@ -154392,7 +399342,7 @@
                 "type": "internal"
             }
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+        "short_id": "T00459",
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             "lotus2"
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@@ -154424,6 +399374,291 @@
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+                            "state": "missing"
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+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
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+                                "2.06+galaxy3",
+                                "2.09",
+                                "2.09.2",
+                                "2.06",
+                                "2.21"
+                            ]
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+                            "state": "inexact",
+                            "versions": [
+                                "2.23+galaxy2"
+                            ]
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+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.32+galaxy0"
+                        },
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+                            "state": "missing"
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+                        {
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+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.32+galaxy0"
+                        },
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+                            "state": "missing"
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+                    ],
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+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "fungi",
@@ -154453,8 +399688,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 30,
-        "visitors": 17,
+        "visit_duration": 92,
+        "visitors": 44,
         "workflows": [
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                 "creators": [
@@ -154580,7 +399815,7 @@
                 ],
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run'",
                 "outputs": [
                     {
@@ -154712,7 +399947,7 @@
                 "workflow_tools": [
                     "toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2/2.32+galaxy0"
                 ],
-                "workflowhub_id": null
+                "workflowhub_id": "1366"
             }
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@@ -154940,24 +400175,24 @@
             "topic_0196"
         ],
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-            "Data handling",
-            "Visualisation",
-            "Sequence trimming",
-            "Read mapping",
-            "Sequencing quality control",
-            "Genome assembly",
-            "Sequence alignment analysis",
-            "Sequence contamination filtering",
-            "Sequence assembly validation",
             "Variant calling",
-            "Statistical calculation",
+            "Genome assembly",
             "Sequence assembly visualisation",
-            "Sequence file editing",
+            "Sequence assembly validation",
+            "Visualisation",
+            "Sequence trimming",
             "Local alignment",
+            "Sequence file editing",
+            "Data handling",
+            "Sequence alignment analysis",
+            "Primer removal",
+            "Formatting",
             "Sequence composition calculation",
+            "Sequencing quality control",
+            "Read mapping",
             "Read pre-processing",
-            "Primer removal",
-            "Formatting"
+            "Sequence contamination filtering",
+            "Statistical calculation"
         ],
         "edam_topic": [
             "Metagenomics",
@@ -154997,7 +400232,7 @@
             "Apply appropriate tools for analyzing the quality of metagenomic assembly",
             "Evaluate the Quality of the Assembly with Quast, Bowtie2, and CoverM-Genome"
         ],
-        "pageviews": 2258,
+        "pageviews": 2337,
         "pub_date": "2022-12-05",
         "questions": [
             "Why metagenomic data should be assembled?",
@@ -155029,24 +400264,24 @@
         ],
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         "short_tools": [
-            "ngsutils_bam_filter",
-            "tp_cat",
-            "bamtools",
             "bandage_image",
-            "filter_tabular",
-            "megahit_contig2fastg",
-            "bandage_info",
-            "bg_uniq",
-            "quast",
             "seqtk_subseq",
+            "megahit_contig2fastg",
             "cutadapt",
             "random_lines1",
-            "collection_column_join",
+            "tp_cat",
             "megahit",
-            "coverm_contig",
             "fastqc",
+            "bg_uniq",
+            "collection_column_join",
+            "bandage_info",
             "metaspades",
-            "bowtie2"
+            "coverm_contig",
+            "bowtie2",
+            "filter_tabular",
+            "quast",
+            "bamtools",
+            "ngsutils_bam_filter"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -155066,6 +400301,3286 @@
                 }
             ]
         },
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+                            "server": "https://galaxy-web.ipk-gatersleben.de",
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+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "4.8+galaxy1",
+                                "4.7+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.16.8",
+                                "1.16.3",
+                                "1.6",
+                                "1.16.1",
+                                "1.16.5"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "4.4+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "4.0+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.16.5"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "4.0+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "4.0+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "4.0+galaxy0"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.15.4+galaxy2",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "3.15.4+galaxy2"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "3.15.5+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "3.9.0",
+                                "1.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "3.15.4+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "3.15.4+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "3.15.4+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "3.15.4+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "3.15.4+galaxy2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "3.15.4+galaxy2"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "assembly",
@@ -155116,8 +403631,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 177,
-        "visitors": 1613,
+        "visit_duration": 179,
+        "visitors": 1671,
         "workflows": [
             {
                 "creators": [],
@@ -155174,7 +403689,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"metaSPAdes\"];\n  0 -->|output| 1;\n  833d79ff-e16f-414c-9c41-db8dbfa8ed6b[\"Output\\nmetaSPAdes on input dataset(s): Scaffolds\"];\n  1 --> 833d79ff-e16f-414c-9c41-db8dbfa8ed6b;\n  style 833d79ff-e16f-414c-9c41-db8dbfa8ed6b stroke:#2c3143,stroke-width:4px;\n  10319152-d2f9-47d8-be41-f956a57e86d3[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph\"];\n  1 --> 10319152-d2f9-47d8-be41-f956a57e86d3;\n  style 10319152-d2f9-47d8-be41-f956a57e86d3 stroke:#2c3143,stroke-width:4px;\n  b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633[\"Output\\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds\"];\n  1 --> b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633;\n  style b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633 stroke:#2c3143,stroke-width:4px;\n  b6b74c9d-5a16-4725-a1d1-11c1f05ee909[\"Output\\nmetaSPAdes on input dataset(s): Contigs\"];\n  1 --> b6b74c9d-5a16-4725-a1d1-11c1f05ee909;\n  style b6b74c9d-5a16-4725-a1d1-11c1f05ee909 stroke:#2c3143,stroke-width:4px;\n  2[\"MEGAHIT\"];\n  0 -->|output| 2;\n  3[\"Bowtie2\"];\n  0 -->|output| 3;\n  2 -->|output| 3;\n  4[\"megahit contig2fastg\"];\n  2 -->|output| 4;\n  5[\"Quast\"];\n  2 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Bandage Image\"];\n  4 -->|fastg| 6;\n  7[\"Bandage Info\"];\n  4 -->|fastg| 7;\n  8[\"Column join\"];\n  7 -->|outfile| 8;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Metagenomics assembly tutorial workflow",
                 "outputs": [
                     {
@@ -155766,7 +404281,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nERR2231567_1.fastq.gz\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nERR2231567_2.fastq.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Cutadapt\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"MEGAHIT\"];\n  2 -->|out1| 3;\n  2 -->|out2| 3;\n  4[\"Bowtie2\"];\n  2 -->|out1| 4;\n  2 -->|out2| 4;\n  3 -->|output| 4;\n  5[\"BAM filter\"];\n  4 -->|output| 5;\n  6[\"BAM filter\"];\n  4 -->|output| 6;\n  7[\"Convert, Merge, Randomize\"];\n  5 -->|outfile| 7;\n  8[\"Convert, Merge, Randomize\"];\n  6 -->|outfile| 8;\n  9[\"Select random lines\"];\n  7 -->|out_file1| 9;\n  10[\"Select random lines\"];\n  8 -->|out_file1| 10;\n  11[\"Filter Tabular\"];\n  9 -->|out_file1| 11;\n  12[\"Filter Tabular\"];\n  10 -->|out_file1| 12;\n  13[\"Unique\"];\n  11 -->|output| 13;\n  14[\"Unique\"];\n  12 -->|output| 14;\n  15[\"Concatenate datasets\"];\n  13 -->|outfile| 15;\n  14 -->|outfile| 15;\n  16[\"seqtk_subseq\"];\n  2 -->|out1| 16;\n  15 -->|out_file1| 16;\n  17[\"seqtk_subseq\"];\n  2 -->|out2| 17;\n  15 -->|out_file1| 17;\n  18[\"FastQC\"];\n  16 -->|default| 18;\n  19[\"FastQC\"];\n  17 -->|default| 19;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "workflow-generate-dataset-for-assembly-tutorial",
                 "outputs": [
                     {
@@ -156803,7 +405318,6 @@
             "GalaxyTrakr",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
@@ -156829,7 +405343,7 @@
             "Explain different metrics to calculate \u03b1 and \u03b2 diversity",
             "Apply Krakentools to calculate \u03b1 and \u03b2 diversity and understand the output"
         ],
-        "pageviews": 370,
+        "pageviews": 449,
         "pub_date": "2024-08-01",
         "questions": [
             "How many different taxons are present in my sample? How do I additionally take their relative abundance into account?",
@@ -156882,8 +405396,140 @@
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
                 {
@@ -156895,9 +405541,286 @@
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
                 }
             ],
-            "inexact": []
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_alpha_diversity/krakentools_alpha_diversity/1.2+galaxy1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "exact",
+                            "version": "1.2+galaxy1"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "1.2+galaxy1"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.2+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.2+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.2+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.2+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.2+galaxy1"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/krakentools_beta_diversity/krakentools_beta_diversity/1.2+galaxy1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
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@@ -157028,7 +405951,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
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@@ -157112,7 +406035,7 @@
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@@ -157152,6 +406075,10 @@
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@@ -157301,7 +406227,7 @@
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@@ -157498,6 +406851,10 @@
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@@ -157846,15 +407203,15 @@
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+            "Sequence read processing",
             "DNA barcoding",
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@@ -157872,7 +407229,6 @@
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@@ -157895,7 +407251,7 @@
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@@ -157909,39 +407265,39 @@
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+            "mothur_make_contigs",
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-            "mothur_make_shared",
-            "mothur_filter_seqs",
             "mothur_dist_seqs",
+            "mothur_pre_cluster",
+            "XY_Plot_1",
             "mothur_remove_seqs",
-            "mothur_rarefaction_single",
+            "mothur_remove_groups",
+            "mothur_sub_sample",
+            "newick_display",
             "mothur_venn",
-            "mothur_classify_otu",
-            "mothur_count_groups",
+            "mothur_rarefaction_single",
+            "mothur_tree_shared",
+            "mothur_summary_single",
+            "mothur_remove_lineage",
+            "mothur_filter_seqs",
+            "mothur_seq_error",
+            "mothur_get_groups",
+            "mothur_heatmap_sim",
             "mothur_align_seqs",
+            "mothur_count_groups",
             "mothur_taxonomy_to_krona",
-            "mothur_heatmap_sim",
-            "mothur_chimera_vsearch",
+            "mothur_make_shared",
             "mothur_cluster_split",
-            "mothur_screen_seqs",
-            "newick_display",
-            "mothur_pre_cluster",
-            "mothur_make_contigs",
-            "mothur_unique_seqs",
-            "XY_Plot_1",
-            "taxonomy_krona_chart",
-            "mothur_cluster",
-            "mothur_tree_shared",
-            "mothur_summary_single",
-            "mothur_sub_sample"
+            "taxonomy_krona_chart"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -157966,10 +407322,141 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -157984,6 +407471,4574 @@
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
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+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
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+                        {
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+                            "state": "inexact",
+                            "versions": [
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+                            ]
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+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "inexact",
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+                            ]
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
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+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
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+                            "server": "https://galaxy-web.ipk-gatersleben.de",
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+                        {
+                            "server": "https://www.immportgalaxy.org/",
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+                        },
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+                        {
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+                            "versions": [
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@@ -158049,8 +412104,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 179,
-        "visitors": 5448,
+        "visit_duration": 178,
+        "visitors": 5547,
         "workflows": [
             {
                 "creators": [],
@@ -158201,7 +412256,7 @@
                 ],
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Training: 16S rRNA Sequencing With Mothur: Main Tutorial",
                 "outputs": [],
                 "parent_id": "microbiome/mothur-miseq-sop",
@@ -158534,15 +412589,15 @@
             "topic_4038"
         ],
         "edam_operation": [
-            "Phylogenetic tree analysis",
+            "Sequence read processing",
             "DNA barcoding",
-            "Visualisation",
-            "Phylogenetic analysis",
-            "Sequencing quality control",
+            "Phylogenetic tree analysis",
             "Phylogenetic tree generation",
-            "Phylogenetic tree reconstruction",
             "Taxonomic classification",
-            "Sequence read processing",
+            "Sequencing quality control",
+            "Visualisation",
+            "Phylogenetic tree reconstruction",
+            "Phylogenetic analysis",
             "Sequence clustering"
         ],
         "edam_topic": [
@@ -158562,8 +412617,7 @@
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         "inexact_supported_servers": [
             "UseGalaxy.be",
-            "UseGalaxy.cz",
-            "UseGalaxy.fr"
+            "UseGalaxy.cz"
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@@ -158583,7 +412637,7 @@
             "Using a mock community to assess the error rate of your sequencing experiment",
             "Visualize sample diversity using Krona and Phinch"
         ],
-        "pageviews": 3572,
+        "pageviews": 3607,
         "priority": 1000,
         "pub_date": "2019-05-13",
         "questions": [
@@ -158626,33 +412680,33 @@
         ],
         "short_id": "T00391",
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-            "mothur_dist_shared",
-            "mothur_summary_seqs",
-            "mothur_remove_lineage",
-            "mothur_count_seqs",
-            "mothur_classify_seqs",
-            "mothur_remove_groups",
-            "mothur_make_shared",
-            "mothur_filter_seqs",
-            "mothur_dist_seqs",
-            "mothur_remove_seqs",
-            "mothur_rarefaction_single",
-            "mothur_venn",
-            "mothur_classify_otu",
-            "mothur_count_groups",
-            "mothur_heatmap_sim",
             "mothur_chimera_vsearch",
-            "mothur_cluster_split",
+            "mothur_count_seqs",
             "mothur_screen_seqs",
+            "mothur_cluster",
+            "mothur_classify_otu",
+            "mothur_summary_seqs",
+            "mothur_unique_seqs",
+            "mothur_dist_shared",
             "collapse_dataset",
-            "newick_display",
+            "mothur_classify_seqs",
+            "mothur_dist_seqs",
             "mothur_pre_cluster",
-            "mothur_unique_seqs",
             "XY_Plot_1",
-            "mothur_cluster",
+            "mothur_remove_seqs",
+            "mothur_remove_groups",
+            "mothur_sub_sample",
+            "newick_display",
+            "mothur_venn",
+            "mothur_rarefaction_single",
             "mothur_tree_shared",
             "mothur_summary_single",
-            "mothur_sub_sample"
+            "mothur_remove_lineage",
+            "mothur_filter_seqs",
+            "mothur_heatmap_sim",
+            "mothur_count_groups",
+            "mothur_make_shared",
+            "mothur_cluster_split"
         ],
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         "slides_recordings": false,
@@ -158690,11 +412744,3865 @@
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
+                }
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-                    "url": "https://usegalaxy.fr/",
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.6+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.6+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.6+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.6+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.6+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.6+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.6+galaxy1"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "5.1.0"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "5.1.0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "5.1.0"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "5.1.0",
+                                "1.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "4.2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "4.2"
                 }
             ]
         },
@@ -158755,7 +416663,7 @@
         "video_versions": 2,
         "video_view": 0,
         "visit_duration": 337,
-        "visitors": 1985,
+        "visitors": 2011,
         "workflows": [
             {
                 "creators": [
@@ -158850,7 +416758,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nContigs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGroups\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Summary.seqs\"];\n  0 -->|output| 2;\n  3[\"Screen.seqs\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Summary.seqs\"];\n  3 -->|fasta_out| 4;\n  5[\"Unique.seqs\"];\n  3 -->|fasta_out| 5;\n  6[\"Count.seqs\"];\n  3 -->|groups_out| 6;\n  5 -->|out_names| 6;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur]",
                 "outputs": [
                     {
@@ -159295,7 +417203,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAligned Sequences\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCount Table\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Summary.seqs\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Screen.seqs\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Filter.seqs\"];\n  3 -->|fasta_out| 4;\n  5[\"Unique.seqs\"];\n  4 -->|filteredfasta| 5;\n  3 -->|count_out| 5;\n  6[\"Pre.cluster\"];\n  5 -->|out_fasta| 6;\n  5 -->|out_count| 6;\n  7[\"Summary.seqs\"];\n  6 -->|count_out| 7;\n  6 -->|fasta_out| 7;\n  a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d[\"Output\\nSummary.seqs on input dataset(s): summary\"];\n  7 --> a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d;\n  style a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d stroke:#2c3143,stroke-width:4px;\n  8[\"Chimera.vsearch\"];\n  6 -->|fasta_out| 8;\n  6 -->|count_out| 8;\n  9[\"Remove.seqs\"];\n  8 -->|out_accnos| 9;\n  8 -->|out_count| 9;\n  6 -->|fasta_out| 9;\n  10[\"Summary.seqs\"];\n  9 -->|count_out| 10;\n  9 -->|fasta_out| 10;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur]",
                 "outputs": [
                     {
@@ -160057,7 +417965,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nCleaned Sequences\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCount Table\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTraining set FASTA\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nTraining set Taxonomy\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Classify.seqs\"];\n  2 -->|output| 4;\n  1 -->|output| 4;\n  0 -->|output| 4;\n  3 -->|output| 4;\n  5[\"Remove.lineage\"];\n  1 -->|output| 5;\n  0 -->|output| 5;\n  4 -->|taxonomy_out| 5;\n  6[\"Summary.seqs\"];\n  5 -->|count_out| 6;\n  5 -->|fasta_out| 6;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]",
                 "outputs": [
                     {
@@ -160385,7 +418293,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMock Count Table\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMock Sequences\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Dist.seqs\"];\n  1 -->|output| 2;\n  3[\"Cluster\"];\n  0 -->|output| 3;\n  2 -->|out_dist| 3;\n  4[\"Make.shared\"];\n  0 -->|output| 4;\n  3 -->|otulist| 4;\n  5[\"Rarefaction.single\"];\n  4 -->|shared| 5;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]",
                 "outputs": [
                     {
@@ -160753,7 +418661,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSequences\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCount Table\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTaxonomy\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Remove.groups\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  2 -->|output| 3;\n  4[\"Cluster.split\"];\n  3 -->|fasta_out| 4;\n  3 -->|count_out| 4;\n  3 -->|taxonomy_out| 4;\n  5[\"Make.shared\"];\n  3 -->|count_out| 5;\n  4 -->|otulist| 5;\n  6[\"Classify.otu\"];\n  3 -->|count_out| 6;\n  4 -->|otulist| 6;\n  3 -->|taxonomy_out| 6;\n  7[\"Count.groups\"];\n  5 -->|shared| 7;\n  8[\"Sub.sample\"];\n  5 -->|shared| 8;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur]",
                 "outputs": [
                     {
@@ -161326,7 +419234,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nShared file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Rarefaction.single\"];\n  0 -->|output| 1;\n  2[\"Summary.single\"];\n  0 -->|output| 2;\n  3[\"Plotting tool\"];\n  1 -->|rarefactioncurves| 3;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow 6: Alpha Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]",
                 "outputs": [
                     {
@@ -161643,7 +419551,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nShared file from Make.shared\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nSub.sample shared\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Dist.shared\"];\n  0 -->|output| 2;\n  3[\"Collapse Collection\"];\n  1 -->|output| 3;\n  4[\"Heatmap.sim\"];\n  2 -->|distfiles| 4;\n  5[\"Tree.shared\"];\n  2 -->|distfiles| 5;\n  6[\"Venn\"];\n  3 -->|output| 6;\n  7[\"Newick Display\"];\n  5 -->|tre| 7;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Workflow7: Beta Diversity [Galaxy Training: 16S Microbial Analysis With Mothur]",
                 "outputs": [
                     {
@@ -162015,7 +419923,6 @@
         "hands_on": true,
         "id": "evolution/mtb_phylogeny",
         "inexact_supported_servers": [
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
         ],
         "js_requirements": {
@@ -162030,7 +419937,7 @@
             "Understand the basic concepts behind phylogenetic trees, as applied to *Mycobacterium tuberculosis*",
             "Be able to read and interrogate a phylogeny encountered in the literature"
         ],
-        "pageviews": 2072,
+        "pageviews": 2079,
         "pub_date": "2022-03-16",
         "questions": [
             "What information can I get from a phylogenetic tree?",
@@ -162054,8 +419961,8 @@
         ],
         "short_id": "T00144",
         "short_tools": [
-            "upload1",
             "interactive_tool_rstudio",
+            "upload1",
             "raxml"
         ],
         "slides": false,
@@ -162070,14 +419977,693 @@
             ],
             "inexact": [
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "interactive_tool_rstudio",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
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+                        {
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+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
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+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
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+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
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+                    "version": "local"
                 }
             ]
         },
@@ -162115,8 +420701,8 @@
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         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 133,
-        "visitors": 1374,
+        "visit_duration": 135,
+        "visitors": 1379,
         "workflows": [
             {
                 "creators": [],
@@ -162187,7 +420773,7 @@
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-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "Mtb phylogeny",
                 "outputs": [
                     {
@@ -162522,9 +421108,9 @@
             "topic_2885"
         ],
         "edam_operation": [
-            "Phylogenetic tree visualisation",
             "Variant calling",
             "Antimicrobial resistance prediction",
+            "Phylogenetic tree visualisation",
             "Phylogenetic tree generation"
         ],
         "edam_topic": [
@@ -162565,7 +421151,7 @@
             "Identify transmission clusters based on SNP distances",
             "Study the emergence and spread of drug resistance based on transmission analysis."
         ],
-        "pageviews": 2499,
+        "pageviews": 2504,
         "pub_date": "2022-03-16",
         "requirements": [
             {
@@ -162585,24 +421171,24 @@
         ],
         "short_id": "T00145",
         "short_tools": [
+            "samtools_view",
+            "tp_replace_in_line",
             "tp_sed_tool",
-            "tp_easyjoin_tool",
-            "tp_cat",
             "bcftools_consensus",
-            "samtools_view",
-            "upload1",
             "snippy",
+            "snp_sites",
+            "collapse_dataset",
+            "trimmomatic",
+            "tp_cat",
+            "tp_easyjoin_tool",
             "tp_grep_tool",
-            "tp_replace_in_line",
-            "snp_dists",
             "Grep1",
             "tb_variant_filter",
+            "addName",
             "tb_profiler_profile",
-            "collapse_dataset",
-            "snp_sites",
-            "trimmomatic",
+            "upload1",
             "__MERGE_COLLECTION__",
-            "addName"
+            "snp_dists"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -162632,6 +421218,3430 @@
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             ]
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+                            "server": "http://smile.hku.hk/SARGs",
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+                            ]
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+                            "server": "http://pepsimili.e-nios.com:8080/",
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+                            "server": "https://usegalaxy.eu",
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+                            "version": "0.38.1"
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+                            "state": "exact",
+                            "version": "0.38.1"
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+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.38.1"
+                        },
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+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
+                                "0.36.6",
+                                "0.36.5"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
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+                    "version": "0.38.1"
+                },
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+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
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+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
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+                            "state": "local"
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+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "prokaryote",
@@ -162684,8 +424694,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 183,
-        "visitors": 1605,
+        "visit_duration": 182,
+        "visitors": 1610,
         "workflows": [
             {
                 "creators": [],
@@ -162781,7 +424791,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nMTB single-end BAMs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nMTB paired-end BAMs\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Merge collections\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  3[\"Samtools view BAM > SAM\"];\n  2 -->|output| 3;\n  aa220027-9d10-4328-b2c2-e4d139d5d5bd[\"Output\\nSamtools view on input dataset(s): filtered alignments\"];\n  3 --> aa220027-9d10-4328-b2c2-e4d139d5d5bd;\n  style aa220027-9d10-4328-b2c2-e4d139d5d5bd stroke:#2c3143,stroke-width:4px;\n  4[\"Sed MTB_anc to Chromosome\"];\n  3 -->|outputsam| 4;\n  5[\"Samtools view SAM > BAM\"];\n  4 -->|output| 5;\n  6[\"TB-profiler\"];\n  5 -->|outputsam| 6;\n  7[\"Get drug resistance profile\"];\n  6 -->|output_txt| 7;\n  8[\"Add Sample Name\"];\n  7 -->|output| 8;\n  9[\"Concatenate DR profiles in a single table\"];\n  8 -->|output| 9;\n  10[\"Cleanup the table\"];\n  9 -->|out_file1| 10;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "From BAMs to drug resistance prediction with TB-profiler",
                 "outputs": [
                     {
@@ -163416,7 +425426,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nSingle-End FASTQs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nPaired-End FASTQs\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nMycobacterium_tuberculosis_ancestral_reference.gbk\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Trimmomatic\"];\n  0 -->|output| 3;\n  4[\"Trimmomatic\"];\n  1 -->|output| 4;\n  5[\"Mapping and variant calling of SINGLE END FASTQs with snippy\"];\n  3 -->|fastq_out| 5;\n  2 -->|output| 5;\n  6[\"Mapping and variant calling of PAIRED END FASTQs with snippy\"];\n  4 -->|fastq_out_paired| 6;\n  2 -->|output| 6;\n  7[\"Merge PE/SE VCFs in a single collection with all samples\"];\n  5 -->|snpvcf| 7;\n  6 -->|snpvcf| 7;\n  8[\"Merge PE/SE BAMs in a single collection with all samples Part the workflow \u201dIdentifying DR with TB-profiler\"];\n  5 -->|snpsbam| 8;\n  6 -->|snpsbam| 8;\n  9[\"TB Variant Filter\"];\n  7 -->|output| 9;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "From Fastqs to VCFs and BAMs",
                 "outputs": [
                     {
@@ -163896,7 +425906,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nCollection of VCFs to analyze\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference genome of the MTBC ancestor\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Filter TB variants\"];\n  0 -->|output| 2;\n  3[\"Generate the complete genome of each of the samples\"];\n  2 -->|output1| 3;\n  1 -->|output| 3;\n  ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a[\"Output\\n#{input_file}\"];\n  3 --> ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a;\n  style ce5dd7a2-c33d-46b4-9f02-68c2bdfcf31a stroke:#2c3143,stroke-width:4px;\n  4[\"Concatenate genomes to build a MSA\"];\n  3 -->|output_file| 4;\n  5[\"Keep only variable positions\"];\n  4 -->|out_file1| 5;\n  6[\"Calculate SNP distances\"];\n  5 -->|output_fasta| 6;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:43 +0000",
                 "name": "From VCFs to SNP distance matrix",
                 "outputs": [
                     {
@@ -164442,8 +426452,8 @@
         ],
         "edam_operation": [
             "Genome visualisation",
-            "Genome annotation",
-            "Read mapping"
+            "Read mapping",
+            "Genome annotation"
         ],
         "edam_topic": [
             "Whole genome sequencing",
@@ -164456,8 +426466,7 @@
         ],
         "exact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -164500,7 +426509,7 @@
             "Get information about ARGs",
             "Visualize the ARGs and plasmid genes in their genomic context"
         ],
-        "pageviews": 1576,
+        "pageviews": 1635,
         "pub_date": "2024-01-23",
         "questions": [
             "Which resistance genes are on a bacterial genome?",
@@ -164524,12 +426533,12 @@
         "short_id": "T00401",
         "short_tools": [
             "jbrowse",
-            "tbl2gff3",
-            "upload1",
             "Grep1",
-            "staramr_search",
+            "tbl2gff3",
             "bakta",
-            "bowtie2"
+            "upload1",
+            "bowtie2",
+            "staramr_search"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -164545,11 +426554,6 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
                 }
             ],
             "inexact": [
@@ -164565,6 +426569,1163 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
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+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
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+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
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+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
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+                    "usegalaxy": false
+                },
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+                },
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+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                {
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+                    "url": "http://pepsimili.e-nios.com:8080/",
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+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "servers": [
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+                            "state": "local"
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+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
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+                            "state": "missing"
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+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
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+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
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+                            "server": "https://galaxy-web.ipk-gatersleben.de",
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+                        },
+                        {
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+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
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+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
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+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
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+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.5.1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.10.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.10.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.7.2+galaxy0",
+                                "0.8.0+galaxy0",
+                                "0.7.1+galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.10.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.10.0+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.10.0+galaxy1"
+                },
+                {
+                    "id": "upload1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "gmod",
@@ -164604,8 +427765,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 165,
-        "visitors": 1138,
+        "visit_duration": 177,
+        "visitors": 1183,
         "workflows": [
             {
                 "creators": [
@@ -164627,7 +427788,7 @@
                     "report": null,
                     "subworkflows": false
                 },
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-                "modified": "2024-10-02 12:08:08 +0000",
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+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "mrsa AMR gene detection",
                 "outputs": [
                     {
@@ -164815,7 +427976,7 @@
                             {
                                 "label": "stararm_detailed_summary",
                                 "output_name": "detailed_summary",
-                                "uuid": "000e2ab9-92db-45bb-a0ef-ecccf06da616"
+                                "uuid": "455bde1a-6195-4ea2-9577-35eea97a546a"
                             }
                         ]
                     },
@@ -164889,7 +428050,7 @@
                             {
                                 "label": "bakta_annotation_summary",
                                 "output_name": "annotation_tsv",
-                                "uuid": "c848b1eb-7262-4627-b7a7-05a13b968935"
+                                "uuid": "065a7e6a-7ce3-4763-8698-959f019c6c76"
                             }
                         ]
                     },
@@ -164946,7 +428107,7 @@
                             {
                                 "label": "bowtie_mapping_stats",
                                 "output_name": "mapping_stats",
-                                "uuid": "352e63d3-8aca-4dff-878c-10497f65bb74"
+                                "uuid": "57f88358-7a42-45c7-a538-55476519e3ec"
                             }
                         ]
                     },
@@ -164999,7 +428160,7 @@
                             {
                                 "label": "jbrowse_output",
                                 "output_name": "output",
-                                "uuid": "3c3bd5fd-419c-45b2-afcd-c6d02af82695"
+                                "uuid": "bac18ad5-2731-45bc-8b53-5cfaca1e06c5"
                             }
                         ]
                     }
@@ -165197,7 +428358,7 @@
             "Replicate the study on a (very) small scale",
             "Gain familiarity with the docking and scoring techniques involved."
         ],
-        "pageviews": 4569,
+        "pageviews": 4577,
         "pub_date": "2020-03-27",
         "questions": [
             "How can candidate ligands be generated and docked to a protein in Galaxy?",
@@ -165215,18 +428376,18 @@
         ],
         "short_id": "T00049",
         "short_tools": [
-            "openbabel_compound_convert",
-            "split_file_to_collection",
-            "enumerate_charges",
-            "rxdock_rbcavity",
-            "sucos_max_score",
+            "rxdock_rbdock",
+            "xchem_transfs_scoring",
             "collapse_dataset",
             "xchem_pose_scoring",
-            "rxdock_rbdock",
-            "ctb_frankenstein_ligand",
             "rdock_rbdock",
+            "rxdock_rbcavity",
+            "sucos_max_score",
+            "ctb_frankenstein_ligand",
+            "openbabel_compound_convert",
+            "enumerate_charges",
             "rdock_rbcavity",
-            "xchem_transfs_scoring"
+            "split_file_to_collection"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -165234,6 +428395,2533 @@
             "exact": [],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
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+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
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+                            "server": "https://www.immportgalaxy.org/",
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+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "covid19",
@@ -165280,7 +430968,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 179,
-        "visitors": 2707,
+        "visitors": 2713,
         "workflows": [
             {
                 "creators": [],
@@ -165422,7 +431110,7 @@
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                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nCandidates\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMpro-x0195_0_apo-desolv.pdb\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nhits.sdf\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Enumerate changes\"];\n  0 -->|output| 3;\n  4[\"Compound conversion\"];\n  1 -->|output| 4;\n  5[\"Create Frankenstein ligand\"];\n  2 -->|output| 5;\n  6[\"Compound conversion\"];\n  3 -->|output| 6;\n  7[\"rDock cavity definition\"];\n  4 -->|outfile| 7;\n  5 -->|outfile| 7;\n  8[\"Split file\"];\n  6 -->|outfile| 8;\n  9[\"rDock docking\"];\n  4 -->|outfile| 9;\n  8 -->|list_output_sdf| 9;\n  7 -->|activesite| 9;\n  10[\"Collapse Collection\"];\n  9 -->|output| 10;\n  11[\"XChem TransFS pose scoring\"];\n  1 -->|output| 11;\n  10 -->|output| 11;\n  12[\"Max SuCOS score\"];\n  11 -->|output| 12;\n  2 -->|output| 12;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring",
                 "outputs": [
                     {
@@ -165794,22 +431482,22 @@
             "topic_3324"
         ],
         "edam_operation": [
-            "Sequence alignment",
-            "Phylogenetic tree generation",
-            "Phylogenetic tree visualisation",
-            "Sequencing quality control",
+            "Variant calling",
             "Sequence alignment analysis",
-            "Genome visualisation",
+            "Antimicrobial resistance prediction",
             "Sequence analysis",
-            "Sequence contamination filtering",
-            "Variant calling",
-            "Global alignment",
-            "Statistical calculation",
+            "Phylogenetic tree generation",
+            "Genome visualisation",
+            "Sequence composition calculation",
             "Taxonomic classification",
+            "Statistical calculation",
             "Validation",
-            "Local alignment",
-            "Sequence composition calculation",
-            "Antimicrobial resistance prediction"
+            "Sequencing quality control",
+            "Global alignment",
+            "Sequence alignment",
+            "Sequence contamination filtering",
+            "Phylogenetic tree visualisation",
+            "Local alignment"
         ],
         "edam_topic": [
             "Genomics",
@@ -165844,7 +431532,7 @@
             "How can we predict drug resistance from those variants",
             "How do we annotate those variants"
         ],
-        "pageviews": 9172,
+        "pageviews": 9186,
         "pub_date": "2020-07-25",
         "questions": [
             "How do we detect differences between a set of reads from _M. tuberculosis_ (Mtb) and the Mtb reference genome"
@@ -165879,26 +431567,26 @@
         ],
         "short_id": "T00319",
         "short_tools": [
+            "mosdepth",
             "tp_sed_tool",
-            "upload1",
-            "snippy",
             "qualimap_bamqc",
-            "tb_variant_filter",
-            "EMBOSS: seqret84",
-            "tb_profiler_profile",
-            "mosdepth",
-            "jvarkit_wgscoverageplotter",
-            "tbvcfreport",
-            "tp_awk_tool",
-            "fastqc",
             "jbrowse",
+            "snippy",
+            "jvarkit_wgscoverageplotter",
             "samtools_stats",
-            "bcftools_consensus",
-            "multiqc",
             "fastp",
-            "kraken2",
+            "upload1",
             "EMBOSS:%20seqret84",
-            "__FLATTEN__"
+            "tp_awk_tool",
+            "tb_variant_filter",
+            "tb_profiler_profile",
+            "multiqc",
+            "kraken2",
+            "tbvcfreport",
+            "EMBOSS: seqret84",
+            "bcftools_consensus",
+            "__FLATTEN__",
+            "fastqc"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -165907,6 +431595,3583 @@
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             "inexact": []
         },
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+                    "url": "http://apostl.moffitt.org/"
+                },
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
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+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
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+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
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+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
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+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
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+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                    "url": "https://www.immportgalaxy.org/"
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.1.7+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.1.10+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.0.1+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.1.7+galaxy0",
+                                "0.1.10+galaxy0",
+                                "0.1.8+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.0.1+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.0.1+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.0.1+galaxy0"
+                },
+                {
+                    "id": "upload1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "prokaryote",
@@ -165960,8 +435225,8 @@
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 177,
-        "visitors": 5788,
+        "visit_duration": 176,
+        "visitors": 5800,
         "workflows": [
             {
                 "creators": [
@@ -166220,7 +435485,7 @@
                 ],
                 "license": "AGPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nReads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference Genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nMinimum depth of coverage\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nMinimum variant allele frequency\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nAdditional BWA-MEM options\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"fastp\"];\n  0 -->|output| 5;\n  6[\"seqret\"];\n  1 -->|output| 6;\n  7[\"snippy\"];\n  4 -->|output| 7;\n  2 -->|output| 7;\n  3 -->|output| 7;\n  5 -->|output_paired_coll| 7;\n  1 -->|output| 7;\n  8[\"Kraken2\"];\n  5 -->|output_paired_coll| 8;\n  c7abf2bf-ed4c-433e-a695-9eca61282bb5[\"Output\\nreport_output\"];\n  8 --> c7abf2bf-ed4c-433e-a695-9eca61282bb5;\n  style c7abf2bf-ed4c-433e-a695-9eca61282bb5 stroke:#2c3143,stroke-width:4px;\n  083a0e51-7780-4c91-a071-dc0e4641d060[\"Output\\noutput\"];\n  8 --> 083a0e51-7780-4c91-a071-dc0e4641d060;\n  style 083a0e51-7780-4c91-a071-dc0e4641d060 stroke:#2c3143,stroke-width:4px;\n  9[\"QualiMap BamQC\"];\n  7 -->|snpsbam| 9;\n  10[\"mosdepth\"];\n  2 -->|output| 10;\n  7 -->|snpsbam| 10;\n  11[\"TB Variant Filter\"];\n  7 -->|snpvcf| 11;\n  12[\"TB-Profiler Profile\"];\n  7 -->|snpsbam| 12;\n  335635b4-a4de-4980-ad02-68f0035daeaa[\"Output\\noutput_txt\"];\n  12 --> 335635b4-a4de-4980-ad02-68f0035daeaa;\n  style 335635b4-a4de-4980-ad02-68f0035daeaa stroke:#2c3143,stroke-width:4px;\n  13[\"TB Variant Filter\"];\n  7 -->|snpvcf| 13;\n  14[\"Flatten collection\"];\n  9 -->|raw_data| 14;\n  15[\"Text reformatting\"];\n  10 -->|output_quantized_bed| 15;\n  16[\"Text transformation\"];\n  11 -->|output1| 16;\n  007df8c2-bd13-495f-8904-abf31d4594d0[\"Output\\nFinal annotated VCF\"];\n  16 --> 007df8c2-bd13-495f-8904-abf31d4594d0;\n  style 007df8c2-bd13-495f-8904-abf31d4594d0 stroke:#2c3143,stroke-width:4px;\n  17[\"MultiQC\"];\n  5 -->|report_json| 17;\n  14 -->|output| 17;\n  59528235-7525-4ef9-8810-36f1ed0f01f6[\"Output\\nhtml_report\"];\n  17 --> 59528235-7525-4ef9-8810-36f1ed0f01f6;\n  style 59528235-7525-4ef9-8810-36f1ed0f01f6 stroke:#2c3143,stroke-width:4px;\n  18[\"bcftools consensus\"];\n  13 -->|output1| 18;\n  6 -->|out_file1| 18;\n  15 -->|outfile| 18;\n  c71b135d-35f9-44d0-a20e-f25528e518af[\"Output\\nconsensus_genome\"];\n  18 --> c71b135d-35f9-44d0-a20e-f25528e518af;\n  style c71b135d-35f9-44d0-a20e-f25528e518af stroke:#2c3143,stroke-width:4px;\n  19[\"TB Variant Report\"];\n  16 -->|output| 19;\n  12 -->|results_json| 19;\n  959528d2-f8f2-4440-99cf-44fddd6c5069[\"Output\\ndrug_resistance_report_html\"];\n  19 --> 959528d2-f8f2-4440-99cf-44fddd6c5069;\n  style 959528d2-f8f2-4440-99cf-44fddd6c5069 stroke:#2c3143,stroke-width:4px;\n  4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0[\"Output\\nvariants_report_html\"];\n  19 --> 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0;\n  style 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "TB Variant Analysis v1.0",
                 "outputs": [
                     {
@@ -166857,15 +436122,15 @@
         "dir": "topics/variant-analysis/tutorials/sars-cov-2",
         "edam_operation": [
             "Data handling",
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
-            "Sequence contamination filtering",
+            "Genome indexing",
+            "Formatting",
             "Generation",
-            "Validation",
             "SNP detection",
-            "Formatting",
-            "Genome indexing"
+            "Validation",
+            "Sequencing quality control",
+            "Read mapping",
+            "Sequence contamination filtering",
+            "Sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -166880,7 +436145,6 @@
             "MISSISSIPPI",
             "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
@@ -166902,7 +436166,7 @@
             "Understand how collections enable processing of sequencing data in batches",
             "Understand the analysis steps required to identify and annotate genomic mutations from sequencing data of SARS-CoV-2 samples"
         ],
-        "pageviews": 18702,
+        "pageviews": 18745,
         "pub_date": "2020-06-24",
         "questions": [
             "How can you download public sequencing data deposited in the NCBI Sequence Read Archive (SRA) into a Galaxy history for analysis?",
@@ -166925,20 +436189,20 @@
         ],
         "short_id": "T00315",
         "short_tools": [
-            "bwa_mem",
-            "samtools_stats",
-            "picard_MarkDuplicates",
-            "fastp",
-            "Filter1",
-            "lofreq_viterbi",
+            "lofreq_call",
             "snpeff_sars_cov_2",
             "multiqc",
             "lofreq_indelqual",
+            "snpSift_extractFields",
+            "bwa_mem",
             "Grep1",
+            "picard_MarkDuplicates",
+            "samtools_stats",
+            "fastp",
+            "lofreq_viterbi",
             "fasterq_dump",
-            "lofreq_call",
             "tp_cut_tool",
-            "snpSift_extractFields"
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -166973,19 +436237,2338 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Filter1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
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+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Grep1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
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+                        {
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+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
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@@ -167034,7 +438617,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 174,
-        "visitors": 12312,
+        "visitors": 12341,
         "workflows": [
             {
                 "creators": [],
@@ -167165,7 +438748,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Faster Download and Extract Reads in FASTQ\"];\n  1 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|list_paired| 3;\n  4[\"Map with BWA-MEM\"];\n  3 -->|output_paired_coll| 4;\n  0 -->|output| 4;\n  5[\"MarkDuplicates\"];\n  4 -->|bam_output| 5;\n  6[\"Realign reads\"];\n  5 -->|outFile| 6;\n  0 -->|output| 6;\n  7[\"Samtools stats\"];\n  5 -->|outFile| 7;\n  8[\"Insert indel qualities\"];\n  6 -->|realigned| 8;\n  0 -->|output| 8;\n  2ca7c89b-999f-41dc-8037-e54e25959a7e[\"Output\\nRealigned Alignments with Indel Qualities\"];\n  8 --> 2ca7c89b-999f-41dc-8037-e54e25959a7e;\n  style 2ca7c89b-999f-41dc-8037-e54e25959a7e stroke:#2c3143,stroke-width:4px;\n  9[\"Call variants\"];\n  8 -->|output| 9;\n  0 -->|output| 9;\n  10[\"SnpEff eff:\"];\n  9 -->|variants| 10;\n  11[\"SnpSift Extract Fields\"];\n  10 -->|snpeff_output| 11;\n  06259137-eaa5-404a-923c-70ee5f1d89d4[\"Output\\nSnpSift tabular output\"];\n  11 --> 06259137-eaa5-404a-923c-70ee5f1d89d4;\n  style 06259137-eaa5-404a-923c-70ee5f1d89d4 stroke:#2c3143,stroke-width:4px;\n  12[\"MultiQC\"];\n  3 -->|report_json| 12;\n  7 -->|output| 12;\n  5 -->|metrics_file| 12;\n  10 -->|csvFile| 12;\n  758ffde5-7ddd-482a-88b2-1504f8335488[\"Output\\nMultiQC Report PE\"];\n  12 --> 758ffde5-7ddd-482a-88b2-1504f8335488;\n  style 758ffde5-7ddd-482a-88b2-1504f8335488 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Simple COVID-19 - PE Variation",
                 "outputs": [
                     {
@@ -167828,17 +439411,17 @@
         ],
         "dir": "topics/variant-analysis/tutorials/pox-tiled-amplicon",
         "edam_operation": [
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
             "Sequence alignment analysis",
+            "Genome indexing",
             "Sequence analysis",
-            "Multiple sequence alignment",
-            "Sequence contamination filtering",
             "Generation",
-            "Global alignment",
+            "Multiple sequence alignment",
+            "Sequencing quality control",
             "Local alignment",
-            "Genome indexing"
+            "Read mapping",
+            "Global alignment",
+            "Sequence contamination filtering",
+            "Sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -167869,7 +439452,7 @@
             "Construct a sample consensus genome from mapped reads",
             "Explore a recombinant pox virus genome via a multiple-sequence alignment of consensus genome and references and through lists of mutations derived from it"
         ],
-        "pageviews": 670,
+        "pageviews": 678,
         "pub_date": "2023-05-15",
         "questions": [
             "Which special challenges does one encounter during sequence data analysis of pox viruses?",
@@ -167888,28 +439471,28 @@
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         "short_id": "T00347",
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-            "ivar_trim",
-            "upload1",
-            "compose_text_param",
             "qualimap_bamqc",
-            "param_value_from_file",
-            "__ZIP_COLLECTION__",
-            "mimodd_info",
-            "datamash_ops",
-            "bwa_mem",
-            "ivar_consensus",
             "fatovcf",
-            "EMBOSS: maskseq51",
-            "__APPLY_RULES__",
+            "fasta_regex_finder",
+            "fastp",
             "samtools_view",
             "rbc_mafft",
+            "bwa_mem",
+            "upload1",
+            "datamash_ops",
+            "ivar_trim",
+            "__APPLY_RULES__",
+            "compose_text_param",
+            "EMBOSS: maskseq51",
+            "ivar_consensus",
             "Grep1",
-            "Cut1",
-            "fasta_regex_finder",
             "samtools_merge",
-            "fastp",
             "fasta_compute_length",
-            "Add_a_column1"
+            "Add_a_column1",
+            "Cut1",
+            "mimodd_info",
+            "__ZIP_COLLECTION__",
+            "param_value_from_file"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -167920,13 +439503,3271 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
-                }
-            ],
-            "inexact": [
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Cut1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
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+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
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+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Grep1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "missing"
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+                        {
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+                            "state": "missing"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
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+                        {
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+                        {
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+                        {
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+                        {
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+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
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+                        },
+                        {
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+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
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+                            "server": "https://usegalaxy.org",
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+                        },
+                        {
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+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
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+                    "version": "local"
+                },
+                {
+                    "id": "__APPLY_RULES__",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
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+                        },
+                        {
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+                        {
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+                            "state": "missing"
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+                            "state": "missing"
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+                        {
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+                        },
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+                            "state": "local"
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+                            "state": "local"
+                        },
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
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+                        },
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+                        {
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+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
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+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "__ZIP_COLLECTION__",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
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+                        {
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+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
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+                        },
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+                        {
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+                            "state": "local"
+                        },
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+                        {
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+                            "state": "local"
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+                        {
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+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
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+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
                 }
             ]
         },
@@ -167981,7 +442822,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 145,
-        "visitors": 562,
+        "visitors": 569,
         "workflows": [
             {
                 "creators": [
@@ -168078,7 +442919,7 @@
                 ],
                 "license": "MIT",
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "pox-virus-tiled-amplicon-ref-masking",
                 "outputs": [
                     {
@@ -168363,10 +443204,10 @@
         ],
         "dir": "topics/variant-analysis/tutorials/sars-cov-2-variant-discovery",
         "edam_operation": [
-            "Tree-based sequence alignment",
             "Variant calling",
+            "Methylation analysis",
             "Variant classification",
-            "Methylation analysis"
+            "Tree-based sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -168401,7 +443242,7 @@
             "Know different SARS-CoV-2 lineage classification systems, and use pangolin and Nextclade to assign samples to predefined lineages",
             "Combine information from different analysis steps to be able to draw appropriate conclusions about individual samples and batches of viral data"
         ],
-        "pageviews": 12061,
+        "pageviews": 12082,
         "pub_date": "2021-06-30",
         "questions": [
             "How can a complete analysis, including viral consensus sequence reconstruction and lineage assignment be performed?",
@@ -168465,11 +443306,11 @@
         "short_id": "T00316",
         "short_tools": [
             "pangolin",
-            "Filter1",
+            "nextclade",
             "upload1",
+            "datamash_ops",
             "fasta_regex_finder",
-            "nextclade",
-            "datamash_ops"
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -168495,6 +443336,987 @@
                 }
             ]
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+                },
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+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
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+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
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+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
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+                },
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+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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@@ -168531,7 +444353,7 @@
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@@ -168542,42 +444364,42 @@
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                     "name": "fastp",
                     "owner": "iuc",
-                    "revisions": "65b93b623c77",
+                    "revisions": "d60c3f704da0",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "iqtree",
                     "owner": "iuc",
-                    "revisions": "24d024316465",
+                    "revisions": "0878b7fd5260",
                     "tool_panel_section_label": "Evolution",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "ivar_consensus",
                     "owner": "iuc",
-                    "revisions": "40737febe339",
+                    "revisions": "3a72fede57ce",
                     "tool_panel_section_label": "Virology",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -168591,14 +444413,14 @@
                 {
                     "name": "samtools_view",
                     "owner": "iuc",
-                    "revisions": "5826298f6a73",
+                    "revisions": "32dc5f781059",
                     "tool_panel_section_label": "SAM/BAM",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "seqtk",
                     "owner": "iuc",
-                    "revisions": "3da72230c066",
+                    "revisions": "4b494533146a",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -168619,13 +444441,13 @@
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                     "owner": "rnateam",
-                    "revisions": "bf28a8cff401",
+                    "revisions": "8e649f27aa0d",
                     "tool_panel_section_label": "Multiple Alignments",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
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         "contributors": [
             {
@@ -168648,20 +444470,20 @@
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         "dir": "topics/variant-analysis/tutorials/aiv-analysis",
         "edam_operation": [
+            "Sequence file editing",
             "Data handling",
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
-            "De-novo assembly",
             "Sequence alignment analysis",
-            "Phylogenetic analysis",
-            "Sequence contamination filtering",
+            "Genome indexing",
+            "De-novo assembly",
+            "Data retrieval",
             "Sequence analysis",
-            "Multiple sequence alignment",
             "Generation",
-            "Sequence file editing",
-            "Data retrieval",
-            "Genome indexing"
+            "Multiple sequence alignment",
+            "Sequencing quality control",
+            "Read mapping",
+            "Phylogenetic analysis",
+            "Sequence contamination filtering",
+            "Sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -168675,6 +444497,16 @@
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             "UseGalaxy.cz"
         ],
+        "input_histories": [
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+                "label": "UseGalaxy.eu"
+            },
+            {
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+                "label": "UseGalaxy.org"
+            }
+        ],
         "js_requirements": {
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@@ -168688,14 +444520,14 @@
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-20",
+        "mod_date": "2024-10-04",
         "objectives": [
             "Determine how reassortment impacts reference-based mapping approaches",
             "Use a collection of per-segment reference sequences to construct a hybrid reference genome that is sufficiently close to a sequenced sample to be useful as a reference for mapping",
             "Construct a sample consensus genome from mapped reads",
             "Generate per-segment phylogenetic trees of AIV consensus sequences"
         ],
-        "pageviews": 1887,
+        "pageviews": 1903,
         "pub_date": "2022-11-21",
         "questions": [
             "With reassortment of gene segments being a common event in avian influenza virus (AIV) evolution, does it make sense to use a reference-based mapping approach for constructing consensus genome sequences for AIV samples?",
@@ -168704,22 +444536,22 @@
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-            "bwa_mem",
-            "fastp",
+            "qualimap_bamqc",
             "samtools_view",
-            "vapor",
-            "upload1",
-            "Show beginning1",
+            "collapse_dataset",
+            "rbc_mafft",
+            "seqtk_subseq",
             "__RELABEL_FROM_FILE__",
+            "iqtree",
+            "Show beginning1",
             "tp_find_and_replace",
             "ivar_consensus",
-            "qualimap_bamqc",
-            "seqtk_subseq",
+            "bwa_mem",
             "Grep1",
+            "upload1",
+            "fastp",
             "bamtools_split_ref",
-            "iqtree",
-            "rbc_mafft",
-            "collapse_dataset"
+            "vapor"
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         "slides": false,
         "slides_recordings": false,
@@ -168745,6 +444577,2511 @@
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@@ -169066,7 +448101,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery chromosome\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference chromosome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Chromeister\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  58cf0c0c-9200-4ba4-9727-6d908ccdfa9a[\"Output\\nChromeister on input dataset(s): Detected events\"];\n  2 --> 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a;\n  style 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a stroke:#2c3143,stroke-width:4px;\n  2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c[\"Output\\nChromeister on input dataset(s): Comparison metainformation\"];\n  2 --> 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c;\n  style 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c stroke:#2c3143,stroke-width:4px;\n  c248576c-1c39-416c-99d0-40c520e3da67[\"Output\\nChromeister on input dataset(s): Comparison dotplot\"];\n  2 --> c248576c-1c39-416c-99d0-40c520e3da67;\n  style c248576c-1c39-416c-99d0-40c520e3da67 stroke:#2c3143,stroke-width:4px;\n  5f9aad77-f9ee-4932-ab22-bb5fd83f416c[\"Output\\nChromeister on input dataset(s): Comparison matrix\"];\n  2 --> 5f9aad77-f9ee-4932-ab22-bb5fd83f416c;\n  style 5f9aad77-f9ee-4932-ab22-bb5fd83f416c stroke:#2c3143,stroke-width:4px;\n  dea450c2-7126-43dc-af7a-9f2b704c76dd[\"Output\\nChromeister on input dataset(s): Comparison score\"];\n  2 --> dea450c2-7126-43dc-af7a-9f2b704c76dd;\n  style dea450c2-7126-43dc-af7a-9f2b704c76dd stroke:#2c3143,stroke-width:4px;\n  9a03f722-5588-4a3f-b70e-0ec9979c16dd[\"Output\\nChromeister on input dataset(s): Detected events plot\"];\n  2 --> 9a03f722-5588-4a3f-b70e-0ec9979c16dd;\n  style 9a03f722-5588-4a3f-b70e-0ec9979c16dd stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "CHROMEISTER chromosome comparison",
                 "outputs": [
                     {
@@ -169382,7 +448417,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nQuery sequence\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference sequence\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Gecko\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  6275abc1-d74e-45a7-b8ab-3c88426cc488[\"Output\\nGecko on input dataset(s): CSV\"];\n  2 --> 6275abc1-d74e-45a7-b8ab-3c88426cc488;\n  style 6275abc1-d74e-45a7-b8ab-3c88426cc488 stroke:#2c3143,stroke-width:4px;\n  3[\"Text reformatting\"];\n  2 -->|alignments2| 3;\n  4[\"ClustalW\"];\n  3 -->|outfile| 4;\n  d63c1172-a591-4bf6-b307-052ca19e7098[\"Output\\nClustalW on input dataset(s): clustal\"];\n  4 --> d63c1172-a591-4bf6-b307-052ca19e7098;\n  style d63c1172-a591-4bf6-b307-052ca19e7098 stroke:#2c3143,stroke-width:4px;\n  d7758e3a-522d-4439-8c9a-03f784284ebd[\"Output\\nClustalW on input dataset(s): dnd\"];\n  4 --> d7758e3a-522d-4439-8c9a-03f784284ebd;\n  style d7758e3a-522d-4439-8c9a-03f784284ebd stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:08 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GECKO pairwise comparison",
                 "outputs": [
                     {
@@ -169758,13 +448793,13 @@
             "topic_4038"
         ],
         "edam_operation": [
-            "Taxonomic classification",
-            "Statistical calculation",
-            "Visualisation",
+            "Sequence contamination filtering",
             "Validation",
             "Sequencing quality control",
+            "Visualisation",
             "Sequence composition calculation",
-            "Sequence contamination filtering"
+            "Statistical calculation",
+            "Taxonomic classification"
         ],
         "edam_topic": [
             "Microbial ecology",
@@ -169802,7 +448837,7 @@
             "Analyze and preprocess Nanopore reads",
             "Use Kraken2 to assign a taxonomic labels"
         ],
-        "pageviews": 3844,
+        "pageviews": 3894,
         "pub_date": "2020-11-24",
         "questions": [
             "How can we analyse the health status of the soil?",
@@ -169816,15 +448851,15 @@
         ],
         "short_id": "T00392",
         "short_tools": [
-            "porechop",
-            "fastp",
             "tp_replace_in_line",
-            "taxonomy_krona_chart",
-            "multiqc",
-            "kraken2",
             "datamash_reverse",
+            "multiqc",
             "fastqc",
-            "Remove beginning1"
+            "Remove beginning1",
+            "fastp",
+            "porechop",
+            "kraken2",
+            "taxonomy_krona_chart"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -169870,6 +448905,1484 @@
                 }
             ]
         },
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+                            "state": "local"
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+                            ]
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@@ -169962,7 +450475,7 @@
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@@ -170126,17 +450639,17 @@
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@@ -170168,7 +450681,7 @@
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         "questions": [
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@@ -170259,6 +450772,2401 @@
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+                        {
+                            "server": "https://usegalaxy.cz/",
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+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.7.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.7.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.7.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.7.0+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.7.0+galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "miRNA",
@@ -170305,7 +453213,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 313,
-        "visitors": 1988915,
+        "visitors": 1999561,
         "workflows": [
             {
                 "creators": [],
@@ -170606,7 +453514,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nControl miRNA FASTQ collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nTreated miRNA FASTQ collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nTreated mRNA FASTQ collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nPrecursor miRNA sequences\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Collection\\nControl mRNA FASTQ collection\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nTranscriptome FASTA\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nAnnotation GTF\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nMature miRNA sequences\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nStar miRNA sequenes\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"FastQC\"];\n  0 -->|output| 9;\n  10[\"Trim Galore!\"];\n  0 -->|output| 10;\n  11[\"FastQC\"];\n  1 -->|output| 11;\n  12[\"Trim Galore!\"];\n  1 -->|output| 12;\n  13[\"FastQC\"];\n  2 -->|output| 13;\n  14[\"FastQC\"];\n  4 -->|output| 14;\n  15[\"Salmon quant\"];\n  6 -->|output| 15;\n  2 -->|output| 15;\n  5 -->|output| 15;\n  16[\"Salmon quant\"];\n  6 -->|output| 16;\n  4 -->|output| 16;\n  5 -->|output| 16;\n  17[\"FastQC\"];\n  10 -->|trimmed_reads_single| 17;\n  18[\"MiRDeep2 Mapper\"];\n  10 -->|trimmed_reads_single| 18;\n  19[\"Merge collections\"];\n  11 -->|text_file| 19;\n  9 -->|text_file| 19;\n  20[\"FastQC\"];\n  12 -->|trimmed_reads_single| 20;\n  21[\"MiRDeep2 Mapper\"];\n  12 -->|trimmed_reads_single| 21;\n  22[\"Merge collections\"];\n  13 -->|text_file| 22;\n  14 -->|text_file| 22;\n  23[\"DESeq2\"];\n  15 -->|output_gene_quant| 23;\n  16 -->|output_gene_quant| 23;\n  6 -->|output| 23;\n  24[\"MiRDeep2 Quantifier\"];\n  7 -->|output| 24;\n  3 -->|output| 24;\n  18 -->|output_reads_collapsed| 24;\n  8 -->|output| 24;\n  25[\"MultiQC\"];\n  19 -->|output| 25;\n  26[\"Merge collections\"];\n  20 -->|text_file| 26;\n  17 -->|text_file| 26;\n  27[\"MiRDeep2 Quantifier\"];\n  7 -->|output| 27;\n  3 -->|output| 27;\n  21 -->|output_reads_collapsed| 27;\n  8 -->|output| 27;\n  28[\"MultiQC\"];\n  22 -->|output| 28;\n  29[\"Filter\"];\n  23 -->|deseq_out| 29;\n  30[\"Cut\"];\n  24 -->|miRNAsExpressed| 30;\n  31[\"MultiQC\"];\n  26 -->|output| 31;\n  32[\"Cut\"];\n  27 -->|miRNAsExpressed| 32;\n  33[\"Filter\"];\n  29 -->|out_file1| 33;\n  34[\"Filter\"];\n  29 -->|out_file1| 34;\n  35[\"DESeq2\"];\n  32 -->|out_file1| 35;\n  30 -->|out_file1| 35;\n  36[\"Cut\"];\n  34 -->|out_file1| 36;\n  37[\"Filter\"];\n  35 -->|deseq_out| 37;\n  38[\"Filter FASTA\"];\n  36 -->|out_file1| 38;\n  5 -->|output| 38;\n  39[\"Filter\"];\n  37 -->|out_file1| 39;\n  40[\"Filter\"];\n  37 -->|out_file1| 40;\n  41[\"Cut\"];\n  40 -->|out_file1| 41;\n  42[\"Filter FASTA\"];\n  41 -->|out_file1| 42;\n  8 -->|output| 42;\n  43[\"Filter FASTA\"];\n  41 -->|out_file1| 43;\n  7 -->|output| 43;\n  44[\"Concatenate datasets\"];\n  43 -->|output| 44;\n  42 -->|output| 44;\n  45[\"TargetFinder\"];\n  38 -->|output| 45;\n  44 -->|out_file1| 45;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Plant bulk RNA-Seq workflow",
                 "outputs": [
                     {
@@ -171271,24 +454179,24 @@
         ],
         "dir": "topics/assembly/tutorials/chloroplast-assembly",
         "edam_operation": [
-            "Scatter plot plotting",
-            "Genome annotation",
-            "Sequence alignment",
-            "Cross-assembly",
-            "Read mapping",
-            "Genome visualisation",
+            "Coding region prediction",
             "Genome assembly",
+            "Genome indexing",
+            "Sequence assembly visualisation",
             "De-novo assembly",
-            "Box-Whisker plot plotting",
-            "Analysis",
-            "Sequence assembly",
-            "Generation",
-            "Gene prediction",
             "Mapping assembly",
-            "Sequence assembly visualisation",
+            "Genome visualisation",
             "Read alignment",
-            "Genome indexing",
-            "Coding region prediction"
+            "Generation",
+            "Sequence assembly",
+            "Box-Whisker plot plotting",
+            "Scatter plot plotting",
+            "Genome annotation",
+            "Gene prediction",
+            "Read mapping",
+            "Cross-assembly",
+            "Sequence alignment",
+            "Analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -171302,7 +454210,6 @@
             "GalaxyTrakr",
             "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)"
         ],
@@ -171325,7 +454232,7 @@
             "Annotate the assembly and view",
             "Map reads to the assembly and view"
         ],
-        "pageviews": 9815,
+        "pageviews": 9850,
         "pub_date": "2020-12-04",
         "questions": [
             "How can we assemble a chloroplast genome?"
@@ -171359,16 +454266,16 @@
         ],
         "short_id": "T00030",
         "short_tools": [
-            "bwa_mem",
-            "prokka",
-            "jbrowse",
             "bandage_image",
-            "upload1",
-            "bandage_info",
+            "jbrowse",
             "fasta-stats",
-            "flye",
+            "pilon",
+            "bandage_info",
+            "bwa_mem",
             "nanoplot",
-            "pilon"
+            "upload1",
+            "prokka",
+            "flye"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -171397,10 +454304,136 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -171410,6 +454443,2114 @@
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.9.4+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "2.6"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
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+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "inexact",
+                            "versions": [
+                                "2.9.1+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
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+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
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+                            "server": "http://pepsimili.e-nios.com:8080/",
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+                            "version": "2.6"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.6"
+                        },
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+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "2.6"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2.6"
+                        },
+                        {
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+                            "state": "exact",
+                            "version": "2.6"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
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+                    "servers": [
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+                        },
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+                            "state": "missing"
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+                                "2.3.7"
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+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
                 }
             ]
         },
@@ -171456,8 +456597,8 @@
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 172,
-        "visitors": 6134,
+        "visit_duration": 173,
+        "visitors": 6160,
         "workflows": [
             {
                 "creators": [],
@@ -171600,7 +456741,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina_reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nNanopore_reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTiny_set_illumina_read\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nTiny_set_nanopore_reads\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Flye assembly\"];\n  1 -->|output| 4;\n  5[\"NanoPlot\"];\n  1 -->|output| 5;\n  6[\"Map with BWA-MEM\"];\n  0 -->|output| 6;\n  4 -->|consensus| 6;\n  7[\"Fasta Statistics\"];\n  4 -->|consensus| 7;\n  8[\"Bandage Info\"];\n  4 -->|assembly_gfa| 8;\n  9[\"Bandage Image\"];\n  4 -->|assembly_gfa| 9;\n  10[\"pilon\"];\n  6 -->|bam_output| 10;\n  4 -->|consensus| 10;\n  11[\"Fasta Statistics\"];\n  10 -->|output_fasta| 11;\n  12[\"Map with BWA-MEM\"];\n  2 -->|output| 12;\n  10 -->|output_fasta| 12;\n  13[\"Map with BWA-MEM\"];\n  3 -->|output| 13;\n  10 -->|output_fasta| 13;\n  14[\"Prokka\"];\n  10 -->|output_fasta| 14;\n  15[\"JBrowse\"];\n  10 -->|output_fasta| 15;\n  12 -->|bam_output| 15;\n  13 -->|bam_output| 15;\n  16[\"JBrowse\"];\n  10 -->|output_fasta| 16;\n  14 -->|out_gff| 16;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Chloroplast-genome-assembly-and-annotation",
                 "outputs": [
                     {
@@ -172591,6 +457732,13 @@
                     "tool_panel_section_label": "Annotation",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "busco",
+                    "owner": "iuc",
+                    "revisions": "2babe6d5c561",
+                    "tool_panel_section_label": "Annotation",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "bwa_mem2",
                     "owner": "iuc",
@@ -172633,6 +457781,13 @@
                     "tool_panel_section_label": "Assembly",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
+                {
+                    "name": "pretext_map",
+                    "owner": "iuc",
+                    "revisions": "79b48f02db49",
+                    "tool_panel_section_label": "Assembly",
+                    "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
+                },
                 {
                     "name": "pretext_snapshot",
                     "owner": "iuc",
@@ -172649,7 +457804,7 @@
                 }
             ]
         },
-        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 7d9ee8cd14b8\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 8c2167481e72\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 5799092ffdff\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 3ef480892a9f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 3a0efe14891f\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: smudgeplot\n  owner: galaxy-australia\n  revisions: 5e0825476fb7\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bellerophon\n  owner: iuc\n  revisions: 25ca5d73aedf\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: bb935709506a\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: b4a22d90cce9\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 01210c4e9144\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n  owner: iuc\n  revisions: f8113c25bc6b\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 5cc34c3f440d\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n  owner: iuc\n  revisions: dfb8a4497339\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_snapshot\n  owner: iuc\n  revisions: 44c66e8d21e6\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 7d9ee8cd14b8\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: blobtoolkit\n  owner: bgruening\n  revisions: 8c2167481e72\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: diamond\n  owner: bgruening\n  revisions: e8ac2b53f262\n  tool_panel_section_label: NCBI Blast\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 5799092ffdff\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: gfastats\n  owner: bgruening\n  revisions: 3ef480892a9f\n  tool_panel_section_label: FASTA/FASTQ\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: text_processing\n  owner: bgruening\n  revisions: d698c222f354\n  tool_panel_section_label: Text Manipulation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: samtools_stats\n  owner: devteam\n  revisions: 3a0efe14891f\n  tool_panel_section_label: SAM/BAM\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: smudgeplot\n  owner: galaxy-australia\n  revisions: 5e0825476fb7\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bandage\n  owner: iuc\n  revisions: ddddce450736\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bellerophon\n  owner: iuc\n  revisions: 25ca5d73aedf\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: bb935709506a\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: busco\n  owner: iuc\n  revisions: 2babe6d5c561\n  tool_panel_section_label: Annotation\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: bwa_mem2\n  owner: iuc\n  revisions: b4a22d90cce9\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: genomescope\n  owner: iuc\n  revisions: 01210c4e9144\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: merqury\n  owner: iuc\n  revisions: f8113c25bc6b\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: meryl\n  owner: iuc\n  revisions: 29dabd8db6f2\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: minimap2\n  owner: iuc\n  revisions: 5cc34c3f440d\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n  owner: iuc\n  revisions: dfb8a4497339\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_map\n  owner: iuc\n  revisions: 79b48f02db49\n  tool_panel_section_label: Assembly\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: pretext_snapshot\n  owner: iuc\n  revisions: 44c66e8d21e6\n  tool_panel_section_label: Graph/Display Data\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: collapse_collections\n  owner: nml\n  revisions: 90981f86000f\n  tool_panel_section_label: Collection Operations\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
         "api": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json",
         "contributors": [
             {
@@ -172680,24 +457835,33 @@
                 "orcid": "0000-0001-8293-4816",
                 "page": "https://training.galaxyproject.org/training-material/hall-of-fame/tbrown91/",
                 "url": "https://training.galaxyproject.org/training-material/api/contributors/tbrown91.json"
+            },
+            {
+                "email": "delphine.lariviere@galaxy.org",
+                "id": "delphine-l",
+                "joined": "2017-09",
+                "name": "Delphine Lariviere",
+                "orcid": "0000-0001-6421-3484",
+                "page": "https://training.galaxyproject.org/training-material/hall-of-fame/delphine-l/",
+                "url": "https://training.galaxyproject.org/training-material/api/contributors/delphine-l.json"
             }
         ],
         "dir": "topics/assembly/tutorials/ERGA-post-assembly-QC",
         "edam_operation": [
-            "Data handling",
-            "Sequence alignment",
-            "Sequence trimming",
+            "Genotyping",
+            "Sequence alignment analysis",
             "Genome assembly",
+            "Transcriptome assembly",
+            "Data handling",
+            "Sequence assembly visualisation",
             "De-novo assembly",
-            "Sequence alignment analysis",
             "Phasing",
+            "k-mer counting",
             "Sequence assembly validation",
             "Scaffolding",
-            "Sequence assembly visualisation",
-            "Pairwise sequence alignment",
-            "k-mer counting",
-            "Transcriptome assembly",
-            "Genotyping"
+            "Sequence trimming",
+            "Sequence alignment",
+            "Pairwise sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -172721,40 +457885,55 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-09-06",
+        "mod_date": "2024-10-08",
         "objectives": [
             "Apply the post-assembly-QC-workflow using the necessary tools",
             "Analyse and evaluate the results of the workflow"
         ],
-        "pageviews": 1211,
+        "pageviews": 1261,
         "pub_date": "2023-06-23",
         "questions": [
             "What combination of tools can assess the quality of a genome assembly?",
-            "What metrics can help to analyse the quality of an asembly?",
+            "What metrics can help to analyse the quality of an assembly?",
             "How do we evaluate the outputs?"
         ],
+        "recordings": [
+            {
+                "bot-timestamp": 1728229662,
+                "captioners": [
+                    "delphine-l"
+                ],
+                "date": "2024-10-06",
+                "galaxy_version": "24.1.3.dev0",
+                "length": "44M",
+                "speakers": [
+                    "delphine-l"
+                ],
+                "youtube_id": "n4PNTTa2d6U"
+            }
+        ],
         "short_id": "T00355",
         "short_tools": [
-            "merqury",
-            "minimap2",
             "busco",
-            "tp_find_and_replace",
+            "CONVERTER_gz_to_uncompressed",
             "pretext_snapshot",
-            "bwa_mem2",
-            "gfastats",
             "bg_diamond",
-            "pretext_map",
-            "__EXTRACT_DATASET__",
             "samtools_stats",
-            "genomescope",
-            "bandage_image",
-            "blobtoolkit",
-            "interactive_tool_blobtoolkit",
             "bellerophon",
+            "__EXTRACT_DATASET__",
+            "smudgeplot",
             "collapse_dataset",
             "meryl",
-            "smudgeplot",
-            "CONVERTER_gz_to_uncompressed"
+            "interactive_tool_blobtoolkit",
+            "blobtoolkit",
+            "bandage_image",
+            "minimap2",
+            "tp_find_and_replace",
+            "pretext_map",
+            "bwa_mem2",
+            "merqury",
+            "gfastats",
+            "genomescope"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -172779,6 +457958,3537 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "CONVERTER_gz_to_uncompressed",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
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+                            ]
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@@ -172804,12 +461514,14 @@
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             "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.4+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2",
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             "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6",
             "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0",
             "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0",
+            "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1",
             "toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0"
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@@ -172828,12 +461540,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/assembly/tutorials/ERGA-post-assembly-QC/tutorial.json"
         },
-        "version": 4,
+        "version": 6,
         "video": false,
-        "video_versions": 0,
+        "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 97,
-        "visitors": 918,
+        "visit_duration": 105,
+        "visitors": 950,
         "workflows": [
             {
                 "creators": [
@@ -173156,7 +461868,7 @@
                 ],
                 "license": "AGPL-3.0-or-later",
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-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Post-assembly workflow",
                 "outputs": [
                     {
@@ -173826,26 +462538,26 @@
         ],
         "dir": "topics/assembly/tutorials/largegenome",
         "edam_operation": [
+            "Variant calling",
+            "Genome assembly",
+            "Sequence assembly visualisation",
+            "Base-calling",
+            "De-novo assembly",
+            "Mapping assembly",
             "Scatter plot plotting",
+            "Sequence assembly validation",
+            "Validation",
+            "Scaffolding",
             "Visualisation",
             "Cross-assembly",
-            "Sequencing quality control",
-            "Genome assembly",
-            "Box-Whisker plot plotting",
-            "Sequence assembly validation",
-            "Mapping assembly",
-            "Base-calling",
-            "Statistical calculation",
             "Pairwise sequence alignment",
-            "Validation",
+            "Transcriptome assembly",
             "Sequence composition calculation",
-            "De-novo assembly",
-            "Sequence contamination filtering",
+            "Box-Whisker plot plotting",
             "Sequence assembly",
-            "Variant calling",
-            "Scaffolding",
-            "Sequence assembly visualisation",
-            "Transcriptome assembly"
+            "Sequencing quality control",
+            "Sequence contamination filtering",
+            "Statistical calculation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -173876,7 +462588,7 @@
             "Polish the assembly",
             "Assess the quality of the assembly"
         ],
-        "pageviews": 5225,
+        "pageviews": 5295,
         "pub_date": "2023-03-06",
         "questions": [
             "How can we assemble a large plant or animal genome?"
@@ -173897,21 +462609,21 @@
         ],
         "short_id": "T00331",
         "short_tools": [
-            "genomescope",
-            "fastp",
-            "minimap2",
             "bandage_image",
-            "barchart_gnuplot",
-            "busco",
-            "racon",
+            "minimap2",
+            "medaka_consensus_pipeline",
+            "meryl",
+            "multiqc",
             "fasta-stats",
+            "busco",
+            "fastqc",
+            "barchart_gnuplot",
+            "nanoplot",
+            "fastp",
+            "genomescope",
             "quast",
-            "multiqc",
             "flye",
-            "nanoplot",
-            "medaka_consensus_pipeline",
-            "fastqc",
-            "meryl"
+            "racon"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -173936,6 +462648,2419 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
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+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.42.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.28.2+galaxy1",
+                                "1.25.0+galaxy1",
+                                "1.36.2+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.42.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.42.0+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.42.0+galaxy1"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.2.0+galaxy1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "5.0.2+galaxy5"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "5.0.2+galaxy0",
+                                "5.0.2+galaxy1",
+                                "4.6.3",
+                                "4.1",
+                                "5.0.2"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "5.2.0+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "5.2.0+galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "assembly",
@@ -173982,7 +465107,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 127,
-        "visitors": 4015,
+        "visitors": 4068,
         "workflows": [
             {
                 "creators": [
@@ -174157,7 +465282,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with long reads, x4 - upgraded\"];\n  style 4 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 4;\n  1 -->|output| 4;\n  2 -->|output| 4;\n  5[\"Medaka polish\"];\n  4 -->|Assembly polished by long reads using Racon| 5;\n  1 -->|output| 5;\n  e3136060-bce7-4af3-87c4-9dcbb0d1f531[\"Output\\nAssembly polished by long reads using Medaka\"];\n  5 --> e3136060-bce7-4af3-87c4-9dcbb0d1f531;\n  style e3136060-bce7-4af3-87c4-9dcbb0d1f531 stroke:#2c3143,stroke-width:4px;\n  6[\"Fasta statistics after Racon long read polish\"];\n  4 -->|Assembly polished by long reads using Racon| 6;\n  7[\"Fasta statistics after Medaka polish\"];\n  5 -->|out_consensus| 7;\n  8[\"\ud83d\udee0\ufe0f Subworkflow\\nRacon polish with Illumina reads R1 only, x2 - upgraded\"];\n  style 8 fill:#edd,stroke:#900,stroke-width:4px;\n  5 -->|out_consensus| 8;\n  3 -->|output| 8;\n  9[\"Fasta statistics after Racon short read polish\"];\n  8 -->|Assembly polished by short reads using Racon| 9;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Assembly polishing - upgraded",
                 "outputs": [
                     {
@@ -174995,7 +466120,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Flye: assembly\"];\n  0 -->|output| 1;\n  3960e31d-7a9e-400c-bb21-f6e47b75e649[\"Output\\nFlye assembly on input dataset(s) (consensus)\"];\n  1 --> 3960e31d-7a9e-400c-bb21-f6e47b75e649;\n  style 3960e31d-7a9e-400c-bb21-f6e47b75e649 stroke:#2c3143,stroke-width:4px;\n  e524f295-a957-4c91-838c-f8e98e809b6c[\"Output\\nFlye assembly on input dataset(s) (assembly_graph)\"];\n  1 --> e524f295-a957-4c91-838c-f8e98e809b6c;\n  style e524f295-a957-4c91-838c-f8e98e809b6c stroke:#2c3143,stroke-width:4px;\n  48b854e2-dd6e-4345-8d05-09abca6659da[\"Output\\nFlye assembly on input dataset(s) (Graphical Fragment Assembly)\"];\n  1 --> 48b854e2-dd6e-4345-8d05-09abca6659da;\n  style 48b854e2-dd6e-4345-8d05-09abca6659da stroke:#2c3143,stroke-width:4px;\n  8672c172-71a7-432c-9679-a8e37f36cf53[\"Output\\nFlye assembly on input dataset(s) (assembly_info)\"];\n  1 --> 8672c172-71a7-432c-9679-a8e37f36cf53;\n  style 8672c172-71a7-432c-9679-a8e37f36cf53 stroke:#2c3143,stroke-width:4px;\n  2[\"Fasta statistics\"];\n  1 -->|consensus| 2;\n  3[\"Quast genome report\"];\n  1 -->|consensus| 3;\n  17cdf8e0-8ad4-4570-afae-1861934fc678[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  3 --> 17cdf8e0-8ad4-4570-afae-1861934fc678;\n  style 17cdf8e0-8ad4-4570-afae-1861934fc678 stroke:#2c3143,stroke-width:4px;\n  4[\"Bandage image: Flye assembly\"];\n  1 -->|assembly_gfa| 4;\n  e66bd129-146f-48dc-95b8-39a2a1ffb68d[\"Output\\nBandage Image on input dataset(s): Assembly Graph Image\"];\n  4 --> e66bd129-146f-48dc-95b8-39a2a1ffb68d;\n  style e66bd129-146f-48dc-95b8-39a2a1ffb68d stroke:#2c3143,stroke-width:4px;\n  5[\"Bar chart: show contig sizes\"];\n  1 -->|assembly_info| 5;\n  6d0a4e23-d631-4e37-8930-3d22fc91369b[\"Output\\nBar chart showing contig sizes\"];\n  5 --> 6d0a4e23-d631-4e37-8930-3d22fc91369b;\n  style 6d0a4e23-d631-4e37-8930-3d22fc91369b stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Assembly with Flye - upgraded",
                 "outputs": [
                     {
@@ -175340,7 +466465,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPolished assembly\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Busco: assess assembly\"];\n  0 -->|output| 2;\n  219e4952-36e0-4b01-a407-e774b5b02dca[\"Output\\nBusco short summary\"];\n  2 --> 219e4952-36e0-4b01-a407-e774b5b02dca;\n  style 219e4952-36e0-4b01-a407-e774b5b02dca stroke:#2c3143,stroke-width:4px;\n  3[\"Quast: assess assembly\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  77ab0186-4cfd-460f-b71e-39a923414ef4[\"Output\\nQuast on input dataset(s):  HTML report\"];\n  3 --> 77ab0186-4cfd-460f-b71e-39a923414ef4;\n  style 77ab0186-4cfd-460f-b71e-39a923414ef4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Assess genome quality - upgraded",
                 "outputs": [
                     {
@@ -175671,7 +466796,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nR1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nR2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nminimap settings for long reads\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nReference genome for Quast\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\ud83d\udee0\ufe0f Subworkflow\\nkmer counting - meryl - upgraded\"];\n  style 5 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 5;\n  6[\"\ud83d\udee0\ufe0f Subworkflow\\nData QC - upgraded\"];\n  style 6 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 6;\n  2 -->|output| 6;\n  0 -->|output| 6;\n  7[\"\ud83d\udee0\ufe0f Subworkflow\\nTrim and filter reads - fastp - upgraded \"];\n  style 7 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  0 -->|output| 7;\n  8[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly with Flye - upgraded\"];\n  style 8 fill:#edd,stroke:#900,stroke-width:4px;\n  7 -->|fastp filtered long reads| 8;\n  9[\"\ud83d\udee0\ufe0f Subworkflow\\nAssembly polishing - upgraded\"];\n  style 9 fill:#edd,stroke:#900,stroke-width:4px;\n  8 -->|Flye assembly on input datasets consensus| 9;\n  7 -->|fastp filtered R1 reads| 9;\n  7 -->|fastp filtered long reads| 9;\n  3 -->|output| 9;\n  10[\"\ud83d\udee0\ufe0f Subworkflow\\nAssess genome quality - upgraded\"];\n  style 10 fill:#edd,stroke:#900,stroke-width:4px;\n  9 -->|Assembly polished by long reads using Medaka| 10;\n  4 -->|output| 10;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Combined workflows for large genome assembly - upgraded ",
                 "outputs": [
                     {
@@ -177207,7 +468332,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput file: long reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R1\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nInput file: Illumina reads R2\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Nanoplot: long reads\"];\n  0 -->|output| 3;\n  73d0e4cf-366e-41c1-810a-b269638826b3[\"Output\\nNanoPlot on input dataset(s): HTML report\"];\n  3 --> 73d0e4cf-366e-41c1-810a-b269638826b3;\n  style 73d0e4cf-366e-41c1-810a-b269638826b3 stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC on R1\"];\n  1 -->|output| 4;\n  5[\"FastQC on R2\"];\n  2 -->|output| 5;\n  6[\"MultiQC: combine fastQC reports\"];\n  4 -->|text_file| 6;\n  5 -->|text_file| 6;\n  8baf8700-876e-4a74-ad99-6e656f3ba618[\"Output\\nMultiQC on input dataset(s): Webpage\"];\n  6 --> 8baf8700-876e-4a74-ad99-6e656f3ba618;\n  style 8baf8700-876e-4a74-ad99-6e656f3ba618 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Data QC - upgraded",
                 "outputs": [
                     {
@@ -177480,7 +468605,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina reads, R1, in fastq.gz format\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Minimap2 round 1: map reads to assembly\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Racon round 1: polish assembly\"];\n  0 -->|output| 3;\n  2 -->|alignment_output| 3;\n  1 -->|output| 3;\n  4[\"Minimap2 round 2: map reads to assembly\"];\n  1 -->|output| 4;\n  3 -->|consensus| 4;\n  5[\"Racon round 2: polish assembly\"];\n  3 -->|consensus| 5;\n  4 -->|alignment_output| 5;\n  1 -->|output| 5;\n  594819c3-668e-4575-b9a6-4459ffacf952[\"Output\\nAssembly polished by short reads using Racon\"];\n  5 --> 594819c3-668e-4575-b9a6-4459ffacf952;\n  style 594819c3-668e-4575-b9a6-4459ffacf952 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Racon polish with Illumina reads (R1 only), x2 - upgraded",
                 "outputs": [
                     {
@@ -177715,7 +468840,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAssembly to be polished\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nminimap setting for long reads \"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"Minimap2: map long reads to assembly\"];\n  2 -->|output| 3;\n  1 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Racon: polish 1\"];\n  0 -->|output| 4;\n  3 -->|alignment_output| 4;\n  1 -->|output| 4;\n  5[\"Minimap2: map long reads to polished assembly 1\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  4 -->|consensus| 5;\n  6[\"Racon: polish 2\"];\n  4 -->|consensus| 6;\n  5 -->|alignment_output| 6;\n  1 -->|output| 6;\n  7[\"Minimap2: map long reads to polished assembly 2\"];\n  2 -->|output| 7;\n  1 -->|output| 7;\n  6 -->|consensus| 7;\n  8[\"Racon: polish 3\"];\n  6 -->|consensus| 8;\n  7 -->|alignment_output| 8;\n  1 -->|output| 8;\n  9[\"Minimap2: map long reads to polished assembly 3\"];\n  2 -->|output| 9;\n  1 -->|output| 9;\n  8 -->|consensus| 9;\n  10[\"Racon: polish 4\"];\n  8 -->|consensus| 10;\n  9 -->|alignment_output| 10;\n  1 -->|output| 10;\n  bcf0f03c-5951-46a7-aa38-545aed9bc183[\"Output\\nAssembly polished by long reads using Racon\"];\n  10 --> bcf0f03c-5951-46a7-aa38-545aed9bc183;\n  style bcf0f03c-5951-46a7-aa38-545aed9bc183 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Racon polish with long reads, x4 - upgraded",
                 "outputs": [
                     {
@@ -177977,7 +469102,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nIllumina reads R2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nlong reads\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"fastp on short reads\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  656e4138-41ab-4561-8989-33de9ac9a2f3[\"Output\\nfastp report on short reads html\"];\n  3 --> 656e4138-41ab-4561-8989-33de9ac9a2f3;\n  style 656e4138-41ab-4561-8989-33de9ac9a2f3 stroke:#2c3143,stroke-width:4px;\n  0d53f347-0368-47cb-953a-2e4dac57e013[\"Output\\nfastp filtered R1 reads\"];\n  3 --> 0d53f347-0368-47cb-953a-2e4dac57e013;\n  style 0d53f347-0368-47cb-953a-2e4dac57e013 stroke:#2c3143,stroke-width:4px;\n  10fbe1e5-400c-4ffe-8794-9b776b0d7322[\"Output\\nfastp report on short reads json\"];\n  3 --> 10fbe1e5-400c-4ffe-8794-9b776b0d7322;\n  style 10fbe1e5-400c-4ffe-8794-9b776b0d7322 stroke:#2c3143,stroke-width:4px;\n  639ed3f7-0e51-4e5d-b6f8-081378962109[\"Output\\nfastp filtered R2 reads\"];\n  3 --> 639ed3f7-0e51-4e5d-b6f8-081378962109;\n  style 639ed3f7-0e51-4e5d-b6f8-081378962109 stroke:#2c3143,stroke-width:4px;\n  4[\"fastp on long reads\"];\n  2 -->|output| 4;\n  5e0d2c3d-41a4-4823-ae9c-b1e4d2826541[\"Output\\nfastp report on long reads html\"];\n  4 --> 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541;\n  style 5e0d2c3d-41a4-4823-ae9c-b1e4d2826541 stroke:#2c3143,stroke-width:4px;\n  e6018ad6-86f4-4e78-8cf2-ccc8b97022fe[\"Output\\nfastp filtered long reads\"];\n  4 --> e6018ad6-86f4-4e78-8cf2-ccc8b97022fe;\n  style e6018ad6-86f4-4e78-8cf2-ccc8b97022fe stroke:#2c3143,stroke-width:4px;\n  69f8383b-a1be-4a74-95f4-3dba35e01426[\"Output\\nfastp report on long reads json\"];\n  4 --> 69f8383b-a1be-4a74-95f4-3dba35e01426;\n  style 69f8383b-a1be-4a74-95f4-3dba35e01426 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "Trim and filter reads - fastp - upgraded ",
                 "outputs": [
                     {
@@ -178304,7 +469429,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nIllumina reads R1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Meryl - count kmers\"];\n  0 -->|output| 1;\n  899ddd93-4c0f-4f81-a973-8120494ed983[\"Output\\nMeryl on input dataset(s): read-db.meryldb\"];\n  1 --> 899ddd93-4c0f-4f81-a973-8120494ed983;\n  style 899ddd93-4c0f-4f81-a973-8120494ed983 stroke:#2c3143,stroke-width:4px;\n  2[\"Meryl - generate histogram\"];\n  1 -->|read_db| 2;\n  3[\"Genomescope\"];\n  2 -->|read_db_hist| 3;\n  efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac[\"Output\\nGenomeScope on input dataset(s) Transformed log plot\"];\n  3 --> efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac;\n  style efc727b6-1ef4-4c4c-8cce-35c7d3cc8aac stroke:#2c3143,stroke-width:4px;\n  701df341-5767-44bc-ade2-6af498ab7467[\"Output\\nGenomeScope on input dataset(s) Transformed linear plot\"];\n  3 --> 701df341-5767-44bc-ade2-6af498ab7467;\n  style 701df341-5767-44bc-ade2-6af498ab7467 stroke:#2c3143,stroke-width:4px;\n  85fa4004-b351-47b3-84aa-6788d338037a[\"Output\\nGenomeScope on input dataset(s) Log plot\"];\n  3 --> 85fa4004-b351-47b3-84aa-6788d338037a;\n  style 85fa4004-b351-47b3-84aa-6788d338037a stroke:#2c3143,stroke-width:4px;\n  c71ce055-98f0-4354-9397-2f8833b90cc4[\"Output\\nGenomeScope on input dataset(s) Linear plot\"];\n  3 --> c71ce055-98f0-4354-9397-2f8833b90cc4;\n  style c71ce055-98f0-4354-9397-2f8833b90cc4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:06 +0000",
+                "modified": "2024-10-08 10:05:41 +0000",
                 "name": "kmer counting - meryl - upgraded",
                 "outputs": [
                     {
@@ -178619,7 +469744,6 @@
         "exact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
@@ -178648,7 +469772,7 @@
             "Load FASTA sequence into Galaxy",
             "Perform NCBI-Blast+ analysis against MAdLandDB"
         ],
-        "pageviews": 1414,
+        "pageviews": 1427,
         "pub_date": "2023-01-16",
         "questions": [
             "What is MAdLand DB?",
@@ -178656,9 +469780,9 @@
         ],
         "short_id": "T00238",
         "short_tools": [
-            "ncbi_blastp_wrapper",
+            "bg_diamond",
             "ncbi_blastx_wrapper",
-            "bg_diamond"
+            "ncbi_blastp_wrapper"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -178674,11 +469798,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -178708,6 +469827,604 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
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+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
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+                    "url": "http://dintor.eurac.edu/"
+                },
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+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
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+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
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+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
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+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
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+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
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+                },
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+                    "usegalaxy": false
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                },
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+                },
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+                },
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+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
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+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
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+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
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+                    "url": "https://viralvariant.anses.fr/"
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+                            "server": "https://usegalaxy.no/",
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+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
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+                                "0.3.3"
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+                            "server": "https://viralvariant.anses.fr/",
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+                            ]
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+                        {
+                            "server": "https://neo.engr.uconn.edu/",
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+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
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+                            "versions": [
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+                            ]
+                        },
+                        {
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+                            "versions": [
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+                                "2.14.1+galaxy2",
+                                "0.3.3",
+                                "0.1.07",
+                                "0.0.11",
+                                "0.3.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "2.10.1+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.10.1+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.10.1+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2.10.1+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.10.1+galaxy2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.10.1+galaxy2"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "plants"
@@ -178738,8 +470455,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 158,
-        "visitors": 1103,
+        "visit_duration": 157,
+        "visitors": 1114,
         "zenodo_link": "https://zenodo.org/records/7524427"
     },
     {
@@ -178898,7 +470615,7 @@
             "Generate a DotPlot emulating the original paper using a different analysis tool",
             "Determine robust clusters across scRNA-seq pipelines"
         ],
-        "pageviews": 2483,
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         "symlink": null,
         "tags": [
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@@ -179020,7 +472025,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 83,
-        "visitors": 1962,
+        "visitors": 1968,
         "workflows": [
             {
                 "creators": [],
@@ -179269,7 +472274,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nLeiden Resolution\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSHR CSV.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nWT CSV.gz\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nMin Genes\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nMin Cells\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Parameter\\nMax Features\"];\n  style 5 fill:#ded,stroke:#393,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Parameter\\nMax Lib Size\"];\n  style 6 fill:#ded,stroke:#393,stroke-width:4px;\n  7[\"Import Anndata and loom\"];\n  1 -->|output| 7;\n  8[\"Import Anndata and loom\"];\n  2 -->|output| 8;\n  9[\"Manipulate AnnData\"];\n  7 -->|anndata| 9;\n  8 -->|anndata| 9;\n  10[\"Rename Batches\"];\n  9 -->|anndata| 10;\n  680180f6-edfc-4f66-b265-7a63aaa22b39[\"Output\\nscRNA Concatenated Datasets\"];\n  10 --> 680180f6-edfc-4f66-b265-7a63aaa22b39;\n  style 680180f6-edfc-4f66-b265-7a63aaa22b39 stroke:#2c3143,stroke-width:4px;\n  11[\"QC metrics\"];\n  10 -->|anndata| 11;\n  12[\"Filter genes\"];\n  11 -->|anndata_out| 12;\n  3 -->|output| 12;\n  13[\"Plot Violin\"];\n  11 -->|anndata_out| 13;\n  14[\"Filter Cells\"];\n  12 -->|anndata_out| 14;\n  4 -->|output| 14;\n  15[\"Filter Max Features\"];\n  14 -->|anndata_out| 15;\n  5 -->|output| 15;\n  16[\"Filter Max Library Size\"];\n  15 -->|anndata| 16;\n  6 -->|output| 16;\n  17[\"Save RAW\"];\n  16 -->|anndata| 17;\n  18[\"Norm to 1e4\"];\n  17 -->|anndata| 18;\n  19[\"Log1p\"];\n  18 -->|anndata_out| 19;\n  20[\"Regress total counts\"];\n  19 -->|anndata_out| 20;\n  21[\"Scale\"];\n  20 -->|anndata_out| 21;\n  22[\"PCA\"];\n  21 -->|anndata_out| 22;\n  23[\"Neighborhod\"];\n  22 -->|anndata_out| 23;\n  24[\"UMAP\"];\n  23 -->|anndata_out| 24;\n  25[\"Leiden\"];\n  24 -->|anndata_out| 25;\n  0 -->|output| 25;\n  48cf0465-84ba-461a-bdb9-61625626de42[\"Output\\nscRNA with clusters Dataset\"];\n  25 --> 48cf0465-84ba-461a-bdb9-61625626de42;\n  style 48cf0465-84ba-461a-bdb9-61625626de42 stroke:#2c3143,stroke-width:4px;\n  26[\"Plot PCA batch\"];\n  24 -->|anndata_out| 26;\n  27[\"Plot UMAP batch\"];\n  24 -->|anndata_out| 27;\n  28[\"Plot UMAP leiden, batch\"];\n  25 -->|anndata_out| 28;\n  29[\"Rename Clusters\"];\n  25 -->|anndata_out| 29;\n  30[\"Complex DotPlot\"];\n  25 -->|anndata_out| 30;\n  31[\"Complex DotPlot with new labels\"];\n  29 -->|anndata| 31;\n  32[\"Plot UMAP with new labels\"];\n  29 -->|anndata| 32;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "scRNA Plant Analysis",
                 "outputs": [
                     {
@@ -179815,8 +472820,8 @@
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@@ -179851,7 +472856,7 @@
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                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPyProphet export tabular\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nComparison matrix\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSample annot MSstats\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"MSstats\"];\n  1 -->|output| 3;\n  2 -->|output| 3;\n  0 -->|output| 3;\n  4[\"Select\"];\n  3 -->|comparison_result| 4;\n  0de65b2c-f62c-4068-8ac0-466e419d495b[\"Output\\nSelect_Ecoli\"];\n  4 --> 0de65b2c-f62c-4068-8ac0-466e419d495b;\n  style 0de65b2c-f62c-4068-8ac0-466e419d495b stroke:#2c3143,stroke-width:4px;\n  5[\"Filter\"];\n  4 -->|out_file1| 5;\n  197e8a45-392f-4981-8684-2c8326af4528[\"Output\\nFilter_Ecoli\"];\n  5 --> 197e8a45-392f-4981-8684-2c8326af4528;\n  style 197e8a45-392f-4981-8684-2c8326af4528 stroke:#2c3143,stroke-width:4px;\n  6[\"Histogram\"];\n  5 -->|out_file1| 6;\n  04c6287d-fd0d-4780-99b6-cf52ee18e06f[\"Output\\nHistogram_Ecoli\"];\n  6 --> 04c6287d-fd0d-4780-99b6-cf52ee18e06f;\n  style 04c6287d-fd0d-4780-99b6-cf52ee18e06f stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "DIA_analysis_MSstats",
                 "outputs": [
                     {
@@ -180619,7 +474306,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPyProphet MSstats input\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nComparison matrix\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"MSstats\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"Select\"];\n  2 -->|comparison_result| 3;\n  6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326[\"Output\\nSelect_Ecoli\"];\n  3 --> 6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326;\n  style 6e8589bd-13fd-4a97-a9c3-ea0a5a0e2326 stroke:#2c3143,stroke-width:4px;\n  4[\"Filter\"];\n  3 -->|out_file1| 4;\n  6997a43a-a17b-418b-bb6d-7d32a6c277ae[\"Output\\nFilter_Ecoli\"];\n  4 --> 6997a43a-a17b-418b-bb6d-7d32a6c277ae;\n  style 6997a43a-a17b-418b-bb6d-7d32a6c277ae stroke:#2c3143,stroke-width:4px;\n  5[\"Histogram\"];\n  4 -->|out_file1| 5;\n  cf3abac3-8227-4af8-a551-6aeae154a0e4[\"Output\\nHistogram_Ecoli\"];\n  5 --> cf3abac3-8227-4af8-a551-6aeae154a0e4;\n  style cf3abac3-8227-4af8-a551-6aeae154a0e4 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "DIA_analysis_MSstats",
                 "outputs": [
                     {
@@ -181193,7 +474880,7 @@
         "objectives": [
             "MS1 feature quantitation and mapping of quantitations to peptide and protein IDs."
         ],
-        "pageviews": 1650,
+        "pageviews": 1653,
         "pub_date": "2017-03-17",
         "questions": [
             "What are MS1 features?",
@@ -181214,22 +474901,22 @@
         "short_id": "T00230",
         "short_tools": [
             "ProteinQuantifier",
-            "IDMapper",
             "FalseDiscoveryRate",
-            "Summary_Statistics1",
-            "MultiplexResolver",
-            "IDScoreSwitcher",
+            "FidoAdapter",
             "TextExporter",
-            "FileInfo",
+            "IDPosteriorErrorProbability",
             "histogram_rpy",
-            "XTandemAdapter",
             "IDConflictResolver",
+            "tp_tail_tool",
+            "PeptideIndexer",
             "Grep1",
+            "Summary_Statistics1",
             "FeatureFinderMultiplex",
-            "PeptideIndexer",
-            "IDPosteriorErrorProbability",
-            "tp_tail_tool",
-            "FidoAdapter"
+            "FileInfo",
+            "IDScoreSwitcher",
+            "XTandemAdapter",
+            "MultiplexResolver",
+            "IDMapper"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -181260,6 +474947,2532 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
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+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
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+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
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+                {
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+                    "url": "http://hyperbrowser.uio.no/hb/"
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+                    "url": "http://gigagalaxy.net/"
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+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
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+                },
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+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
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+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                    "url": "https://usegalaxy.no/",
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+                    "url": "https://usegalaxy.org.au",
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+                        {
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+                            "state": "local"
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+                            "server": "https://usegalaxy.eu",
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+                            "server": "https://usegalaxy.org.au",
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+                            "state": "local"
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+                            ]
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+                            "state": "exact",
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+                            "state": "exact",
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+                        },
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+                            "server": "https://viralvariant.anses.fr/",
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         "tags": [
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@@ -181306,7 +477519,7 @@
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         "video_view": 0,
         "visit_duration": 101,
-        "visitors": 1141,
+        "visitors": 1144,
         "workflows": [
             {
                 "creators": [],
@@ -181477,7 +477690,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Proteomics: Peptide and Protein Quantification via stable istobe labeling",
                 "outputs": [
                     {
@@ -182732,14 +478945,14 @@
         ],
         "dir": "topics/proteomics/tutorials/clinical-mp-4-quantitation",
         "edam_operation": [
+            "Clustering",
             "Principal component plotting",
+            "Imputation",
+            "Heat map generation",
             "Visualisation",
-            "Clustering",
             "Protein quantification",
             "Standardisation and normalisation",
-            "Imputation",
-            "Statistical calculation",
-            "Heat map generation"
+            "Statistical calculation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -182778,7 +478991,7 @@
         "objectives": [
             "Perform quantitation using MaxQuant and extract microbial and human proteins and peptides."
         ],
-        "pageviews": 74,
+        "pageviews": 81,
         "pub_date": "2024-02-06",
         "questions": [
             "How to perform quantitation?"
@@ -182810,10 +479023,10 @@
         ],
         "short_id": "T00416",
         "short_tools": [
-            "Grep1",
             "Cut1",
-            "maxquant",
-            "Grouping1"
+            "Grep1",
+            "Grouping1",
+            "maxquant"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -182854,6 +479067,685 @@
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             ]
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@@ -183315,7 +482468,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 159,
-        "visitors": 6339,
+        "visitors": 6380,
         "workflows": [
             {
                 "creators": [],
@@ -183482,7 +482635,7 @@
                 ],
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Proteomics: MaxQuant and MSstats LFQ workflow",
                 "outputs": [
                     {
@@ -185023,11 +484176,11 @@
         ],
         "dir": "topics/proteomics/tutorials/proteogenomics-dbcreation",
         "edam_operation": [
-            "Statistical calculation",
             "Variant calling",
-            "Sequence annotation",
-            "Sequence alignment",
             "Transcriptome assembly",
+            "Sequence alignment",
+            "Statistical calculation",
+            "Sequence annotation",
             "RNA-Seq analysis"
         ],
         "edam_topic": [],
@@ -185070,7 +484223,7 @@
         "objectives": [
             "Generating a customized Protein sequence database with variants, indels, splice junctions and known sequences."
         ],
-        "pageviews": 7973,
+        "pageviews": 8013,
         "pub_date": "2018-11-20",
         "questions": [
             "How to create a customized Protein Database from RNAseq data?"
@@ -185091,23 +484244,23 @@
         ],
         "short_id": "T00231",
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+            "translate_bed",
+            "tp_cat",
+            "tab2fasta",
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-            "tp_cat",
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             "fasta_merge_files_and_filter_unique_sequences",
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-            "bed_to_protein_map",
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+            "custom_pro_db",
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+            "tp_replace_in_column",
+            "bed_to_protein_map",
+            "filter_tabular",
+            "stringtie",
+            "gffcompare"
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         "slides": false,
         "slides_recordings": false,
@@ -185148,6 +484301,2542 @@
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+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.2.1+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "2.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.1.1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.1.1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "proteogenomics"
@@ -185193,7 +486882,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 156,
-        "visitors": 4619,
+        "visitors": 4651,
         "workflows": [
             {
                 "creators": [],
@@ -185409,7 +487098,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nFASTQ_ProB_22LIST.fastqsanger\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nMus_musculus.GRCm38.86.gtf\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nTrimmed_ref_5000_uniprot_cRAP.fasta\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"HISAT2\"];\n  0 -->|output| 3;\n  4[\"Editing GTF File\"];\n  1 -->|output| 4;\n  70b6f719-803f-4fa9-8394-a3b64b71ec01[\"Output\\nchr_corrected_gtf\"];\n  4 --> 70b6f719-803f-4fa9-8394-a3b64b71ec01;\n  style 70b6f719-803f-4fa9-8394-a3b64b71ec01 stroke:#2c3143,stroke-width:4px;\n  5[\"FASTA-to-Tabular\"];\n  2 -->|output| 5;\n  6[\"FreeBayes\"];\n  3 -->|output_alignments| 6;\n  7[\"StringTie\"];\n  4 -->|outfile| 7;\n  3 -->|output_alignments| 7;\n  8[\"Filter Tabular\"];\n  5 -->|output| 8;\n  9[\"CustomProDB\"];\n  3 -->|output_alignments| 9;\n  6 -->|output_vcf| 9;\n  10[\"GffCompare\"];\n  4 -->|outfile| 10;\n  7 -->|output_gtf| 10;\n  11[\"SQLite to tabular\"];\n  9 -->|output_genomic_mapping_sqlite| 11;\n  12[\"SQLite to tabular\"];\n  9 -->|output_variant_annotation_sqlite| 12;\n  13[\"FASTA Merge Files and Filter Unique Sequences\"];\n  9 -->|output_rpkm| 13;\n  9 -->|output_snv| 13;\n  9 -->|output_indel| 13;\n  a5054be9-dd74-4d60-a4c6-494fdbcb97a1[\"Output\\nCustomProDB_FASTA\"];\n  13 --> a5054be9-dd74-4d60-a4c6-494fdbcb97a1;\n  style a5054be9-dd74-4d60-a4c6-494fdbcb97a1 stroke:#2c3143,stroke-width:4px;\n  14[\"FASTA-to-Tabular\"];\n  9 -->|output_rpkm| 14;\n  15[\"Convert gffCompare annotated GTF to BED\"];\n  10 -->|transcripts_annotated| 15;\n  16[\"Column Regex Find And Replace\"];\n  11 -->|query_results| 16;\n  17[\"Column Regex Find And Replace\"];\n  12 -->|query_results| 17;\n  18[\"FASTA-to-Tabular\"];\n  13 -->|output| 18;\n  19[\"Filter Tabular\"];\n  14 -->|output| 19;\n  20[\"Translate BED transcripts\"];\n  15 -->|output| 20;\n  21[\"Query Tabular\"];\n  17 -->|out_file1| 21;\n  e9468479-4ebd-4ced-8086-c10e916b97c5[\"Output\\nvariant_annoation_sqlite\"];\n  21 --> e9468479-4ebd-4ced-8086-c10e916b97c5;\n  style e9468479-4ebd-4ced-8086-c10e916b97c5 stroke:#2c3143,stroke-width:4px;\n  22[\"Column Regex Find And Replace\"];\n  18 -->|output| 22;\n  23[\"Reference Protein Accessions\"];\n  19 -->|output| 23;\n  8 -->|output| 23;\n  19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85[\"Output\\nReference_Protein_Accessions\"];\n  23 --> 19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85;\n  style 19aa5a85-5933-4ab5-ae76-e4b1ec5b2f85 stroke:#2c3143,stroke-width:4px;\n  24[\"bed to protein map\"];\n  20 -->|translation_bed| 24;\n  25[\"Tabular-to-FASTA\"];\n  22 -->|out_file1| 25;\n  26[\"Concatenate datasets\"];\n  24 -->|output| 26;\n  16 -->|out_file1| 26;\n  27[\"FASTA Merge Files and Filter Unique Sequences\"];\n  2 -->|output| 27;\n  25 -->|output| 27;\n  20 -->|translation_fasta| 27;\n  924bce7c-5c6a-4cb3-a459-18784a55ae01[\"Output\\nUniprot_cRAP_SAV_indel_translatedbed_FASTA\"];\n  27 --> 924bce7c-5c6a-4cb3-a459-18784a55ae01;\n  style 924bce7c-5c6a-4cb3-a459-18784a55ae01 stroke:#2c3143,stroke-width:4px;\n  28[\"Genomic_mapping_sqlite\"];\n  26 -->|out_file1| 28;\n  6542c4e5-289a-4be4-9b42-7a4e170ba198[\"Output\\ngenomic_mapping_sqlite\"];\n  28 --> 6542c4e5-289a-4be4-9b42-7a4e170ba198;\n  style 6542c4e5-289a-4be4-9b42-7a4e170ba198 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GTN Proteogenomics1 Database Creation",
                 "outputs": [
                     {
@@ -187146,17 +488835,17 @@
         ],
         "dir": "topics/proteomics/tutorials/maxquant-label-free",
         "edam_operation": [
-            "Principal component plotting",
-            "Visualisation",
             "Clustering",
-            "Protein quantification",
-            "Standardisation and normalisation",
-            "Imputation",
             "Spectrum calculation",
+            "Principal component plotting",
             "Differential protein expression profiling",
-            "Statistical calculation",
+            "Imputation",
             "Heat map generation",
-            "Tag-based peptide identification"
+            "Tag-based peptide identification",
+            "Visualisation",
+            "Protein quantification",
+            "Standardisation and normalisation",
+            "Statistical calculation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -187188,7 +488877,7 @@
         "objectives": [
             "Analysis of human serum proteome samples with label-free quantification in MaxQuant"
         ],
-        "pageviews": 24393,
+        "pageviews": 24435,
         "pub_date": "2020-04-29",
         "questions": [
             "How to perform label-free analysis in Maxquant?",
@@ -187197,14 +488886,14 @@
         ],
         "short_id": "T00218",
         "short_tools": [
-            "Filter1",
+            "Cut1",
+            "maxquant",
+            "msstats",
             "tp_sort_header_tool",
             "histogram_rpy",
             "Grep1",
             "Add_a_column1",
-            "Cut1",
-            "maxquant",
-            "msstats"
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -187245,6 +488934,1252 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
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+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
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+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
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+                    "usegalaxy": false
+                },
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+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
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+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
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+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "id": "Cut1",
+                    "servers": [
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+                            "state": "local"
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+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
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+                                "3.22.0.1"
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         "tags": [
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@@ -187282,7 +490217,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 101,
-        "visitors": 16500,
+        "visitors": 16538,
         "workflows": [
             {
                 "creators": [],
@@ -187470,7 +490405,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Proteomics: MaxQuant workflow",
                 "outputs": [
                     {
@@ -188312,7 +491247,7 @@
             "Understanding DIA data principles and characteristics",
             "Using OpenSwathworkflow to analyze HEK-Ecoli Spike-in DIA data"
         ],
-        "pageviews": 3351,
+        "pageviews": 3357,
         "pub_date": "2020-12-02",
         "questions": [
             "How to analyze data independent acquisition (DIA) mass spectrometry (MS) data using OpenSwathWorkflow?",
@@ -188329,14 +491264,14 @@
         ],
         "short_id": "T00211",
         "short_tools": [
-            "pyprophet_protein",
-            "msconvert",
+            "pyprophet_merge",
             "OpenSwathWorkflow",
+            "pyprophet_protein",
             "pyprophet_peptide",
+            "pyprophet_score",
             "Grep1",
-            "pyprophet_merge",
-            "pyprophet_export",
-            "pyprophet_score"
+            "msconvert",
+            "pyprophet_export"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -188367,6 +491302,1376 @@
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@@ -188404,7 +492709,7 @@
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@@ -188588,7 +492893,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
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@@ -189541,7 +493846,7 @@
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@@ -189564,11 +493869,11 @@
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-            "sqlite_to_tabular"
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@@ -189609,6 +493914,849 @@
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+                            "state": "exact",
+                            "version": "2.0.0"
+                        },
+                        {
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+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.0.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
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         "tags": [
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@@ -189642,7 +494790,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 158,
-        "visitors": 2310,
+        "visitors": 2320,
         "workflows": [
             {
                 "creators": [],
@@ -189844,7 +494992,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSixgill generated protein FASTA File\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nDataset Collection of Bering Strait MGF Files\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGene Ontology Terms Selected\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Search GUI\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  7516674a-b5aa-45b5-b2e8-38c1889ad2e9[\"Output\\nSearch GUI on input dataset(s)\"];\n  3 --> 7516674a-b5aa-45b5-b2e8-38c1889ad2e9;\n  style 7516674a-b5aa-45b5-b2e8-38c1889ad2e9 stroke:#2c3143,stroke-width:4px;\n  4[\"Peptide Shaker\"];\n  3 -->|searchgui_results| 4;\n  ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0[\"Output\\nPeptide Shaker on input dataset(s): mzidentML file\"];\n  4 --> ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0;\n  style ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0 stroke:#2c3143,stroke-width:4px;\n  5[\"Query Tabular Select Peptides\"];\n  4 -->|output_psm| 5;\n  6[\"Unipept pept2prot\"];\n  5 -->|output| 6;\n  7[\"Unipept lca\"];\n  5 -->|output| 7;\n  8[\"Go Pop2Prot DB\"];\n  2 -->|output| 8;\n  6 -->|output_tsv| 8;\n  6 -->|output_tsv| 8;\n  4 -->|output_psm| 8;\n  9[\"Genera | PSMs | Peptides\"];\n  4 -->|output_psm| 9;\n  7 -->|output_tsv| 9;\n  10[\"GO Terms: Biological Processes\"];\n  8 -->|sqlitedb| 10;\n  11[\"GO Terms: Molecular Functions\"];\n  8 -->|sqlitedb| 11;\n  12[\"GO Terms: Cellular Localization\"];\n  8 -->|sqlitedb| 12;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Metaproteomics_GTN",
                 "outputs": [
                     {
@@ -190709,18 +495857,18 @@
             "Learn, how to create training data set from features?",
             "Assessment of best ML algorithm in predicting anticancer peptide"
         ],
-        "pageviews": 1335,
+        "pageviews": 1344,
         "pub_date": "2021-01-22",
         "questions": [
             "Which machine learning (ML) algorithm is superior in classifying anticancer peptides (ACPs) and non-anticancer peptides (non-ACPs)?"
         ],
         "short_id": "T00225",
         "short_tools": [
-            "pdaug_basic_plots",
             "pdaug_ml_models",
-            "pdaug_addclasslabel",
+            "pdaug_basic_plots",
+            "pdaug_sequence_property_based_descriptors",
             "pdaug_merge_dataframes",
-            "pdaug_sequence_property_based_descriptors"
+            "pdaug_addclasslabel"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -190735,6 +495883,803 @@
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+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
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+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
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+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
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+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
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+                    "url": "http://hyperbrowser.uio.no/hb/"
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+                    "url": "http://gigagalaxy.net/"
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+                    "name": "HyPhy HIV NGS Tools",
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+                    "usegalaxy": false
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                    "url": "https://www.immportgalaxy.org/"
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+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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@@ -190769,7 +496714,7 @@
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         "visit_duration": 115,
-        "visitors": 874,
+        "visitors": 881,
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@@ -190858,7 +496803,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "PeptideML",
                 "outputs": [
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@@ -191380,16 +497325,16 @@
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+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.0.0-0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.0.0-0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
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+                                "2.0.0-1",
+                                "2.0.0-2",
+                                "2.0.1+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.0.0-0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "microgalaxy"
@@ -191530,7 +498481,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 164,
-        "visitors": 377,
+        "visitors": 378,
         "workflows": [
             {
                 "creators": [],
@@ -191633,7 +498584,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"metaQuantome: create samples file\"];\n  1[\"\u2139\ufe0f Input Dataset\\nTaxa\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nIntensity\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"metaQuantome: database\"];\n  4[\"metaQuantome: expand\"];\n  3 -->|outfile| 4;\n  2 -->|output| 4;\n  1 -->|output| 4;\n  0 -->|samples_file| 4;\n  5[\"metaQuantome: filter\"];\n  4 -->|outfile| 5;\n  0 -->|samples_file| 5;\n  6[\"metaQuantome: stat\"];\n  5 -->|outfile| 6;\n  0 -->|samples_file| 6;\n  7[\"T2-Bar-Plot\"];\n  6 -->|outfile| 7;\n  0 -->|samples_file| 7;\n  8[\"T7-T2_volcano-plot\"];\n  6 -->|outfile| 8;\n  0 -->|samples_file| 8;\n  9[\"T4-Bar-Plot\"];\n  6 -->|outfile| 9;\n  0 -->|samples_file| 9;\n  10[\"T7-Bar-Plot\"];\n  6 -->|outfile| 10;\n  0 -->|samples_file| 10;\n  11[\"T4-T2_volcano-plot\"];\n  6 -->|outfile| 11;\n  0 -->|samples_file| 11;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "metaquantome-taxonomy-workflow",
                 "outputs": [
                     {
@@ -192400,16 +499351,16 @@
         ],
         "dir": "topics/proteomics/tutorials/clinical-mp-2-discovery",
         "edam_operation": [
+            "Clustering",
             "Principal component plotting",
+            "Filtering",
+            "Imputation",
+            "Heat map generation",
+            "Formatting",
             "Visualisation",
-            "Clustering",
             "Protein quantification",
             "Standardisation and normalisation",
-            "Imputation",
-            "Statistical calculation",
-            "Heat map generation",
-            "Filtering",
-            "Formatting"
+            "Statistical calculation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -192447,7 +499398,7 @@
             "Extract confident peptides and proteins",
             "Generate a microbial peptide panel for verification"
         ],
-        "pageviews": 166,
+        "pageviews": 180,
         "pub_date": "2024-02-06",
         "questions": [
             "How to perform database searching?",
@@ -192480,23 +499431,23 @@
         ],
         "short_id": "T00414",
         "short_tools": [
-            "query_tabular",
+            "Cut1",
+            "maxquant",
             "tp_cat",
-            "fasta_merge_files_and_filter_unique_sequences",
-            "filter_tabular",
-            "Filter1",
-            "dbbuilder",
-            "peptide_shaker",
             "ident_params",
-            "msconvert",
+            "fasta_cli",
+            "fasta_merge_files_and_filter_unique_sequences",
             "search_gui",
+            "query_tabular",
+            "peptide_shaker",
             "Grep1",
-            "Cut1",
-            "maxquant",
             "Remove beginning1",
             "fasta2tab",
-            "fasta_cli",
-            "Grouping1"
+            "msconvert",
+            "filter_tabular",
+            "Grouping1",
+            "dbbuilder",
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -192521,6 +499472,2475 @@
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             "inexact": []
         },
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+                },
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                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHuman UniProt Microbial Proteins from MetaNovo and cRAP \"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Identification Parameters: PAR file\"];\n  2[\"\u2139\ufe0f Input Collection\\nRAW files Dataset Collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Human SwissProt reviewed only\"];\n  e0de9f90-a710-4b55-af62-41ba1c2d8e1f[\"Output\\nHuman SwissProt (reviewed only)\"];\n  3 --> e0de9f90-a710-4b55-af62-41ba1c2d8e1f;\n  style e0de9f90-a710-4b55-af62-41ba1c2d8e1f stroke:#2c3143,stroke-width:4px;\n  4[\"Contaminants cRAP\"];\n  5[\"\u2139\ufe0f Input Dataset\\nExperimental Design Discovery MaxQuant\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"FastaCLI__MetaNovo_Human_SwissProt_cRAP_with_decoys_on_data_1_MetaNovo_Human_SwissProt_cRAP_concatenated_target_decoy.fasta\"];\n  0 -->|output| 6;\n  7[\"msconvert\"];\n  2 -->|output| 7;\n  8[\"Human SwissProt+cRAP\"];\n  3 -->|output_database| 8;\n  4 -->|output_database| 8;\n  2f14902f-b005-4c08-b6d1-6d7ee0b4b199[\"Output\\nHuman SwissProt+cRAP\"];\n  8 --> 2f14902f-b005-4c08-b6d1-6d7ee0b4b199;\n  style 2f14902f-b005-4c08-b6d1-6d7ee0b4b199 stroke:#2c3143,stroke-width:4px;\n  9[\"MaxQuant\"];\n  0 -->|output| 9;\n  2 -->|output| 9;\n  5 -->|output| 9;\n  10[\"Search GUI\"];\n  6 -->|input_database_concatenated_target_decoy| 10;\n  1 -->|Identification_Parameters_File| 10;\n  7 -->|output| 10;\n  11[\"FASTA-to-Tabular\"];\n  8 -->|output| 11;\n  12[\"Select microbial peptides MQ\"];\n  9 -->|peptides| 12;\n  d7718bab-9e75-4729-bfb6-03bc3112a0e2[\"Output\\nSelect microbial peptides (MQ)\"];\n  12 --> d7718bab-9e75-4729-bfb6-03bc3112a0e2;\n  style d7718bab-9e75-4729-bfb6-03bc3112a0e2 stroke:#2c3143,stroke-width:4px;\n  13[\"Peptide Shaker\"];\n  10 -->|searchgui_results| 13;\n  14[\"Filter Tabular\"];\n  11 -->|output| 14;\n  15[\"MQ Peptide Sequences\"];\n  12 -->|out_file1| 15;\n  16[\"Select microbial peptides SGPS\"];\n  13 -->|output_peptides| 16;\n  14fd9080-df92-4c61-b1f1-3f700a166700[\"Output\\nSelect microbial peptides (SGPS)\"];\n  16 --> 14fd9080-df92-4c61-b1f1-3f700a166700;\n  style 14fd9080-df92-4c61-b1f1-3f700a166700 stroke:#2c3143,stroke-width:4px;\n  17[\"Select microbial PSMs\"];\n  13 -->|output_psm| 17;\n  18[\"Remove beginning\"];\n  15 -->|out_file1| 18;\n  19[\"Filter confident microbial peptides\"];\n  16 -->|out_file1| 19;\n  1c6c953f-d192-4953-938a-9f401315bc0d[\"Output\\nFilter confident microbial peptides\"];\n  19 --> 1c6c953f-d192-4953-938a-9f401315bc0d;\n  style 1c6c953f-d192-4953-938a-9f401315bc0d stroke:#2c3143,stroke-width:4px;\n  20[\"Filter confident microbial PSMs\"];\n  17 -->|out_file1| 20;\n  d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2[\"Output\\nFilter confident microbial PSMs\"];\n  20 --> d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2;\n  style d8ec7f0c-7ba1-4733-a3dc-74a9ef298dc2 stroke:#2c3143,stroke-width:4px;\n  21[\"MQ Distinct Peptides\"];\n  18 -->|out_file1| 21;\n  07cae017-0b39-4065-b83e-b5f2e27fe740[\"Output\\nMQ Peptides\"];\n  21 --> 07cae017-0b39-4065-b83e-b5f2e27fe740;\n  style 07cae017-0b39-4065-b83e-b5f2e27fe740 stroke:#2c3143,stroke-width:4px;\n  22[\"Query Tabular\"];\n  20 -->|out_file1| 22;\n  20 -->|out_file1| 22;\n  14 -->|output| 22;\n  23[\"Cut\"];\n  22 -->|output| 23;\n  24[\"SGPS Distinct Peptides\"];\n  23 -->|out_file1| 24;\n  b6c61697-ff52-43c0-8fb4-765d7b4204cc[\"Output\\nSGPS Distinct Peptides\"];\n  24 --> b6c61697-ff52-43c0-8fb4-765d7b4204cc;\n  style b6c61697-ff52-43c0-8fb4-765d7b4204cc stroke:#2c3143,stroke-width:4px;\n  25[\"SGPS-MQ Peptides\"];\n  21 -->|out_file1| 25;\n  24 -->|out_file1| 25;\n  a8c2de2e-e322-4830-9d28-2f79bf937013[\"Output\\nSGPS-MQ Peptides\"];\n  25 --> a8c2de2e-e322-4830-9d28-2f79bf937013;\n  style a8c2de2e-e322-4830-9d28-2f79bf937013 stroke:#2c3143,stroke-width:4px;\n  26[\"Distinct Peptides\"];\n  25 -->|out_file1| 26;\n  ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7[\"Output\\nDistinct Peptides\"];\n  26 --> ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7;\n  style ef0d91b1-042f-4a9f-a2b6-bf73d82f24f7 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "WF2_Discovery-Workflow",
                 "outputs": [
                     {
@@ -193652,16 +503072,16 @@
             "topic_3174"
         ],
         "edam_operation": [
-            "Visualisation",
-            "Indexing",
             "Differential protein expression analysis",
-            "Functional clustering",
-            "Statistical inference",
-            "Principal component visualisation",
-            "Query and retrieval",
+            "Filtering",
             "Heat map generation",
+            "Indexing",
+            "Query and retrieval",
+            "Visualisation",
+            "Principal component visualisation",
             "Quantification",
-            "Filtering"
+            "Functional clustering",
+            "Statistical inference"
         ],
         "edam_topic": [
             "Proteomics",
@@ -193715,7 +503135,7 @@
         "objectives": [
             "A functional and quantitational analysis of metaproteomic mass spectrometry data."
         ],
-        "pageviews": 508,
+        "pageviews": 509,
         "pub_date": "2020-10-29",
         "questions": [
             "How do I look at differentially expressed proteins?",
@@ -193733,12 +503153,12 @@
         ],
         "short_id": "T00223",
         "short_tools": [
-            "metaquantome_filter",
-            "metaquantome_sample",
+            "metaquantome_db",
             "metaquantome_stat",
-            "metaquantome_expand",
+            "metaquantome_sample",
             "metaquantome_viz",
-            "metaquantome_db"
+            "metaquantome_expand",
+            "metaquantome_filter"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -193774,6 +503194,1846 @@
                 }
             ]
         },
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+                },
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+                },
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+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
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+                        },
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+                            "state": "exact",
+                            "version": "2.0.2+galaxy0"
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+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
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+                        },
+                        {
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+                            "state": "missing"
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+                        {
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+                        {
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+                        },
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
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+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
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@@ -193814,7 +505074,7 @@
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         "video_view": 0,
         "visit_duration": 226,
-        "visitors": 352,
+        "visitors": 353,
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@@ -193924,7 +505184,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "metaquantome-function-worklow",
                 "outputs": [
                     {
@@ -194687,7 +505947,7 @@
         "objectives": [
             "Verification of peptides helps in confirming the presence of the peptides in our samplle"
         ],
-        "pageviews": 89,
+        "pageviews": 94,
         "pub_date": "2024-02-06",
         "questions": [
             "Why do we need to verify our identified peptides",
@@ -194720,17 +505980,17 @@
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-            "query_tabular",
-            "tp_cat",
-            "fasta_merge_files_and_filter_unique_sequences",
-            "Filter1",
-            "dbbuilder",
             "Cut1",
+            "pepquery2",
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             "collapse_dataset",
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             "Remove beginning1",
-            "pepquery2",
-            "Grouping1"
+            "Grouping1",
+            "dbbuilder",
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -194756,6 +506016,1643 @@
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+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "4.2",
+                                "4.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "5.1.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "5.1.0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "label-TMT11"
@@ -194795,7 +507692,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 634,
-        "visitors": 53,
+        "visitors": 58,
         "workflows": [
             {
                 "creators": [
@@ -194934,7 +507831,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"Human UniProt+Isoforms FASTA\"];\n  4bdae9fb-eb48-4821-a806-e7dd3a8c7101[\"Output\\nHuman UniProt+Isoforms FASTA\"];\n  0 --> 4bdae9fb-eb48-4821-a806-e7dd3a8c7101;\n  style 4bdae9fb-eb48-4821-a806-e7dd3a8c7101 stroke:#2c3143,stroke-width:4px;\n  1[\"cRAP\"];\n  13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa[\"Output\\ncRAP\"];\n  1 --> 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa;\n  style 13ddaf34-d346-4cc4-b5b6-fee2b5e0c1aa stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nInput MGFs Dataset Collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSGPS_peptide-report\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nDistinct Peptides for PepQuery\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nMaxQuant-peptide-report\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"Human UniProt+Isoforms+cRAP FASTA\"];\n  0 -->|output_database| 6;\n  1 -->|output_database| 6;\n  62c376eb-85a3-4976-8024-bd72ac528af3[\"Output\\nHuman UniProt+Isoforms+cRAP FASTA\"];\n  6 --> 62c376eb-85a3-4976-8024-bd72ac528af3;\n  style 62c376eb-85a3-4976-8024-bd72ac528af3 stroke:#2c3143,stroke-width:4px;\n  7[\"Cut\"];\n  3 -->|output| 7;\n  8[\"Cut\"];\n  5 -->|output| 8;\n  9[\"PepQuery2\"];\n  6 -->|output| 9;\n  4 -->|output| 9;\n  2 -->|output| 9;\n  10[\"Remove beginning\"];\n  7 -->|out_file1| 10;\n  11[\"Remove beginning\"];\n  8 -->|out_file1| 11;\n  12[\"Collapse Collection\"];\n  9 -->|psm_rank_txt| 12;\n  13[\"Concatenate datasets\"];\n  10 -->|out_file1| 13;\n  11 -->|out_file1| 13;\n  14[\"Filter\"];\n  12 -->|output| 14;\n  15[\"Remove beginning\"];\n  14 -->|out_file1| 15;\n  16[\"Cut\"];\n  15 -->|out_file1| 16;\n  17[\"Peptide and Protein from Peptide reports\"];\n  16 -->|out_file1| 17;\n  13 -->|out_file1| 17;\n  bc4e33da-4064-4b78-bb15-5732b08b9316[\"Output\\nPeptide and Protein from Peptide reports\"];\n  17 --> bc4e33da-4064-4b78-bb15-5732b08b9316;\n  style bc4e33da-4064-4b78-bb15-5732b08b9316 stroke:#2c3143,stroke-width:4px;\n  18[\"Remove beginning\"];\n  17 -->|output| 18;\n  19[\"Group\"];\n  18 -->|out_file1| 19;\n  20[\"Uniprot-ID from verified Peptides\"];\n  19 -->|out_file1| 20;\n  cd6c81d8-1f44-4129-b505-2ee4dde10cd2[\"Output\\nUniprot-ID from verified Peptides\"];\n  20 --> cd6c81d8-1f44-4129-b505-2ee4dde10cd2;\n  style cd6c81d8-1f44-4129-b505-2ee4dde10cd2 stroke:#2c3143,stroke-width:4px;\n  21[\"UniProt\"];\n  20 -->|output| 21;\n  22[\"Quantitation Database for MaxQuant\"];\n  0 -->|output_database| 22;\n  1 -->|output_database| 22;\n  21 -->|proteome| 22;\n  a52b5136-db74-496f-9b66-ec1064f2301d[\"Output\\nQuantitation Database for MaxQuant\"];\n  22 --> a52b5136-db74-496f-9b66-ec1064f2301d;\n  style a52b5136-db74-496f-9b66-ec1064f2301d stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "WF3_VERIFICATION_WORKFLOW",
                 "outputs": [
                     {
@@ -195393,7 +508290,6 @@
         "id": "proteomics/mass-spectrometry-imaging-loading-exploring-data",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
@@ -195415,7 +508311,7 @@
             "Getting an overview of the MSI data with the MSI quality control tool",
             "How to export MSI data as tabular files"
         ],
-        "pageviews": 3657,
+        "pageviews": 3661,
         "pub_date": "2018-11-27",
         "questions": [
             "Did the tryptic digestions work?",
@@ -195424,10 +508320,10 @@
         ],
         "short_id": "T00217",
         "short_tools": [
-            "tp_sort_header_tool",
+            "cardinal_data_exporter",
             "Grep1",
-            "cardinal_quality_report",
-            "cardinal_data_exporter"
+            "tp_sort_header_tool",
+            "cardinal_quality_report"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -195452,19 +508348,723 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Grep1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "9.3+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
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+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.1.1"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
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         "tags": [
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@@ -195856,7 +510426,7 @@
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         "video_view": 0,
         "visit_duration": 112,
-        "visitors": 1417,
+        "visitors": 1435,
         "workflows": [
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                 "creators": [
@@ -196038,7 +510608,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "EncyclopeDIA-GTN",
                 "outputs": [
                     {
@@ -196482,14 +511052,14 @@
         ],
         "dir": "topics/proteomics/tutorials/DIA_lib_OSW",
         "edam_operation": [
+            "Clustering",
             "Principal component plotting",
+            "Imputation",
+            "Heat map generation",
             "Visualisation",
-            "Clustering",
             "Protein quantification",
             "Standardisation and normalisation",
-            "Imputation",
-            "Statistical calculation",
-            "Heat map generation"
+            "Statistical calculation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -196521,7 +511091,7 @@
             "Understanding DIA data principles and characteristics",
             "Optimizing and refining a spectral library for the analysis of DIA data"
         ],
-        "pageviews": 5003,
+        "pageviews": 5012,
         "pub_date": "2020-12-02",
         "questions": [
             "How does the peptide identification work in data independent acquisition (DIA) mass spectrometry (MS) data?",
@@ -196529,12 +511099,12 @@
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         "short_id": "T00212",
         "short_tools": [
-            "Filter1",
-            "OpenSwathDecoyGenerator",
-            "diapysef",
             "maxquant",
+            "diapysef",
+            "TargetedFileConverter",
+            "OpenSwathDecoyGenerator",
             "OpenSwathAssayGenerator",
-            "TargetedFileConverter"
+            "Filter1"
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         "slides": false,
         "slides_recordings": false,
@@ -196565,6 +511135,1391 @@
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             ]
         },
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         "tags": [
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@@ -196602,7 +512557,7 @@
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         "video_view": 0,
         "visit_duration": 82,
-        "visitors": 3790,
+        "visitors": 3799,
         "workflows": [
             {
                 "creators": [],
@@ -196786,7 +512741,7 @@
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                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHEK_Ecoli_exp_design.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\niRTassays.tsv\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nFASTA collection\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Collection\\nDDA_data collection\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"MaxQuant\"];\n  2 -->|output| 4;\n  3 -->|output| 4;\n  0 -->|output| 4;\n  5[\"Filter\"];\n  4 -->|evidence| 5;\n  6[\"Filter\"];\n  4 -->|msms| 6;\n  7[\"diapysef library generation\"];\n  5 -->|out_file1| 7;\n  1 -->|output| 7;\n  6 -->|out_file1| 7;\n  8[\"OpenSwathAssayGenerator\"];\n  7 -->|output_tabular| 8;\n  9[\"OpenSwathDecoyGenerator\"];\n  8 -->|out| 9;\n  10[\"TargetedFileConverter\"];\n  9 -->|out| 10;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "DIA_lib_OSW",
                 "outputs": [
                     {
@@ -197496,7 +513451,7 @@
         "objectives": [
             "Protein identification from LC-MS/MS raw files."
         ],
-        "pageviews": 4157,
+        "pageviews": 4173,
         "pub_date": "2017-06-12",
         "questions": [
             "How to convert LC-MS/MS raw files?",
@@ -197507,8 +513462,8 @@
         "short_id": "T00229",
         "short_tools": [
             "PeakPickerHiRes",
-            "peptide_shaker",
             "search_gui",
+            "peptide_shaker",
             "Grep1",
             "FileConverter"
         ],
@@ -197519,6 +513474,846 @@
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             "inexact": []
         },
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+                    "url": "http://apostl.moffitt.org/"
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+                },
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+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
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@@ -197553,7 +514348,7 @@
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         "video_view": 0,
         "visit_duration": 124,
-        "visitors": 2412,
+        "visitors": 2426,
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@@ -197663,7 +514458,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Peptide And Protein ID Tutorial",
                 "outputs": [
                     {
@@ -198146,7 +514941,7 @@
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+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "ProteinID SG PS Tutorial WF datasetCollection",
                 "outputs": [
                     {
@@ -198445,7 +515240,7 @@
         "objectives": [
             "Creation of a protein FASTA database ready for use with database search algorithms."
         ],
-        "pageviews": 6523,
+        "pageviews": 6537,
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@@ -198456,11 +515251,11 @@
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         "short_tools": [
             "DecoyDatabase",
-            "fasta_merge_files_and_filter_unique_sequences",
-            "dbbuilder",
             "tab2fasta",
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             "fasta2tab",
-            "addValue"
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@@ -198491,6 +515286,975 @@
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+                            "server": "https://usegalaxy.org",
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+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
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+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
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+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.6+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.3.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "inexact",
+                            "versions": [
+                                "2.8+galaxy0",
+                                "3.1+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.6+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.6+galaxy0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "DDA"
@@ -198525,7 +516289,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 120,
-        "visitors": 3941,
+        "visitors": 3954,
         "workflows": [
             {
                 "creators": [],
@@ -198584,7 +516348,7 @@
                 "inputs": [],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"Protein Database Downloader\"];\n  1[\"Protein Database Downloader\"];\n  2[\"FASTA-to-Tabular\"];\n  0 -->|output_database| 2;\n  3[\"Add column\"];\n  2 -->|output| 3;\n  4[\"Tabular-to-FASTA\"];\n  3 -->|out_file1| 4;\n  5[\"FASTA Merge Files and Filter Unique Sequences\"];\n  4 -->|output| 5;\n  1 -->|output_database| 5;\n  6[\"DecoyDatabase\"];\n  5 -->|output| 6;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Proteomics: database handling",
                 "outputs": [
                     {
@@ -199024,7 +516788,7 @@
                 "inputs": [],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"Protein Database Downloader\"];\n  1[\"Protein Database Downloader\"];\n  2[\"Protein Database Downloader\"];\n  3[\"Protein Database Downloader\"];\n  4[\"Protein Database Downloader\"];\n  5[\"Protein Database Downloader\"];\n  6[\"Protein Database Downloader\"];\n  7[\"Protein Database Downloader\"];\n  8[\"FASTA-to-Tabular\"];\n  2 -->|output_database| 8;\n  9[\"FASTA Merge Files and Filter Unique Sequences\"];\n  5 -->|output_database| 9;\n  4 -->|output_database| 9;\n  3 -->|output_database| 9;\n  1 -->|output_database| 9;\n  0 -->|output_database| 9;\n  6 -->|output_database| 9;\n  10[\"Add column\"];\n  8 -->|output| 10;\n  11[\"FASTA-to-Tabular\"];\n  9 -->|output| 11;\n  12[\"Tabular-to-FASTA\"];\n  10 -->|out_file1| 12;\n  13[\"Add column\"];\n  11 -->|output| 13;\n  14[\"Tabular-to-FASTA\"];\n  13 -->|out_file1| 14;\n  15[\"FASTA Merge Files and Filter Unique Sequences\"];\n  12 -->|output| 15;\n  7 -->|output_database| 15;\n  14 -->|output| 15;\n  16[\"DecoyDatabase\"];\n  15 -->|output| 16;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Proteomics: database handling including mycoplasma",
                 "outputs": [
                     {
@@ -199945,9 +517709,7 @@
         "feedback_number": 0,
         "hands_on": true,
         "id": "proteomics/proteome_annotation",
-        "inexact_supported_servers": [
-            "UseGalaxy.fr"
-        ],
+        "inexact_supported_servers": [],
         "js_requirements": {
             "mathjax": null,
             "mermaid": false
@@ -199963,7 +517725,7 @@
         "objectives": [
             "Execute a complete annotation pipeline of a protein list identified by LC-MS/MS experiments"
         ],
-        "pageviews": 3736,
+        "pageviews": 3765,
         "pub_date": "2019-09-12",
         "questions": [
             "How to filter out technical contaminants?",
@@ -199988,13 +517750,13 @@
         ],
         "short_id": "T00234",
         "short_tools": [
+            "retrieve_from_hpa",
+            "reactome_analysis",
+            "cluter_profiler",
             "MQoutputfilter",
-            "Jvenn",
             "IDconverter",
-            "rna_abbased_data",
-            "reactome_analysis",
-            "retrieve_from_hpa",
-            "cluter_profiler"
+            "Jvenn",
+            "rna_abbased_data"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -200007,11 +517769,1198 @@
                     "usegalaxy": false
                 }
             ],
-            "inexact": [
+            "inexact": []
+        },
+        "supported_servers_matrix": {
+            "servers": [
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
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+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
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+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
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+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.be/",
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+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "servers": [
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+                            "state": "missing"
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+                        {
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+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
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+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
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@@ -200052,7 +519001,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 174,
-        "visitors": 2483,
+        "visitors": 2505,
         "workflows": [
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@@ -200169,7 +519118,7 @@
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                 "license": null,
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "'Proteome Annotation'",
                 "outputs": [],
                 "parent_id": "proteomics/proteome_annotation",
@@ -200322,7 +519271,7 @@
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                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nLacombe_et_al_2017.txt\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nBredberg.txt\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"View proteins on Reactome maps\"];\n  9 -->|kept_lines| 10;\n  11[\"GO terms classification and enrichment analysis\"];\n  5 -->|output| 11;\n  9 -->|kept_lines| 11;\n  2[\"\u2139\ufe0f Input Dataset\\nMucilli.txt\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Build a lung proteome as a background \"];\n  4[\"Filter technical contaminants\"];\n  0 -->|output| 4;\n  5[\"ID Converter\"];\n  3 -->|output| 5;\n  6[\"ID mapping UniProt <-> ENSG ID\"];\n  4 -->|kept_lines| 6;\n  7[\"MS/MS datasets comparison\"];\n  4 -->|kept_lines| 7;\n  1 -->|output| 7;\n  2 -->|output| 7;\n  8[\"Add expression data\"];\n  6 -->|output| 8;\n  9[\"Filter biological contaminants\"];\n  8 -->|output| 9;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "ProteoRE ProteomeAnnotation Tutorial (release 2.0)",
                 "outputs": [],
                 "parent_id": "proteomics/proteome_annotation",
@@ -200439,7 +519388,7 @@
         "objectives": [
             "Run an N-TAILS data analysis."
         ],
-        "pageviews": 982,
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         "pub_date": "2017-02-14",
         "questions": [
             "How can protein N-termini be enriched for LC-MS/MS?",
@@ -200447,19 +519396,19 @@
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             "FalseDiscoveryRate",
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             "FileFilter",
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-            "IDMerger",
-            "FileMerger",
-            "PeptideIndexer"
+            "IDMapper",
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         "slides_recordings": false,
@@ -200468,6 +519417,1838 @@
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         "tags": [],
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@@ -200507,7 +521288,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 84,
-        "visitors": 674,
+        "visitors": 677,
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@@ -200617,7 +521398,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Tails Triple Dimethyl OpenMS2.1",
                 "outputs": [
                     {
@@ -201784,8 +522565,8 @@
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         "dir": "topics/proteomics/tutorials/proteogenomics-dbsearch",
         "edam_operation": [
-            "Conversion",
-            "Peptide database search"
+            "Peptide database search",
+            "Conversion"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -201825,7 +522606,7 @@
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             "A proteogenomic data analysis of mass spectrometry data to identify and visualize variant peptides."
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         "questions": [
             "How to identify variant proteoforms in MS data by searching with the customized Protein database?"
@@ -201855,10 +522636,10 @@
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             "tab2fasta",
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@@ -201900,6 +522681,849 @@
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+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "inexact",
+                            "versions": [
+                                "3.3.1"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "3.3.1"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "3.0.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "3.3.1",
+                                "3.3.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "3.0.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "3.0.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "3.0.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "3.0.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "3.0.0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "proteogenomics"
@@ -201932,8 +523556,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 301,
-        "visitors": 1242,
+        "visit_duration": 300,
+        "visitors": 1247,
         "workflows": [
             {
                 "creators": [],
@@ -202121,7 +523745,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nUniprot_cRAP_SAV_indel_translatedbed.FASTA\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nMGF Collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nReference Protein Accessions\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Search GUI\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  d14f9481-80db-4c15-8afc-6fa38ef61deb[\"Output\\nSearch GUI on input dataset(s)\"];\n  3 --> d14f9481-80db-4c15-8afc-6fa38ef61deb;\n  style d14f9481-80db-4c15-8afc-6fa38ef61deb stroke:#2c3143,stroke-width:4px;\n  4[\"Peptide Shaker\"];\n  3 -->|searchgui_results| 4;\n  afe0f1a5-28bb-44bd-b32b-c634aa2154f3[\"Output\\nPeptide Shaker on input dataset(s): mzidentML file\"];\n  4 --> afe0f1a5-28bb-44bd-b32b-c634aa2154f3;\n  style afe0f1a5-28bb-44bd-b32b-c634aa2154f3 stroke:#2c3143,stroke-width:4px;\n  5[\"mz to sqlite\"];\n  4 -->|mzidentML| 5;\n  1 -->|output| 5;\n  0 -->|output| 5;\n  b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9[\"Output\\nmz to sqlite on input dataset(s)\"];\n  5 --> b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9;\n  style b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9 stroke:#2c3143,stroke-width:4px;\n  6[\"Removing reference proteins\"];\n  4 -->|output_psm| 6;\n  4 -->|output_psm| 6;\n  2 -->|output| 6;\n  a06ad5fa-9a00-4867-b976-3745c5e59c80[\"Output\\nRemoving reference proteins\"];\n  6 --> a06ad5fa-9a00-4867-b976-3745c5e59c80;\n  style a06ad5fa-9a00-4867-b976-3745c5e59c80 stroke:#2c3143,stroke-width:4px;\n  7[\"Selecting sequence with length >6 and <30\"];\n  6 -->|output| 7;\n  b71e5417-2864-4712-b5c1-c90725976baf[\"Output\\nSelecting sequence with length >6 and <30\"];\n  7 --> b71e5417-2864-4712-b5c1-c90725976baf;\n  style b71e5417-2864-4712-b5c1-c90725976baf stroke:#2c3143,stroke-width:4px;\n  8[\"Peptides for BlastP analysis\"];\n  7 -->|output| 8;\n  1ac3c776-8095-4db1-8518-3643dc081006[\"Output\\nPeptides_for_BlastP_analysis\"];\n  8 --> 1ac3c776-8095-4db1-8518-3643dc081006;\n  style 1ac3c776-8095-4db1-8518-3643dc081006 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GTN Proteogemics2 Database Search",
                 "outputs": [
                     {
@@ -202802,18 +524426,18 @@
         ],
         "short_id": "T00235",
         "short_tools": [
-            "tp_sorted_uniq",
+            "uniprot",
+            "term_id_vs_term_name",
             "tp_easyjoin_tool",
-            "wolf_psort",
-            "comp1",
-            "Filter1",
             "Convert characters1",
-            "get_subontology_from",
+            "tp_sorted_uniq",
+            "comp1",
             "bg_uniq",
-            "term_id_vs_term_name",
+            "wolf_psort",
+            "get_subontology_from",
             "Grep1",
             "tp_cut_tool",
-            "uniprot"
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -202822,6 +524446,1830 @@
             "exact": [],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Convert characters1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Filter1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Grep1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
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         "symlink": null,
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@@ -203005,7 +526453,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Secreted Proteins Via GO Annotation And WoLF PSORT For shCTSB Paper",
                 "outputs": [
                     {
@@ -203301,21 +526749,21 @@
             "Calculate descriptors",
             "Quantitative analysis of peptide sequence properties"
         ],
-        "pageviews": 821,
+        "pageviews": 822,
         "pub_date": "2021-01-22",
         "questions": [
             "How to utilize quantitative properties of amino acids and peptide sequence to analyse peptide data?"
         ],
         "short_id": "T00227",
         "short_tools": [
-            "pdaug_peptide_sequence_analysis",
-            "pdaug_basic_plots",
-            "pdaug_peptide_data_access",
-            "pdaug_addclasslabel",
             "pdaug_fishers_plot",
+            "pdaug_basic_plots",
+            "pdaug_sequence_property_based_descriptors",
             "pdaug_tsvtofasta",
             "pdaug_merge_dataframes",
-            "pdaug_sequence_property_based_descriptors"
+            "pdaug_peptide_data_access",
+            "pdaug_addclasslabel",
+            "pdaug_peptide_sequence_analysis"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -203330,6 +526778,1196 @@
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@@ -203364,7 +528002,7 @@
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         "video_view": 0,
         "visit_duration": 159,
-        "visitors": 589,
+        "visitors": 590,
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@@ -203388,7 +528026,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Copy of PeptideDataAnalysis (imported from uploaded file)",
                 "outputs": [
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@@ -203797,7 +528435,7 @@
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             "Protein identification from LC-MS/MS raw files."
         ],
-        "pageviews": 4800,
+        "pageviews": 4826,
         "pub_date": "2017-10-16",
         "questions": [
             "How to convert LC-MS/MS raw files?",
@@ -203816,21 +528454,21 @@
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-            "IDPosteriorErrorProbability",
-            "PeptideIndexer",
-            "FidoAdapter"
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@@ -203860,6 +528498,3383 @@
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+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.3.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.2.0.1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
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+                    "version": "2.2.0.1"
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+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
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+                        {
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+                            "state": "missing"
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+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
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+                        },
+                        {
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+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
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+                        {
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+                        },
+                        {
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+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.2.0.1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.8+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.6+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.3.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.6+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.6+galaxy0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "DDA",
@@ -203912,7 +531927,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 172,
-        "visitors": 2767,
+        "visitors": 2788,
         "workflows": [
             {
                 "creators": [],
@@ -204069,7 +532084,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmzml input\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nfasta input\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"PeakPickerHiRes\"];\n  0 -->|output| 2;\n  3[\"XTandemAdapter\"];\n  1 -->|output| 3;\n  2 -->|param_out| 3;\n  4[\"FileInfo\"];\n  3 -->|out| 4;\n  5[\"PeptideIndexer\"];\n  1 -->|output| 5;\n  3 -->|out| 5;\n  6[\"IDPosteriorErrorProbability\"];\n  5 -->|out| 6;\n  7[\"FalseDiscoveryRate\"];\n  6 -->|out| 7;\n  8[\"IDScoreSwitcher\"];\n  7 -->|out| 8;\n  9[\"FileInfo\"];\n  8 -->|out| 9;\n  10[\"FidoAdapter\"];\n  8 -->|out| 10;\n  11[\"FalseDiscoveryRate\"];\n  10 -->|out| 11;\n  12[\"FileInfo\"];\n  11 -->|out| 12;\n  13[\"TextExporter\"];\n  11 -->|out| 13;\n  14[\"Select\"];\n  13 -->|out| 14;\n  15[\"Select\"];\n  13 -->|out| 15;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Proteomics: Peptide and Protein ID using OpenMS",
                 "outputs": [
                     {
@@ -204984,7 +532999,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nmzML_test_dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nHuman_database_including_decoys\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"XTandemAdapter\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"MSGFPlusAdapter\"];\n  1 -->|output| 3;\n  4[\"IDPosteriorErrorProbability\"];\n  2 -->|param_out| 4;\n  5[\"IDPosteriorErrorProbability\"];\n  3 -->|param_out| 5;\n  6[\"IDMerger\"];\n  5 -->|param_out| 6;\n  4 -->|param_out| 6;\n  7[\"ConsensusID\"];\n  6 -->|param_out| 7;\n  8[\"PeptideIndexer\"];\n  1 -->|output| 8;\n  7 -->|param_out| 8;\n  9[\"FalseDiscoveryRate\"];\n  8 -->|param_out| 9;\n  10[\"IDScoreSwitcher\"];\n  9 -->|param_out| 10;\n  11[\"FileInfo\"];\n  9 -->|param_out| 11;\n  12[\"FidoAdapter\"];\n  10 -->|param_out| 12;\n  13[\"FalseDiscoveryRate\"];\n  12 -->|param_out| 13;\n  14[\"IDFilter\"];\n  13 -->|param_out| 14;\n  15[\"FileInfo\"];\n  14 -->|param_out| 15;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Peptide And Protein ID Via OMS Using Two Search Engines",
                 "outputs": [
                     {
@@ -205477,8 +533492,7 @@
         "hands_on": true,
         "id": "proteomics/biomarker_selection",
         "inexact_supported_servers": [
-            "UseGalaxy.be",
-            "UseGalaxy.fr"
+            "UseGalaxy.be"
         ],
         "js_requirements": {
             "mathjax": null,
@@ -205493,7 +533507,7 @@
         "objectives": [
             "Build a workflow implementing a strategy for the selection of tissue-leakage biomarkers using ProteoRE"
         ],
-        "pageviews": 1926,
+        "pageviews": 1928,
         "pub_date": "2019-06-13",
         "questions": [
             "How to mine public databases to retrieve info?",
@@ -205503,13 +533517,13 @@
         "short_id": "T00213",
         "short_tools": [
             "prot_features",
-            "MQoutputfilter",
-            "retr_pepatlas1",
-            "rna_abbased_data",
+            "retrieve_from_hpa",
             "Jvenn",
+            "MQoutputfilter",
             "IDconverter",
+            "retr_pepatlas1",
             "tp_cut_tool",
-            "retrieve_from_hpa"
+            "rna_abbased_data"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -205521,11 +533535,1228 @@
                     "name": "UseGalaxy.be",
                     "url": "https://usegalaxy.be/",
                     "usegalaxy": false
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "servers": [
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+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
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+                        },
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+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "1.1.0"
+                            ]
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.1.0"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
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+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
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+                                "1.1.0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
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+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "9.3+galaxy1",
+                                "9.3+galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                            ]
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+                            "server": "https://usegalaxy.no/",
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+                            ]
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+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
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+                        },
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+                                "1.1.0",
+                                "9.3+galaxy1",
+                                "9.3+galaxy2",
+                                "9.3+galaxy0"
+                            ]
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+                        {
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+                            "state": "missing"
+                        }
+                    ],
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+                    "servers": [
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+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
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+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
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+                        {
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+                        {
+                            "server": "https://galaxytrakr.org/",
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+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
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+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
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+                        {
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+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
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+                            "server": "https://www.immportgalaxy.org/",
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+                        {
+                            "server": "http://galaxy.interactomix.com/",
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+                        },
+                        {
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+                        {
+                            "server": "https://neo.engr.uconn.edu/",
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+                        {
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+                        {
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+                        },
+                        {
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+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
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+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
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+                        },
+                        {
+                            "server": "https://usegalaxy.org",
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+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
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@@ -205566,7 +534797,7 @@
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@@ -205604,7 +534835,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
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@@ -205761,7 +534992,7 @@
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@@ -205794,9 +535025,9 @@
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@@ -205821,6 +535052,560 @@
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@@ -205852,7 +535637,7 @@
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-        "visitors": 63,
+        "visitors": 69,
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@@ -206025,7 +535810,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "WF5_Data_Interpretation_Worklow",
                 "outputs": [],
                 "parent_id": "proteomics/clinical-mp-5-data-interpretation",
@@ -206192,7 +535977,7 @@
         "objectives": [
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         ],
-        "pageviews": 1853,
+        "pageviews": 1861,
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         "questions": [
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@@ -206214,10 +535999,10 @@
         ],
         "short_id": "T00233",
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-            "ncbi_blastp_wrapper",
+            "pep_pointer",
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+            "ncbi_blastp_wrapper"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -206258,6 +536043,733 @@
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         "tags": [
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@@ -206290,7 +536802,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
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                 "name": "GTN Proteogemics3 Novel Peptide Analysis",
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@@ -207234,11 +537746,11 @@
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-            "Tag-based peptide identification",
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@@ -207275,7 +537787,7 @@
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@@ -207308,10 +537820,10 @@
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+                        {
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+                            "state": "missing"
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+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
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+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
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+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "2.3.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.3.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.4.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.3.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.3.0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "label-TMT11"
@@ -207367,8 +538565,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 225,
-        "visitors": 215,
+        "visit_duration": 239,
+        "visitors": 237,
         "workflows": [
             {
                 "creators": [
@@ -207507,7 +538705,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nHUMAN SwissProt Protein Database\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nInput MGF files Dataset Collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSpecies_UniProt_FASTA\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nContaminants cRAP Protein Database \"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Human UniProt Microbial Proteins cRAP for MetaNovo\"];\n  0 -->|output| 4;\n  2 -->|output| 4;\n  3 -->|output| 4;\n  286f5bd4-fb0d-4649-8dac-f191acc72722[\"Output\\nHuman UniProt Microbial Proteins cRAP for MetaNovo\"];\n  4 --> 286f5bd4-fb0d-4649-8dac-f191acc72722;\n  style 286f5bd4-fb0d-4649-8dac-f191acc72722 stroke:#2c3143,stroke-width:4px;\n  5[\"MetaNovo\"];\n  4 -->|output| 5;\n  1 -->|output| 5;\n  6[\"FASTA Merge Files and Filter Unique Sequences\"];\n  0 -->|output| 6;\n  5 -->|output_fasta| 6;\n  3 -->|output| 6;\n  de57cd9d-ac05-4397-9d44-e65620913447[\"Output\\nHuman UniProt Microbial Proteins (from MetaNovo) and cRAP \"];\n  6 --> de57cd9d-ac05-4397-9d44-e65620913447;\n  style de57cd9d-ac05-4397-9d44-e65620913447 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "WF1_Database_Generation_Workflow",
                 "outputs": [
                     {
@@ -207891,8 +539089,8 @@
             "Prediction and recognition",
             "Visualisation",
             "Filtering",
-            "Label-free quantification",
-            "Formatting"
+            "Formatting",
+            "Label-free quantification"
         ],
         "edam_topic": [
             "Proteomics",
@@ -207938,7 +539136,7 @@
         "objectives": [
             "A taxonomy, functional and quantitational analysis of metaproteomic mass spectrometry data."
         ],
-        "pageviews": 1353,
+        "pageviews": 1355,
         "pub_date": "2020-10-16",
         "questions": [
             "How do I perform functional and taxonomy analysis on metaproteomics data?",
@@ -207947,19 +539145,19 @@
         ],
         "short_id": "T00222",
         "short_tools": [
-            "query_tabular",
+            "Cut1",
+            "tp_replace_in_line",
             "flashlfq",
-            "Filter1",
-            "peptide_shaker",
             "regex1",
-            "tp_replace_in_line",
-            "msconvert",
+            "query_tabular",
             "search_gui",
-            "unipept",
+            "peptide_shaker",
             "Grep1",
-            "Cut1",
             "Remove beginning1",
-            "tp_replace_in_column"
+            "msconvert",
+            "tp_replace_in_column",
+            "unipept",
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -207995,6 +539193,2261 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
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+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
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+                    "url": "http://gigagalaxy.net/"
+                },
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+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
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+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
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+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
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+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
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+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
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@@ -208037,8 +541490,8 @@
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-        "visit_duration": 229,
-        "visitors": 781,
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+        "visitors": 782,
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@@ -208245,7 +541698,7 @@
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+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "metaQuantome_datacreation_workflow",
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                     {
@@ -209055,14 +542508,14 @@
         ],
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         "edam_operation": [
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             "Protein quantification",
             "Standardisation and normalisation",
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-            "Statistical calculation",
-            "Heat map generation"
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@@ -209091,7 +542544,7 @@
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@@ -209099,8 +542552,8 @@
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-            "maxquant"
+            "maxquant",
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@@ -209126,6 +542579,438 @@
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+                                "1.6",
+                                "1.16.1",
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+                            "state": "inexact",
+                            "versions": [
+                                "4.4+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "3.4+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.16.5"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "3.4+galaxy2"
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+                        {
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+                            "state": "exact",
+                            "version": "3.4+galaxy2"
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+                        {
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+                            "state": "missing"
+                        }
+                    ],
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         },
@@ -210311,12 +545600,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-control/tutorial.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/sequence-analysis/tutorials/quality-control/tutorial.json"
         },
-        "version": 41,
+        "version": 42,
         "video": false,
-        "video_versions": 2,
+        "video_versions": 3,
         "video_view": 0,
         "visit_duration": 335,
-        "visitors": 2218100,
+        "visitors": 2229364,
         "workflows": [
             {
                 "creators": [],
@@ -210440,7 +545729,7 @@
                 ],
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "GTN - Sequence Analyses - Quality Control (imported from uploaded file)",
                 "outputs": [
                     {
@@ -212068,16 +547357,15 @@
         ],
         "dir": "topics/sequence-analysis/tutorials/human-reads-removal",
         "edam_operation": [
-            "Generation",
-            "Data handling",
-            "Sequence alignment",
             "Sequence file editing",
+            "Data handling",
+            "Genome indexing",
             "Read mapping",
-            "Genome indexing"
+            "Sequence alignment",
+            "Generation"
         ],
         "edam_topic": [],
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-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
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         "feedback_mean_note": null,
@@ -212113,7 +547401,7 @@
             "Preprocess and map the data against the human reference genome",
             "Eliminate reads/read pairs that map to the human genome from the original data"
         ],
-        "pageviews": 4842,
+        "pageviews": 4864,
         "pub_date": "2021-08-04",
         "questions": [
             "How can you remove traces of human sequence data from a sequenced viral sample?"
@@ -212137,24 +547425,19 @@
         ],
         "short_id": "T00236",
         "short_tools": [
-            "bwa_mem",
-            "seqtk_subseq",
             "tp_replace_in_line",
-            "samtools_fastx",
-            "Grep1",
-            "__UNZIP_COLLECTION__",
+            "seqtk_subseq",
             "trimmomatic",
-            "__ZIP_COLLECTION__"
+            "__ZIP_COLLECTION__",
+            "bwa_mem",
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+            "samtools_fastx",
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                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -212204,6 +547487,1447 @@
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+                            "state": "exact",
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+                        },
+                        {
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+                            "state": "exact",
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+                        },
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+                            "state": "inexact",
+                            "versions": [
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+                                "0.36.5"
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+                        },
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         "tags": [
             "covid19"
@@ -212241,7 +548965,7 @@
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         "video_view": 0,
         "visit_duration": 140,
-        "visitors": 3422,
+        "visitors": 3439,
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@@ -212311,7 +549035,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data",
                 "outputs": [
                     {
@@ -213030,16 +549754,16 @@
         ],
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             "Data handling",
-            "Sequence trimming",
-            "Read mapping",
-            "Sequencing quality control",
-            "Genome visualisation",
             "Sequence alignment analysis",
-            "Statistical calculation",
-            "Validation",
+            "Primer removal",
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             "Read pre-processing",
-            "Primer removal"
+            "Sequence trimming",
+            "Statistical calculation"
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             "Mapping"
@@ -213074,7 +549798,6 @@
             "GalaxyTrakr",
             "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no"
         ],
         "js_requirements": {
@@ -213095,7 +549818,7 @@
             "Explain what is a BAM file and what it contains",
             "Use genome browser to understand your data"
         ],
-        "pageviews": 5993272,
+        "pageviews": 6025555,
         "pub_date": "2016-10-04",
         "questions": [
             "What is mapping?",
@@ -213140,13 +549863,13 @@
         ],
         "short_id": "T00237",
         "short_tools": [
-            "jbrowse",
-            "samtools_stats",
             "bamFilter",
-            "multiqc",
+            "trim_galore",
+            "jbrowse",
             "fastqc",
+            "samtools_stats",
             "bowtie2",
-            "trim_galore"
+            "multiqc"
         ],
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         "slides_recordings": [
@@ -213203,14 +549926,2009 @@
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                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                    "url": "https://www.immportgalaxy.org/"
+                },
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+                            "server": "https://palfinder.ls.manchester.ac.uk/",
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+                            "server": "https://usegalaxy.be/",
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+                            "versions": [
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+                            ]
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+                            "version": "1.9+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.9+galaxy1"
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+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.9+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
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+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.9+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.9+galaxy1"
                 }
             ]
         },
@@ -213250,8 +551968,8 @@
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 314,
-        "visitors": 2188054,
+        "visit_duration": 315,
+        "visitors": 2199132,
         "workflows": [
             {
                 "creators": [],
@@ -213368,7 +552086,7 @@
                 ],
                 "license": null,
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GTN - Sequence Analyses - Mapping - Jbrowse (imported from uploaded file)",
                 "outputs": [
                     {
@@ -213737,7 +552455,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nreads_1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nreads_2\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FastQC\"];\n  0 -->|output| 2;\n  3[\"FastQC\"];\n  1 -->|output| 3;\n  4[\"Trim Galore!\"];\n  0 -->|output| 4;\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  3 -->|text_file| 5;\n  2 -->|text_file| 5;\n  6[\"Bowtie2\"];\n  4 -->|trimmed_reads_pair1| 6;\n  4 -->|trimmed_reads_pair2| 6;\n  d2674912-28a6-45f3-ac48-6635eabe47b7[\"Output\\nbowtie2_mapping_stats\"];\n  6 --> d2674912-28a6-45f3-ac48-6635eabe47b7;\n  style d2674912-28a6-45f3-ac48-6635eabe47b7 stroke:#2c3143,stroke-width:4px;\n  7[\"Stats\"];\n  6 -->|output| 7;\n  96de3c0c-4d7e-423b-8e9b-9a12a011d726[\"Output\\nbam_stats_1\"];\n  7 --> 96de3c0c-4d7e-423b-8e9b-9a12a011d726;\n  style 96de3c0c-4d7e-423b-8e9b-9a12a011d726 stroke:#2c3143,stroke-width:4px;\n  8[\"Filter\"];\n  6 -->|output| 8;\n  9[\"Stats\"];\n  8 -->|out_file1| 9;\n  9603a94a-dcd8-4c1f-89cd-bb31d8572783[\"Output\\nbam_stats_2\"];\n  9 --> 9603a94a-dcd8-4c1f-89cd-bb31d8572783;\n  style 9603a94a-dcd8-4c1f-89cd-bb31d8572783 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "GTN - Sequence Analyses - Mapping (imported from uploaded file)",
                 "outputs": [
                     {
@@ -215761,8 +554479,8 @@
         "dir": "topics/sequence-analysis/tutorials/ncbi-fcs",
         "edam_operation": [
             "Sequence assembly validation",
-            "Sequence trimming",
-            "Sequence contamination filtering"
+            "Sequence contamination filtering",
+            "Sequence trimming"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -215789,15 +554507,15 @@
             "Learn how to screen a genome assembly for adaptor and vector contamination.",
             "Learn how to screen a genome assembly for non-host organism contamination."
         ],
-        "pageviews": 634,
+        "pageviews": 653,
         "pub_date": "2024-04-16",
         "questions": [
             "Are the sequences in a genome assembly contaminant-free?"
         ],
         "short_id": "T00439",
         "short_tools": [
-            "ncbi_fcs_gx",
-            "ncbi_fcs_adaptor"
+            "ncbi_fcs_adaptor",
+            "ncbi_fcs_gx"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -215816,6 +554534,413 @@
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+                },
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+                            "state": "missing"
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+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.5.0+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.5.0+galaxy0"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "90M",
         "title": "Screening assembled genomes for contamination using NCBI FCS",
@@ -215842,8 +554967,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 142,
-        "visitors": 448,
+        "visit_duration": 138,
+        "visitors": 465,
         "workflows": [
             {
                 "creators": [
@@ -215908,7 +555033,7 @@
                 ],
                 "license": "http://www.usa.gov/publicdomain/label/1.0/",
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "NCBI Foreign Contamination Screen",
                 "outputs": [
                     {
@@ -216341,22 +555466,21 @@
         ],
         "dir": "topics/sequence-analysis/tutorials/Manage_AB1_Sanger",
         "edam_operation": [
+            "Sequence file editing",
+            "Sequence read processing",
             "Data handling",
             "DNA barcoding",
-            "Visualisation",
-            "Phylogenetic analysis",
-            "Sequencing quality control",
+            "Sequence clustering",
             "Demultiplexing",
             "Taxonomic classification",
-            "Sequence read processing",
-            "Sequence file editing",
-            "Sequence clustering"
+            "Sequencing quality control",
+            "Visualisation",
+            "Phylogenetic analysis"
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             "UseGalaxy.cz",
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu"
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@@ -216377,33 +555501,33 @@
             "Learn how to manage sequencing files (AB1, FASTQ, FASTA)",
             "Learn how to clean your Sanger sequences in an automated and reproducible way"
         ],
-        "pageviews": 1988,
+        "pageviews": 2008,
         "pub_date": "2024-01-08",
         "questions": [
             "How to clean Sanger sequencing files?"
         ],
         "short_id": "T00383",
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-            "seqtk_trimfq",
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-            "fastq_masker_by_quality",
-            "mothur_degap_seqs",
-            "qiime_align_seqs",
             "regex1",
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             "mothur_merge_files",
-            "ncbi_blastn_wrapper",
+            "__SORTLIST__",
+            "fastq_masker_by_quality",
+            "fastq_to_tabular",
+            "tab2fasta",
+            "unzip",
             "cshl_fastq_to_fasta",
-            "ab1_fastq_converter",
-            "cshl_fastx_reverse_complement",
+            "filter_by_fasta_ids",
             "seqtk_mergepe",
-            "aligned_to_consensus",
-            "__SORTLIST__",
-            "__FILTER_FROM_FILE__"
+            "ncbi_blastn_wrapper",
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+            "__FILTER_FROM_FILE__",
+            "mothur_degap_seqs",
+            "fastq_groomer",
+            "seqtk_trimfq",
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@@ -216418,14 +555542,2933 @@
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+                            "state": "missing"
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+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "1.4+galaxy0"
+                            ]
+                        },
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+                            "state": "missing"
+                        },
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+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        }
+                    ],
+                    "version": "1.3.1"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
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+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "1.4+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "exact",
+                            "version": "1.3.1"
+                        }
+                    ],
+                    "version": "1.3.1"
+                }
+            ]
         },
         "symlink": null,
         "time_estimation": "1H",
@@ -216471,8 +558514,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 128,
-        "visitors": 1530,
+        "visit_duration": 127,
+        "visitors": 1549,
         "workflows": [
             {
                 "creators": [
@@ -216617,7 +558660,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nL sequences Forward\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nH sequences Reverse\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nLCOI primers\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nHCOI primers\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"ab1 to FASTQ converter\"];\n  0 -->|output| 4;\n  5[\"ab1 to FASTQ converter\"];\n  1 -->|output| 5;\n  6[\"What\u2019s your LCOI primer sequence identifier ?\"];\n  2 -->|output| 6;\n  7[\"What\u2019s your HCOI primer sequence identifier ?\"];\n  3 -->|output| 7;\n  8[\"seqtk_trimfq\"];\n  4 -->|output| 8;\n  9[\"seqtk_trimfq\"];\n  5 -->|output| 9;\n  10[\"Degap.seqs\"];\n  6 -->|output| 10;\n  11[\"Degap.seqs\"];\n  7 -->|output| 11;\n  12[\"Sort collection\"];\n  8 -->|default| 12;\n  13[\"FASTQ Groomer\"];\n  9 -->|default| 13;\n  14[\"Reverse-Complement\"];\n  11 -->|out_fasta| 14;\n  15[\"Reverse-Complement\"];\n  13 -->|output_file| 15;\n  16[\"Sort collection\"];\n  15 -->|output| 16;\n  17[\"seqtk_mergepe\"];\n  12 -->|output| 17;\n  16 -->|output| 17;\n  18[\"FASTQ Groomer\"];\n  17 -->|default| 18;\n  19[\"FASTQ to Tabular\"];\n  18 -->|output_file| 19;\n  20[\"Tabular-to-FASTA\"];\n  19 -->|output_file| 20;\n  21[\"Align sequences\"];\n  20 -->|output| 21;\n  22[\"Consensus sequence from aligned FASTA\"];\n  21 -->|aligned_sequences| 22;\n  23[\"Merge.files\"];\n  22 -->|output| 23;\n  24[\"Merge.files\"];\n  23 -->|output| 24;\n  14 -->|output| 24;\n  10 -->|out_fasta| 24;\n  25[\"Regex Find And Replace\"];\n  24 -->|output| 25;\n  26[\"Align sequences\"];\n  25 -->|out_file1| 26;\n  27[\"NCBI BLAST+ blastn\"];\n  25 -->|out_file1| 27;\n  31c2dd1a-918e-4648-a407-d0e3d7172253[\"Output\\nw_blast_output\"];\n  27 --> 31c2dd1a-918e-4648-a407-d0e3d7172253;\n  style 31c2dd1a-918e-4648-a407-d0e3d7172253 stroke:#2c3143,stroke-width:4px;\n  7514514f-809a-4a14-8981-cb08c950b523[\"Output\\nw_consensus_aligned_sequences\"];\n  27 --> 7514514f-809a-4a14-8981-cb08c950b523;\n  style 7514514f-809a-4a14-8981-cb08c950b523 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST",
                 "outputs": [
                     {
@@ -217584,7 +559627,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAOPEP_and_CHD8_sequences_20220907.zip?download=1\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nPrim\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Unzip\"];\n  0 -->|output| 2;\n  3[\"Filter FASTA\"];\n  1 -->|output| 3;\n  4[\"Filter FASTA\"];\n  1 -->|output| 4;\n  5[\"Extract element identifiers\"];\n  2 -->|unzipped| 5;\n  6[\"Degap.seqs\"];\n  3 -->|output| 6;\n  7[\"Degap.seqs\"];\n  4 -->|output| 7;\n  8[\"Regex Find And Replace\"];\n  5 -->|output| 8;\n  9[\"Regex Find And Replace\"];\n  5 -->|output| 9;\n  10[\"Reverse-Complement\"];\n  7 -->|out_fasta| 10;\n  11[\"Filter collection\"];\n  8 -->|out_file1| 11;\n  2 -->|unzipped| 11;\n  12[\"Filter collection\"];\n  9 -->|out_file1| 12;\n  11 -->|output_discarded| 12;\n  13[\"ab1 to FASTQ converter\"];\n  11 -->|output_filtered| 13;\n  14[\"ab1 to FASTQ converter\"];\n  12 -->|output_filtered| 14;\n  15[\"seqtk_trimfq\"];\n  13 -->|output| 15;\n  16[\"seqtk_trimfq\"];\n  14 -->|output| 16;\n  17[\"FASTQ Groomer\"];\n  15 -->|default| 17;\n  18[\"Sort collection\"];\n  16 -->|default| 18;\n  19[\"Sort collection\"];\n  17 -->|output_file| 19;\n  20[\"Reverse-Complement\"];\n  19 -->|output| 20;\n  21[\"seqtk_mergepe\"];\n  18 -->|output| 21;\n  20 -->|output| 21;\n  22[\"FASTQ Groomer\"];\n  21 -->|default| 22;\n  23[\"FASTQ to Tabular\"];\n  22 -->|output_file| 23;\n  24[\"Tabular-to-FASTA\"];\n  23 -->|output_file| 24;\n  25[\"Align sequences\"];\n  24 -->|output| 25;\n  26[\"Consensus sequence from aligned FASTA\"];\n  25 -->|aligned_sequences| 26;\n  27[\"Merge.files\"];\n  26 -->|output| 27;\n  28[\"Merge.files\"];\n  27 -->|output| 28;\n  10 -->|output| 28;\n  6 -->|out_fasta| 28;\n  29[\"Regex Find And Replace\"];\n  28 -->|output| 29;\n  30[\"Align sequences\"];\n  29 -->|out_file1| 30;\n  31[\"NCBI BLAST+ blastn\"];\n  29 -->|out_file1| 31;",
-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:44 +0000",
                 "name": "Training Sanger sequences CHD8",
                 "outputs": [
                     {
@@ -217810,13 +559853,13 @@
             "topic_3697"
         ],
         "edam_operation": [
-            "Cross-assembly",
-            "Sequencing quality control",
+            "Expression analysis",
             "Sequence contamination filtering",
+            "Sequencing quality control",
+            "Cross-assembly",
+            "Sequence composition calculation",
             "Statistical calculation",
-            "Taxonomic classification",
-            "Expression analysis",
-            "Sequence composition calculation"
+            "Taxonomic classification"
         ],
         "edam_topic": [
             "Whole genome sequencing",
@@ -217825,8 +559868,7 @@
             "Microbial ecology"
         ],
         "exact_supported_servers": [
-            "UseGalaxy.eu",
-            "UseGalaxy.fr"
+            "UseGalaxy.eu"
         ],
         "feedback_mean_note": null,
         "feedback_number": 0,
@@ -217860,7 +559902,7 @@
             "Run a series of tool to identify species in bacterial isolate sequencing data",
             "Visualize the species abundance"
         ],
-        "pageviews": 225,
+        "pageviews": 296,
         "pub_date": "2024-07-15",
         "questions": [
             "How to check the quality of MiSeq data?",
@@ -217883,12 +559925,12 @@
         ],
         "short_id": "T00446",
         "short_tools": [
-            "fastp",
-            "est_abundance",
-            "recentrifuge",
+            "fastqc",
             "upload1",
-            "kraken2",
-            "fastqc"
+            "recentrifuge",
+            "est_abundance",
+            "fastp",
+            "kraken2"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -217898,33 +559940,1542 @@
                     "name": "UseGalaxy.eu",
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
+                }
+            ],
+            "inexact": [
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
                 }
-            ],
-            "inexact": [
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
                 {
                     "name": "Galaxy@AuBi",
                     "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "GalaxyTrakr",
                     "url": "https://galaxytrakr.org/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "0.72+galaxy1",
+                                "0.72",
+                                "0.73+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "exact",
+                            "version": "0.74+galaxy0"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.72+galaxy1",
+                                "0.73+galaxy0",
+                                "0.69"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.73+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "exact",
+                            "version": "0.74+galaxy0"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
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@@ -217966,8 +561517,8 @@
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         "video_view": 0,
-        "visit_duration": 151,
-        "visitors": 185,
+        "visit_duration": 163,
+        "visitors": 229,
         "workflows": [
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@@ -218059,7 +561610,7 @@
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-                "modified": "2024-10-02 12:08:09 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Quality and contamination control in bacterial isolate using Illumina MiSeq Data",
                 "outputs": [
                     {
@@ -218643,7 +562194,6 @@
         "exact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
@@ -218672,7 +562222,7 @@
             "Load FASTA sequence into Galaxy",
             "Perform NCBI-Blast+ analysis against MAdLandDB"
         ],
-        "pageviews": 1414,
+        "pageviews": 1427,
         "pub_date": "2023-01-16",
         "questions": [
             "What is MAdLand DB?",
@@ -218680,9 +562230,9 @@
         ],
         "short_id": "T00238",
         "short_tools": [
-            "ncbi_blastp_wrapper",
+            "bg_diamond",
             "ncbi_blastx_wrapper",
-            "bg_diamond"
+            "ncbi_blastp_wrapper"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -218698,11 +562248,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -218732,6 +562277,604 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
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+                        },
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+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
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+                            "state": "missing"
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+                        },
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+                            "state": "inexact",
+                            "versions": [
+                                "2.0.8.0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
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+                            "versions": [
+                                "2.0.8.0"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
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+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "exact",
+                            "version": "2.0.15+galaxy0"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
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+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "2.0.15+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.0.15+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "2.0.15+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2.0.15+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.0.15+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.0.15+galaxy0"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.10.1+galaxy2",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "2.10.1+galaxy2"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
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+                                "2.14.1+galaxy2",
+                                "0.3.3"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
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+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
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+                        {
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+                            "state": "inexact",
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+                            ]
+                        },
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+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                            "state": "inexact",
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+                            ]
+                        },
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+                            "state": "inexact",
+                            "versions": [
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+                                "2.14.1+galaxy2",
+                                "0.3.3",
+                                "0.3.0",
+                                "0.1.07",
+                                "0.0.11"
+                            ]
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+                        {
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+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.10.1+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.10.1+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2.10.1+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.10.1+galaxy2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.10.1+galaxy2"
+                },
+                {
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+                    "servers": [
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "2.10.1+galaxy2"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.14.1+galaxy2",
+                                "2.10.1+galaxy1",
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+                            "state": "exact",
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         "tags": [
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@@ -218762,8 +562905,8 @@
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         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 158,
-        "visitors": 1103,
+        "visit_duration": 157,
+        "visitors": 1114,
         "zenodo_link": "https://zenodo.org/records/7524427"
     },
     {
@@ -218927,19 +563070,18 @@
         ],
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         "edam_operation": [
-            "Generation",
-            "Statistical calculation",
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
             "Sequence composition calculation",
+            "Sequencing quality control",
+            "Genome indexing",
+            "Read mapping",
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+            "Statistical calculation",
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+            "Generation"
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@@ -218973,7 +563115,7 @@
             "Critique large data sets and use bioinformatics to assess genetics data",
             "Tap into the interdisciplinary nature of science"
         ],
-        "pageviews": 956,
+        "pageviews": 961,
         "pub_date": "2023-07-10",
         "questions": [
             "How do I check my data quality?",
@@ -218983,8 +563125,8 @@
         "short_id": "T00356",
         "short_tools": [
             "bwa_mem",
-            "fastqc",
-            "jbrowse"
+            "jbrowse",
+            "fastqc"
         ],
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         "slides_recordings": false,
@@ -218995,11 +563137,6 @@
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                     "usegalaxy": true
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                 {
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                     "url": "https://usegalaxy.no/",
@@ -219049,6 +563186,620 @@
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+                            "state": "exact",
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+                        {
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+                            "state": "exact",
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+                        },
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+                            "state": "exact",
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         "tags": [
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@@ -219081,8 +563832,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 271,
-        "visitors": 739,
+        "visit_duration": 270,
+        "visitors": 744,
         "zenodo_link": "https://doi.org/10.5281/zenodo.8115178"
     },
     {
@@ -219177,7 +563928,7 @@
             "Compare enrichment across experimental conditions (e.g., wild type vs. knockout) to uncover functional changes associated with genetic or environmental perturbations.",
             "Link GO enrichment results with previously annotated cell clusters, providing a clearer picture of the functional roles of different cell populations."
         ],
-        "pageviews": 70216,
+        "pageviews": 102243,
         "pub_date": "2024-09-17",
         "questions": [
             "What is Gene Ontology (GO) enrichment analysis, and why should I perform it on my marker genes?",
@@ -219196,10 +563947,10 @@
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         "short_tools": [
-            "gprofiler_gost",
             "Cut1",
             "tp_split_on_column",
-            "goenrichment"
+            "goenrichment",
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         ],
         "slides": true,
         "slides_recordings": false,
@@ -219228,6 +563979,689 @@
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         "symlink": null,
         "tags": [
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@@ -219674,7 +565786,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 98,
-        "visitors": 2865,
+        "visitors": 2870,
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@@ -220010,7 +566122,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "MuSiC Workflow",
                 "outputs": [
                     {
@@ -220886,9 +566998,9 @@
         ],
         "dir": "topics/single-cell/tutorials/scrna-scater-qc",
         "edam_operation": [
-            "Sequence visualisation",
             "Sequencing quality control",
-            "Read pre-processing"
+            "Read pre-processing",
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@@ -220930,7 +567042,7 @@
             "Visualise data with various types of plots",
             "Filtering low-quality cells with the appropriate approach"
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-        "pageviews": 645,
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         "pub_date": "2019-10-23",
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@@ -220953,10 +567065,10 @@
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-            "scater_create_qcmetric_ready_sce",
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-            "scater_plot_dist_scatter"
+            "scater_create_qcmetric_ready_sce"
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         "slides_recordings": false,
@@ -220992,6 +567104,696 @@
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@@ -221125,7 +567927,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Scater",
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@@ -221308,9 +568110,9 @@
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         "edam_operation": [
-            "Gene expression analysis",
             "RNA-Seq quantification",
-            "Sequence composition calculation"
+            "Sequence composition calculation",
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@@ -221353,7 +568155,7 @@
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         ],
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@@ -221391,15 +568193,15 @@
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+            "join1",
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-            "_salmon_kallisto_mtx_to_10x"
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         "slides": false,
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@@ -221419,6 +568221,1355 @@
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+                            "state": "missing"
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+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
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+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
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+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
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+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
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+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
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+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.0.7+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.0.7+galaxy2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.0.7+galaxy2"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "10x",
@@ -221456,8 +569607,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 202,
-        "visitors": 2590,
+        "visit_duration": 205,
+        "visitors": 2604,
         "workflows": [
             {
                 "creators": [
@@ -221608,7 +569759,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGTF file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference FASTA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nRead 1 - containing cell barcode & UMI\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nRead 2 - containing transcript\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"GTF2GeneList\"];\n  0 -->|output| 4;\n  5[\"Transcript-gene mapping\"];\n  1 -->|output| 5;\n  0 -->|output| 5;\n  773cb4ae-56c3-49c0-b582-ee69d620def3[\"Output\\nfasta_output\"];\n  5 --> 773cb4ae-56c3-49c0-b582-ee69d620def3;\n  style 773cb4ae-56c3-49c0-b582-ee69d620def3 stroke:#2c3143,stroke-width:4px;\n  a30424b5-1ddc-4324-9ff6-dc5883adcce0[\"Output\\nfeature_annotation\"];\n  5 --> a30424b5-1ddc-4324-9ff6-dc5883adcce0;\n  style a30424b5-1ddc-4324-9ff6-dc5883adcce0 stroke:#2c3143,stroke-width:4px;\n  6[\"Alevin Processed\"];\n  2 -->|output| 6;\n  3 -->|output| 6;\n  5 -->|fasta_output| 6;\n  1 -->|output| 6;\n  5 -->|feature_annotation| 6;\n  a87beb55-1baf-458e-bd09-bb5ac6ea6e9a[\"Output\\nraw_cb_frequency_txt\"];\n  6 --> a87beb55-1baf-458e-bd09-bb5ac6ea6e9a;\n  style a87beb55-1baf-458e-bd09-bb5ac6ea6e9a stroke:#2c3143,stroke-width:4px;\n  c9390a50-775c-4f0f-88e5-0984d570902c[\"Output\\nsalmon_quant_log\"];\n  6 --> c9390a50-775c-4f0f-88e5-0984d570902c;\n  style c9390a50-775c-4f0f-88e5-0984d570902c stroke:#2c3143,stroke-width:4px;\n  2cebc438-ddc0-41e0-89ba-49b4bd3e2160[\"Output\\nquants_mat_mtx\"];\n  6 --> 2cebc438-ddc0-41e0-89ba-49b4bd3e2160;\n  style 2cebc438-ddc0-41e0-89ba-49b4bd3e2160 stroke:#2c3143,stroke-width:4px;\n  89fa1aad-9ec6-4351-97d5-f05cac09e08e[\"Output\\nquants_mat_cols_txt\"];\n  6 --> 89fa1aad-9ec6-4351-97d5-f05cac09e08e;\n  style 89fa1aad-9ec6-4351-97d5-f05cac09e08e stroke:#2c3143,stroke-width:4px;\n  3b3dda80-5d35-4c51-9ca0-90a2f909755f[\"Output\\nquants_mat_rows_txt\"];\n  6 --> 3b3dda80-5d35-4c51-9ca0-90a2f909755f;\n  style 3b3dda80-5d35-4c51-9ca0-90a2f909755f stroke:#2c3143,stroke-width:4px;\n  7[\"Alevin - no processing\"];\n  2 -->|output| 7;\n  3 -->|output| 7;\n  5 -->|fasta_output| 7;\n  1 -->|output| 7;\n  5 -->|feature_annotation| 7;\n  25d4d8f6-d166-4470-80fe-d0fdb0702371[\"Output\\nquants_mat_rows_txt_1\"];\n  7 --> 25d4d8f6-d166-4470-80fe-d0fdb0702371;\n  style 25d4d8f6-d166-4470-80fe-d0fdb0702371 stroke:#2c3143,stroke-width:4px;\n  d9ed1457-792b-4eaf-a9fc-2407bcd90da7[\"Output\\nquants_mat_mtx_1\"];\n  7 --> d9ed1457-792b-4eaf-a9fc-2407bcd90da7;\n  style d9ed1457-792b-4eaf-a9fc-2407bcd90da7 stroke:#2c3143,stroke-width:4px;\n  40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e[\"Output\\nquants_mat_cols_txt_1\"];\n  7 --> 40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e;\n  style 40df6aa8-3dfa-4946-bbc8-cacf4ca2a20e stroke:#2c3143,stroke-width:4px;\n  8[\"Droplet rank plot - raw barcodes\"];\n  6 -->|raw_cb_frequency_txt| 8;\n  9[\"Droplet rank plot - Alevin barcodes\"];\n  6 -->|quants_mat_mtx| 9;\n  10[\"salmonKallistoMtxTo10x\"];\n  7 -->|quants_mat_rows_txt| 10;\n  7 -->|quants_mat_cols_txt| 10;\n  7 -->|quants_mat_mtx| 10;\n  11[\"Join two Datasets\"];\n  10 -->|genes_out| 11;\n  4 -->|feature_annotation| 11;\n  12[\"Cut\"];\n  11 -->|out_file1| 12;\n  13[\"DropletUtils Read10x\"];\n  10 -->|barcodes_out| 13;\n  12 -->|out_file1| 13;\n  10 -->|matrix_out| 13;\n  14[\"DropletUtils emptyDrops\"];\n  13 -->|output_rds| 14;\n  15[\"SCEasy Converter\"];\n  14 -->|output_rdata| 15;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Generating a single cell matrix using Alevin",
                 "outputs": [
                     {
@@ -221984,6 +570135,13 @@
             ]
         },
         "admin_install_yaml": "---\ninstall_tool_dependencies: true\ninstall_repository_dependencies: true\ninstall_resolver_dependencies: true\ntools:\n- name: dropletutils\n  owner: iuc\n  revisions: a9caad671439\n  tool_panel_section_label: Single-cell\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: multiqc\n  owner: iuc\n  revisions: 75c93c70d094\n  tool_panel_section_label: Quality Control\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n- name: rna_starsolo\n  owner: iuc\n  revisions: 13022c3d3076\n  tool_panel_section_label: Mapping\n  tool_shed_url: https://toolshed.g2.bx.psu.edu/\n",
+        "answer_histories": [
+            {
+                "date": "2024-10-04",
+                "history": "https://usegalaxy.org/u/videmp/h/pre-processing-of-10x-single-cell-rna-datasets",
+                "label": "UseGalaxy.org"
+            }
+        ],
         "api": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.json",
         "contributors": [
             {
@@ -222067,11 +570225,11 @@
         ],
         "dir": "topics/single-cell/tutorials/scrna-preprocessing-tenx",
         "edam_operation": [
-            "Sequence alignment",
+            "Loading",
             "Validation",
             "Sequencing quality control",
             "Community profiling",
-            "Loading"
+            "Sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -222097,7 +570255,6 @@
         "inexact_supported_servers": [
             "HyPhy HIV NGS Tools",
             "UseGalaxy.be",
-            "UseGalaxy.fr",
             "UseGalaxy.no"
         ],
         "js_requirements": {
@@ -222110,13 +570267,13 @@
         ],
         "layout": "tutorial_hands_on",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-06-14",
+        "mod_date": "2024-10-04",
         "objectives": [
             "Demultiplex single-cell FASTQ data from 10X Genomics",
             "Learn about transparent matrix formats",
             "Understand the importance of high and low quality cells"
         ],
-        "pageviews": 11241,
+        "pageviews": 11325,
         "priority": 1,
         "pub_date": "2019-09-11",
         "questions": [
@@ -222167,9 +570324,9 @@
         ],
         "short_id": "T00252",
         "short_tools": [
-            "multiqc",
+            "rna_starsolo",
             "dropletutils",
-            "rna_starsolo"
+            "multiqc"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -222209,14 +570366,599 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                }
+            ]
+        },
+        "supported_servers_matrix": {
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+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
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+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
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+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "servers": [
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+                            "state": "missing"
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+                            "state": "missing"
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
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+                        {
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+                            "state": "missing"
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+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
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+                            "server": "http://gigagalaxy.net/",
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+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                            "state": "missing"
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+                            "server": "https://palfinder.ls.manchester.ac.uk/",
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+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
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+                            "state": "inexact",
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+                                "1.2.1+3",
+                                "1.2.1+4",
+                                "1.2.1+2",
+                                "1.2.1+5",
+                                "1.10.0+galaxy1",
+                                "1.2.1+1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.10.0+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.10.0+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.10.0+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.10.0+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.10.0+galaxy2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.10.0+galaxy2"
+                },
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+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
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+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "1.7",
+                                "1.6",
+                                "1.11+galaxy1",
+                                "1.11+galaxy0"
+                            ]
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@@ -222285,11 +571027,20 @@
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+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.9.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.9.0+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.9.0+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.9.0+galaxy1"
+                }
+            ]
+        },
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         "tags": [
             "10x",
@@ -222785,8 +573561,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 67,
-        "visitors": 3827,
+        "visit_duration": 66,
+        "visitors": 3864,
         "workflows": [
             {
                 "creators": [
@@ -222844,7 +573620,7 @@
                 ],
                 "license": "CC-BY-4.0",
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "scATAC-seq Count Matrix Filtering",
                 "outputs": [],
                 "parent_id": "single-cell/scatac-preprocessing-tenx",
@@ -222978,7 +573754,7 @@
                 ],
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "scATAC-seq FASTQ to Count Matrix",
                 "outputs": [],
                 "parent_id": "single-cell/scatac-preprocessing-tenx",
@@ -223275,8 +574051,8 @@
         ],
         "dir": "topics/single-cell/tutorials/scrna-data-ingest",
         "edam_operation": [
-            "Community profiling",
-            "Loading"
+            "Loading",
+            "Community profiling"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -223311,7 +574087,7 @@
             "You will perform conversions between the most common single cell formats.",
             "You will downsample FASTQ files."
         ],
-        "pageviews": 1011,
+        "pageviews": 1037,
         "priority": 1,
         "pub_date": "2024-02-13",
         "questions": [
@@ -223323,23 +574099,23 @@
         ],
         "short_id": "T00418",
         "short_tools": [
-            "monocle3_create",
-            "join1",
-            "datamash_transpose",
+            "Cut1",
             "dropletutils_read_10x",
-            "Filter1",
-            "seurat_read10x",
-            "anndata_ops",
+            "dropletutils",
             "fastq_to_tabular",
+            "tabular_to_fastq",
             "scanpy_filter_cells",
+            "regexColumn1",
+            "tp_tail_tool",
+            "join1",
+            "anndata_ops",
             "sceasy_convert",
-            "Cut1",
+            "monocle3_create",
             "anndata_inspect",
-            "dropletutils",
-            "regexColumn1",
+            "datamash_transpose",
+            "seurat_read10x",
             "tp_cut_tool",
-            "tp_tail_tool",
-            "tabular_to_fastq"
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -223354,6 +574130,3095 @@
             ],
             "inexact": []
         },
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+                    "url": "http://apostl.moffitt.org/"
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
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+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
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+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
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+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
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+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
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+                    "url": "https://galaxytrakr.org/",
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+                    "url": "http://hyperbrowser.uio.no/hb/"
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+                    "usegalaxy": false
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
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+                    "url": "https://palfinder.ls.manchester.ac.uk/"
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+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
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+                    "url": "https://usegalaxy.no/",
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+                    "url": "https://usegalaxy.org",
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+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
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+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
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+                    "servers": [
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+                            "state": "local"
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                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAnnData\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Inspect AnnData\"];\n  0 -->|output| 1;\n  7bdb825c-6a89-4a34-bbd9-a79c309c9750[\"Output\\nInspect AnnData: obs\"];\n  1 --> 7bdb825c-6a89-4a34-bbd9-a79c309c9750;\n  style 7bdb825c-6a89-4a34-bbd9-a79c309c9750 stroke:#2c3143,stroke-width:4px;\n  2[\"Inspect AnnData\"];\n  0 -->|output| 2;\n  79a2e3e5-4bd6-42de-864c-a5dc2412cb86[\"Output\\nInspect AnnData: var\"];\n  2 --> 79a2e3e5-4bd6-42de-864c-a5dc2412cb86;\n  style 79a2e3e5-4bd6-42de-864c-a5dc2412cb86 stroke:#2c3143,stroke-width:4px;\n  3[\"Inspect AnnData\"];\n  0 -->|output| 3;\n  7a254954-7e32-4e8a-bd4c-a79abf9db8d8[\"Output\\nInspect AnnData: X\"];\n  3 --> 7a254954-7e32-4e8a-bd4c-a79abf9db8d8;\n  style 7a254954-7e32-4e8a-bd4c-a79abf9db8d8 stroke:#2c3143,stroke-width:4px;\n  4[\"Transpose\"];\n  3 -->|X| 4;\n  5[\"Monocle3 create\"];\n  1 -->|obs| 5;\n  4 -->|out_file| 5;\n  2 -->|var| 5;\n  6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c[\"Output\\nCDS Monocle file\"];\n  5 --> 6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c;\n  style 6bf4a0ea-3cb9-470c-9863-0a7eb0bc3d8c stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "AnnData to Cell Data Set (CDS) conversion",
                 "outputs": [
                     {
@@ -223797,7 +577662,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAnnData\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Inspect AnnData\"];\n  0 -->|output| 1;\n  6d03d713-8d71-4f6a-9f83-cd999f423ebf[\"Output\\nInspect AnnData: obs\"];\n  1 --> 6d03d713-8d71-4f6a-9f83-cd999f423ebf;\n  style 6d03d713-8d71-4f6a-9f83-cd999f423ebf stroke:#2c3143,stroke-width:4px;\n  2[\"Inspect AnnData\"];\n  0 -->|output| 2;\n  ea025a8a-6f3a-4e38-a3af-db406886c7de[\"Output\\nInspect AnnData: X\"];\n  2 --> ea025a8a-6f3a-4e38-a3af-db406886c7de;\n  style ea025a8a-6f3a-4e38-a3af-db406886c7de stroke:#2c3143,stroke-width:4px;\n  3[\"Transpose\"];\n  2 -->|X| 3;\n  4[\"DropletUtils\"];\n  3 -->|out_file| 4;\n  5[\"Seurat Read10x\"];\n  4 -->|barcodes_out| 5;\n  4 -->|genes_out| 5;\n  4 -->|matrix_out| 5;\n  1 -->|obs| 5;\n  e5fec5dc-4706-48e5-8326-05e70290552d[\"Output\\nConverted Seurat object\"];\n  5 --> e5fec5dc-4706-48e5-8326-05e70290552d;\n  style e5fec5dc-4706-48e5-8326-05e70290552d stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "AnnData to Seurat conversion",
                 "outputs": [
                     {
@@ -224103,7 +577968,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAnnData\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Parameter\\nCell ID column\"];\n  style 1 fill:#ded,stroke:#393,stroke-width:4px;\n  2[\"Inspect AnnData\"];\n  0 -->|output| 2;\n  8b9200c2-96e6-40fa-a8e9-1e99638c733f[\"Output\\nInspect AnnData: obs\"];\n  2 --> 8b9200c2-96e6-40fa-a8e9-1e99638c733f;\n  style 8b9200c2-96e6-40fa-a8e9-1e99638c733f stroke:#2c3143,stroke-width:4px;\n  3[\"Inspect AnnData\"];\n  0 -->|output| 3;\n  9fc4ce5a-8384-484d-b1cd-c0f5137cf821[\"Output\\nInspect AnnData: X\"];\n  3 --> 9fc4ce5a-8384-484d-b1cd-c0f5137cf821;\n  style 9fc4ce5a-8384-484d-b1cd-c0f5137cf821 stroke:#2c3143,stroke-width:4px;\n  4[\"Transpose\"];\n  3 -->|X| 4;\n  5[\"DropletUtils\"];\n  4 -->|out_file| 5;\n  6[\"DropletUtils Read10x\"];\n  1 -->|output| 6;\n  2 -->|obs| 6;\n  5 -->|barcodes_out| 6;\n  5 -->|genes_out| 6;\n  5 -->|matrix_out| 6;\n  3256e23f-2026-407d-aa25-0f8c0f3ae3f7[\"Output\\nConverted SCE object\"];\n  6 --> 3256e23f-2026-407d-aa25-0f8c0f3ae3f7;\n  style 3256e23f-2026-407d-aa25-0f8c0f3ae3f7 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "AnnData to SingleCellExperiment (SCE) conversion",
                 "outputs": [
                     {
@@ -224526,13 +578391,13 @@
         ],
         "dir": "topics/single-cell/tutorials/scrna-preprocessing",
         "edam_operation": [
-            "RNA-Seq quantification",
             "Data handling",
-            "Sequence alignment",
+            "Sequence alignment analysis",
             "Validation",
             "Sequencing quality control",
-            "Sequence alignment analysis",
-            "Read summarisation"
+            "RNA-Seq quantification",
+            "Read summarisation",
+            "Sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -224555,7 +578420,6 @@
         "inexact_supported_servers": [
             "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
@@ -224579,7 +578443,7 @@
             "Obtain an overview of general alignment and quantification techniques",
             "Generate a count matrix for downstream single-cell RNA analysis"
         ],
-        "pageviews": 5903735,
+        "pageviews": 5935777,
         "priority": 1,
         "pub_date": "2019-02-22",
         "questions": [
@@ -224605,16 +578469,16 @@
         ],
         "short_id": "T00251",
         "short_tools": [
-            "rna_star",
-            "samtools_stats",
+            "bamFilter",
             "tp_sed_tool",
+            "rna_star",
             "umi_tools_count",
-            "bamFilter",
-            "multiqc",
             "umi_tools_extract",
-            "collection_column_join",
             "__FLATTEN__",
-            "featurecounts"
+            "collection_column_join",
+            "featurecounts",
+            "samtools_stats",
+            "multiqc"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -224639,10 +578503,141 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -224657,6 +578652,2313 @@
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "id": "__FLATTEN__",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "9.3+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
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+                        {
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
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+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
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+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.1.1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.1.1"
+                },
+                {
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+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
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+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "2.5.2+galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "2.4.1"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
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@@ -224807,7 +581109,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
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@@ -225868,7 +582170,7 @@
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@@ -226396,7 +582698,7 @@
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@@ -226475,6 +582777,10 @@
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@@ -226662,7 +582968,7 @@
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             "Find relevant information in GTF files for the particulars of their study, and include this in data matrix metadata"
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@@ -226716,6 +583022,10 @@
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@@ -226795,13 +583070,6 @@
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@@ -226809,13 +583077,6 @@
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@@ -227222,11 +585072,20 @@
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-                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nBarcodes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGenes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nMatrix\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nmito header\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Import Anndata and loom\"];\n  2 -->|output| 4;\n  0 -->|output| 4;\n  1 -->|output| 4;\n  5[\"Inspect AnnData\"];\n  4 -->|anndata| 5;\n  6[\"Inspect AnnData\"];\n  4 -->|anndata| 6;\n  7[\"Inspect AnnData\"];\n  4 -->|anndata| 7;\n  8[\"Filter\"];\n  4 -->|anndata| 8;\n  9[\"Inspect AnnData\"];\n  4 -->|anndata| 9;\n  10[\"Inspect AnnData\"];\n  8 -->|anndata_out| 10;\n  11[\"Select last\"];\n  10 -->|var| 11;\n  12[\"Text reformatting\"];\n  11 -->|outfile| 12;\n  13[\"Search in textfiles\"];\n  11 -->|outfile| 13;\n  14[\"Replace Text\"];\n  12 -->|outfile| 14;\n  15[\"Concatenate datasets\"];\n  3 -->|output| 15;\n  14 -->|outfile| 15;\n  16[\"Manipulate AnnData\"];\n  8 -->|anndata_out| 16;\n  15 -->|out_file1| 16;\n  17[\"Inspect and manipulate\"];\n  16 -->|anndata| 17;\n  18[\"Inspect AnnData\"];\n  16 -->|anndata| 18;\n  19[\"Plot\"];\n  17 -->|anndata_out| 19;\n  4ab8b810-4e79-46b2-b740-74e267f5e209[\"Output\\nout_png\"];\n  19 --> 4ab8b810-4e79-46b2-b740-74e267f5e209;\n  style 4ab8b810-4e79-46b2-b740-74e267f5e209 stroke:#2c3143,stroke-width:4px;\n  20[\"Filter\"];\n  17 -->|anndata_out| 20;\n  21[\"Plot\"];\n  17 -->|anndata_out| 21;\n  02478047-eb04-4a4e-b1ff-f3cb3c7673d5[\"Output\\nout_png\"];\n  21 --> 02478047-eb04-4a4e-b1ff-f3cb3c7673d5;\n  style 02478047-eb04-4a4e-b1ff-f3cb3c7673d5 stroke:#2c3143,stroke-width:4px;\n  22[\"Plot\"];\n  17 -->|anndata_out| 22;\n  3eb66a4a-79fe-43a3-889b-d43daeae5e17[\"Output\\nout_png\"];\n  22 --> 3eb66a4a-79fe-43a3-889b-d43daeae5e17;\n  style 3eb66a4a-79fe-43a3-889b-d43daeae5e17 stroke:#2c3143,stroke-width:4px;\n  23[\"Filter\"];\n  20 -->|anndata_out| 23;\n  24[\"Manipulate AnnData\"];\n  23 -->|anndata_out| 24;\n  25[\"Normalize\"];\n  24 -->|anndata| 25;\n  26[\"Inspect and manipulate\"];\n  25 -->|anndata_out| 26;\n  27[\"Manipulate AnnData\"];\n  26 -->|anndata_out| 27;\n  28[\"Filter\"];\n  27 -->|anndata| 28;\n  29[\"Manipulate AnnData\"];\n  28 -->|anndata_out| 29;\n  30[\"Plot\"];\n  28 -->|anndata_out| 30;\n  31[\"Remove confounders\"];\n  29 -->|anndata| 31;\n  32[\"Inspect and manipulate\"];\n  31 -->|anndata_out| 32;\n  33[\"Cluster, infer trajectories and embed\"];\n  32 -->|anndata_out| 33;\n  96cbb37e-e755-4479-9f14-f0e14f689868[\"Output\\nanndata_out\"];\n  33 --> 96cbb37e-e755-4479-9f14-f0e14f689868;\n  style 96cbb37e-e755-4479-9f14-f0e14f689868 stroke:#2c3143,stroke-width:4px;\n  34[\"Plot\"];\n  33 -->|anndata_out| 34;\n  35[\"Plot\"];\n  33 -->|anndata_out| 35;\n  5dc45ef9-c56e-4dbd-9817-367c981a2041[\"Output\\nout_png\"];\n  35 --> 5dc45ef9-c56e-4dbd-9817-367c981a2041;\n  style 5dc45ef9-c56e-4dbd-9817-367c981a2041 stroke:#2c3143,stroke-width:4px;\n  36[\"Inspect and manipulate\"];\n  33 -->|anndata_out| 36;\n  37[\"Plot\"];\n  33 -->|anndata_out| 37;\n  38[\"Plot\"];\n  33 -->|anndata_out| 38;\n  39[\"Cluster, infer trajectories and embed\"];\n  36 -->|anndata_out| 39;\n  40[\"Cluster, infer trajectories and embed\"];\n  39 -->|anndata_out| 40;\n  41[\"Plot\"];\n  39 -->|anndata_out| 41;\n  29513947-d16c-48b2-93ff-dd78cd99ecb7[\"Output\\nout_png\"];\n  41 --> 29513947-d16c-48b2-93ff-dd78cd99ecb7;\n  style 29513947-d16c-48b2-93ff-dd78cd99ecb7 stroke:#2c3143,stroke-width:4px;\n  42[\"Inspect and manipulate\"];\n  40 -->|anndata_out| 42;\n  43[\"Inspect and manipulate\"];\n  40 -->|anndata_out| 43;\n  da91ad5a-dd9c-482e-accc-8e42d645e7b1[\"Output\\nanndata_out\"];\n  43 --> da91ad5a-dd9c-482e-accc-8e42d645e7b1;\n  style da91ad5a-dd9c-482e-accc-8e42d645e7b1 stroke:#2c3143,stroke-width:4px;\n  44[\"Plot\"];\n  40 -->|anndata_out| 44;\n  45[\"Inspect AnnData\"];\n  42 -->|anndata_out| 45;\n  868797a3-ab74-45bf-96d1-84451a16f882[\"Output\\nuns_rank_genes_groups_names\"];\n  45 --> 868797a3-ab74-45bf-96d1-84451a16f882;\n  style 868797a3-ab74-45bf-96d1-84451a16f882 stroke:#2c3143,stroke-width:4px;\n  46[\"Plot\"];\n  42 -->|anndata_out| 46;\n  47[\"Plot\"];\n  43 -->|anndata_out| 47;\n  2d042636-8fd1-42e3-af8d-83b4d613f075[\"Output\\nout_png\"];\n  47 --> 2d042636-8fd1-42e3-af8d-83b4d613f075;\n  style 2d042636-8fd1-42e3-af8d-83b4d613f075 stroke:#2c3143,stroke-width:4px;\n  48[\"Manipulate AnnData\"];\n  43 -->|anndata_out| 48;\n  51289df3-101f-4c6c-ae85-a8f46c2f33ea[\"Output\\nanndata\"];\n  48 --> 51289df3-101f-4c6c-ae85-a8f46c2f33ea;\n  style 51289df3-101f-4c6c-ae85-a8f46c2f33ea stroke:#2c3143,stroke-width:4px;\n  49[\"Inspect and manipulate\"];\n  43 -->|anndata_out| 49;\n  50[\"Inspect AnnData\"];\n  43 -->|anndata_out| 50;\n  e617acd1-e59d-4f20-b39d-9dc0f832b0db[\"Output\\nuns_rank_genes_groups_names\"];\n  50 --> e617acd1-e59d-4f20-b39d-9dc0f832b0db;\n  style e617acd1-e59d-4f20-b39d-9dc0f832b0db stroke:#2c3143,stroke-width:4px;\n  51[\"Plot\"];\n  43 -->|anndata_out| 51;\n  983e7cee-7028-456c-9db2-bf0ad3e52de5[\"Output\\nout_png\"];\n  51 --> 983e7cee-7028-456c-9db2-bf0ad3e52de5;\n  style 983e7cee-7028-456c-9db2-bf0ad3e52de5 stroke:#2c3143,stroke-width:4px;\n  52[\"Inspect clusters\"];\n  43 -->|anndata_out| 52;\n  53[\"Plot\"];\n  43 -->|anndata_out| 53;\n  734099bb-f454-4d8c-bc78-a269b0570c41[\"Output\\nout_png\"];\n  53 --> 734099bb-f454-4d8c-bc78-a269b0570c41;\n  style 734099bb-f454-4d8c-bc78-a269b0570c41 stroke:#2c3143,stroke-width:4px;\n  54[\"Plot\"];\n  43 -->|anndata_out| 54;\n  55[\"Plot\"];\n  43 -->|anndata_out| 55;\n  39f2d4b6-f2e8-41b3-a00a-a2c5b54face2[\"Output\\nout_png\"];\n  55 --> 39f2d4b6-f2e8-41b3-a00a-a2c5b54face2;\n  style 39f2d4b6-f2e8-41b3-a00a-a2c5b54face2 stroke:#2c3143,stroke-width:4px;\n  56[\"Plot\"];\n  48 -->|anndata| 56;\n  e0979d1e-eb87-4a7b-904f-a5116c7b8fff[\"Output\\nout_svg\"];\n  56 --> e0979d1e-eb87-4a7b-904f-a5116c7b8fff;\n  style e0979d1e-eb87-4a7b-904f-a5116c7b8fff stroke:#2c3143,stroke-width:4px;\n  57[\"Plot\"];\n  48 -->|anndata| 57;\n  58[\"Plot\"];\n  48 -->|anndata| 58;\n  bd14e644-2a32-4a81-bd83-042ee46d118a[\"Output\\nout_png\"];\n  58 --> bd14e644-2a32-4a81-bd83-042ee46d118a;\n  style bd14e644-2a32-4a81-bd83-042ee46d118a stroke:#2c3143,stroke-width:4px;\n  59[\"Plot\"];\n  49 -->|anndata_out| 59;\n  e9cf90db-ac42-4876-8abd-183fea271666[\"Output\\ncollection_png\"];\n  59 --> e9cf90db-ac42-4876-8abd-183fea271666;\n  style e9cf90db-ac42-4876-8abd-183fea271666 stroke:#2c3143,stroke-width:4px;\n  60[\"Plot\"];\n  49 -->|anndata_out| 60;\n  aef215b1-dbb4-447b-9297-c90536842c8e[\"Output\\nout_png\"];\n  60 --> aef215b1-dbb4-447b-9297-c90536842c8e;\n  style aef215b1-dbb4-447b-9297-c90536842c8e stroke:#2c3143,stroke-width:4px;\n  61[\"Datamash\"];\n  52 -->|obs| 61;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nBarcodes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGenes\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nMatrix\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Import Anndata\"];\n  2 -->|output| 3;\n  0 -->|output| 3;\n  1 -->|output| 3;\n  4[\"Inspect AnnData\"];\n  3 -->|anndata| 4;\n  5[\"Scanpy filter\"];\n  3 -->|anndata| 5;\n  6[\"Inspect AnnData\"];\n  3 -->|anndata| 6;\n  7[\"Inspect AnnData\"];\n  3 -->|anndata| 7;\n  8[\"Inspect AnnData\"];\n  3 -->|anndata| 8;\n  9[\"Manipulate AnnData\"];\n  5 -->|anndata_out| 9;\n  10[\"Scanpy Inspect and manipulate\"];\n  9 -->|anndata| 10;\n  11[\"Inspect AnnData\"];\n  9 -->|anndata| 11;\n  12[\"Scanpy plot\"];\n  10 -->|anndata_out| 12;\n  a13ef439-dade-4aa1-91d3-0e050da961af[\"Output\\npl_scatter_total_counts_vs_n_genes_by_counts\"];\n  12 --> a13ef439-dade-4aa1-91d3-0e050da961af;\n  style a13ef439-dade-4aa1-91d3-0e050da961af stroke:#2c3143,stroke-width:4px;\n  13[\"Scanpy filter\"];\n  10 -->|anndata_out| 13;\n  14[\"Scanpy plot\"];\n  10 -->|anndata_out| 14;\n  f3ed5faf-e274-4575-91d4-c6a49d1aef6d[\"Output\\npl_scatter_n_genes_by_counts_vs_pct_mito\"];\n  14 --> f3ed5faf-e274-4575-91d4-c6a49d1aef6d;\n  style f3ed5faf-e274-4575-91d4-c6a49d1aef6d stroke:#2c3143,stroke-width:4px;\n  15[\"Scanpy plot\"];\n  10 -->|anndata_out| 15;\n  51634f2e-a033-4ef8-a785-079c415ccfae[\"Output\\npl_violin\"];\n  15 --> 51634f2e-a033-4ef8-a785-079c415ccfae;\n  style 51634f2e-a033-4ef8-a785-079c415ccfae stroke:#2c3143,stroke-width:4px;\n  16[\"Scanpy filter\"];\n  13 -->|anndata_out| 16;\n  17[\"Manipulate AnnData\"];\n  16 -->|anndata_out| 17;\n  18[\"Scanpy normalize\"];\n  17 -->|anndata| 18;\n  19[\"Scanpy Inspect and manipulate\"];\n  18 -->|anndata_out| 19;\n  20[\"Manipulate AnnData\"];\n  19 -->|anndata_out| 20;\n  21[\"Scanpy filter\"];\n  20 -->|anndata| 21;\n  22[\"Manipulate AnnData\"];\n  21 -->|anndata_out| 22;\n  23[\"Scanpy plot\"];\n  21 -->|anndata_out| 23;\n  7c1818c2-b46f-4274-b309-68b45c7387f9[\"Output\\npl_highly_variable\"];\n  23 --> 7c1818c2-b46f-4274-b309-68b45c7387f9;\n  style 7c1818c2-b46f-4274-b309-68b45c7387f9 stroke:#2c3143,stroke-width:4px;\n  24[\"Scanpy remove confounders\"];\n  22 -->|anndata| 24;\n  25[\"Scanpy Inspect and manipulate\"];\n  24 -->|anndata_out| 25;\n  26[\"Scanpy cluster, embed\"];\n  25 -->|anndata_out| 26;\n  27[\"Scanpy plot\"];\n  26 -->|anndata_out| 27;\n  9fa13332-20f5-4cf3-8b21-f4cf0be0f7d3[\"Output\\npl_pca_overview\"];\n  27 --> 9fa13332-20f5-4cf3-8b21-f4cf0be0f7d3;\n  style 9fa13332-20f5-4cf3-8b21-f4cf0be0f7d3 stroke:#2c3143,stroke-width:4px;\n  28[\"Scanpy plot\"];\n  26 -->|anndata_out| 28;\n  23fad9ca-caed-4cb5-bf9c-77dccd7fff09[\"Output\\npl_pca_overview_genes\"];\n  28 --> 23fad9ca-caed-4cb5-bf9c-77dccd7fff09;\n  style 23fad9ca-caed-4cb5-bf9c-77dccd7fff09 stroke:#2c3143,stroke-width:4px;\n  29[\"Scanpy plot\"];\n  26 -->|anndata_out| 29;\n  d80530df-fb7b-4d72-8c12-ae09d9eccc7c[\"Output\\npl_pca_loadings\"];\n  29 --> d80530df-fb7b-4d72-8c12-ae09d9eccc7c;\n  style d80530df-fb7b-4d72-8c12-ae09d9eccc7c stroke:#2c3143,stroke-width:4px;\n  30[\"Scanpy Inspect and manipulate\"];\n  26 -->|anndata_out| 30;\n  31[\"Scanpy plot\"];\n  26 -->|anndata_out| 31;\n  2e3480a4-1dfb-4e43-b70c-459d155853e9[\"Output\\npl_pca_variance_ratio\"];\n  31 --> 2e3480a4-1dfb-4e43-b70c-459d155853e9;\n  style 2e3480a4-1dfb-4e43-b70c-459d155853e9 stroke:#2c3143,stroke-width:4px;\n  32[\"Scanpy cluster, embed\"];\n  30 -->|anndata_out| 32;\n  33[\"Scanpy plot\"];\n  32 -->|anndata_out| 33;\n  504ea6ab-68a6-4c37-ae97-c58a99ff8381[\"Output\\npl_umap_initial\"];\n  33 --> 504ea6ab-68a6-4c37-ae97-c58a99ff8381;\n  style 504ea6ab-68a6-4c37-ae97-c58a99ff8381 stroke:#2c3143,stroke-width:4px;\n  34[\"Scanpy cluster, embed\"];\n  32 -->|anndata_out| 34;\n  35[\"Scanpy plot\"];\n  34 -->|anndata_out| 35;\n  c674ba29-f097-4242-8dc2-b22441233e73[\"Output\\npl_umap_louvain\"];\n  35 --> c674ba29-f097-4242-8dc2-b22441233e73;\n  style c674ba29-f097-4242-8dc2-b22441233e73 stroke:#2c3143,stroke-width:4px;\n  36[\"Scanpy Inspect and manipulate\"];\n  34 -->|anndata_out| 36;\n  37[\"Scanpy Inspect and manipulate\"];\n  34 -->|anndata_out| 37;\n  38[\"Inspect clusters\"];\n  36 -->|anndata_out| 38;\n  39[\"Scanpy plot\"];\n  36 -->|anndata_out| 39;\n  249d7c38-140c-403d-a0ed-effe1a17fdd6[\"Output\\npl_rank_gene_groups_t_test_wilcoxon_test\"];\n  39 --> 249d7c38-140c-403d-a0ed-effe1a17fdd6;\n  style 249d7c38-140c-403d-a0ed-effe1a17fdd6 stroke:#2c3143,stroke-width:4px;\n  40[\"Scanpy plot\"];\n  36 -->|anndata_out| 40;\n  c1395d95-9c53-48c9-972e-cf93116e85db[\"Output\\npl_rank_genes_heatmap\"];\n  40 --> c1395d95-9c53-48c9-972e-cf93116e85db;\n  style c1395d95-9c53-48c9-972e-cf93116e85db stroke:#2c3143,stroke-width:4px;\n  41[\"Scanpy plot\"];\n  36 -->|anndata_out| 41;\n  6b30a9d8-01be-4757-999d-cade6b516df6[\"Output\\npl_stacked_violin_marker_genes\"];\n  41 --> 6b30a9d8-01be-4757-999d-cade6b516df6;\n  style 6b30a9d8-01be-4757-999d-cade6b516df6 stroke:#2c3143,stroke-width:4px;\n  42[\"Scanpy plot\"];\n  36 -->|anndata_out| 42;\n  30bc8ca7-37b7-4efc-b442-8bc4cb986d7e[\"Output\\npl_umap_marker_genes\"];\n  42 --> 30bc8ca7-37b7-4efc-b442-8bc4cb986d7e;\n  style 30bc8ca7-37b7-4efc-b442-8bc4cb986d7e stroke:#2c3143,stroke-width:4px;\n  43[\"Scanpy Inspect and manipulate\"];\n  36 -->|anndata_out| 43;\n  44[\"Inspect AnnData\"];\n  36 -->|anndata_out| 44;\n  9092ecc8-cace-45c4-8efa-bd4d27275060[\"Output\\nuns_rank_genes_groups_names_wilcoxon_test\"];\n  44 --> 9092ecc8-cace-45c4-8efa-bd4d27275060;\n  style 9092ecc8-cace-45c4-8efa-bd4d27275060 stroke:#2c3143,stroke-width:4px;\n  45[\"Manipulate AnnData\"];\n  36 -->|anndata_out| 45;\n  545a105c-1202-4209-aff2-201fd953e398[\"Output\\nanndata_out\"];\n  45 --> 545a105c-1202-4209-aff2-201fd953e398;\n  style 545a105c-1202-4209-aff2-201fd953e398 stroke:#2c3143,stroke-width:4px;\n  46[\"Scanpy plot\"];\n  36 -->|anndata_out| 46;\n  ad91827e-e8cc-45ec-b32f-935cf44a77d1[\"Output\\npl_violin_louvain\"];\n  46 --> ad91827e-e8cc-45ec-b32f-935cf44a77d1;\n  style ad91827e-e8cc-45ec-b32f-935cf44a77d1 stroke:#2c3143,stroke-width:4px;\n  47[\"Scanpy plot\"];\n  37 -->|anndata_out| 47;\n  4011556e-85f9-470e-b902-7ef9df11fef5[\"Output\\npl_rank_gene_groups_t_test\"];\n  47 --> 4011556e-85f9-470e-b902-7ef9df11fef5;\n  style 4011556e-85f9-470e-b902-7ef9df11fef5 stroke:#2c3143,stroke-width:4px;\n  48[\"Inspect AnnData\"];\n  37 -->|anndata_out| 48;\n  55f664c3-b771-4115-890f-3eb4637813b0[\"Output\\nuns_rank_genes_groups_names_t_test\"];\n  48 --> 55f664c3-b771-4115-890f-3eb4637813b0;\n  style 55f664c3-b771-4115-890f-3eb4637813b0 stroke:#2c3143,stroke-width:4px;\n  49[\"Datamash\"];\n  38 -->|obs| 49;\n  10693ba5-026d-443b-aa80-b4dedbf4f940[\"Output\\ncells_per_cluster\"];\n  49 --> 10693ba5-026d-443b-aa80-b4dedbf4f940;\n  style 10693ba5-026d-443b-aa80-b4dedbf4f940 stroke:#2c3143,stroke-width:4px;\n  50[\"Scanpy plot\"];\n  43 -->|anndata_out| 50;\n  51878bf2-d055-4acc-b365-cc7f7a673f66[\"Output\\npl_rank_gene_groups_0_vs_1\"];\n  50 --> 51878bf2-d055-4acc-b365-cc7f7a673f66;\n  style 51878bf2-d055-4acc-b365-cc7f7a673f66 stroke:#2c3143,stroke-width:4px;\n  51[\"Scanpy plot\"];\n  43 -->|anndata_out| 51;\n  10a46aa1-5685-4480-a6eb-362f32b91fa1[\"Output\\npl_rank_gene_groups_violin_0_vs_1\"];\n  51 --> 10a46aa1-5685-4480-a6eb-362f32b91fa1;\n  style 10a46aa1-5685-4480-a6eb-362f32b91fa1 stroke:#2c3143,stroke-width:4px;\n  52[\"Scanpy plot\"];\n  45 -->|anndata| 52;\n  c8ae2d77-361a-41e0-b238-0f494d12b6d7[\"Output\\npl_umap_celltypes\"];\n  52 --> c8ae2d77-361a-41e0-b238-0f494d12b6d7;\n  style c8ae2d77-361a-41e0-b238-0f494d12b6d7 stroke:#2c3143,stroke-width:4px;\n  53[\"Scanpy plot\"];\n  45 -->|anndata| 53;\n  a3ceb616-64b8-4c79-ba94-4272a5bd747f[\"Output\\npl_dotplot_marker_genes\"];\n  53 --> a3ceb616-64b8-4c79-ba94-4272a5bd747f;\n  style a3ceb616-64b8-4c79-ba94-4272a5bd747f stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Clustering 3k PBMC with Scanpy",
                 "outputs": [
                     {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0",
                         "errors": null,
-                        "id": 19,
+                        "id": 12,
                         "input_connections": {
                             "adata": {
-                                "id": 17,
+                                "id": 10,
                                 "output_name": "anndata_out"
                             }
                         },
                         "inputs": [],
                         "label": null,
-                        "name": "Plot",
+                        "name": "Scanpy plot",
                         "outputs": [
                             {
                                 "name": "out_png",
@@ -227385,44 +585217,44 @@
                             }
                         ],
                         "position": {
-                            "left": 2799.999999999996,
-                            "top": 931
+                            "left": 1400.0005445845704,
+                            "top": 163
                         },
                         "post_job_actions": {},
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "9b0cdb8cf6be",
+                            "changeset_revision": "0185bd174ea0",
                             "name": "scanpy_plot",
                             "owner": "iuc",
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             "You will manipulate the metadata and matrix files.",
             "You will combine the metadata and matrix files into an AnnData or Seurat object for downstream analysis."
         ],
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+        "pageviews": 421,
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         "questions": [
@@ -228668,14 +586585,14 @@
         ],
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@@ -228691,6 +586608,1550 @@
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+                            "state": "exact",
+                            "version": "0.0.7+galaxy1"
+                        },
+                        {
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+                        },
+                        {
+                            "server": "https://usegalaxy.org",
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+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
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         "symlink": null,
         "tags": [
             "data import",
@@ -228729,8 +588190,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 325,
-        "visitors": 272,
+        "visit_duration": 318,
+        "visitors": 277,
         "workflows": [
             {
                 "creators": [
@@ -228801,7 +588262,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nSC-Atlas experiment accession\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"EBI SCXA Data Retrieval\"];\n  0 -->|output| 1;\n  2[\"Rename batch numbers\"];\n  1 -->|design_tsv| 2;\n  3[\"Mito genes check\"];\n  1 -->|genes_tsv| 3;\n  b0762cfd-58bd-4c39-ae41-2dca4289c541[\"Output\\nMito genes check\"];\n  3 --> b0762cfd-58bd-4c39-ae41-2dca4289c541;\n  style b0762cfd-58bd-4c39-ae41-2dca4289c541 stroke:#2c3143,stroke-width:4px;\n  4[\"Rename cell metadata headers\"];\n  2 -->|out_file1| 4;\n  5[\"Create AnnData\"];\n  1 -->|barcode_tsv| 5;\n  4 -->|outfile| 5;\n  1 -->|genes_tsv| 5;\n  1 -->|matrix_mtx| 5;\n  938cd594-61cf-4037-a58b-c09c065db505[\"Output\\nAnnData object\"];\n  5 --> 938cd594-61cf-4037-a58b-c09c065db505;\n  style 938cd594-61cf-4037-a58b-c09c065db505 stroke:#2c3143,stroke-width:4px;\n  6[\"Seurat Read10x\"];\n  1 -->|barcode_tsv| 6;\n  1 -->|genes_tsv| 6;\n  1 -->|matrix_mtx| 6;\n  4 -->|outfile| 6;\n  c24e9d83-c175-40a2-9c36-eeb486fe323e[\"Output\\nSeurat object\"];\n  6 --> c24e9d83-c175-40a2-9c36-eeb486fe323e;\n  style c24e9d83-c175-40a2-9c36-eeb486fe323e stroke:#2c3143,stroke-width:4px;\n  7[\"AnnData Operations\"];\n  5 -->|output_h5ad| 7;\n  b47f801f-bedb-4136-a5e9-378a815a1799[\"Output\\nMito-counted AnnData for downstream analysis\"];\n  7 --> b47f801f-bedb-4136-a5e9-378a815a1799;\n  style b47f801f-bedb-4136-a5e9-378a815a1799 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "EBI SCXA to AnnData (Scanpy) or Seurat Object",
                 "outputs": [
                     {
@@ -229246,7 +588707,7 @@
             "Determining the top most expressive genes per cluster",
             "Correcting for unwanted variation"
         ],
-        "pageviews": 960,
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         "pub_date": "2019-03-25",
         "questions": [
@@ -229272,15 +588733,15 @@
         ],
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-            "tp_head_tool",
             "raceid_inspectclusters",
             "datamash_transpose",
-            "datamash_ops"
+            "raceid_trajectory",
+            "datamash_ops",
+            "raceid_inspecttrajectory",
+            "raceid_clustering",
+            "tp_head_tool"
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         "slides": false,
         "slides_recordings": false,
@@ -229289,6 +588750,2087 @@
             "exact": [],
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+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
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         "tags": null,
         "time_estimation": "3H",
@@ -229328,8 +590870,8 @@
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         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 82,
-        "visitors": 800,
+        "visit_duration": 81,
+        "visitors": 809,
         "workflows": [
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@@ -229392,7 +590934,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "RaceID Workflow",
                 "outputs": [
                     {
@@ -230096,7 +591638,7 @@
             "Use the cell cycle genes to regress out the effects of the cell cycle",
             "Create PCA plots to understand the impact of the regression"
         ],
-        "pageviews": 1730,
+        "pageviews": 1752,
         "priority": 2,
         "pub_date": "2023-01-25",
         "questions": [
@@ -230115,17 +591657,17 @@
         ],
         "short_id": "T00248",
         "short_tools": [
-            "table_compute",
-            "tp_easyjoin_tool",
+            "cat1",
             "sort1",
-            "scanpy_plot",
+            "tp_easyjoin_tool",
             "scanpy_cluster_reduce_dimension",
+            "table_compute",
             "anndata_inspect",
             "anndata_manipulate",
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             "scanpy_inspect",
-            "scanpy_regress_variable",
-            "cat1",
-            "addValue"
+            "scanpy_regress_variable"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -230146,6 +591688,1681 @@
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@@ -230184,8 +593401,8 @@
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-        "visitors": 1435,
+        "visit_duration": 49,
+        "visitors": 1454,
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@@ -230314,7 +593531,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Cell Cycle Regression Workflow",
                 "outputs": [
                     {
@@ -231345,7 +594562,7 @@
             "Combine data matrices from different samples in the same experiment",
             "Label the metadata for downstream processing"
         ],
-        "pageviews": 2665,
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         "questions": [
@@ -231394,14 +594611,14 @@
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             "anndata_manipulate",
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@@ -231427,6 +594644,1284 @@
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@@ -231463,8 +595958,8 @@
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 144,
-        "visitors": 1846,
+        "visit_duration": 146,
+        "visitors": 1868,
         "workflows": [
             {
                 "creators": [
@@ -231689,7 +596184,7 @@
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                 "license": "CC-BY-4.0",
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Combining datasets after pre-processing",
                 "outputs": [
                     {
@@ -232294,7 +596789,7 @@
             "Appraise data outputs and decisions",
             "Explain why single cell analysis is an iterative process (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly)"
         ],
-        "pageviews": 2391,
+        "pageviews": 2438,
         "priority": 2,
         "pub_date": "2023-10-02",
         "questions": [
@@ -232350,6 +596845,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
+        },
         "symlink": null,
         "tags": [
             "10x",
@@ -232378,8 +596877,8 @@
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-        "visit_duration": 50,
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+        "visit_duration": 53,
+        "visitors": 2160,
         "zenodo_link": "https://zenodo.org/record/7053673"
     },
     {
@@ -232584,11 +597083,11 @@
         ],
         "dir": "topics/single-cell/tutorials/scatac-standard-processing-snapatac2",
         "edam_operation": [
-            "Generation",
-            "Sequence alignment",
             "Differential gene expression analysis",
+            "Genome indexing",
             "Read mapping",
-            "Genome indexing"
+            "Sequence alignment",
+            "Generation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -232618,7 +597117,7 @@
             "Generate and filter a cell-by-gene matrix",
             "Identify marker genes for the clusters and annotate the cell types"
         ],
-        "pageviews": 421,
+        "pageviews": 433,
         "priority": 2,
         "pub_date": "2024-07-11",
         "questions": [
@@ -232642,21 +597141,21 @@
         ],
         "short_id": "T00445",
         "short_tools": [
-            "bwa_mem",
-            "snapatac2_peaks_and_motif",
-            "fasta_compute_length",
-            "replace_column_with_key_value_file",
+            "Cut1",
+            "scanpy_normalize",
+            "scanpy_plot",
+            "scanpy_filter",
             "snapatac2_clustering",
-            "snapatac2_preprocessing",
             "anndata_ops",
-            "scanpy_plot",
+            "bwa_mem",
+            "snapatac2_peaks_and_motif",
             "snapatac2_plotting",
             "anndata_inspect",
-            "Cut1",
+            "snapatac2_preprocessing",
             "anndata_manipulate",
-            "scanpy_filter",
-            "scanpy_inspect",
-            "scanpy_normalize"
+            "replace_column_with_key_value_file",
+            "fasta_compute_length",
+            "scanpy_inspect"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -232665,6 +597164,2400 @@
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.6.4+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2.6.4+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.6.4+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.6.4+galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "10x",
@@ -232710,8 +599603,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 61,
-        "visitors": 319,
+        "visit_duration": 59,
+        "visitors": 331,
         "workflows": [
             {
                 "creators": [
@@ -232919,7 +599812,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nFragment_file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nchromosome_sizes.tabular\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\ngene_annotation\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nBam-file\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nKeys for annotations of obs/cells or vars/genes\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nReplace_file\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"pp.import_data\"];\n  1 -->|output| 6;\n  0 -->|output| 6;\n  7[\"pp.make_fragment_file\"];\n  3 -->|output| 7;\n  8[\"pl.frag_size_distr\"];\n  6 -->|anndata_out| 8;\n  265d6020-44e2-408c-9eb6-02cbc9ac23a7[\"Output\\nplot frag_size\"];\n  8 --> 265d6020-44e2-408c-9eb6-02cbc9ac23a7;\n  style 265d6020-44e2-408c-9eb6-02cbc9ac23a7 stroke:#2c3143,stroke-width:4px;\n  9[\"pl.frag_size_distr_log\"];\n  6 -->|anndata_out| 9;\n  a37cd3c3-e07e-4bea-899f-ee44cee8370b[\"Output\\nplot log frag_size\"];\n  9 --> a37cd3c3-e07e-4bea-899f-ee44cee8370b;\n  style a37cd3c3-e07e-4bea-899f-ee44cee8370b stroke:#2c3143,stroke-width:4px;\n  10[\"metrics.tsse\"];\n  6 -->|anndata_out| 10;\n  2 -->|output| 10;\n  233284e5-c184-4330-a1d3-2d03951c4ce7[\"Output\\nanndata tsse\"];\n  10 --> 233284e5-c184-4330-a1d3-2d03951c4ce7;\n  style 233284e5-c184-4330-a1d3-2d03951c4ce7 stroke:#2c3143,stroke-width:4px;\n  11[\"pp.import_data-sorted_by_barcodes\"];\n  1 -->|output| 11;\n  7 -->|fragments_out| 11;\n  50ef9fe7-bb08-4957-bc45-079ed78f9ee8[\"Output\\nanndata\"];\n  11 --> 50ef9fe7-bb08-4957-bc45-079ed78f9ee8;\n  style 50ef9fe7-bb08-4957-bc45-079ed78f9ee8 stroke:#2c3143,stroke-width:4px;\n  12[\"pl.tsse\"];\n  10 -->|anndata_out| 12;\n  9a5c0f9c-0423-4822-871e-ba8317f2fa7b[\"Output\\nplot tsse\"];\n  12 --> 9a5c0f9c-0423-4822-871e-ba8317f2fa7b;\n  style 9a5c0f9c-0423-4822-871e-ba8317f2fa7b stroke:#2c3143,stroke-width:4px;\n  13[\"pp.filter_cells\"];\n  10 -->|anndata_out| 13;\n  b58dc4ad-6bf0-4f31-99f4-4f8deb13427c[\"Output\\nanndata filter cells\"];\n  13 --> b58dc4ad-6bf0-4f31-99f4-4f8deb13427c;\n  style b58dc4ad-6bf0-4f31-99f4-4f8deb13427c stroke:#2c3143,stroke-width:4px;\n  14[\"pp.add_tile_matrix\"];\n  13 -->|anndata_out| 14;\n  d4b64fc4-fd35-4781-b799-0d07fe8fe438[\"Output\\nanndata tile matrix\"];\n  14 --> d4b64fc4-fd35-4781-b799-0d07fe8fe438;\n  style d4b64fc4-fd35-4781-b799-0d07fe8fe438 stroke:#2c3143,stroke-width:4px;\n  15[\"pp.select_features\"];\n  14 -->|anndata_out| 15;\n  f531f6bd-3fc6-48b9-bb33-66de7928e670[\"Output\\nanndata select features\"];\n  15 --> f531f6bd-3fc6-48b9-bb33-66de7928e670;\n  style f531f6bd-3fc6-48b9-bb33-66de7928e670 stroke:#2c3143,stroke-width:4px;\n  16[\"pp.scrublet\"];\n  15 -->|anndata_out| 16;\n  5b17aa3a-3694-440f-9022-cf9761feb760[\"Output\\nanndata scrublet\"];\n  16 --> 5b17aa3a-3694-440f-9022-cf9761feb760;\n  style 5b17aa3a-3694-440f-9022-cf9761feb760 stroke:#2c3143,stroke-width:4px;\n  17[\"pp.filter_doublets\"];\n  16 -->|anndata_out| 17;\n  3838cf9d-a018-4aa7-8852-893b2f60ec2a[\"Output\\nanndata filter doublets\"];\n  17 --> 3838cf9d-a018-4aa7-8852-893b2f60ec2a;\n  style 3838cf9d-a018-4aa7-8852-893b2f60ec2a stroke:#2c3143,stroke-width:4px;\n  18[\"tl.spectral\"];\n  17 -->|anndata_out| 18;\n  77883516-8ac4-40b5-8b75-5750639d9fc4[\"Output\\nanndata spectral\"];\n  18 --> 77883516-8ac4-40b5-8b75-5750639d9fc4;\n  style 77883516-8ac4-40b5-8b75-5750639d9fc4 stroke:#2c3143,stroke-width:4px;\n  19[\"tl.umap\"];\n  18 -->|anndata_out| 19;\n  062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad[\"Output\\nanndata umap\"];\n  19 --> 062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad;\n  style 062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad stroke:#2c3143,stroke-width:4px;\n  20[\"pp.knn\"];\n  19 -->|anndata_out| 20;\n  b7ebe580-9938-48e5-8718-4df197126615[\"Output\\nanndata knn\"];\n  20 --> b7ebe580-9938-48e5-8718-4df197126615;\n  style b7ebe580-9938-48e5-8718-4df197126615 stroke:#2c3143,stroke-width:4px;\n  21[\"tl.leiden\"];\n  20 -->|anndata_out| 21;\n  9970eb96-013b-4d97-bbbf-2d1f4663b73c[\"Output\\nanndata_leiden_clustering\"];\n  21 --> 9970eb96-013b-4d97-bbbf-2d1f4663b73c;\n  style 9970eb96-013b-4d97-bbbf-2d1f4663b73c stroke:#2c3143,stroke-width:4px;\n  22[\"pl.umap\"];\n  21 -->|anndata_out| 22;\n  4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9[\"Output\\numap_leiden-clusters\"];\n  22 --> 4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9;\n  style 4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9 stroke:#2c3143,stroke-width:4px;\n  23[\"make_gene_matrix\"];\n  21 -->|anndata_out| 23;\n  2 -->|output| 23;\n  9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a[\"Output\\nanndata gene matrix\"];\n  23 --> 9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a;\n  style 9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a stroke:#2c3143,stroke-width:4px;\n  24[\"scanpy_filter_genes\"];\n  23 -->|anndata_out| 24;\n  7a9b22df-e0e5-49d9-9fa1-2efe316d6d66[\"Output\\nanndata filter genes\"];\n  24 --> 7a9b22df-e0e5-49d9-9fa1-2efe316d6d66;\n  style 7a9b22df-e0e5-49d9-9fa1-2efe316d6d66 stroke:#2c3143,stroke-width:4px;\n  25[\"Normalize\"];\n  24 -->|anndata_out| 25;\n  7dddd4c8-1944-4f50-b331-857d03cc9631[\"Output\\nanndata normalize\"];\n  25 --> 7dddd4c8-1944-4f50-b331-857d03cc9631;\n  style 7dddd4c8-1944-4f50-b331-857d03cc9631 stroke:#2c3143,stroke-width:4px;\n  26[\"pp.log1p\"];\n  25 -->|anndata_out| 26;\n  40ace30a-21e1-4bf2-8e08-ad93b62fb2ee[\"Output\\nanndata log1p\"];\n  26 --> 40ace30a-21e1-4bf2-8e08-ad93b62fb2ee;\n  style 40ace30a-21e1-4bf2-8e08-ad93b62fb2ee stroke:#2c3143,stroke-width:4px;\n  27[\"external.pp.magic\"];\n  26 -->|anndata_out| 27;\n  8c1c7aa9-b9dd-467b-9715-73773aea093f[\"Output\\nanndata_magic\"];\n  27 --> 8c1c7aa9-b9dd-467b-9715-73773aea093f;\n  style 8c1c7aa9-b9dd-467b-9715-73773aea093f stroke:#2c3143,stroke-width:4px;\n  28[\"Copy obsm\"];\n  21 -->|anndata_out| 28;\n  27 -->|anndata_out| 28;\n  2c3825d3-7151-4eef-97d0-c8a31ca6fd3e[\"Output\\nanndata_gene-matrix_leiden\"];\n  28 --> 2c3825d3-7151-4eef-97d0-c8a31ca6fd3e;\n  style 2c3825d3-7151-4eef-97d0-c8a31ca6fd3e stroke:#2c3143,stroke-width:4px;\n  29[\"umap_plot_with_scanpy\"];\n  28 -->|output_h5ad| 29;\n  4 -->|output| 29;\n  4cfbbb70-156b-48d7-b14b-db21198d9b6d[\"Output\\numap_marker-genes\"];\n  29 --> 4cfbbb70-156b-48d7-b14b-db21198d9b6d;\n  style 4cfbbb70-156b-48d7-b14b-db21198d9b6d stroke:#2c3143,stroke-width:4px;\n  30[\"Inspect observations\"];\n  28 -->|output_h5ad| 30;\n  31[\"Cut leiden from table\"];\n  30 -->|obs| 31;\n  11c22200-a54e-4585-82c4-8457dbbfb53c[\"Output\\nleiden annotation\"];\n  31 --> 11c22200-a54e-4585-82c4-8457dbbfb53c;\n  style 11c22200-a54e-4585-82c4-8457dbbfb53c stroke:#2c3143,stroke-width:4px;\n  32[\"Replace leiden\"];\n  31 -->|out_file1| 32;\n  5 -->|output| 32;\n  467de061-79e6-4148-8a65-c06383a14012[\"Output\\ncell type annotation\"];\n  32 --> 467de061-79e6-4148-8a65-c06383a14012;\n  style 467de061-79e6-4148-8a65-c06383a14012 stroke:#2c3143,stroke-width:4px;\n  33[\"Manipulate AnnData\"];\n  28 -->|output_h5ad| 33;\n  32 -->|outfile_replace| 33;\n  cbba6173-f439-4fd5-8423-946aa625112b[\"Output\\nanndata_cell_type\"];\n  33 --> cbba6173-f439-4fd5-8423-946aa625112b;\n  style cbba6173-f439-4fd5-8423-946aa625112b stroke:#2c3143,stroke-width:4px;\n  34[\"Plot cell types\"];\n  33 -->|anndata| 34;\n  c28c53ae-8ee7-47d7-8a00-352908bb7c1a[\"Output\\numap_cell-type\"];\n  34 --> c28c53ae-8ee7-47d7-8a00-352908bb7c1a;\n  style c28c53ae-8ee7-47d7-8a00-352908bb7c1a stroke:#2c3143,stroke-width:4px;\n  35[\"Final Anndata general info\"];\n  33 -->|anndata| 35;\n  379a85d1-a204-4b0b-8b33-86e5582fc51f[\"Output\\ngeneral\"];\n  35 --> 379a85d1-a204-4b0b-8b33-86e5582fc51f;\n  style 379a85d1-a204-4b0b-8b33-86e5582fc51f stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2",
                 "outputs": [
                     {
@@ -234478,8 +601371,8 @@
         ],
         "dir": "topics/single-cell/tutorials/scrna-umis",
         "edam_operation": [
-            "Sequencing quality control",
             "Statistical calculation",
+            "Sequencing quality control",
             "Sequence composition calculation"
         ],
         "edam_topic": [],
@@ -234495,8 +601388,7 @@
         "hands_on": true,
         "id": "single-cell/scrna-umis",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr"
+            "UseGalaxy.cz"
         ],
         "js_requirements": {
             "mathjax": null,
@@ -234514,7 +601406,7 @@
             "Demultiplex FASTQ data via UMI-tools",
             "Understand and validate the extraction of barcodes"
         ],
-        "pageviews": 6185,
+        "pageviews": 6214,
         "priority": 2,
         "pub_date": "2019-02-20",
         "questions": [
@@ -234544,8 +601436,8 @@
         "short_id": "T00256",
         "short_tools": [
             "fastqc",
-            "seq_filter_by_id",
-            "umi_tools_extract"
+            "umi_tools_extract",
+            "seq_filter_by_id"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -234578,11 +601470,588 @@
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
                     "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "0.72+galaxy1"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.74+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "exact",
+                            "version": "0.72+galaxy1"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
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+                                "1.4.4.post1+galaxy1",
+                                "1.4",
+                                "1.4.4.post1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.7.1+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.7.1+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.7.1+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.7.1+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.7.1+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.7.1+galaxy0"
+                }
+            ]
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         "symlink": null,
         "tags": [
             "plants",
@@ -235102,7 +603863,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 83,
-        "visitors": 1962,
+        "visitors": 1968,
         "workflows": [
             {
                 "creators": [],
@@ -235351,7 +604112,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Parameter\\nLeiden Resolution\"];\n  style 0 fill:#ded,stroke:#393,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSHR CSV.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nWT CSV.gz\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nMin Genes\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nMin Cells\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Parameter\\nMax Features\"];\n  style 5 fill:#ded,stroke:#393,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Parameter\\nMax Lib Size\"];\n  style 6 fill:#ded,stroke:#393,stroke-width:4px;\n  7[\"Import Anndata and loom\"];\n  1 -->|output| 7;\n  8[\"Import Anndata and loom\"];\n  2 -->|output| 8;\n  9[\"Manipulate AnnData\"];\n  7 -->|anndata| 9;\n  8 -->|anndata| 9;\n  10[\"Rename Batches\"];\n  9 -->|anndata| 10;\n  680180f6-edfc-4f66-b265-7a63aaa22b39[\"Output\\nscRNA Concatenated Datasets\"];\n  10 --> 680180f6-edfc-4f66-b265-7a63aaa22b39;\n  style 680180f6-edfc-4f66-b265-7a63aaa22b39 stroke:#2c3143,stroke-width:4px;\n  11[\"QC metrics\"];\n  10 -->|anndata| 11;\n  12[\"Filter genes\"];\n  11 -->|anndata_out| 12;\n  3 -->|output| 12;\n  13[\"Plot Violin\"];\n  11 -->|anndata_out| 13;\n  14[\"Filter Cells\"];\n  12 -->|anndata_out| 14;\n  4 -->|output| 14;\n  15[\"Filter Max Features\"];\n  14 -->|anndata_out| 15;\n  5 -->|output| 15;\n  16[\"Filter Max Library Size\"];\n  15 -->|anndata| 16;\n  6 -->|output| 16;\n  17[\"Save RAW\"];\n  16 -->|anndata| 17;\n  18[\"Norm to 1e4\"];\n  17 -->|anndata| 18;\n  19[\"Log1p\"];\n  18 -->|anndata_out| 19;\n  20[\"Regress total counts\"];\n  19 -->|anndata_out| 20;\n  21[\"Scale\"];\n  20 -->|anndata_out| 21;\n  22[\"PCA\"];\n  21 -->|anndata_out| 22;\n  23[\"Neighborhod\"];\n  22 -->|anndata_out| 23;\n  24[\"UMAP\"];\n  23 -->|anndata_out| 24;\n  25[\"Leiden\"];\n  24 -->|anndata_out| 25;\n  0 -->|output| 25;\n  48cf0465-84ba-461a-bdb9-61625626de42[\"Output\\nscRNA with clusters Dataset\"];\n  25 --> 48cf0465-84ba-461a-bdb9-61625626de42;\n  style 48cf0465-84ba-461a-bdb9-61625626de42 stroke:#2c3143,stroke-width:4px;\n  26[\"Plot PCA batch\"];\n  24 -->|anndata_out| 26;\n  27[\"Plot UMAP batch\"];\n  24 -->|anndata_out| 27;\n  28[\"Plot UMAP leiden, batch\"];\n  25 -->|anndata_out| 28;\n  29[\"Rename Clusters\"];\n  25 -->|anndata_out| 29;\n  30[\"Complex DotPlot\"];\n  25 -->|anndata_out| 30;\n  31[\"Complex DotPlot with new labels\"];\n  29 -->|anndata| 31;\n  32[\"Plot UMAP with new labels\"];\n  29 -->|anndata| 32;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "scRNA Plant Analysis",
                 "outputs": [
                     {
@@ -236070,7 +604831,7 @@
             "Convert raw gene expression data into the AnnData format.",
             "Add metadata to the AnnData object to prepare it for analysis."
         ],
-        "pageviews": 213,
+        "pageviews": 215,
         "priority": 3,
         "pub_date": "2023-12-13",
         "questions": [
@@ -236090,15 +604851,15 @@
         ],
         "short_id": "T00380",
         "short_tools": [
-            "Paste1",
-            "anndata_ops",
+            "Cut1",
+            "scanpy_filter_cells",
             "anndata_import",
+            "anndata_ops",
             "unzip",
-            "scanpy_filter_cells",
             "anndata_inspect",
-            "Cut1",
             "anndata_manipulate",
-            "tp_replace_in_column"
+            "tp_replace_in_column",
+            "Paste1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -236119,6 +604880,1541 @@
                 }
             ]
         },
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
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+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
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+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
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+                    "usegalaxy": false
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                    "url": "https://www.immportgalaxy.org/"
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+                    "url": "http://pepsimili.e-nios.com:8080/",
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+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
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+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
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+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
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+                    "url": "https://viralvariant.anses.fr/"
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+                            "state": "local"
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+                        {
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+                        {
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+                            "server": "https://usegalaxy.no/",
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+                        {
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         "symlink": null,
         "tags": [
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@@ -236157,8 +606453,8 @@
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         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 90,
-        "visitors": 179,
+        "visit_duration": 100,
+        "visitors": 180,
         "workflows": [
             {
                 "creators": [
@@ -236471,7 +606767,7 @@
                 ],
                 "license": "CC-BY-4.0",
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "NCBI to Anndata",
                 "outputs": [
                     {
@@ -236739,7 +607035,7 @@
             "Operate tools working on dataset collections",
             "Compare plots resulting from different parameters values"
         ],
-        "pageviews": 149,
+        "pageviews": 151,
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         "questions": [
@@ -236760,12 +607056,12 @@
         ],
         "short_id": "T00357",
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-            "scanpy_run_umap",
-            "scanpy_plot_embed",
-            "scanpy_find_cluster",
             "scanpy_parameter_iterator",
             "scanpy_compute_graph",
-            "scanpy_run_tsne"
+            "scanpy_run_umap",
+            "scanpy_run_tsne",
+            "scanpy_plot_embed",
+            "scanpy_find_cluster"
         ],
         "slides": false,
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@@ -236791,6 +607087,993 @@
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+                            ]
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+                                "1.4.3+galaxy1"
+                            ]
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+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.8.1+galaxy9"
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+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
+                                "1.8.1+1+galaxy1",
+                                "1.9.3+galaxy0"
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+                            "state": "missing"
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+                            "server": "http://apostl.moffitt.org/",
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+                            "server": "https://galaxy-web.ipk-gatersleben.de",
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+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
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+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.4.3+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.8.1+galaxy9"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.4.3+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.8.1+galaxy9"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
+                                "1.8.1+1+galaxy0",
+                                "1.9.3+galaxy0",
+                                "1.8.1+3+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
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+                    ],
+                    "version": "1.8.1+galaxy9"
+                }
+            ]
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         "symlink": null,
         "tags": null,
         "time_estimation": "2H",
@@ -236822,8 +608105,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 83,
-        "visitors": 132,
+        "visit_duration": 82,
+        "visitors": 134,
         "workflows": [
             {
                 "creators": [
@@ -236942,7 +608225,7 @@
                 ],
                 "license": "CC-BY-4.0",
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Scanpy Parameter Iterator workflow full (imported from URL)",
                 "outputs": [
                     {
@@ -238018,7 +609301,7 @@
             "Appraise data outputs and decisions",
             "Explain why single cell analysis is an iterative (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly) process"
         ],
-        "pageviews": 6346,
+        "pageviews": 6374,
         "priority": 3,
         "pub_date": "2021-03-24",
         "questions": [
@@ -238058,25 +609341,25 @@
         ],
         "short_id": "T00247",
         "short_tools": [
-            "join1",
-            "scanpy_plot_embed",
-            "scanpy_run_pca",
-            "scanpy_run_tsne",
+            "interactive_tool_cellxgene",
+            "scanpy_plot",
             "scanpy_scale_data",
-            "anndata_manipulate",
+            "scanpy_find_markers",
+            "scanpy_filter_cells",
+            "scanpy_run_pca",
+            "scanpy_plot_embed",
             "scanpy_filter_genes",
-            "scanpy_compute_graph",
             "scanpy_find_variable_genes",
-            "scanpy_normalise_data",
-            "scanpy_run_umap",
-            "interactive_tool_cellxgene",
-            "scanpy_filter_cells",
+            "anndata_ops",
             "anndata_inspect",
-            "Cut1",
+            "scanpy_run_umap",
+            "anndata_manipulate",
+            "scanpy_run_tsne",
             "scanpy_find_cluster",
-            "anndata_ops",
-            "scanpy_plot",
-            "scanpy_find_markers"
+            "Cut1",
+            "scanpy_normalise_data",
+            "join1",
+            "scanpy_compute_graph"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -238097,6 +609380,4716 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "id": "Cut1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
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+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
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+                        {
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+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
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+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
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+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
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+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.4.4.post1+galaxy2",
+                                "1.4.4.post1+galaxy1",
+                                "1.4.4+galaxy0",
+                                "1.4.4.post1+galaxy0",
+                                "1.4+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.7.1+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.7.1+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.7.1+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.7.1+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.7.1+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.7.1+galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "10x",
@@ -238158,7 +614151,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 160,
-        "visitors": 4039,
+        "visitors": 4059,
         "workflows": [
             {
                 "creators": [],
@@ -238209,7 +614202,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMito-counted AnnData\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Inspect AnnData\"];\n  0 -->|output| 1;\n  2[\"Scanpy FilterCells\"];\n  0 -->|output| 2;\n  08175d7f-f4f4-413c-ad86-f59587ff692e[\"Output\\nGenes-filtered Object\"];\n  2 --> 08175d7f-f4f4-413c-ad86-f59587ff692e;\n  style 08175d7f-f4f4-413c-ad86-f59587ff692e stroke:#2c3143,stroke-width:4px;\n  3[\"Plot\"];\n  0 -->|output| 3;\n  bfc499ee-630a-498b-9be6-696d9bb78837[\"Output\\nScatter - genes x UMIs\"];\n  3 --> bfc499ee-630a-498b-9be6-696d9bb78837;\n  style bfc499ee-630a-498b-9be6-696d9bb78837 stroke:#2c3143,stroke-width:4px;\n  4[\"Plot\"];\n  0 -->|output| 4;\n  f2c78ef3-7d31-4930-954c-0133cce27a41[\"Output\\nScatter - mito x genes\"];\n  4 --> f2c78ef3-7d31-4930-954c-0133cce27a41;\n  style f2c78ef3-7d31-4930-954c-0133cce27a41 stroke:#2c3143,stroke-width:4px;\n  5[\"Plot\"];\n  0 -->|output| 5;\n  348818e6-9def-41fd-a390-6f8525c57cd8[\"Output\\nViolin - genotype - log\"];\n  5 --> 348818e6-9def-41fd-a390-6f8525c57cd8;\n  style 348818e6-9def-41fd-a390-6f8525c57cd8 stroke:#2c3143,stroke-width:4px;\n  6[\"Plot\"];\n  0 -->|output| 6;\n  844f5e7c-78c8-4f28-8e15-cea35ada8fef[\"Output\\nViolin - batch - log\"];\n  6 --> 844f5e7c-78c8-4f28-8e15-cea35ada8fef;\n  style 844f5e7c-78c8-4f28-8e15-cea35ada8fef stroke:#2c3143,stroke-width:4px;\n  7[\"Inspect AnnData\"];\n  0 -->|output| 7;\n  8[\"Plot\"];\n  0 -->|output| 8;\n  3b1232c5-d16a-434d-806e-79fd77f7c05f[\"Output\\nScatter - mito x UMIs\"];\n  8 --> 3b1232c5-d16a-434d-806e-79fd77f7c05f;\n  style 3b1232c5-d16a-434d-806e-79fd77f7c05f stroke:#2c3143,stroke-width:4px;\n  9[\"Inspect AnnData\"];\n  0 -->|output| 9;\n  10[\"Plot\"];\n  0 -->|output| 10;\n  a639cdc0-da40-4df9-8348-23117528b24a[\"Output\\nViolin - sex - log\"];\n  10 --> a639cdc0-da40-4df9-8348-23117528b24a;\n  style a639cdc0-da40-4df9-8348-23117528b24a stroke:#2c3143,stroke-width:4px;\n  11[\"Plot\"];\n  2 -->|output_h5ad| 11;\n  69bf3e42-63e2-4b5b-9d63-5aac9d6b5691[\"Output\\nViolin - Filterbygenes\"];\n  11 --> 69bf3e42-63e2-4b5b-9d63-5aac9d6b5691;\n  style 69bf3e42-63e2-4b5b-9d63-5aac9d6b5691 stroke:#2c3143,stroke-width:4px;\n  12[\"Scanpy FilterCells\"];\n  2 -->|output_h5ad| 12;\n  f378cb4e-0a77-49d9-b92a-752dbea4b09a[\"Output\\nCounts-filtered Object\"];\n  12 --> f378cb4e-0a77-49d9-b92a-752dbea4b09a;\n  style f378cb4e-0a77-49d9-b92a-752dbea4b09a stroke:#2c3143,stroke-width:4px;\n  13[\"Inspect AnnData\"];\n  2 -->|output_h5ad| 13;\n  f9e862db-eb22-4124-8fe0-0fdcfcfb8393[\"Output\\nGeneral - Filterbygenes\"];\n  13 --> f9e862db-eb22-4124-8fe0-0fdcfcfb8393;\n  style f9e862db-eb22-4124-8fe0-0fdcfcfb8393 stroke:#2c3143,stroke-width:4px;\n  14[\"Inspect AnnData\"];\n  12 -->|output_h5ad| 14;\n  794f72b5-c2c3-46a0-ac15-b9f1e94941d2[\"Output\\nGeneral - Filterbycounts\"];\n  14 --> 794f72b5-c2c3-46a0-ac15-b9f1e94941d2;\n  style 794f72b5-c2c3-46a0-ac15-b9f1e94941d2 stroke:#2c3143,stroke-width:4px;\n  15[\"Scanpy FilterCells\"];\n  12 -->|output_h5ad| 15;\n  b915da66-6435-4871-baa0-3e494ba73c96[\"Output\\nMito-filtered Object\"];\n  15 --> b915da66-6435-4871-baa0-3e494ba73c96;\n  style b915da66-6435-4871-baa0-3e494ba73c96 stroke:#2c3143,stroke-width:4px;\n  16[\"Plot\"];\n  12 -->|output_h5ad| 16;\n  3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa[\"Output\\nViolin - Filterbycounts\"];\n  16 --> 3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa;\n  style 3aef86d7-d34d-4b24-bc97-bf8c97d8d2fa stroke:#2c3143,stroke-width:4px;\n  17[\"Inspect AnnData\"];\n  15 -->|output_h5ad| 17;\n  cd94a4c6-5665-4bdf-88ea-4f4d41efa893[\"Output\\nGeneral - Filterbymito\"];\n  17 --> cd94a4c6-5665-4bdf-88ea-4f4d41efa893;\n  style cd94a4c6-5665-4bdf-88ea-4f4d41efa893 stroke:#2c3143,stroke-width:4px;\n  18[\"Scanpy FilterGenes\"];\n  15 -->|output_h5ad| 18;\n  ee63ef0a-98ed-45cb-b144-1154f84ae452[\"Output\\nFiltered Object\"];\n  18 --> ee63ef0a-98ed-45cb-b144-1154f84ae452;\n  style ee63ef0a-98ed-45cb-b144-1154f84ae452 stroke:#2c3143,stroke-width:4px;\n  19[\"Plot\"];\n  15 -->|output_h5ad| 19;\n  7e48a14f-08fd-45ab-b613-606bf64dcf9d[\"Output\\nViolin - Filterbymito\"];\n  19 --> 7e48a14f-08fd-45ab-b613-606bf64dcf9d;\n  style 7e48a14f-08fd-45ab-b613-606bf64dcf9d stroke:#2c3143,stroke-width:4px;\n  20[\"Inspect AnnData\"];\n  18 -->|output_h5ad| 20;\n  d59efa9b-d049-4f0e-8bd8-8ae982a45d0a[\"Output\\nGeneral - Filtered object\"];\n  20 --> d59efa9b-d049-4f0e-8bd8-8ae982a45d0a;\n  style d59efa9b-d049-4f0e-8bd8-8ae982a45d0a stroke:#2c3143,stroke-width:4px;\n  21[\"Scanpy NormaliseData\"];\n  18 -->|output_h5ad| 21;\n  22[\"Scanpy FindVariableGenes\"];\n  21 -->|output_h5ad| 22;\n  23[\"Scanpy ScaleData\"];\n  22 -->|output_h5ad| 23;\n  24[\"Scanpy RunPCA\"];\n  23 -->|output_h5ad| 24;\n  25[\"Plot\"];\n  24 -->|output_h5ad| 25;\n  993dea99-990f-460a-beb9-46e5c97ee898[\"Output\\nPCA Variance\"];\n  25 --> 993dea99-990f-460a-beb9-46e5c97ee898;\n  style 993dea99-990f-460a-beb9-46e5c97ee898 stroke:#2c3143,stroke-width:4px;\n  26[\"Scanpy ComputeGraph\"];\n  24 -->|output_h5ad| 26;\n  27[\"Scanpy RunTSNE\"];\n  26 -->|output_h5ad| 27;\n  28[\"Scanpy RunUMAP\"];\n  27 -->|output_h5ad| 28;\n  29[\"Scanpy FindCluster\"];\n  28 -->|output_h5ad| 29;\n  30[\"Scanpy FindMarkers\"];\n  29 -->|output_h5ad| 30;\n  308b4961-4d50-442b-9bca-bbb1992426ba[\"Output\\nMarkers - cluster\"];\n  30 --> 308b4961-4d50-442b-9bca-bbb1992426ba;\n  style 308b4961-4d50-442b-9bca-bbb1992426ba stroke:#2c3143,stroke-width:4px;\n  035bbbce-fb57-48c8-83d5-2b0cd0376541[\"Output\\nFinal object\"];\n  30 --> 035bbbce-fb57-48c8-83d5-2b0cd0376541;\n  style 035bbbce-fb57-48c8-83d5-2b0cd0376541 stroke:#2c3143,stroke-width:4px;\n  31[\"Scanpy FindMarkers\"];\n  29 -->|output_h5ad| 31;\n  1705e219-192a-4f52-9b26-64fcbcd303ea[\"Output\\nMarkers - genotype\"];\n  31 --> 1705e219-192a-4f52-9b26-64fcbcd303ea;\n  style 1705e219-192a-4f52-9b26-64fcbcd303ea stroke:#2c3143,stroke-width:4px;\n  32[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 32;\n  33[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 33;\n  34[\"Manipulate AnnData\"];\n  30 -->|output_h5ad| 34;\n  35[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 35;\n  36[\"Inspect AnnData\"];\n  30 -->|output_h5ad| 36;\n  37[\"AnnData Operations\"];\n  34 -->|anndata| 37;\n  30 -->|output_h5ad| 37;\n  38[\"Join two Datasets\"];\n  30 -->|output_tsv| 38;\n  36 -->|var| 38;\n  39[\"Join two Datasets\"];\n  31 -->|output_tsv| 39;\n  36 -->|var| 39;\n  40[\"AnnData Operations\"];\n  37 -->|output_h5ad| 40;\n  a6d48df0-403f-4efc-a75f-9504a960884e[\"Output\\nFinal cell annotated object\"];\n  40 --> a6d48df0-403f-4efc-a75f-9504a960884e;\n  style a6d48df0-403f-4efc-a75f-9504a960884e stroke:#2c3143,stroke-width:4px;\n  41[\"Cut\"];\n  38 -->|out_file1| 41;\n  0ee7f9b6-b065-4e26-93df-6e6e2fe458a9[\"Output\\nMarkers - cluster - named\"];\n  41 --> 0ee7f9b6-b065-4e26-93df-6e6e2fe458a9;\n  style 0ee7f9b6-b065-4e26-93df-6e6e2fe458a9 stroke:#2c3143,stroke-width:4px;\n  42[\"Cut\"];\n  39 -->|out_file1| 42;\n  fdb88faa-9b76-4edb-b89b-427c098a473e[\"Output\\nMarkers - genotype - named\"];\n  42 --> fdb88faa-9b76-4edb-b89b-427c098a473e;\n  style fdb88faa-9b76-4edb-b89b-427c098a473e stroke:#2c3143,stroke-width:4px;\n  43[\"Scanpy PlotEmbed\"];\n  40 -->|output_h5ad| 43;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "CS3_Filter, Plot and Explore Single-cell RNA-seq Data",
                 "outputs": [
                     {
@@ -240456,7 +616449,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nMito-counted AnnData\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Inspect AnnData\"];\n  0 -->|output| 1;\n  2[\"Scanpy FilterCells\"];\n  0 -->|output| 2;\n  6a00b14b-d3f8-4771-963a-76115c8eaf2f[\"Output\\nGenes-filtered Object\"];\n  2 --> 6a00b14b-d3f8-4771-963a-76115c8eaf2f;\n  style 6a00b14b-d3f8-4771-963a-76115c8eaf2f stroke:#2c3143,stroke-width:4px;\n  3[\"Plot\"];\n  0 -->|output| 3;\n  c123842e-b2d2-43ad-81f0-6ba3b45d4021[\"Output\\nScatter - genes x UMIs\"];\n  3 --> c123842e-b2d2-43ad-81f0-6ba3b45d4021;\n  style c123842e-b2d2-43ad-81f0-6ba3b45d4021 stroke:#2c3143,stroke-width:4px;\n  4[\"Plot\"];\n  0 -->|output| 4;\n  f1020d4d-555e-42fa-ba21-52a151b91a5b[\"Output\\nScatter - mito x genes\"];\n  4 --> f1020d4d-555e-42fa-ba21-52a151b91a5b;\n  style f1020d4d-555e-42fa-ba21-52a151b91a5b stroke:#2c3143,stroke-width:4px;\n  5[\"Plot\"];\n  0 -->|output| 5;\n  a7fe6020-8f1e-470a-9ed3-f2b5e95516e0[\"Output\\nViolin - genotype - log\"];\n  5 --> a7fe6020-8f1e-470a-9ed3-f2b5e95516e0;\n  style a7fe6020-8f1e-470a-9ed3-f2b5e95516e0 stroke:#2c3143,stroke-width:4px;\n  6[\"Plot\"];\n  0 -->|output| 6;\n  15e501bc-8ddb-4519-89eb-dde431ea96c1[\"Output\\nViolin - batch - log\"];\n  6 --> 15e501bc-8ddb-4519-89eb-dde431ea96c1;\n  style 15e501bc-8ddb-4519-89eb-dde431ea96c1 stroke:#2c3143,stroke-width:4px;\n  7[\"Inspect AnnData\"];\n  0 -->|output| 7;\n  8[\"Plot\"];\n  0 -->|output| 8;\n  eff22f46-baa6-4e00-ba82-d5e12ce26ff0[\"Output\\nScatter - mito x UMIs\"];\n  8 --> eff22f46-baa6-4e00-ba82-d5e12ce26ff0;\n  style eff22f46-baa6-4e00-ba82-d5e12ce26ff0 stroke:#2c3143,stroke-width:4px;\n  9[\"Inspect AnnData\"];\n  0 -->|output| 9;\n  10[\"Plot\"];\n  0 -->|output| 10;\n  56677ca4-129c-476c-85ec-69d1bb3d800d[\"Output\\nViolin - sex - log\"];\n  10 --> 56677ca4-129c-476c-85ec-69d1bb3d800d;\n  style 56677ca4-129c-476c-85ec-69d1bb3d800d stroke:#2c3143,stroke-width:4px;\n  11[\"Plot\"];\n  2 -->|output_h5ad| 11;\n  acb61ea4-bcb9-45db-beef-e2bf1a176701[\"Output\\nViolin - Filterbygenes\"];\n  11 --> acb61ea4-bcb9-45db-beef-e2bf1a176701;\n  style acb61ea4-bcb9-45db-beef-e2bf1a176701 stroke:#2c3143,stroke-width:4px;\n  12[\"Scanpy FilterCells\"];\n  2 -->|output_h5ad| 12;\n  51853662-4519-4229-a2ea-b22a53e7ef73[\"Output\\nCounts-filtered Object\"];\n  12 --> 51853662-4519-4229-a2ea-b22a53e7ef73;\n  style 51853662-4519-4229-a2ea-b22a53e7ef73 stroke:#2c3143,stroke-width:4px;\n  13[\"Inspect AnnData\"];\n  2 -->|output_h5ad| 13;\n  362a7fe6-24bb-4398-ae48-870f4b4bb774[\"Output\\nGeneral - Filterbygenes\"];\n  13 --> 362a7fe6-24bb-4398-ae48-870f4b4bb774;\n  style 362a7fe6-24bb-4398-ae48-870f4b4bb774 stroke:#2c3143,stroke-width:4px;\n  14[\"Inspect AnnData\"];\n  12 -->|output_h5ad| 14;\n  edf24149-9341-4fe7-b10c-3fcf092faaa5[\"Output\\nGeneral - Filterbycounts\"];\n  14 --> edf24149-9341-4fe7-b10c-3fcf092faaa5;\n  style edf24149-9341-4fe7-b10c-3fcf092faaa5 stroke:#2c3143,stroke-width:4px;\n  15[\"Scanpy FilterCells\"];\n  12 -->|output_h5ad| 15;\n  a88ec405-265f-4a59-a75e-34e3b05b0096[\"Output\\nMito-filtered Object\"];\n  15 --> a88ec405-265f-4a59-a75e-34e3b05b0096;\n  style a88ec405-265f-4a59-a75e-34e3b05b0096 stroke:#2c3143,stroke-width:4px;\n  16[\"Plot\"];\n  12 -->|output_h5ad| 16;\n  a7c8b0d9-82d3-4438-a212-b5f7c56d36b8[\"Output\\nViolin - Filterbycounts\"];\n  16 --> a7c8b0d9-82d3-4438-a212-b5f7c56d36b8;\n  style a7c8b0d9-82d3-4438-a212-b5f7c56d36b8 stroke:#2c3143,stroke-width:4px;\n  17[\"Inspect AnnData\"];\n  15 -->|output_h5ad| 17;\n  56882809-e19f-451a-8010-bc55dcee482f[\"Output\\nGeneral - Filterbymito\"];\n  17 --> 56882809-e19f-451a-8010-bc55dcee482f;\n  style 56882809-e19f-451a-8010-bc55dcee482f stroke:#2c3143,stroke-width:4px;\n  18[\"Scanpy FilterGenes\"];\n  15 -->|output_h5ad| 18;\n  00846477-dec5-408a-83b2-105fff7ce05b[\"Output\\nFiltered Object\"];\n  18 --> 00846477-dec5-408a-83b2-105fff7ce05b;\n  style 00846477-dec5-408a-83b2-105fff7ce05b stroke:#2c3143,stroke-width:4px;\n  19[\"Plot\"];\n  15 -->|output_h5ad| 19;\n  7582e113-2004-4255-a1f3-d3123373f342[\"Output\\nViolin - Filterbymito\"];\n  19 --> 7582e113-2004-4255-a1f3-d3123373f342;\n  style 7582e113-2004-4255-a1f3-d3123373f342 stroke:#2c3143,stroke-width:4px;\n  20[\"Inspect AnnData\"];\n  18 -->|output_h5ad| 20;\n  2d870a40-c602-4a1c-afef-450489354d39[\"Output\\nGeneral - Filtered object\"];\n  20 --> 2d870a40-c602-4a1c-afef-450489354d39;\n  style 2d870a40-c602-4a1c-afef-450489354d39 stroke:#2c3143,stroke-width:4px;\n  21[\"Scanpy NormaliseData\"];\n  18 -->|output_h5ad| 21;\n  22[\"Scanpy FindVariableGenes\"];\n  21 -->|output_h5ad| 22;\n  a0eb92b1-0263-4179-b7af-4bd9bcc9c960[\"Output\\nUse_me_FVG\"];\n  22 --> a0eb92b1-0263-4179-b7af-4bd9bcc9c960;\n  style a0eb92b1-0263-4179-b7af-4bd9bcc9c960 stroke:#2c3143,stroke-width:4px;\n  23[\"Scanpy ScaleData\"];\n  22 -->|output_h5ad| 23;\n  5776dbb9-0cac-40c0-9bae-9accae16a7a0[\"Output\\nUse_me_Scaled\"];\n  23 --> 5776dbb9-0cac-40c0-9bae-9accae16a7a0;\n  style 5776dbb9-0cac-40c0-9bae-9accae16a7a0 stroke:#2c3143,stroke-width:4px;\n  24[\"Scanpy RunPCA\"];\n  23 -->|output_h5ad| 24;\n  25[\"Plot\"];\n  24 -->|output_h5ad| 25;\n  f0b6f578-050f-4936-9ee7-9956b0760c6f[\"Output\\nPCA Variance\"];\n  25 --> f0b6f578-050f-4936-9ee7-9956b0760c6f;\n  style f0b6f578-050f-4936-9ee7-9956b0760c6f stroke:#2c3143,stroke-width:4px;\n  26[\"Scanpy ComputeGraph\"];\n  24 -->|output_h5ad| 26;\n  27[\"Scanpy RunTSNE\"];\n  26 -->|output_h5ad| 27;\n  28[\"Scanpy RunUMAP\"];\n  27 -->|output_h5ad| 28;\n  29[\"Scanpy FindCluster\"];\n  28 -->|output_h5ad| 29;\n  30[\"Scanpy FindMarkers\"];\n  29 -->|output_h5ad| 30;\n  7cfe5c9c-1c80-41b4-b669-633b1d7d40e3[\"Output\\nMarkers - cluster\"];\n  30 --> 7cfe5c9c-1c80-41b4-b669-633b1d7d40e3;\n  style 7cfe5c9c-1c80-41b4-b669-633b1d7d40e3 stroke:#2c3143,stroke-width:4px;\n  98e98405-951e-4c6c-be01-3c925ae35449[\"Output\\nFinal object\"];\n  30 --> 98e98405-951e-4c6c-be01-3c925ae35449;\n  style 98e98405-951e-4c6c-be01-3c925ae35449 stroke:#2c3143,stroke-width:4px;\n  31[\"Scanpy FindMarkers\"];\n  29 -->|output_h5ad| 31;\n  1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4[\"Output\\nMarkers - genotype\"];\n  31 --> 1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4;\n  style 1e9f229d-eb34-4a5b-a6d9-e70c7b0581f4 stroke:#2c3143,stroke-width:4px;\n  32[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 32;\n  33[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 33;\n  34[\"Manipulate AnnData\"];\n  30 -->|output_h5ad| 34;\n  35[\"Scanpy PlotEmbed\"];\n  30 -->|output_h5ad| 35;\n  36[\"Inspect AnnData\"];\n  30 -->|output_h5ad| 36;\n  37[\"AnnData Operations\"];\n  34 -->|anndata| 37;\n  30 -->|output_h5ad| 37;\n  38[\"Join two Datasets\"];\n  30 -->|output_tsv| 38;\n  36 -->|var| 38;\n  39[\"Join two Datasets\"];\n  31 -->|output_tsv| 39;\n  36 -->|var| 39;\n  40[\"AnnData Operations\"];\n  37 -->|output_h5ad| 40;\n  10bd70f8-ffcb-442b-9647-e5b947b6d35e[\"Output\\nFinal cell annotated object\"];\n  40 --> 10bd70f8-ffcb-442b-9647-e5b947b6d35e;\n  style 10bd70f8-ffcb-442b-9647-e5b947b6d35e stroke:#2c3143,stroke-width:4px;\n  41[\"Cut\"];\n  38 -->|out_file1| 41;\n  4f822c1c-91c5-4be4-8f9b-d5bdda0a037e[\"Output\\nMarkers - cluster - named\"];\n  41 --> 4f822c1c-91c5-4be4-8f9b-d5bdda0a037e;\n  style 4f822c1c-91c5-4be4-8f9b-d5bdda0a037e stroke:#2c3143,stroke-width:4px;\n  42[\"Cut\"];\n  39 -->|out_file1| 42;\n  3b471f3d-263d-4299-9b7d-8a8ae1aa556e[\"Output\\nMarkers - genotype - named\"];\n  42 --> 3b471f3d-263d-4299-9b7d-8a8ae1aa556e;\n  style 3b471f3d-263d-4299-9b7d-8a8ae1aa556e stroke:#2c3143,stroke-width:4px;\n  43[\"Scanpy PlotEmbed\"];\n  40 -->|output_h5ad| 43;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Filter, Plot and Explore Single-cell RNA-seq Data updated",
                 "outputs": [
                     {
@@ -242805,7 +618798,7 @@
             "How to set up plates to prevent batch effect",
             "Proper naming conventions when dealing with scRNA-seq samples"
         ],
-        "pageviews": 5897561,
+        "pageviews": 5929579,
         "priority": 3,
         "pub_date": "2019-02-16",
         "questions": [
@@ -242857,6 +618850,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
+        },
         "symlink": null,
         "tags": null,
         "time_estimation": "1h",
@@ -242882,7 +618879,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2133613,
+        "visitors": 2144471,
         "zenodo_link": ""
     },
     {
@@ -243029,7 +619026,7 @@
             "Execute multiple plotting methods designed to maintain lineage relationships between cells",
             "Interpret these plots"
         ],
-        "pageviews": 3602,
+        "pageviews": 3640,
         "priority": 3,
         "pub_date": "2021-04-07",
         "questions": [
@@ -243111,6 +619108,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
+        },
         "symlink": null,
         "tags": [
             "10x",
@@ -243140,7 +619141,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 88,
-        "visitors": 2983,
+        "visitors": 3014,
         "zenodo_link": "https://zenodo.org/record/7075718"
     },
     {
@@ -243311,7 +619312,6 @@
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
@@ -243340,7 +619340,7 @@
             "Appraise data outputs and decisions",
             "Explain why single cell analysis is an iterative process (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly)"
         ],
-        "pageviews": 561,
+        "pageviews": 581,
         "priority": 3,
         "pub_date": "2024-04-09",
         "questions": [
@@ -243360,18 +619360,18 @@
         ],
         "short_id": "T00438",
         "short_tools": [
-            "seurat_normalise_data",
-            "retrieve_scxa",
-            "seurat_find_variable_genes",
-            "seurat_plot",
-            "seurat_read10x",
-            "seurat_run_umap",
-            "seurat_filter_cells",
             "seurat_find_markers",
-            "seurat_run_pca",
             "seurat_find_clusters",
             "seurat_find_neighbours",
-            "seurat_scale_data"
+            "seurat_find_variable_genes",
+            "seurat_filter_cells",
+            "seurat_run_umap",
+            "seurat_normalise_data",
+            "retrieve_scxa",
+            "seurat_scale_data",
+            "seurat_read10x",
+            "seurat_plot",
+            "seurat_run_pca"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -243384,8 +619384,140 @@
                     "usegalaxy": true
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ],
+            "inexact": []
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
                 {
@@ -243397,9 +619529,1623 @@
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
                 }
             ],
-            "inexact": []
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2",
+                    "servers": [
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "v0.0.2+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "v0.0.2+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "v0.0.2+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "v0.0.2+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "v0.0.2+galaxy2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "v0.0.2+galaxy2"
+                },
+                {
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+                    "servers": [
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
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@@ -243682,15 +621428,15 @@
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.6.19+galaxy0",
+                                "0.6.22.post1+galaxy0",
+                                "0.6.22.post1+galaxy3",
+                                "0.6.22.post1+galaxy2",
+                                "0.6.22.post1+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.7.5+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.7.5+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "0.7.5+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.7.5+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.7.5+galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.7.5+galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "10x",
@@ -243737,8 +623016,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 223,
-        "visitors": 578,
+        "visit_duration": 227,
+        "visitors": 593,
         "workflows": [
             {
                 "creators": [
@@ -243795,7 +623074,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput Anndata\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Manipulate AnnData\"];\n  0 -->|output| 1;\n  2[\"Scanpy RunFDG\"];\n  1 -->|anndata| 2;\n  3[\"Scanpy PlotEmbed\"];\n  2 -->|output_h5ad| 3;\n  4[\"Scanpy DiffusionMap\"];\n  2 -->|output_h5ad| 4;\n  5[\"Scanpy ComputeGraph\"];\n  4 -->|output_h5ad| 5;\n  6[\"Scanpy RunFDG\"];\n  5 -->|output_h5ad| 6;\n  7[\"Scanpy PlotEmbed\"];\n  6 -->|output_h5ad| 7;\n  8[\"Scanpy PAGA\"];\n  6 -->|output_h5ad| 8;\n  9[\"Scanpy PlotTrajectory\"];\n  8 -->|output_h5ad| 9;\n  10[\"Scanpy RunFDG\"];\n  9 -->|output_h5ad| 10;\n  11[\"Scanpy PlotEmbed\"];\n  10 -->|output_h5ad| 11;\n  12[\"Scanpy PlotEmbed\"];\n  10 -->|output_h5ad| 12;\n  13[\"Scanpy PlotEmbed\"];\n  10 -->|output_h5ad| 13;\n  14[\"Final Anndata with Trajectory and DPT\"];\n  10 -->|output_h5ad| 14;\n  15[\"Scanpy PlotEmbed\"];\n  14 -->|output_h5ad| 15;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Inferring Trajectories with Scanpy Tutorial Workflow",
                 "outputs": [],
                 "parent_id": "single-cell/scrna-case_trajectories",
@@ -243979,6 +623258,282 @@
             ],
             "inexact": []
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/bgruening/music_compare/music_compare/0.1.1+galaxy4",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.1.1+galaxy4"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.1.1+galaxy4"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.1.1+galaxy4"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.1.1+galaxy4"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.1.1+galaxy4"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "transcriptomics"
@@ -244174,7 +623729,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell:T2D\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell:normal\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nESet Object - Bulk:normal\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nESet Object - Bulk:T2D\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nESet Object - Single cell Total\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"MuSiC Compare: Like with like\"];\n  2 -->|output| 5;\n  1 -->|output| 5;\n  3 -->|output| 5;\n  0 -->|output| 5;\n  6[\"MuSiC Compare: healthyscref\"];\n  2 -->|output| 6;\n  3 -->|output| 6;\n  1 -->|output| 6;\n  7[\"MuSiC Compare - Altogether\"];\n  2 -->|output| 7;\n  3 -->|output| 7;\n  4 -->|output| 7;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "MuSiC-Deconvolution: Compare",
                 "outputs": [
                     {
@@ -244910,7 +624465,7 @@
             "You will combine the metadata and matrix files into an ESet object for MuSiC deconvolution.",
             "You will create multiple ESet objects - both combined and separated out by disease phenotype for your single cell reference."
         ],
-        "pageviews": 1050,
+        "pageviews": 1051,
         "priority": 4,
         "pub_date": "2023-01-20",
         "questions": [
@@ -244928,23 +624483,23 @@
         ],
         "short_id": "T00241",
         "short_tools": [
-            "music_manipulate_eset",
-            "annotatemyids",
-            "join1",
+            "Cut1",
+            "sort1",
             "tp_sed_tool",
-            "table_compute",
+            "regex1",
             "tp_easyjoin_tool",
-            "sort1",
-            "retrieve_scxa",
+            "annotatemyids",
+            "music_manipulate_eset",
+            "music_construct_eset",
+            "join1",
             "tp_awk_tool",
             "add_line_to_file",
-            "music_construct_eset",
+            "table_compute",
+            "retrieve_scxa",
             "anndata_inspect",
-            "Cut1",
-            "tp_cut_tool",
-            "scanpy_read_10x",
             "datamash_transpose",
-            "regex1"
+            "scanpy_read_10x",
+            "tp_cut_tool"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -244964,6 +624519,2670 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Cut1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
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@@ -245010,7 +627229,7 @@
         "video_versions": 0,
         "video_view": 0,
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@@ -245072,7 +627291,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "MuSiC-Deconvolution: Data generation | sc | matrix + ESet",
                 "outputs": [
                     {
@@ -246152,7 +628371,7 @@
                 "inputs": [],
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "MuSiC-Deconvolution: Data generation | sc | metadata",
                 "outputs": [
                     {
@@ -246564,7 +628783,7 @@
             "Be able to choose the most appropriate method for your data",
             "Recognise the common issues and be able to resolve them"
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         "questions": [
@@ -246620,6 +628839,10 @@
                 }
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         "title": "Automated Cell Annotation",
@@ -246643,8 +628866,8 @@
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@@ -246724,14 +628947,14 @@
         "layout": "tutorial_slides",
         "license": "CC-BY-4.0",
         "logo": "GTN",
-        "mod_date": "2024-07-26",
+        "mod_date": "2024-10-04",
         "objectives": [
             "Learn the basic structure of single-cell data",
             "Be able to recognise different types of single-cell metadata",
             "Learn the common data formats used for storing single-cell data",
             "Become familiar with some popular sources for public single-cell data"
         ],
-        "pageviews": 242332,
+        "pageviews": 274350,
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         "questions": [
@@ -246739,6 +628962,20 @@
             "What are the common single-cell formats?",
             "Where can public single-cell data be found?"
         ],
+        "recordings": [
+            {
+                "bot-timestamp": 1727719569,
+                "captioners": [
+                    "hexhowells"
+                ],
+                "date": "2024-09-30",
+                "length": "19M",
+                "speakers": [
+                    "hexhowells"
+                ],
+                "youtube_id": "_GsIlvWxdFw"
+            }
+        ],
         "requirements": [
             {
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@@ -246751,7 +628988,20 @@
         "short_id": "S00123",
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         "slides": true,
-        "slides_recordings": false,
+        "slides_recordings": [
+            {
+                "bot-timestamp": 1727719569,
+                "captioners": [
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+                "date": "2024-09-30",
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+                "speakers": [
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+                ],
+                "youtube_id": "_GsIlvWxdFw"
+            }
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         "supported_servers": {
             "exact": [],
@@ -246786,6 +629036,10 @@
                 }
             ]
         },
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         "tags": null,
         "title": "Single-cell Formats and Resources",
@@ -246805,12 +629059,12 @@
             "hands_on": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-data-formats/slides.json",
             "slides": "https://training.galaxyproject.org/training-material/api/topics/single-cell/tutorials/scrna-data-formats/slides.json"
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-        "visitors": 99484
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@@ -246958,7 +629212,7 @@
             "Compare the outputs from Scanpy, Monocle in Galaxy and Monocle in R",
             "Describe differential expression analysis methods"
         ],
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         "priority": 4,
         "pub_date": "2023-04-12",
         "questions": [
@@ -247017,6 +629271,10 @@
                 }
             ]
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         "tags": [
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@@ -247046,7 +629304,7 @@
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@@ -247296,7 +629554,7 @@
             "Compare the outputs from Scanpy and Monocle",
             "Interpet trajectory analysis results"
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@@ -247337,22 +629595,22 @@
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-            "monocle3_preprocess",
-            "monocle3_create",
-            "join1",
-            "monocle3_partition",
+            "Cut1",
             "monocle3_plotCells",
-            "monocle3_reduceDim",
-            "datamash_transpose",
-            "Filter1",
-            "monocle3_diffExp",
             "monocle3_orderCells",
+            "regexColumn1",
+            "monocle3_diffExp",
+            "join1",
+            "monocle3_partition",
+            "monocle3_create",
             "anndata_inspect",
-            "Cut1",
-            "tp_cut_tool",
+            "monocle3_preprocess",
+            "monocle3_topmarkers",
+            "datamash_transpose",
             "monocle3_learnGraph",
-            "regexColumn1",
-            "monocle3_topmarkers"
+            "monocle3_reduceDim",
+            "tp_cut_tool",
+            "Filter1"
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@@ -247372,6 +629630,2310 @@
             ],
             "inexact": []
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                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAnnData to extract genes & cells annotations\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nAnnData before processing to extract clean expression matrix\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Extract cell annotations\"];\n  0 -->|output| 2;\n  9d66a217-4269-4fb4-9a4e-520eedbb0c9d[\"Output\\nExtracted cell annotations (obs)\"];\n  2 --> 9d66a217-4269-4fb4-9a4e-520eedbb0c9d;\n  style 9d66a217-4269-4fb4-9a4e-520eedbb0c9d stroke:#2c3143,stroke-width:4px;\n  3[\"Extract gene annotations\"];\n  0 -->|output| 3;\n  03537e97-d668-4ce2-ba6b-2952a18a2752[\"Output\\nExtracted gene annotations (var)\"];\n  3 --> 03537e97-d668-4ce2-ba6b-2952a18a2752;\n  style 03537e97-d668-4ce2-ba6b-2952a18a2752 stroke:#2c3143,stroke-width:4px;\n  4[\"Extract clean expression matrix\"];\n  1 -->|output| 4;\n  963462c8-4ae0-486c-8173-d98339127850[\"Output\\nUnprocessed expression matrix\"];\n  4 --> 963462c8-4ae0-486c-8173-d98339127850;\n  style 963462c8-4ae0-486c-8173-d98339127850 stroke:#2c3143,stroke-width:4px;\n  5[\"Filter out unwanted cell types\"];\n  2 -->|obs| 5;\n  5dcb7029-8d03-445d-bb3e-a3119e502be4[\"Output\\nCells without macrophages\"];\n  5 --> 5dcb7029-8d03-445d-bb3e-a3119e502be4;\n  style 5dcb7029-8d03-445d-bb3e-a3119e502be4 stroke:#2c3143,stroke-width:4px;\n  6[\"gene_short_name annotation\"];\n  3 -->|var| 6;\n  15fd415b-2d73-4a1d-92ad-200bb2e73853[\"Output\\nGenes table with gene_short_name colname\"];\n  6 --> 15fd415b-2d73-4a1d-92ad-200bb2e73853;\n  style 15fd415b-2d73-4a1d-92ad-200bb2e73853 stroke:#2c3143,stroke-width:4px;\n  7[\"Cut cells IDs\"];\n  5 -->|out_file1| 7;\n  f9bde249-43b9-4424-8285-e437549223e2[\"Output\\nFiltered cells IDs \"];\n  7 --> f9bde249-43b9-4424-8285-e437549223e2;\n  style f9bde249-43b9-4424-8285-e437549223e2 stroke:#2c3143,stroke-width:4px;\n  8[\"Cut genes IDs\"];\n  6 -->|out_file1| 8;\n  b22efa1d-db99-435f-9357-74150ac9a437[\"Output\\nGenes IDs\"];\n  8 --> b22efa1d-db99-435f-9357-74150ac9a437;\n  style b22efa1d-db99-435f-9357-74150ac9a437 stroke:#2c3143,stroke-width:4px;\n  9[\"Filter matrix by cells\"];\n  7 -->|out_file1| 9;\n  4 -->|X| 9;\n  b45f18b6-e385-41a1-a8f0-f94e6616e2b3[\"Output\\nPre-filtered matrix (by cells)\"];\n  9 --> b45f18b6-e385-41a1-a8f0-f94e6616e2b3;\n  style b45f18b6-e385-41a1-a8f0-f94e6616e2b3 stroke:#2c3143,stroke-width:4px;\n  10[\"Remove duplicate column cells IDs\"];\n  9 -->|out_file1| 10;\n  f4d6a581-9b42-41dc-9a4a-278fe5d6591c[\"Output\\nFiltered matrix (by cells) \"];\n  10 --> f4d6a581-9b42-41dc-9a4a-278fe5d6591c;\n  style f4d6a581-9b42-41dc-9a4a-278fe5d6591c stroke:#2c3143,stroke-width:4px;\n  11[\"Transpose matrix\"];\n  10 -->|output| 11;\n  e4eb8fb3-2028-41fb-8aca-b1c0a6e6bfe5[\"Output\\nfiltered matrix (by cells) transposed\"];\n  11 --> e4eb8fb3-2028-41fb-8aca-b1c0a6e6bfe5;\n  style e4eb8fb3-2028-41fb-8aca-b1c0a6e6bfe5 stroke:#2c3143,stroke-width:4px;\n  12[\"Filter matrix by genes\"];\n  8 -->|out_file1| 12;\n  11 -->|out_file| 12;\n  c0481255-0187-407c-9f29-f4c0069d9285[\"Output\\nPre-filtered matrix (by cells & genes)\"];\n  12 --> c0481255-0187-407c-9f29-f4c0069d9285;\n  style c0481255-0187-407c-9f29-f4c0069d9285 stroke:#2c3143,stroke-width:4px;\n  13[\"Remove duplicate column genes IDs\"];\n  12 -->|out_file1| 13;\n  4dcd8e60-1298-4886-be8f-af1eac9f20f7[\"Output\\nFiltered matrix (by cells & genes)\"];\n  13 --> 4dcd8e60-1298-4886-be8f-af1eac9f20f7;\n  style 4dcd8e60-1298-4886-be8f-af1eac9f20f7 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "AnnData object to Monocle input files",
                 "outputs": [
                     {
@@ -248245,7 +632807,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nExpression matrix input\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nCell annotations input\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nGene annotations input\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Monocle3 create\"];\n  1 -->|output| 3;\n  0 -->|output| 3;\n  2 -->|output| 3;\n  30db218d-f9e5-426d-ac9b-7823743ab5fb[\"Output\\nMonocle3 create on input dataset(s): cds3\"];\n  3 --> 30db218d-f9e5-426d-ac9b-7823743ab5fb;\n  style 30db218d-f9e5-426d-ac9b-7823743ab5fb stroke:#2c3143,stroke-width:4px;\n  4[\"Monocle3 preprocess\"];\n  3 -->|output_rds| 4;\n  38996ee0-0c00-4a01-ad18-f2e505eaf780[\"Output\\nMonocle3 preprocess on input dataset(s): cds3\"];\n  4 --> 38996ee0-0c00-4a01-ad18-f2e505eaf780;\n  style 38996ee0-0c00-4a01-ad18-f2e505eaf780 stroke:#2c3143,stroke-width:4px;\n  5[\"Monocle3 reduceDim\"];\n  4 -->|output_rds| 5;\n  21edf68f-72df-457d-aad7-c5fc5afa2b6b[\"Output\\nMonocle3 reduceDim on input dataset(s): cds3\"];\n  5 --> 21edf68f-72df-457d-aad7-c5fc5afa2b6b;\n  style 21edf68f-72df-457d-aad7-c5fc5afa2b6b stroke:#2c3143,stroke-width:4px;\n  6[\"Monocle3 partition\"];\n  5 -->|output_rds| 6;\n  fdb0e520-27c4-43a0-8f27-a25832a0816d[\"Output\\nMonocle3 partition on input dataset(s): cds3\"];\n  6 --> fdb0e520-27c4-43a0-8f27-a25832a0816d;\n  style fdb0e520-27c4-43a0-8f27-a25832a0816d stroke:#2c3143,stroke-width:4px;\n  7[\"Plot cell type\"];\n  5 -->|output_rds| 7;\n  5e309658-e20f-4da1-8841-818f16fa8f01[\"Output\\nCell type plot\"];\n  7 --> 5e309658-e20f-4da1-8841-818f16fa8f01;\n  style 5e309658-e20f-4da1-8841-818f16fa8f01 stroke:#2c3143,stroke-width:4px;\n  8[\"Plot genotype\"];\n  5 -->|output_rds| 8;\n  aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4[\"Output\\nGenotype plot\"];\n  8 --> aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4;\n  style aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4 stroke:#2c3143,stroke-width:4px;\n  9[\"Plot batch\"];\n  5 -->|output_rds| 9;\n  c8eec2e4-1a64-47bb-812b-4002968c57c8[\"Output\\nBatch plot\"];\n  9 --> c8eec2e4-1a64-47bb-812b-4002968c57c8;\n  style c8eec2e4-1a64-47bb-812b-4002968c57c8 stroke:#2c3143,stroke-width:4px;\n  10[\"Plot sex\"];\n  5 -->|output_rds| 10;\n  c75954dd-34d5-4a20-bcf3-e5cd92d74885[\"Output\\nSex plot\"];\n  10 --> c75954dd-34d5-4a20-bcf3-e5cd92d74885;\n  style c75954dd-34d5-4a20-bcf3-e5cd92d74885 stroke:#2c3143,stroke-width:4px;\n  11[\"Monocle3 top markers\"];\n  6 -->|output_rds| 11;\n  12[\"Plot genes\"];\n  6 -->|output_rds| 12;\n  f91c22a3-8c6d-432a-92c5-cb010115fa86[\"Output\\nGene expression plot\"];\n  12 --> f91c22a3-8c6d-432a-92c5-cb010115fa86;\n  style f91c22a3-8c6d-432a-92c5-cb010115fa86 stroke:#2c3143,stroke-width:4px;\n  13[\"Plot partition\"];\n  6 -->|output_rds| 13;\n  f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d[\"Output\\nPartition plot\"];\n  13 --> f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d;\n  style f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d stroke:#2c3143,stroke-width:4px;\n  14[\"Plot cluster\"];\n  6 -->|output_rds| 14;\n  a2c1a628-d79d-4e37-ad33-de92033021a8[\"Output\\nCluster plot\"];\n  14 --> a2c1a628-d79d-4e37-ad33-de92033021a8;\n  style a2c1a628-d79d-4e37-ad33-de92033021a8 stroke:#2c3143,stroke-width:4px;\n  15[\"Monocle3 learnGraph\"];\n  6 -->|output_rds| 15;\n  ed2003aa-4680-409f-8d79-e79b878a786c[\"Output\\nMonocle3 learnGraph on input dataset(s): cds3\"];\n  15 --> ed2003aa-4680-409f-8d79-e79b878a786c;\n  style ed2003aa-4680-409f-8d79-e79b878a786c stroke:#2c3143,stroke-width:4px;\n  16[\"Plot learned trajectory\"];\n  15 -->|output_rds| 16;\n  6fa555f1-b4f2-4e5d-bce1-ed462d8e056d[\"Output\\nCell types & learned trajectory path plot\"];\n  16 --> 6fa555f1-b4f2-4e5d-bce1-ed462d8e056d;\n  style 6fa555f1-b4f2-4e5d-bce1-ed462d8e056d stroke:#2c3143,stroke-width:4px;\n  17[\"Monocle3 orderCells\"];\n  15 -->|output_rds| 17;\n  96d10412-3d7f-4970-b541-6f4367fa3f37[\"Output\\nMonocle3 orderCells on input dataset(s): cds3\"];\n  17 --> 96d10412-3d7f-4970-b541-6f4367fa3f37;\n  style 96d10412-3d7f-4970-b541-6f4367fa3f37 stroke:#2c3143,stroke-width:4px;\n  18[\"Monocle3 diffExp\"];\n  17 -->|output_rds| 18;\n  db1dc457-2d6e-47cc-b7ce-d0a4d23e9498[\"Output\\nDifferential expression of genes - table\"];\n  18 --> db1dc457-2d6e-47cc-b7ce-d0a4d23e9498;\n  style db1dc457-2d6e-47cc-b7ce-d0a4d23e9498 stroke:#2c3143,stroke-width:4px;\n  19[\"Plot pseudotime\"];\n  17 -->|output_rds| 19;\n  d1b3efd2-0a81-4dad-8652-589c2678fbaa[\"Output\\nPseudotime plot\"];\n  19 --> d1b3efd2-0a81-4dad-8652-589c2678fbaa;\n  style d1b3efd2-0a81-4dad-8652-589c2678fbaa stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Monocle3 workflow",
                 "outputs": [
                     {
@@ -249229,7 +633791,7 @@
                 ],
                 "license": "CC-BY-4.0",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nAnnData to extract genes & cells annotations\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nAnnData before processing to extract clean expression matrix\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Extract cell annotations\"];\n  0 -->|output| 2;\n  0646798d-3a5d-420a-a7cf-cde6cec722d5[\"Output\\nExtracted cell annotations (obs)\"];\n  2 --> 0646798d-3a5d-420a-a7cf-cde6cec722d5;\n  style 0646798d-3a5d-420a-a7cf-cde6cec722d5 stroke:#2c3143,stroke-width:4px;\n  3[\"Extract gene annotations\"];\n  0 -->|output| 3;\n  84162745-68b0-41a5-b06e-a285440ba095[\"Output\\nExtracted gene annotations (var)\"];\n  3 --> 84162745-68b0-41a5-b06e-a285440ba095;\n  style 84162745-68b0-41a5-b06e-a285440ba095 stroke:#2c3143,stroke-width:4px;\n  4[\"Extract clean expression matrix\"];\n  1 -->|output| 4;\n  3f03af0c-ac41-4450-b5ba-639a79ea543b[\"Output\\nUnprocessed expression matrix\"];\n  4 --> 3f03af0c-ac41-4450-b5ba-639a79ea543b;\n  style 3f03af0c-ac41-4450-b5ba-639a79ea543b stroke:#2c3143,stroke-width:4px;\n  5[\"Filter out macrophages\"];\n  2 -->|obs| 5;\n  fb81e9a1-0603-419a-83f5-0c9f94939b16[\"Output\\nCells without macrophages\"];\n  5 --> fb81e9a1-0603-419a-83f5-0c9f94939b16;\n  style fb81e9a1-0603-419a-83f5-0c9f94939b16 stroke:#2c3143,stroke-width:4px;\n  6[\"gene_short_name annotation\"];\n  3 -->|var| 6;\n  94a60e6c-cdf7-48e5-8b55-d221cef22688[\"Output\\nGenes table with gene_short_name colname\"];\n  6 --> 94a60e6c-cdf7-48e5-8b55-d221cef22688;\n  style 94a60e6c-cdf7-48e5-8b55-d221cef22688 stroke:#2c3143,stroke-width:4px;\n  7[\"Cut cells IDs\"];\n  5 -->|out_file1| 7;\n  34146c30-2666-481f-8d49-a849d5d3aa91[\"Output\\nFiltered cells IDs \"];\n  7 --> 34146c30-2666-481f-8d49-a849d5d3aa91;\n  style 34146c30-2666-481f-8d49-a849d5d3aa91 stroke:#2c3143,stroke-width:4px;\n  8[\"Cut genes IDs\"];\n  6 -->|out_file1| 8;\n  8f38fb93-cb30-4fbc-90c5-7f6bd023feea[\"Output\\nGenes IDs\"];\n  8 --> 8f38fb93-cb30-4fbc-90c5-7f6bd023feea;\n  style 8f38fb93-cb30-4fbc-90c5-7f6bd023feea stroke:#2c3143,stroke-width:4px;\n  9[\"Filter matrix by cells\"];\n  7 -->|out_file1| 9;\n  4 -->|X| 9;\n  f654c045-5fea-43f9-96d6-492c810593d2[\"Output\\nPre-filtered matrix (by cells)\"];\n  9 --> f654c045-5fea-43f9-96d6-492c810593d2;\n  style f654c045-5fea-43f9-96d6-492c810593d2 stroke:#2c3143,stroke-width:4px;\n  10[\"Remove duplicate column cells IDs\"];\n  9 -->|out_file1| 10;\n  f633c125-a4d0-4fa7-ab87-022349f4ac70[\"Output\\nFiltered matrix (by cells) \"];\n  10 --> f633c125-a4d0-4fa7-ab87-022349f4ac70;\n  style f633c125-a4d0-4fa7-ab87-022349f4ac70 stroke:#2c3143,stroke-width:4px;\n  11[\"Transpose matrix\"];\n  10 -->|output| 11;\n  3202091e-1afc-4f50-8922-1f9e50c490fc[\"Output\\nfiltered matrix (by cells) transposed\"];\n  11 --> 3202091e-1afc-4f50-8922-1f9e50c490fc;\n  style 3202091e-1afc-4f50-8922-1f9e50c490fc stroke:#2c3143,stroke-width:4px;\n  12[\"Filter matrix by genes\"];\n  8 -->|out_file1| 12;\n  11 -->|out_file| 12;\n  6c23cbd5-a1b5-428e-8ff9-ebac4893ad88[\"Output\\nPre-filtered matrix (by cells & genes)\"];\n  12 --> 6c23cbd5-a1b5-428e-8ff9-ebac4893ad88;\n  style 6c23cbd5-a1b5-428e-8ff9-ebac4893ad88 stroke:#2c3143,stroke-width:4px;\n  13[\"Remove duplicate column genes IDs\"];\n  12 -->|out_file1| 13;\n  25839326-0b5d-4e74-91ec-24e22c08f7c5[\"Output\\nFiltered matrix (by cells & genes)\"];\n  13 --> 25839326-0b5d-4e74-91ec-24e22c08f7c5;\n  style 25839326-0b5d-4e74-91ec-24e22c08f7c5 stroke:#2c3143,stroke-width:4px;\n  14[\"Monocle3 create\"];\n  5 -->|out_file1| 14;\n  13 -->|output| 14;\n  6 -->|out_file1| 14;\n  f8c5589c-a70d-416e-a9de-ebc987f61fc3[\"Output\\nMonocle3 create on input dataset(s): cds3\"];\n  14 --> f8c5589c-a70d-416e-a9de-ebc987f61fc3;\n  style f8c5589c-a70d-416e-a9de-ebc987f61fc3 stroke:#2c3143,stroke-width:4px;\n  15[\"Monocle3 preprocess\"];\n  14 -->|output_rds| 15;\n  c134942f-60e7-4cd0-8c32-da4a303b879d[\"Output\\nMonocle3 preprocess on input dataset(s): cds3\"];\n  15 --> c134942f-60e7-4cd0-8c32-da4a303b879d;\n  style c134942f-60e7-4cd0-8c32-da4a303b879d stroke:#2c3143,stroke-width:4px;\n  16[\"Monocle3 reduceDim\"];\n  15 -->|output_rds| 16;\n  2c9fb108-2a1c-41df-a8d8-81a18b66d2a1[\"Output\\nMonocle3 reduceDim on input dataset(s): cds3\"];\n  16 --> 2c9fb108-2a1c-41df-a8d8-81a18b66d2a1;\n  style 2c9fb108-2a1c-41df-a8d8-81a18b66d2a1 stroke:#2c3143,stroke-width:4px;\n  17[\"Monocle3 partition\"];\n  16 -->|output_rds| 17;\n  93371c10-6583-47fc-830f-9a90dc980766[\"Output\\nMonocle3 partition on input dataset(s): cds3\"];\n  17 --> 93371c10-6583-47fc-830f-9a90dc980766;\n  style 93371c10-6583-47fc-830f-9a90dc980766 stroke:#2c3143,stroke-width:4px;\n  18[\"Plot cell type\"];\n  16 -->|output_rds| 18;\n  f096d060-82e8-4847-9e8f-b22c9288f565[\"Output\\nCell type plot\"];\n  18 --> f096d060-82e8-4847-9e8f-b22c9288f565;\n  style f096d060-82e8-4847-9e8f-b22c9288f565 stroke:#2c3143,stroke-width:4px;\n  19[\"Plot genotype\"];\n  16 -->|output_rds| 19;\n  aab28bb1-e2e7-4b7d-9b2b-1cab64bea287[\"Output\\nGenotype plot\"];\n  19 --> aab28bb1-e2e7-4b7d-9b2b-1cab64bea287;\n  style aab28bb1-e2e7-4b7d-9b2b-1cab64bea287 stroke:#2c3143,stroke-width:4px;\n  20[\"Plot batch\"];\n  16 -->|output_rds| 20;\n  9b362eee-9238-47c5-a4c2-85f3995430f4[\"Output\\nBatch plot\"];\n  20 --> 9b362eee-9238-47c5-a4c2-85f3995430f4;\n  style 9b362eee-9238-47c5-a4c2-85f3995430f4 stroke:#2c3143,stroke-width:4px;\n  21[\"Plot sex\"];\n  16 -->|output_rds| 21;\n  c2a1e104-ef2d-4b66-ac2b-bf0251714434[\"Output\\nSex plot\"];\n  21 --> c2a1e104-ef2d-4b66-ac2b-bf0251714434;\n  style c2a1e104-ef2d-4b66-ac2b-bf0251714434 stroke:#2c3143,stroke-width:4px;\n  22[\"Monocle3 top markers\"];\n  17 -->|output_rds| 22;\n  23[\"Plot genes\"];\n  17 -->|output_rds| 23;\n  e8867379-82c6-4c32-a2d3-0b24670269ae[\"Output\\nGene expression plot\"];\n  23 --> e8867379-82c6-4c32-a2d3-0b24670269ae;\n  style e8867379-82c6-4c32-a2d3-0b24670269ae stroke:#2c3143,stroke-width:4px;\n  24[\"Plot partition\"];\n  17 -->|output_rds| 24;\n  3f7b0a7c-85d6-430b-8385-fa9a76385c0e[\"Output\\nPartition plot\"];\n  24 --> 3f7b0a7c-85d6-430b-8385-fa9a76385c0e;\n  style 3f7b0a7c-85d6-430b-8385-fa9a76385c0e stroke:#2c3143,stroke-width:4px;\n  25[\"Plot cluster\"];\n  17 -->|output_rds| 25;\n  40b65826-f73e-4054-a56d-b241985d6996[\"Output\\nCluster plot\"];\n  25 --> 40b65826-f73e-4054-a56d-b241985d6996;\n  style 40b65826-f73e-4054-a56d-b241985d6996 stroke:#2c3143,stroke-width:4px;\n  26[\"Monocle3 learnGraph\"];\n  17 -->|output_rds| 26;\n  294b1a49-cec6-49d0-bcd4-3a954da67bec[\"Output\\nMonocle3 learnGraph on input dataset(s): cds3\"];\n  26 --> 294b1a49-cec6-49d0-bcd4-3a954da67bec;\n  style 294b1a49-cec6-49d0-bcd4-3a954da67bec stroke:#2c3143,stroke-width:4px;\n  27[\"Plot learned trajectory\"];\n  26 -->|output_rds| 27;\n  c85ddefe-8eaf-4d21-93ed-ca0859286bf0[\"Output\\nCell types & learned trajectory path plot\"];\n  27 --> c85ddefe-8eaf-4d21-93ed-ca0859286bf0;\n  style c85ddefe-8eaf-4d21-93ed-ca0859286bf0 stroke:#2c3143,stroke-width:4px;\n  28[\"Monocle3 orderCells\"];\n  26 -->|output_rds| 28;\n  5aea5752-b767-4fc8-8741-1f4d1c659a41[\"Output\\nMonocle3 orderCells on input dataset(s): cds3\"];\n  28 --> 5aea5752-b767-4fc8-8741-1f4d1c659a41;\n  style 5aea5752-b767-4fc8-8741-1f4d1c659a41 stroke:#2c3143,stroke-width:4px;\n  29[\"Monocle3 diffExp\"];\n  28 -->|output_rds| 29;\n  3c298624-9f06-4e52-b2a8-fb834b87c296[\"Output\\nDifferential expression of genes - table\"];\n  29 --> 3c298624-9f06-4e52-b2a8-fb834b87c296;\n  style 3c298624-9f06-4e52-b2a8-fb834b87c296 stroke:#2c3143,stroke-width:4px;\n  30[\"Plot pseudotime\"];\n  28 -->|output_rds| 30;\n  813d15bb-0771-4aed-9226-4874c1ddba59[\"Output\\nPseudotime plot\"];\n  30 --> 813d15bb-0771-4aed-9226-4874c1ddba59;\n  style 813d15bb-0771-4aed-9226-4874c1ddba59 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Trajectory analysis using Monocle3 - full tutorial workflow",
                 "outputs": [
                     {
@@ -250961,7 +635523,7 @@
             "You will combine the metadata and matrix files into an ESet object for MuSiC deconvolution.",
             "You will create multiple ESet objects - both combined and separated out by disease phenotype for your bulk dataset."
         ],
-        "pageviews": 877,
+        "pageviews": 882,
         "priority": 5,
         "pub_date": "2023-01-20",
         "questions": [
@@ -250980,17 +635542,17 @@
         ],
         "short_id": "T00242",
         "short_tools": [
-            "music_manipulate_eset",
-            "annotatemyids",
-            "tp_sed_tool",
-            "table_compute",
-            "tp_easyjoin_tool",
             "sort1",
+            "tp_sed_tool",
             "column_remove_by_header",
-            "tp_awk_tool",
+            "regex1",
+            "tp_easyjoin_tool",
+            "annotatemyids",
+            "music_manipulate_eset",
             "music_construct_eset",
-            "tp_cut_tool",
-            "regex1"
+            "tp_awk_tool",
+            "table_compute",
+            "tp_cut_tool"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -251011,6 +635573,1699 @@
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@@ -251086,7 +637341,7 @@
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+                "modified": "2024-10-08 10:05:45 +0000",
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@@ -252113,7 +638368,7 @@
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@@ -252174,6 +638429,10 @@
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@@ -252198,7 +638457,7 @@
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@@ -252316,7 +638575,7 @@
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             "Visualize the predictions."
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@@ -252325,9 +638584,9 @@
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-            "sklearn_ensemble",
             "plotly_regression_performance_plots",
+            "sklearn_ensemble",
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@@ -252367,6 +638626,692 @@
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         "time_estimation": "1H",
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@@ -252396,7 +639341,7 @@
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@@ -252537,7 +639482,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Classification LSVC",
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@@ -252903,7 +639848,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Regression GradientBoosting",
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@@ -253200,8 +640145,7 @@
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@@ -253222,7 +640166,7 @@
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             "Learn how to visualize clusters"
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@@ -253268,11 +640212,559 @@
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@@ -253303,8 +640795,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 57,
-        "visitors": 7784,
+        "visit_duration": 58,
+        "visitors": 7802,
         "workflows": [
             {
                 "creators": [],
@@ -253414,7 +640906,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\niris\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\ncircles\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Numeric Clustering\"];\n  2 -->|output| 10;\n  11[\"Numeric Clustering\"];\n  2 -->|output| 11;\n  12[\"Numeric Clustering\"];\n  3 -->|tabular| 12;\n  13[\"Numeric Clustering\"];\n  3 -->|tabular| 13;\n  14[\"Numeric Clustering\"];\n  3 -->|tabular| 14;\n  15[\"Scatterplot with ggplot2\"];\n  5 -->|outfile| 15;\n  275528af-4af3-4dc6-a958-737f4d2f89bd[\"Output\\nheirarchical_clustering_circles\"];\n  15 --> 275528af-4af3-4dc6-a958-737f4d2f89bd;\n  style 275528af-4af3-4dc6-a958-737f4d2f89bd stroke:#2c3143,stroke-width:4px;\n  16[\"Scatterplot with ggplot2\"];\n  6 -->|outfile| 16;\n  870b03ca-6b2c-42ab-bbcc-6c4bbecf8ea9[\"Output\\nkmeans_clustering_circles\"];\n  16 --> 870b03ca-6b2c-42ab-bbcc-6c4bbecf8ea9;\n  style 870b03ca-6b2c-42ab-bbcc-6c4bbecf8ea9 stroke:#2c3143,stroke-width:4px;\n  17[\"Scatterplot with ggplot2\"];\n  7 -->|outfile| 17;\n  9664ba05-4664-4ceb-8f93-0974b20bf9e1[\"Output\\ndbscan_clustering_circles\"];\n  17 --> 9664ba05-4664-4ceb-8f93-0974b20bf9e1;\n  style 9664ba05-4664-4ceb-8f93-0974b20bf9e1 stroke:#2c3143,stroke-width:4px;\n  18[\"Scatterplot with ggplot2\"];\n  9 -->|outfile| 18;\n  d82a4483-7f38-4614-96b4-2a9b3316c808[\"Output\\nheirarchical_clustering_moon\"];\n  18 --> d82a4483-7f38-4614-96b4-2a9b3316c808;\n  style d82a4483-7f38-4614-96b4-2a9b3316c808 stroke:#2c3143,stroke-width:4px;\n  19[\"Scatterplot with ggplot2\"];\n  10 -->|outfile| 19;\n  00c0ca58-4ee5-4606-8c1b-c172431e5dbd[\"Output\\ndbscan_clustering_moon\"];\n  19 --> 00c0ca58-4ee5-4606-8c1b-c172431e5dbd;\n  style 00c0ca58-4ee5-4606-8c1b-c172431e5dbd stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nmoon\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  20[\"Scatterplot with ggplot2\"];\n  11 -->|outfile| 20;\n  5717bf22-83e3-46a2-8f6d-12a1fa41439b[\"Output\\nkmeans_clustering_moon\"];\n  20 --> 5717bf22-83e3-46a2-8f6d-12a1fa41439b;\n  style 5717bf22-83e3-46a2-8f6d-12a1fa41439b stroke:#2c3143,stroke-width:4px;\n  21[\"Scatterplot with ggplot2\"];\n  12 -->|outfile| 21;\n  0ace8714-ff3a-4efd-a649-70924b1e6230[\"Output\\nheirarchical_clustering_iris\"];\n  21 --> 0ace8714-ff3a-4efd-a649-70924b1e6230;\n  style 0ace8714-ff3a-4efd-a649-70924b1e6230 stroke:#2c3143,stroke-width:4px;\n  22[\"Scatterplot with ggplot2\"];\n  13 -->|outfile| 22;\n  e6f69d7d-c9e3-4023-8daf-87f6b0afc3fd[\"Output\\nkmeans_clustering_iris\"];\n  22 --> e6f69d7d-c9e3-4023-8daf-87f6b0afc3fd;\n  style e6f69d7d-c9e3-4023-8daf-87f6b0afc3fd stroke:#2c3143,stroke-width:4px;\n  23[\"Scatterplot with ggplot2\"];\n  14 -->|outfile| 23;\n  119d1cde-567a-47f0-99de-00d3557c38a2[\"Output\\ndbscan_clustering_iris\"];\n  23 --> 119d1cde-567a-47f0-99de-00d3557c38a2;\n  style 119d1cde-567a-47f0-99de-00d3557c38a2 stroke:#2c3143,stroke-width:4px;\n  3[\"Convert CSV to tabular\"];\n  0 -->|output| 3;\n  4[\"Scatterplot with ggplot2\"];\n  1 -->|output| 4;\n  5[\"Numeric Clustering\"];\n  1 -->|output| 5;\n  6[\"Numeric Clustering\"];\n  1 -->|output| 6;\n  7[\"Numeric Clustering\"];\n  1 -->|output| 7;\n  8[\"Scatterplot with ggplot2\"];\n  2 -->|output| 8;\n  9[\"Numeric Clustering\"];\n  2 -->|output| 9;",
-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Clustering in Machine Learning",
                 "outputs": [
                     {
@@ -253958,7 +641450,7 @@
             "Learn how to create a CNN using Galaxy's deep learning tools",
             "Solve an image classification problem on fruit 360 dataset using CNN in Galaxy"
         ],
-        "pageviews": 4268424,
+        "pageviews": 4300446,
         "pub_date": "2021-12-01",
         "questions": [
             "How to solve an image classification problem using convolutional neural network (CNN)?"
@@ -253988,13 +641480,13 @@
         ],
         "short_id": "T00265",
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-            "model_prediction",
-            "keras_model_config",
-            "tp_cut_tool",
-            "ml_visualization_ex",
             "keras_train_and_eval",
+            "ml_visualization_ex",
             "sklearn_to_categorical",
-            "keras_model_builder"
+            "model_prediction",
+            "keras_model_config",
+            "keras_model_builder",
+            "tp_cut_tool"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -254023,6 +641515,1520 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "fruit_360",
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                     {
@@ -255054,7 +644060,7 @@
             "Learn ageing biomarkers and predict age from DNA methylation datasets",
             "Learn how visualizations can be used to analyze predictions"
         ],
-        "pageviews": 3167,
+        "pageviews": 3190,
         "pub_date": "2020-01-25",
         "questions": [
             "How to use regression techniques to create predictive models from biological datasets?"
@@ -255075,12 +644081,12 @@
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+            "sklearn_generalized_linear",
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@@ -255120,6 +644126,1035 @@
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         "time_estimation": "2H",
         "title": "Regression in Machine Learning",
@@ -255151,7 +645186,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 55,
-        "visitors": 2569,
+        "visitors": 2588,
         "workflows": [
             {
                 "creators": [
@@ -255263,7 +645298,7 @@
                 ],
                 "license": "MIT",
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "ml_regression",
                 "outputs": [],
                 "parent_id": "statistics/regression_machinelearning",
@@ -255393,7 +645428,7 @@
             "Learn how to create a neural network using Galaxy's deep learning tools",
             "Solve a simple regression problem, car purchase price prediction, via FNN in Galaxy"
         ],
-        "pageviews": 5351360,
+        "pageviews": 5383454,
         "pub_date": "2021-04-28",
         "questions": [
             "What is a feedforward neural network (FNN)?",
@@ -255424,10 +645459,10 @@
         ],
         "short_id": "T00258",
         "short_tools": [
+            "keras_train_and_eval",
             "plotly_regression_performance_plots",
             "model_prediction",
             "keras_model_config",
-            "keras_train_and_eval",
             "keras_model_builder"
         ],
         "slides": true,
@@ -255468,6 +645503,854 @@
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@@ -255637,7 +646520,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Intro_To_FNN_v1_0_10_0",
                 "outputs": [],
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@@ -255761,7 +646644,7 @@
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             "Solve an image classification problem on MNIST digit classification dataset using CNN in Galaxy"
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         "questions": [
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@@ -255794,11 +646677,11 @@
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-            "ml_visualization_ex",
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+            "ml_visualization_ex",
             "sklearn_to_categorical",
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@@ -255829,6 +646712,1016 @@
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@@ -256377,7 +649092,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Intro_To_Deep_Learning",
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                 "parent_id": "statistics/intro_deep_learning",
@@ -256493,7 +649208,7 @@
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@@ -256501,9 +649216,9 @@
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-        "visit_duration": 127,
-        "visitors": 398,
+        "visit_duration": 126,
+        "visitors": 400,
         "workflows": [
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@@ -256606,7 +649859,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Simtext training workflow",
                 "outputs": [
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@@ -256883,7 +650136,7 @@
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             "Solve a sentiment analysis problem on IMDB movie review dataset using RNN in Galaxy"
         ],
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+        "pageviews": 5678125,
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             "What is a recurrent neural network (RNN)?",
@@ -256915,10 +650168,10 @@
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@@ -256959,6 +650212,861 @@
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@@ -257507,7 +652440,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
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                 "name": "Age Prediction DNA Methylation",
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@@ -257965,7 +652898,7 @@
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+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "Age Prediction RNA-Seq",
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@@ -258318,11 +653249,283 @@
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+                            "version": "1.0.8.1"
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+                        {
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+                            "state": "missing"
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@@ -258351,8 +653554,8 @@
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         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 170,
-        "visitors": 2008,
+        "visit_duration": 171,
+        "visitors": 2015,
         "workflows": [
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                 "creators": [],
@@ -258457,7 +653660,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Machine Learning",
                 "outputs": [
                     {
@@ -259089,7 +654292,7 @@
             "Send long-running jobs to Galaxy's cluster and save results in its history",
             "Reproduce results from recent scientific publications - COVID CT scan segmentation and 3D protein structure prediction"
         ],
-        "pageviews": 1148,
+        "pageviews": 1155,
         "pub_date": "2022-04-06",
         "questions": [
             "How to use Jupyterlab and it several features?",
@@ -259113,9 +654316,9 @@
         ],
         "short_id": "T00266",
         "short_tools": [
-            "Filter1",
+            "Cut1",
             "interactive_tool_ml_jupyter_notebook",
-            "Cut1"
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -259129,6 +654332,538 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Workflow Constructed From History 'IWTomics Workflow'",
                 "outputs": [],
                 "parent_id": "statistics/iwtomics",
@@ -259993,25 +656278,25 @@
             "Learn to predict aberrant pathway activity using RNA-Seq data, mutational status and copy number variation data from TCGA.",
             "Apply logistic regression based machine learning algorithms on TCGA data."
         ],
-        "pageviews": 1098,
+        "pageviews": 1099,
         "pub_date": "2021-05-06",
         "questions": [
             "How to predict aberrant pathway activity in The Cancer Genome Atlas (TCGA) using Machine learning approaches?"
         ],
         "short_id": "T00260",
         "short_tools": [
+            "pancancer_apply_weights",
+            "pancancer_within_disease_analysis",
             "pancancer_targene_pharmacology",
-            "pancancer_classifier",
-            "pancancer_map_mutation_class",
+            "pancancer_visualize_decisions",
             "pancancer_pathway_count_heatmaps",
-            "pancancer_targene_summary_figures",
-            "pancancer_within_disease_analysis",
-            "pancancer_targene_cell_line_predictions",
-            "pancancer_apply_weights",
             "pancancer_external_sample_status_prediction",
-            "pancancer_compare_within_models",
-            "pancancer_visualize_decisions",
-            "pancancer_alternative_genes_pathwaymapper"
+            "pancancer_alternative_genes_pathwaymapper",
+            "pancancer_map_mutation_class",
+            "pancancer_targene_cell_line_predictions",
+            "pancancer_targene_summary_figures",
+            "pancancer_classifier",
+            "pancancer_compare_within_models"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -260019,6 +656304,1708 @@
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@@ -260789,7 +658776,7 @@
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@@ -260823,14 +658810,14 @@
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+                                "1.0.8.4",
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+                            "state": "exact",
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+                    "version": "1.0.11.0"
+                }
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         "symlink": null,
         "time_estimation": "2H",
         "title": "Classification in Machine Learning",
@@ -260903,7 +660237,7 @@
         "video_versions": 2,
         "video_view": 0,
         "visit_duration": 116,
-        "visitors": 2078,
+        "visitors": 2087,
         "workflows": [
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@@ -261080,7 +660414,7 @@
                 ],
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:45 +0000",
                 "name": "ml_classification",
                 "outputs": [],
                 "parent_id": "statistics/classification_machinelearning",
@@ -261177,7 +660511,6 @@
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         "exact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
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             "UseGalaxy.org.au"
         ],
@@ -261214,7 +660547,7 @@
             "Interpret and visualize the results obtained from ML analyses on omics datasets",
             "Apply the ML techniques to analyse their own datasets"
         ],
-        "pageviews": 5315,
+        "pageviews": 5327,
         "pub_date": "2021-05-21",
         "questions": [
             "What are the main categories in Machine Learning algorithms?",
@@ -261268,8 +660601,140 @@
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-                    "url": "https://usegalaxy.fr/",
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+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
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+                },
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@@ -261281,9 +660746,144 @@
                     "name": "UseGalaxy.org.au",
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                     "usegalaxy": true
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@@ -261731,12 +661876,12 @@
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         "time_estimation": "30M",
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@@ -261774,8 +662841,8 @@
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-        "visit_duration": 144,
-        "visitors": 356,
+        "visit_duration": 142,
+        "visitors": 358,
         "workflows": [
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@@ -261845,7 +662912,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "RetroSynthesis",
                 "outputs": [
                     {
@@ -262384,7 +663451,7 @@
             "Design plasmids encoding predicted pathways using rpbasicdesign tool.",
             "Generate dnabot scripts enabling the automatic build of plasmids."
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-        "pageviews": 1144,
+        "pageviews": 1145,
         "pub_date": "2022-05-12",
         "questions": [
             "How to design plasmids encoding predicted pathways using BASIC assembly method ?",
@@ -262407,8 +663474,8 @@
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             "dnabot",
-            "selenzy-wrapper",
-            "rpbasicdesign"
+            "rpbasicdesign",
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         "symlink": null,
         "time_estimation": "15M",
         "title": "Designing plasmids encoding predicted pathways by using the BASIC assembly method",
@@ -262444,7 +664043,7 @@
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         "video_view": 0,
         "visit_duration": 146,
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@@ -262643,7 +664242,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Genetic Design (BASIC Assembly)",
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                     {
@@ -263040,7 +664639,7 @@
             "Compute the global score for the previous annotated pathways.",
             "Rank the computed heterologous pathways depending on their score."
         ],
-        "pageviews": 635,
+        "pageviews": 638,
         "pub_date": "2022-09-26",
         "questions": [
             "How to evaluate a set of heterologous pathways ?"
@@ -263061,10 +664660,10 @@
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+                            "state": "missing"
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+                        {
+                            "server": "https://usegalaxy.eu",
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+                        {
+                            "server": "https://usegalaxy.no/",
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+                        {
+                            "server": "https://usegalaxy.org",
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+                            "server": "https://usegalaxy.org.au",
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+                            "server": "https://viralvariant.anses.fr/",
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+                    "version": "5.12.1"
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         "time_estimation": "20M",
         "title": "Evaluating and ranking a set of pathways based on multiple metrics",
@@ -263100,8 +665361,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 187,
-        "visitors": 407,
+        "visit_duration": 186,
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@@ -263261,7 +665522,7 @@
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-                "modified": "2024-10-02 12:08:10 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Pathway Analysis",
                 "outputs": [
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@@ -263575,7 +665836,7 @@
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@@ -263588,6 +665849,7 @@
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         "subtopic": "prepare",
         "supported_servers": [],
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         "time_estimation": "30m",
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@@ -263612,7 +665874,7 @@
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-        "visitors": 2133613
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@@ -263677,7 +665939,7 @@
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@@ -263689,6 +665951,7 @@
         "slides": true,
         "slides_recordings": false,
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "10M",
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@@ -263712,8 +665975,8 @@
         "video": true,
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         "video_view": 0,
-        "visit_duration": 143,
-        "visitors": 1186473
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@@ -263806,7 +666069,7 @@
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             "Create a docker image for a training topic"
         ],
-        "pageviews": 268,
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         "questions": [
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@@ -263823,6 +666086,7 @@
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         "subtopic": "prepare",
         "supported_servers": [],
+        "supported_servers_matrix": [],
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         "time_estimation": "2h",
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@@ -263846,8 +666110,8 @@
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-        "visitors": 236
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@@ -263943,7 +666207,7 @@
         "objectives": [
             "Identify if it is appropriate"
         ],
-        "pageviews": 67,
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@@ -263960,6 +666224,7 @@
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@@ -263987,7 +666252,7 @@
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@@ -264087,6 +666352,7 @@
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         "subtopic": "practises",
         "supported_servers": [],
+        "supported_servers_matrix": [],
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@@ -264201,7 +666467,7 @@
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-        "pageviews": 157,
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@@ -264218,6 +666484,7 @@
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         "subtopic": "prepare",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "3H",
         "title": "Organizing a workshop",
@@ -264241,8 +666508,8 @@
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         "video_view": 0,
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-        "visitors": 140
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@@ -264369,6 +666636,7 @@
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+        "supported_servers_matrix": [],
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@@ -264534,7 +666802,7 @@
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             "Identify what instructors can do to motivate and avoid demotivating learners"
         ],
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@@ -264574,6 +666842,7 @@
         "slides_recordings": false,
         "subtopic": "pedagogy",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "60m",
         "title": "Motivation and Demotivation",
@@ -264598,7 +666867,7 @@
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         "video_view": 0,
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@@ -264663,7 +666932,7 @@
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             "Interact with the service administrators to arrange for infrastructure"
         ],
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@@ -264679,6 +666948,7 @@
         "slides_recordings": false,
         "subtopic": "prepare",
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+        "supported_servers_matrix": [],
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@@ -264706,7 +666976,7 @@
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-        "visitors": 140
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@@ -264847,7 +667117,7 @@
             "Describe a few techniques for formative feedback",
             "List a few techniques to cope with feedback on your teaching efforts"
         ],
-        "pageviews": 1112,
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@@ -264904,6 +667174,7 @@
         "slides_recordings": false,
         "subtopic": "pedagogy",
         "supported_servers": [],
+        "supported_servers_matrix": [],
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         "time_estimation": "3h30m",
         "title": "Assessment and feedback in training and teachings",
@@ -264927,8 +667198,8 @@
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         "video_view": 0,
-        "visit_duration": 43,
-        "visitors": 943
+        "visit_duration": 44,
+        "visitors": 949
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@@ -265004,7 +667275,7 @@
         "objectives": [
             "Learn how others teach using Galaxy"
         ],
-        "pageviews": 406,
+        "pageviews": 407,
         "pub_date": "2022-09-23",
         "questions": [
             "How to teach using Galaxy?",
@@ -265021,6 +667292,7 @@
         "slides_recordings": false,
         "subtopic": "practises",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "1h",
         "title": "Teaching experiences",
@@ -265045,7 +667317,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 192,
-        "visitors": 192
+        "visitors": 193
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     {
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@@ -265170,6 +667442,7 @@
         "slides_recordings": false,
         "subtopic": "practises",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "tags": [
             "work-in-progress"
@@ -265356,6 +667629,7 @@
         "slides_recordings": false,
         "subtopic": "practises",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "tags": [
             "work-in-progress"
@@ -265525,7 +667799,7 @@
             "Describe what makes a trainer effective",
             "Identify some strategies that facilitate active, interactive and collaborative learning"
         ],
-        "pageviews": 1634,
+        "pageviews": 1638,
         "pub_date": "2022-09-23",
         "questions": [
             "What does make a training effective?",
@@ -265589,6 +667863,7 @@
         "slides_recordings": false,
         "subtopic": "pedagogy",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "60m",
         "title": "Training techniques to enhance learner participation and engagement",
@@ -265613,7 +667888,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 44,
-        "visitors": 1373
+        "visitors": 1377
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     {
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@@ -265761,7 +668036,7 @@
         "license": "CC-BY-4.0",
         "mod_date": "2023-11-09",
         "objectives": null,
-        "pageviews": 192,
+        "pageviews": 206,
         "pub_date": "2018-11-15",
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         "redirect_from": [
@@ -265775,6 +668050,7 @@
         "slides_recordings": false,
         "subtopic": "prepare",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "3H",
         "title": "Running a workshop as instructor",
@@ -265798,8 +668074,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 54,
-        "visitors": 74
+        "visit_duration": 44,
+        "visitors": 85
     },
     {
         "admin_install": {
@@ -265938,7 +668214,7 @@
             "Deliver a 5 minute training",
             "Deliver and receive feedback"
         ],
-        "pageviews": 50,
+        "pageviews": 52,
         "pub_date": "2023-06-12",
         "questions": [
             "How can we apply all pedagogical concepts together for training?"
@@ -265967,6 +668243,7 @@
         "slides_recordings": false,
         "subtopic": "pedagogy",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "60m",
         "title": "Train-the-Trainer: putting it all together",
@@ -265990,8 +668267,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 50,
-        "visitors": 43
+        "visit_duration": 45,
+        "visitors": 45
     },
     {
         "admin_install": {
@@ -266057,7 +668334,7 @@
             "Interact with the UseGalaxy.eu admins to arrange for infrastructure",
             "Run a great training!"
         ],
-        "pageviews": 108,
+        "pageviews": 110,
         "pub_date": "2020-11-04",
         "questions": [
             "How do I organise a Galaxy Admin Training (GAT)",
@@ -266085,6 +668362,7 @@
         "slides_recordings": false,
         "subtopic": "prepare",
         "supported_servers": [],
+        "supported_servers_matrix": [],
         "symlink": null,
         "time_estimation": "60m",
         "title": "Galaxy Admin Training",
@@ -266108,8 +668386,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 205,
-        "visitors": 98
+        "visit_duration": 200,
+        "visitors": 100
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     {
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@@ -266286,14 +668564,14 @@
         ],
         "dir": "topics/transcriptomics/tutorials/clipseq",
         "edam_operation": [
-            "Statistical calculation",
-            "Sequence alignment",
-            "Sequence trimming",
-            "Sequencing quality control",
+            "Primer removal",
             "Sequence composition calculation",
-            "Mapping",
+            "Sequencing quality control",
             "Read pre-processing",
-            "Primer removal"
+            "Sequence trimming",
+            "Statistical calculation",
+            "Sequence alignment",
+            "Mapping"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -266328,7 +668606,7 @@
             "Analyse the peaks and find potential binding motifs and targets",
             "Check the quality of the peak calling"
         ],
-        "pageviews": 14792,
+        "pageviews": 14814,
         "pub_date": "2018-08-17",
         "questions": [
             "How is raw CLIP-Seq data processed and analysed?",
@@ -266336,26 +668614,26 @@
         ],
         "short_id": "T00288",
         "short_tools": [
-            "deeptools_plot_fingerprint",
             "rna_star",
-            "deeptools_multi_bam_summary",
-            "wig_to_bigWig",
-            "__MERGE_COLLECTION__",
-            "meme_chip",
-            "deeptools_plot_correlation",
-            "tp_awk_tool",
             "umi_tools_dedup",
+            "__SORTLIST__",
+            "sort1",
+            "deeptools_plot_correlation",
+            "cutadapt",
+            "bedtools_slopbed",
+            "meme_chip",
+            "bedtools_genomecoveragebed_bedgraph",
             "bctools_extract_alignment_ends",
             "umi_tools_extract",
+            "wig_to_bigWig",
+            "tp_awk_tool",
+            "rcas",
+            "__MERGE_COLLECTION__",
             "peakachu",
             "Extract genomic DNA 1",
             "fastqc",
-            "bedtools_slopbed",
-            "cutadapt",
-            "bedtools_genomecoveragebed_bedgraph",
-            "sort1",
-            "rcas",
-            "__SORTLIST__"
+            "deeptools_plot_fingerprint",
+            "deeptools_multi_bam_summary"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -266379,6 +668657,3022 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
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+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "__MERGE_COLLECTION__",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
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+                        {
+                            "server": "https://usegalaxy.eu",
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+                        },
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+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
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+                            "server": "https://usegalaxy.org",
+                            "state": "missing"
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+                        {
+                            "server": "https://usegalaxy.org.au",
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+                    ],
+                    "version": "local"
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+            ]
+        },
         "symlink": null,
         "time_estimation": "6h",
         "title": "CLIP-Seq data analysis from pre-processing to motif detection",
@@ -266424,7 +671718,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 116,
-        "visitors": 7053,
+        "visitors": 7075,
         "workflows": [
             {
                 "creators": [],
@@ -266602,7 +671896,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nBackground\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nEnriched set as a paired-end reads collection\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nAnnotation Reference File for RCAS\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nGenome Chromosome Sizes\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"FastQC\"];\n  0 -->|output| 4;\n  5[\"Cutadapt\"];\n  0 -->|output| 5;\n  6[\"FastQC\"];\n  1 -->|output| 6;\n  7[\"Cutadapt\"];\n  1 -->|output| 7;\n  8[\"UMI-tools extract\"];\n  5 -->|out_pairs| 8;\n  9[\"UMI-tools extract\"];\n  7 -->|out_pairs| 9;\n  10[\"RNA STAR\"];\n  2 -->|output| 10;\n  8 -->|out_paired_collection| 10;\n  11[\"RNA STAR\"];\n  2 -->|output| 11;\n  9 -->|out_paired_collection| 11;\n  12[\"UMI-tools deduplicate\"];\n  10 -->|mapped_reads| 12;\n  13[\"UMI-tools deduplicate\"];\n  11 -->|mapped_reads| 13;\n  14[\"Extract alignment ends\"];\n  12 -->|output| 14;\n  15[\"FastQC\"];\n  12 -->|output| 15;\n  16[\"PEAKachu\"];\n  12 -->|output| 16;\n  13 -->|output| 16;\n  17[\"Merge collections\"];\n  12 -->|output| 17;\n  13 -->|output| 17;\n  18[\"Extract alignment ends\"];\n  13 -->|output| 18;\n  19[\"FastQC\"];\n  13 -->|output| 19;\n  20[\"Sort\"];\n  14 -->|alignment_ends| 20;\n  21[\"Text reformatting\"];\n  16 -->|peak_tables| 21;\n  22[\"Sort collection\"];\n  17 -->|output| 22;\n  23[\"Sort\"];\n  18 -->|alignment_ends| 23;\n  24[\"Create a BedGraph of genome coverage\"];\n  20 -->|out_file1| 24;\n  25[\"bedtools SlopBed\"];\n  3 -->|output| 25;\n  21 -->|outfile| 25;\n  26[\"plotFingerprint\"];\n  22 -->|output| 26;\n  27[\"multiBamSummary\"];\n  22 -->|output| 27;\n  28[\"Create a BedGraph of genome coverage\"];\n  23 -->|out_file1| 28;\n  29[\"Wig/BedGraph-to-bigWig\"];\n  24 -->|output| 29;\n  30[\"Extract Genomic DNA\"];\n  25 -->|output| 30;\n  31[\"Text reformatting\"];\n  25 -->|output| 31;\n  32[\"plotCorrelation\"];\n  27 -->|outFile| 32;\n  33[\"Wig/BedGraph-to-bigWig\"];\n  28 -->|output| 33;\n  34[\"MEME-ChIP\"];\n  30 -->|output| 34;\n  35[\"RCAS\"];\n  31 -->|outfile| 35;\n  2 -->|output| 35;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Tutorial CLIPseq Explorer Demultiplexed PEAKachu eCLIP Hg38 ",
                 "outputs": [
                     {
@@ -267468,8 +672762,8 @@
         ],
         "dir": "topics/transcriptomics/tutorials/rna-seq-counts-to-genes",
         "edam_operation": [
-            "RNA-Seq analysis",
-            "Annotation"
+            "Annotation",
+            "RNA-Seq analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -267494,7 +672788,6 @@
         "id": "transcriptomics/rna-seq-counts-to-genes",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.org.au"
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@@ -267515,7 +672808,7 @@
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         ],
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@@ -267533,10 +672826,10 @@
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+                            "version": "3.34.9.9"
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+                            "state": "inexact",
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+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
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+                        },
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+                                "3.48.0+galaxy1",
+                                "3.48.0",
+                                "3.48.0+galaxy2",
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+                            ]
+                        },
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+                            "state": "inexact",
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+                                "3.34.9.8",
+                                "3.38.3+galaxy2",
+                                "3.50.1+galaxy0",
+                                "3.48.0+galaxy1",
+                                "3.58.1+galaxy0",
+                                "3.48.0",
+                                "3.48.0+galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
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+                                "3.38.3+galaxy2",
+                                "3.50.1+galaxy0",
+                                "3.48.0+galaxy1",
+                                "3.58.1+galaxy0",
+                                "3.48.0",
+                                "3.48.0+galaxy2",
+                                "3.50.0+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
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+                    "version": "3.34.9.9"
                 }
             ]
         },
@@ -267608,7 +673794,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 134,
-        "visitors": 36908,
+        "visitors": 37006,
         "workflows": [
             {
                 "creators": [],
@@ -267699,7 +673885,7 @@
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                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nseqdata\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nsampleinfo\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Cut\"];\n  0 -->|output| 2;\n  3[\"Merge Columns\"];\n  1 -->|output| 3;\n  4[\"Replace Text\"];\n  2 -->|output| 4;\n  5[\"Cut\"];\n  3 -->|out_file1| 5;\n  6[\"annotateMyIDs\"];\n  4 -->|outfile| 6;\n  7[\"limma\"];\n  4 -->|outfile| 7;\n  6 -->|out_tab| 7;\n  5 -->|output| 7;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "RNA Seq Counts To Genes",
                 "outputs": [],
                 "parent_id": "transcriptomics/rna-seq-counts-to-genes",
@@ -267837,19 +674023,19 @@
         "objectives": [
             "Identification of differentially expressed pathways"
         ],
-        "pageviews": 37169,
+        "pageviews": 37279,
         "pub_date": "2018-12-31",
         "questions": [
             "What are the differentially expressed pathways in the mammary gland of pregnant versus lactating mice?"
         ],
         "short_id": "T00300",
         "short_tools": [
-            "join1",
+            "Cut1",
+            "goseq",
             "tp_sort_header_tool",
+            "join1",
             "egsea",
-            "goseq",
             "Add_a_column1",
-            "Cut1",
             "fgsea",
             "tp_cut_tool"
         ],
@@ -267892,6 +674078,1280 @@
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             ]
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+                },
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+                },
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+                },
+                {
+                    "name": "InteractoMIX",
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+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.36.0+galaxy0",
+                                "0.2.2",
+                                "1.34.0+galaxy1",
+                                "1.30.0",
+                                "1.30.1",
+                                "1.26.0",
+                                "1.34.0",
+                                "1.32.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.50.0+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.44.0+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.44.0+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.44.0+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.44.0+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.44.0+galaxy0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "mouse"
@@ -267928,7 +675388,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 112,
-        "visitors": 22384,
+        "visitors": 22453,
         "workflows": [
             {
                 "creators": [],
@@ -268141,7 +675601,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nseqdata\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nfactordata\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nDE table\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nmouse_hallmark_sets\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nlimma_filtered_counts\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"Compute\"];\n  2 -->|output| 5;\n  6[\"Cut\"];\n  2 -->|output| 6;\n  7[\"Advanced Cut\"];\n  4 -->|output| 7;\n  8[\"Advanced Cut\"];\n  4 -->|output| 8;\n  9[\"Join two Datasets\"];\n  5 -->|out_file1| 9;\n  0 -->|output| 9;\n  10[\"Sort\"];\n  6 -->|out_file1| 10;\n  11[\"EGSEA\"];\n  8 -->|output| 11;\n  7 -->|output| 11;\n  1 -->|output| 11;\n  12[\"Cut\"];\n  9 -->|out_file1| 12;\n  13[\"Cut\"];\n  9 -->|out_file1| 13;\n  14[\"fgsea\"];\n  10 -->|outfile| 14;\n  3 -->|output| 14;\n  15[\"goseq\"];\n  12 -->|out_file1| 15;\n  13 -->|out_file1| 15;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "RNA Seq Genes To Pathways (imported from uploaded file)",
                 "outputs": [
                     {
@@ -268808,7 +676268,6 @@
         "id": "transcriptomics/rna-seq-viz-with-heatmap2",
         "inexact_supported_servers": [
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
@@ -268825,17 +676284,17 @@
         "objectives": [
             "Create heatmaps of RNA-seq data"
         ],
-        "pageviews": 117773,
+        "pageviews": 117964,
         "pub_date": "2018-12-31",
         "questions": [
             "How to generate heatmaps from RNA-seq data?"
         ],
         "short_id": "T00303",
         "short_tools": [
-            "ggplot2_heatmap2",
-            "join1",
             "Cut1",
-            "datamash_transpose"
+            "ggplot2_heatmap2",
+            "datamash_transpose",
+            "join1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -268865,19 +676324,712 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Cut1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "join1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.8+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.0.6",
+                                "1.1.0+galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
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+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.1.0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.1.0"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
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+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
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+                            "state": "inexact",
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+                            ]
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
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+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
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+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
+                            "versions": [
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+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
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+                        {
+                            "server": "https://www.immportgalaxy.org/",
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+                            "state": "missing"
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "2.2.1+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "3.1.3+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.2.1+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "3.1.1+galaxy1",
+                                "3.0.1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2.2.1+galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
+                                "3.1.3.1+galaxy0",
+                                "3.1.1+galaxy1",
+                                "3.0.1",
+                                "3.1.3+galaxy0",
+                                "3.1.1"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "2.2.1+galaxy1"
                 }
             ]
         },
@@ -268910,7 +677062,7 @@
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         "video_view": 0,
         "visit_duration": 83,
-        "visitors": 69038,
+        "visitors": 69203,
         "workflows": [
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@@ -268921,7 +677073,7 @@
                     "report": null,
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+                "graph_dot": "digraph main {\n  node [fontname=\"Atkinson Hyperlegible\", shape=box, color=white,style=filled,color=peachpuff,margin=\"0.2,0.2\"];\n  edge [fontname=\"Atkinson Hyperlegible\"];\n  0[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nheatmap_genes\"]\n  1[color=lightblue,label=\"\u2139\ufe0f Input Dataset\\nnormalized_counts\"]\n  2[label=\"Join two Datasets\"]\n  1 -> 2 [label=\"output\"]\n  0 -> 2 [label=\"output\"]\n  3[label=\"Cut\"]\n  2 -> 3 [label=\"out_file1\"]\n  4[label=\"Transpose\"]\n  3 -> 4 [label=\"out_file1\"]\n  5[label=\"heatmap2\"]\n  4 -> 5 [label=\"out_file\"]\n  k99497a451d0d43eda67662f474fbd822[color=lightseagreen,label=\"Output\\nheatmap_pdf\"]\n  5 -> k99497a451d0d43eda67662f474fbd822\n}",
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@@ -269014,8 +677166,8 @@
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-                "modified": "2024-10-02 12:08:11 +0000",
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                 "outputs": [
                     {
@@ -269063,7 +677215,7 @@
                             {
                                 "label": "heatmap_pdf",
                                 "output_name": "output1",
-                                "uuid": "b3f63523-62fb-4615-9a9c-b6b36b340172"
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@@ -269266,17 +677418,17 @@
         "dir": "topics/transcriptomics/tutorials/rna-seq-reads-to-counts",
         "edam_operation": [
             "Data handling",
-            "Sequence alignment",
-            "Sequence trimming",
-            "Sequencing quality control",
-            "Read summarisation",
-            "Statistical calculation",
             "RNA-Seq quantification",
-            "Validation",
+            "Primer removal",
+            "Formatting",
             "Sequence composition calculation",
+            "Validation",
+            "Sequencing quality control",
             "Read pre-processing",
-            "Primer removal",
-            "Formatting"
+            "Sequence trimming",
+            "Read summarisation",
+            "Sequence alignment",
+            "Statistical calculation"
         ],
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         "exact_supported_servers": [
@@ -269299,7 +677451,6 @@
             "MISSISSIPPI",
             "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
@@ -269326,7 +677477,7 @@
             "Make use of Galaxy Collections for a tidy analysis",
             "Create a Galaxy Workflow that converts RNA-seq reads into counts"
         ],
-        "pageviews": 126626,
+        "pageviews": 126832,
         "pub_date": "2018-09-23",
         "questions": [
             "How to convert RNA-seq reads into counts?",
@@ -269352,17 +677503,17 @@
         ],
         "short_id": "T00301",
         "short_tools": [
+            "cutadapt",
             "hisat2",
-            "picard_MarkDuplicates",
+            "fastqc",
+            "featurecounts",
+            "collection_column_join",
             "rseqc_geneBody_coverage",
-            "cutadapt",
-            "samtools_idxstats",
+            "picard_MarkDuplicates",
             "multiqc",
-            "collection_column_join",
+            "samtools_idxstats",
             "rseqc_infer_experiment",
-            "rseqc_read_distribution",
-            "fastqc",
-            "featurecounts"
+            "rseqc_read_distribution"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -269392,10 +677543,141 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
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+                },
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+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
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+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
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+                    "url": "http://dintor.eurac.edu/"
+                },
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+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
                     "usegalaxy": false
                 },
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+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
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+                    "usegalaxy": false
+                },
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+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
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+                    "url": "https://usegalaxy.cz/",
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+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
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                     "url": "https://usegalaxy.no/",
@@ -269410,6 +677692,2987 @@
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
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+                    "url": "https://viralvariant.anses.fr/"
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+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
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+                            "state": "missing"
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+                            "state": "missing"
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+                            "state": "exact",
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+                            "versions": [
+                                "0.74+galaxy0"
+                            ]
+                        },
+                        {
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+                                "0.72+galaxy1",
+                                "0.73+galaxy0",
+                                "0.69"
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+                        {
+                            "server": "https://usegalaxy.eu",
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+                            "versions": [
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+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "2.6.4.1"
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+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "2.6.4.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "2.6.4.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "2.6.4.1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
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             ]
         },
@@ -269462,7 +680725,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 149,
-        "visitors": 66867,
+        "visitors": 67023,
         "workflows": [
             {
                 "creators": [],
@@ -269584,7 +680847,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nReference genes\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\nBAM files\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Infer Experiment\"];\n  1 -->|output| 2;\n  0 -->|output| 2;\n  3[\"MarkDuplicates\"];\n  1 -->|output| 3;\n  4[\"Samtools idxstats\"];\n  1 -->|output| 4;\n  5[\"MultiQC\"];\n  2 -->|output| 5;\n  3 -->|metrics_file| 5;\n  4 -->|output| 5;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "QC report",
                 "outputs": [
                     {
@@ -269852,7 +681115,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput FASTQs collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput Reference gene BED\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Infer Experiment\"];\n  5 -->|output_alignments| 10;\n  1 -->|output| 10;\n  11[\"Read Distribution\"];\n  5 -->|output_alignments| 11;\n  1 -->|output| 11;\n  12[\"Column Join\"];\n  6 -->|output_short| 12;\n  13[\"MultiQC\"];\n  4 -->|text_file| 13;\n  3 -->|report| 13;\n  10 -->|output| 13;\n  7 -->|metrics_file| 13;\n  8 -->|output| 13;\n  9 -->|outputtxt| 13;\n  11 -->|output| 13;\n  6 -->|output_summary| 13;\n  5 -->|summary_file| 13;\n  2[\"FastQC raw reads\"];\n  0 -->|output| 2;\n  3[\"Cutadapt\"];\n  0 -->|output| 3;\n  4[\"FastQC post QC\"];\n  3 -->|out1| 4;\n  5[\"HISAT2\"];\n  3 -->|out1| 5;\n  6[\"featureCounts\"];\n  5 -->|output_alignments| 6;\n  7[\"MarkDuplicates\"];\n  5 -->|output_alignments| 7;\n  8[\"Samtools idxstats\"];\n  5 -->|output_alignments| 8;\n  9[\"Gene Body Coverage BAM\"];\n  5 -->|output_alignments| 9;\n  1 -->|output| 9;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "RNA Seq Reads To Counts",
                 "outputs": [],
                 "parent_id": "transcriptomics/rna-seq-reads-to-counts",
@@ -270010,7 +681273,7 @@
                 {
                     "name": "gffcompare",
                     "owner": "iuc",
-                    "revisions": "f99dd58de04f",
+                    "revisions": "3c5e024a18cf",
                     "tool_panel_section_label": "Filter and Sort",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
@@ -270135,7 +681398,7 @@
                 }
             ]
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         "contributions": {
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@@ -270194,23 +681457,23 @@
         ],
         "dir": "topics/transcriptomics/tutorials/differential-isoform-expression",
         "edam_operation": [
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-            "Sequencing quality control",
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-            "Statistical calculation",
-            "Validation",
-            "Sequence composition calculation",
-            "Sequence comparison",
-            "Formatting",
             "Data handling",
-            "Sequence alignment",
+            "Transcriptome assembly",
+            "Protein sequence analysis",
             "De-novo assembly",
+            "Sequence comparison",
             "Sequence analysis",
+            "Formatting",
+            "Sequence composition calculation",
+            "Sequence assembly validation",
+            "Validation",
+            "Statistical calculation",
+            "Sequencing quality control",
+            "Visualisation",
             "Sequence contamination filtering",
+            "Sequence alignment",
             "Sequence annotation",
-            "Transcriptome assembly",
-            "Protein sequence analysis"
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         "exact_supported_servers": [],
@@ -270221,7 +681484,6 @@
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             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org.au"
         ],
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@@ -270241,7 +681503,7 @@
             "Perform genome-wide isoform analysis in order to evaluate differences in expression profiles between two conditions",
             "Evaluate the differential alternative splicing in specific genes"
         ],
-        "pageviews": 1799801,
+        "pageviews": 1831859,
         "pub_date": "2023-05-17",
         "questions": [
             "Are there statistically significant differences in gene splicing patterns between samples?",
@@ -270249,41 +681511,41 @@
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             "rna_star",
-            "pygenomeTracks",
-            "gffcompare",
-            "collection_element_identifiers",
-            "rseqc_inner_distance",
             "cpat",
-            "rna_quast",
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-            "fastqc",
-            "rseqc_geneBody_coverage",
-            "tp_cat",
+            "tp_uniq_tool",
+            "addValue",
+            "rseqc_read_distribution",
+            "rseqc_inner_distance",
             "Filter1",
-            "isoformswitchanalyzer",
+            "stringtie_merge",
+            "collection_element_identifiers",
+            "tp_awk_tool",
+            "__FILTER_FROM_FILE__",
             "multiqc",
-            "pfamscan",
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-            "rseqc_infer_experiment",
-            "gene2exon1",
-            "rseqc_read_distribution",
-            "tp_uniq_tool",
-            "Remove beginning1",
+            "pygenomeTracks",
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-            "addValue",
-            "fastp",
-            "sort1",
-            "tp_grep_tool",
-            "stringtie",
-            "Add_a_column1",
+            "tp_cat",
             "__FLATTEN__",
+            "fastqc",
+            "pfamscan",
+            "rseqc_geneBody_coverage",
+            "gffcompare",
             "gffread",
-            "__FILTER_FROM_FILE__"
+            "isoformswitchanalyzer"
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         "slides": true,
         "slides_recordings": false,
@@ -270301,14 +681563,6458 @@
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-                    "url": "https://usegalaxy.fr/",
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+                                "5.0.1+galaxy2"
+                            ]
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+                            "versions": [
+                                "2.6.4.1",
+                                "2.6.4",
+                                "2.4"
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+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
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+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
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+                },
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+                        },
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+                        },
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+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
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+                            "server": "http://dintor.eurac.edu/",
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+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
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+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
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+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
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+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
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+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.6.4.1"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.6.4.1",
+                                "2.4galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.4galaxy1",
+                                "5.0.1+galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.6.4.1",
+                                "2.6.4",
+                                "2.4"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "5.0.3+galaxy0"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.6.4.1"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.6.4.1",
+                                "2.4galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.4galaxy1",
+                                "5.0.1+galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.6.4.1",
+                                "2.6.4",
+                                "2.4"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "5.0.3+galaxy0"
                 }
             ]
         },
@@ -270383,8 +688089,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 268,
-        "visitors": 772528,
+        "visit_duration": 269,
+        "visitors": 782835,
         "workflows": [
             {
                 "creators": [
@@ -270716,7 +688422,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nRNA-seq data collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGenome annotation\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nReference genome\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nPfam-A HMM library\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nPfam-A HMM Stockholm file\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nActive sites dataset\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nCPAT header\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"Flatten collection\"];\n  0 -->|output| 7;\n  8[\"fastp\"];\n  0 -->|output| 8;\n  9[\"Convert GTF to BED12\"];\n  1 -->|output| 9;\n  10[\"Search in textfiles\"];\n  1 -->|output| 10;\n  11[\"Search in textfiles\"];\n  1 -->|output| 11;\n  12[\"FastQC\"];\n  7 -->|output| 12;\n  13[\"gather fastp reports\"];\n  8 -->|report_json| 13;\n  14[\"RNA STAR\"];\n  1 -->|output| 14;\n  2 -->|output| 14;\n  8 -->|output_paired_coll| 14;\n  15[\"Gene BED To Exon/Intron/Codon BED\"];\n  9 -->|bed_file| 15;\n  16[\"gffread\"];\n  10 -->|output| 16;\n  2 -->|output| 16;\n  17[\"gffread\"];\n  11 -->|output| 17;\n  2 -->|output| 17;\n  18[\"gather FastQC reports\"];\n  12 -->|text_file| 18;\n  19[\"Concatenate datasets\"];\n  14 -->|splice_junctions| 19;\n  20[\"Compute\"];\n  15 -->|out_file1| 20;\n  21[\"Filter\"];\n  19 -->|out_file1| 21;\n  22[\"Sort\"];\n  20 -->|out_file1| 22;\n  23[\"Cut\"];\n  21 -->|out_file1| 23;\n  24[\"Text reformatting\"];\n  22 -->|out_file1| 24;\n  25[\"Text reformatting\"];\n  22 -->|out_file1| 25;\n  26[\"Sort\"];\n  23 -->|out_file1| 26;\n  27[\"Unique lines\"];\n  26 -->|out_file1| 27;\n  28[\"RNA STAR\"];\n  1 -->|output| 28;\n  2 -->|output| 28;\n  8 -->|output_paired_coll| 28;\n  27 -->|outfile| 28;\n  29[\"StringTie\"];\n  1 -->|output| 29;\n  28 -->|mapped_reads| 29;\n  30[\"Infer Experiment\"];\n  28 -->|mapped_reads| 30;\n  9 -->|bed_file| 30;\n  31[\"Gene Body Coverage BAM\"];\n  28 -->|mapped_reads| 31;\n  9 -->|bed_file| 31;\n  32[\"Junction Saturation\"];\n  28 -->|mapped_reads| 32;\n  9 -->|bed_file| 32;\n  33[\"Junction Annotation\"];\n  28 -->|mapped_reads| 33;\n  9 -->|bed_file| 33;\n  34[\"Inner Distance\"];\n  28 -->|mapped_reads| 34;\n  9 -->|bed_file| 34;\n  35[\"Read Distribution\"];\n  28 -->|mapped_reads| 35;\n  9 -->|bed_file| 35;\n  36[\"StringTie merge\"];\n  1 -->|output| 36;\n  29 -->|output_gtf| 36;\n  37[\"gffread\"];\n  29 -->|output_gtf| 37;\n  2 -->|output| 37;\n  38[\"MultiQC\"];\n  28 -->|output_log| 38;\n  28 -->|reads_per_gene| 38;\n  30 -->|output| 38;\n  32 -->|outputr| 38;\n  31 -->|outputtxt| 38;\n  34 -->|outputfreqtxt| 38;\n  35 -->|output| 38;\n  33 -->|stats| 38;\n  39[\"StringTie\"];\n  36 -->|out_gtf| 39;\n  28 -->|mapped_reads| 39;\n  40[\"GffCompare\"];\n  1 -->|output| 40;\n  36 -->|out_gtf| 40;\n  41[\"Plot a transcript in intron\"];\n  28 -->|signal_unique_str2| 41;\n  28 -->|signal_unique_str1| 41;\n  36 -->|out_gtf| 41;\n  42[\"gffread\"];\n  36 -->|out_gtf| 42;\n  2 -->|output| 42;\n  43[\"Plot ADD3\"];\n  28 -->|signal_unique_str2| 43;\n  28 -->|signal_unique_str1| 43;\n  36 -->|out_gtf| 43;\n  44[\"Plot ADD3 zoomed\"];\n  28 -->|signal_unique_str2| 44;\n  28 -->|signal_unique_str1| 44;\n  36 -->|out_gtf| 44;\n  45[\"rnaQUAST\"];\n  1 -->|output| 45;\n  2 -->|output| 45;\n  37 -->|output_exons| 45;\n  46[\"Extract element identifiers\"];\n  39 -->|transcript_expression| 46;\n  47[\"Filter\"];\n  40 -->|tmap_output| 47;\n  48[\"Search in textfiles\"];\n  46 -->|output| 48;\n  49[\"Filter collection\"];\n  48 -->|output| 49;\n  39 -->|transcript_expression| 49;\n  50[\"IsoformSwitchAnalyzeR\"];\n  1 -->|output| 50;\n  49 -->|output_discarded| 50;\n  36 -->|out_gtf| 50;\n  49 -->|output_filtered| 50;\n  42 -->|output_exons| 50;\n  51[\"IsoformSwitchAnalyzeR\"];\n  50 -->|switchList| 51;\n  52[\"PfamScan\"];\n  5 -->|output| 52;\n  51 -->|isoformAA| 52;\n  4 -->|output| 52;\n  3 -->|output| 52;\n  53[\"CPAT\"];\n  16 -->|output_exons| 53;\n  51 -->|isoformNT| 53;\n  17 -->|output_exons| 53;\n  2 -->|output| 53;\n  54[\"Cut\"];\n  53 -->|orf_seqs_prob_best| 54;\n  55[\"Add column\"];\n  54 -->|out_file1| 55;\n  56[\"Remove beginning\"];\n  55 -->|out_file1| 56;\n  57[\"Concatenate datasets\"];\n  6 -->|output| 57;\n  56 -->|out_file1| 57;\n  58[\"IsoformSwitchAnalyzeR\"];\n  57 -->|out_file1| 58;\n  52 -->|output| 58;\n  51 -->|switchList| 58;\n  59[\"IsoformSwitchAnalyzeR\"];\n  57 -->|out_file1| 59;\n  52 -->|output| 59;\n  51 -->|switchList| 59;\n  d2f0865b-20ba-43ef-8ebc-ad9f517ec60d[\"Output\\nconsequencesSummary\"];\n  59 --> d2f0865b-20ba-43ef-8ebc-ad9f517ec60d;\n  style d2f0865b-20ba-43ef-8ebc-ad9f517ec60d stroke:#2c3143,stroke-width:4px;\n  8dd90968-6ef6-48e1-a104-547cbeaa80c8[\"Output\\nconsequencesEnrichment\"];\n  59 --> 8dd90968-6ef6-48e1-a104-547cbeaa80c8;\n  style 8dd90968-6ef6-48e1-a104-547cbeaa80c8 stroke:#2c3143,stroke-width:4px;\n  6b812e8d-997d-4a53-9c4f-cb2aa3bb26bc[\"Output\\nsplicingEnrichment\"];\n  59 --> 6b812e8d-997d-4a53-9c4f-cb2aa3bb26bc;\n  style 6b812e8d-997d-4a53-9c4f-cb2aa3bb26bc stroke:#2c3143,stroke-width:4px;\n  9c8369e2-8f86-4984-a47a-a35415ecb9b9[\"Output\\nmostSwitching\"];\n  59 --> 9c8369e2-8f86-4984-a47a-a35415ecb9b9;\n  style 9c8369e2-8f86-4984-a47a-a35415ecb9b9 stroke:#2c3143,stroke-width:4px;\n  292b9609-061f-49f7-94fc-7831526bb48b[\"Output\\nsplicingSummary\"];\n  59 --> 292b9609-061f-49f7-94fc-7831526bb48b;\n  style 292b9609-061f-49f7-94fc-7831526bb48b stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "GTN_differential_isoform_expression",
                 "outputs": [
                     {
@@ -270934,7 +688640,6 @@
             "MISSISSIPPI",
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
@@ -270970,7 +688675,7 @@
         "objectives": [
             "Create a volcano plot of RNA-seq data to visualize significant genes"
         ],
-        "pageviews": 228436,
+        "pageviews": 228850,
         "pub_date": "2018-12-31",
         "questions": [
             "How to generate a volcano plot from RNA-seq data?"
@@ -271040,11 +688745,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -271074,6 +688774,294 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
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         "time_estimation": "30m",
         "title": "Visualization of RNA-Seq results with Volcano Plot",
@@ -271099,8 +689087,8 @@
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         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 82,
-        "visitors": 133762,
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@@ -271238,7 +689226,7 @@
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Visualization Of RNA-Seq Results With Volcano Plot",
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@@ -271371,7 +689359,6 @@
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@@ -271397,16 +689384,16 @@
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             "How to interpret and simplify the results"
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-        "pageviews": 34415,
+        "pageviews": 34469,
         "pub_date": "2019-01-23",
         "questions": [
             "How can I functionally interpret a list of genes of interest that I obtained from my experiment?"
         ],
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             "goslimmer",
-            "goenrichment"
+            "goenrichment",
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@@ -271428,10 +689415,142 @@
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@@ -271446,9 +689565,416 @@
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+                            "state": "missing"
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+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "1.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.0.1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.0.1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.0.1"
+                }
+            ]
         },
         "symlink": null,
         "time_estimation": "1h",
@@ -271477,8 +690003,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 77,
-        "visitors": 20487,
+        "visit_duration": 78,
+        "visitors": 20531,
         "workflows": [
             {
                 "creators": [],
@@ -271751,7 +690277,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGO annotations Drosophila melanogaster\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nGO\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  10[\"Filter\"];\n  2 -->|output| 10;\n  11[\"GOEnrichment\"];\n  3 -->|output| 11;\n  1 -->|output| 11;\n  4 -->|output| 11;\n  5 -->|output| 11;\n  12[\"GOEnrichment\"];\n  3 -->|output| 12;\n  1 -->|output| 12;\n  4 -->|output| 12;\n  5 -->|output| 12;\n  13[\"GOSlimmer\"];\n  3 -->|output| 13;\n  1 -->|output| 13;\n  6 -->|output| 13;\n  14[\"GOEnrichment\"];\n  3 -->|output| 14;\n  1 -->|output| 14;\n  4 -->|output| 14;\n  7 -->|output| 14;\n  15[\"GOEnrichment\"];\n  3 -->|output| 15;\n  1 -->|output| 15;\n  4 -->|output| 15;\n  8 -->|output| 15;\n  16[\"GOEnrichment\"];\n  0 -->|output| 16;\n  1 -->|output| 16;\n  2 -->|output| 16;\n  9 -->|out_file1| 16;\n  17[\"GOEnrichment\"];\n  0 -->|output| 17;\n  1 -->|output| 17;\n  10 -->|out_file1| 17;\n  9 -->|out_file1| 17;\n  18[\"GOEnrichment\"];\n  13 -->|output| 18;\n  6 -->|output| 18;\n  4 -->|output| 18;\n  5 -->|output| 18;\n  2[\"\u2139\ufe0f Input Dataset\\ntrapnellPopulation.tab\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nGO annotations Mus musculus\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nMouse population\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nMouse diff\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nGO Slim\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nmouseUnderexpressed.txt\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nmouseOverexpressed.txt\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"Filter\"];\n  2 -->|output| 9;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "GO Enrichment Workflow",
                 "outputs": [],
                 "parent_id": "transcriptomics/goenrichment",
@@ -271838,9 +690364,9 @@
         ],
         "dir": "topics/transcriptomics/tutorials/network-analysis-with-heinz",
         "edam_operation": [
+            "Differential gene expression analysis",
             "Pathway or network analysis",
-            "RNA-Seq analysis",
-            "Differential gene expression analysis"
+            "RNA-Seq analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -271874,19 +690400,19 @@
         "objectives": [
             "Network Analysis of metatranscriptomics data using Heinz in Galaxy to pinpoint the optimal scoring subnetwork."
         ],
-        "pageviews": 5900522,
+        "pageviews": 5932544,
         "pub_date": "2018-10-11",
         "questions": [
             "Which pathways are potentially contributing to dental caries?"
         ],
         "short_id": "T00293",
         "short_tools": [
-            "heinz",
-            "heinz_scoring",
             "Cut1",
             "deseq2",
+            "heinz_bum",
+            "heinz",
             "heinz_visualization",
-            "heinz_bum"
+            "heinz_scoring"
         ],
         "slides": true,
         "slides_recordings": false,
@@ -271926,6 +690452,992 @@
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             ]
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+                },
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+                },
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+                },
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@@ -271961,7 +691473,7 @@
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@@ -272073,7 +691585,7 @@
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Workflow Constructed From History 'Heinz Workflow Trial Sep 11'",
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@@ -272192,7 +691704,7 @@
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             "Clustering of the read profiles by machine learning algorithm"
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@@ -272200,10 +691712,10 @@
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         "time_estimation": "1H",
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@@ -272271,8 +692500,8 @@
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-        "visit_duration": 175,
-        "visitors": 865,
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@@ -272350,7 +692579,7 @@
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                 "name": "Blockclust 1.1.0 Clustering",
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@@ -272652,17 +692881,17 @@
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-            "Differential gene expression analysis",
-            "Sequencing quality control",
-            "RNA-Seq analysis",
-            "Statistical calculation",
-            "Gene expression analysis",
             "RNA-Seq quantification",
+            "Gene expression analysis",
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             "Sequence composition calculation",
+            "Differential gene expression analysis",
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             "Read pre-processing",
-            "Primer removal"
+            "Sequence trimming",
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+            "Statistical calculation",
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@@ -272696,7 +692925,7 @@
             "Differentiate between subclasses of small RNAs based on their characteristics.",
             "Identify differently abundant small RNAs and their targets."
         ],
-        "pageviews": 11082,
+        "pageviews": 11091,
         "pub_date": "2017-06-29",
         "questions": [
             "What small RNAs are expressed?",
@@ -272704,15 +692933,15 @@
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@@ -272752,6 +692981,1522 @@
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@@ -272785,8 +694530,8 @@
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@@ -272914,7 +694659,7 @@
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@@ -273536,7 +695281,7 @@
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                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nDataset collection - Control\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nDataset - Ref Txome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nDataset collection - Case\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Salmon\"];\n  1 -->|output| 4;\n  0 -->|output| 4;\n  5[\"Salmon\"];\n  1 -->|output| 5;\n  0 -->|output| 5;\n  6[\"Salmon\"];\n  1 -->|output| 6;\n  2 -->|output| 6;\n  7[\"Salmon\"];\n  1 -->|output| 7;\n  2 -->|output| 7;\n  8[\"DESeq2\"];\n  6 -->|output_quant| 8;\n  4 -->|output_quant| 8;\n  3 -->|output| 8;\n  9[\"DESeq2\"];\n  7 -->|output_quant| 9;\n  5 -->|output_quant| 9;\n  3 -->|output| 9;\n  10[\"Filter\"];\n  8 -->|deseq_out| 10;\n  11[\"Filter\"];\n  9 -->|deseq_out| 11;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "sRNA Seq Step 2: Salmon And DESeq2",
                 "outputs": [],
                 "parent_id": "transcriptomics/srna",
@@ -273740,15 +695485,15 @@
         "dir": "topics/transcriptomics/tutorials/full-de-novo",
         "draft": true,
         "edam_operation": [
-            "Sequencing quality control",
+            "Coding region prediction",
+            "Transcriptome assembly",
             "de Novo sequencing",
             "De-novo assembly",
-            "Statistical calculation",
-            "Validation",
-            "Transcriptome assembly",
-            "Sequence composition calculation",
             "Gene functional annotation",
-            "Coding region prediction"
+            "Sequence composition calculation",
+            "Validation",
+            "Sequencing quality control",
+            "Statistical calculation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -273781,7 +695526,7 @@
             "They are single sentences describing what a learner should be able to do once they have completed the tutorial",
             "You can use Bloom's Taxonomy to write effective learning objectives"
         ],
-        "pageviews": 21999,
+        "pageviews": 22071,
         "pub_date": "2020-02-13",
         "questions": [
             "Which biological questions are addressed by the tutorial?",
@@ -273789,21 +695534,21 @@
         ],
         "short_id": "T00290",
         "short_tools": [
-            "trinotate",
+            "trinity_align_and_estimate_abundance",
+            "trinity_define_clusters_by_cutting_tree",
+            "trinity_filter_low_expr_transcripts",
+            "trimmomatic",
+            "trinity_run_de_analysis",
             "transdecoder",
-            "trinity_abundance_estimates_to_matrix",
+            "trinotate",
+            "fastqc",
             "describe_samples",
-            "trinity_run_de_analysis",
             "trinity_samples_qccheck",
-            "trinity_filter_low_expr_transcripts",
-            "trinity_align_and_estimate_abundance",
-            "multiqc",
+            "trinity_abundance_estimates_to_matrix",
             "trinity_analyze_diff_expr",
-            "trinity",
             "trinity_contig_exn50_statistic",
-            "trinity_define_clusters_by_cutting_tree",
-            "fastqc",
-            "trimmomatic"
+            "multiqc",
+            "trinity"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -273838,6 +695583,2419 @@
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+                            "state": "exact",
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+                            "state": "inexact",
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+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
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+        },
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         "tags": [
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@@ -273880,8 +698038,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 151,
-        "visitors": 11314,
+        "visit_duration": 150,
+        "visitors": 11372,
         "workflows": [
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@@ -274004,7 +698162,7 @@
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                 "license": null,
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "trinity NG",
                 "outputs": [
                     {
@@ -274733,12 +698891,12 @@
         ],
         "dir": "topics/transcriptomics/tutorials/rna-interactome",
         "edam_operation": [
-            "Statistical calculation",
-            "Sequence trimming",
-            "Sequencing quality control",
             "Sequence composition calculation",
+            "Sequencing quality control",
             "Read pre-processing",
-            "Primer removal"
+            "Sequence trimming",
+            "Primer removal",
+            "Statistical calculation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -274772,7 +698930,7 @@
             "Quantification of the mapped loci",
             "Visualization and filtering of results"
         ],
-        "pageviews": 1935,
+        "pageviews": 1946,
         "pub_date": "2020-03-23",
         "questions": [
             "What are the difficulties in mapping chimeric reads from RNA interactome data?",
@@ -274781,14 +698939,14 @@
         ],
         "short_id": "T00296",
         "short_tools": [
-            "chira_merge",
-            "chira_quantify",
-            "query_tabular",
-            "cutadapt",
-            "chira_map",
             "chira_collapse",
+            "chira_map",
+            "cutadapt",
             "fastqc",
-            "chira_extract"
+            "query_tabular",
+            "chira_quantify",
+            "chira_extract",
+            "chira_merge"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -274828,6 +698986,1333 @@
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+                                "1.1.a",
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+                                "3.5+galaxy0",
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         "symlink": null,
         "time_estimation": "2H",
         "title": "RNA-RNA interactome data analysis",
@@ -274860,8 +700345,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 178,
-        "visitors": 1217,
+        "visit_duration": 179,
+        "visitors": 1225,
         "workflows": [
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                 "creators": [],
@@ -275083,7 +700568,7 @@
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "RNA-RNA interactome data analysis - chira  v1.4.3",
                 "outputs": [
                     {
@@ -276005,17 +701490,17 @@
         ],
         "dir": "topics/transcriptomics/tutorials/mirna-target-finder",
         "edam_operation": [
-            "Sequence trimming",
-            "Differential gene expression analysis",
-            "Sequencing quality control",
-            "RNA-Seq analysis",
-            "Statistical calculation",
-            "Gene expression analysis",
             "RNA-Seq quantification",
-            "Validation",
+            "Gene expression analysis",
+            "Primer removal",
             "Sequence composition calculation",
+            "Differential gene expression analysis",
+            "Validation",
+            "Sequencing quality control",
             "Read pre-processing",
-            "Primer removal"
+            "Sequence trimming",
+            "Statistical calculation",
+            "RNA-Seq analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -276047,7 +701532,7 @@
             "Understand the quasi-mapping-based Salmon method for quantifying the expression of transcripts using RNA-Seq data",
             "Idenfity potential miRNAs involved in brassinosteroid-mediated regulation networks"
         ],
-        "pageviews": 5390935,
+        "pageviews": 5423014,
         "pub_date": "2021-04-08",
         "questions": [
             "Which miRNAs are upregulated in response to brassinosteroids?",
@@ -276069,21 +701554,21 @@
         ],
         "short_id": "T00292",
         "short_tools": [
-            "filter_by_fasta_ids",
-            "targetfinder",
-            "sample_seqs",
+            "Cut1",
             "sort1",
-            "rbc_mirdeep2_mapper",
-            "Filter1",
+            "cat1",
+            "trim_galore",
             "multiqc",
-            "rbc_mirdeep2_quantifier",
-            "Cut1",
             "deseq2",
+            "sample_seqs",
             "fastqc",
-            "salmon",
+            "rbc_mirdeep2_quantifier",
+            "targetfinder",
+            "rbc_mirdeep2_mapper",
             "__MERGE_COLLECTION__",
-            "cat1",
-            "trim_galore"
+            "filter_by_fasta_ids",
+            "salmon",
+            "Filter1"
         ],
         "slides": true,
         "slides_recordings": [
@@ -276138,6 +701623,2401 @@
                 }
             ]
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@@ -276485,7 +704365,7 @@
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Plant bulk RNA-Seq workflow",
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@@ -277094,7 +704974,7 @@
             "Extract genes for producing differential gene expression analysis visualizations",
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-        "pageviews": 5901051,
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         "questions": [
             "How are RNA-Seq results stored?",
@@ -277139,6 +705019,10 @@
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@@ -277269,7 +705153,7 @@
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-        "pageviews": 5898685,
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         "questions": [
             "How to integrate RNA-Seq results with other datasets using AskOmics?",
@@ -277322,6 +705206,10 @@
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         "time_estimation": "2H",
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@@ -277346,7 +705234,7 @@
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@@ -277430,7 +705318,7 @@
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@@ -277505,6 +705393,10 @@
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@@ -277575,7 +705467,7 @@
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         "questions": [
             "How to perform analysis of RNAseq data when reference genome is available?"
@@ -277617,6 +705509,10 @@
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@@ -277824,7 +705720,7 @@
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         "questions": [
             "What are the first steps to process RNA-seq data?"
@@ -277866,6 +705762,10 @@
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@@ -278011,7 +705910,7 @@
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@@ -278071,8 +705970,140 @@
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-                    "url": "https://usegalaxy.fr/",
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@@ -278084,9 +706115,144 @@
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@@ -278117,7 +706283,7 @@
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@@ -278152,7 +706318,6 @@
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@@ -278176,7 +706341,7 @@
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@@ -278222,8 +706387,8 @@
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-            "volcanoplot",
-            "interactive_tool_rstudio"
+            "interactive_tool_rstudio",
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@@ -278236,8 +706401,140 @@
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-                    "url": "https://usegalaxy.fr/",
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+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
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+                },
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+                    "url": "http://gigagalaxy.net/"
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+                    "url": "https://galaxy.hyphy.org/",
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
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+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
                     "usegalaxy": false
                 },
                 {
@@ -278249,9 +706546,290 @@
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
                 }
             ],
-            "inexact": []
+            "tools": [
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+                    "id": "interactive_tool_rstudio",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
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+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
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+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.5",
+                    "servers": [
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+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
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+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
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+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
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+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
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+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
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+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "0.0.5"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.0.6",
+                                "0.0.3"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "exact",
+                            "version": "0.0.5"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.0.3",
+                                "0.0.1",
+                                "0.0.2"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "0.0.5"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "0.0.5"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "0.0.5"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.0.5"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.0.5"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.0.5"
+                }
+            ]
         },
         "symlink": null,
         "tags": [
@@ -278283,7 +706861,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 102,
-        "visitors": 28758,
+        "visitors": 28798,
         "zenodo_link": "https://zenodo.org/record/2529117"
     },
     {
@@ -278789,31 +707367,30 @@
         ],
         "dir": "topics/transcriptomics/tutorials/ref-based",
         "edam_operation": [
-            "Visualisation",
-            "Differential gene expression analysis",
-            "Sequencing quality control",
-            "RNA-Seq analysis",
-            "Statistical calculation",
             "RNA-Seq quantification",
-            "Pathway or network visualisation",
+            "Gene functional annotation",
             "Validation",
-            "Exonic splicing enhancer prediction",
-            "Sequence composition calculation",
-            "Formatting",
-            "Data handling",
-            "Sequence alignment",
-            "Sequence trimming",
+            "Pathway or network analysis",
+            "Visualisation",
             "Enrichment analysis",
+            "Sequence trimming",
+            "Pathway or network visualisation",
             "Read summarisation",
-            "Pathway or network analysis",
-            "Read pre-processing",
+            "Sequence alignment",
+            "Data handling",
+            "Exonic splicing enhancer prediction",
             "Primer removal",
-            "Gene functional annotation"
+            "Formatting",
+            "Sequence composition calculation",
+            "Differential gene expression analysis",
+            "Sequencing quality control",
+            "Read pre-processing",
+            "Statistical calculation",
+            "RNA-Seq analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
         ],
@@ -278862,7 +707439,7 @@
             "Perform a gene ontology enrichment analysis",
             "Perform and visualize an enrichment analysis for KEGG pathways"
         ],
-        "pageviews": 289636,
+        "pageviews": 290452,
         "priority": 2,
         "pub_date": "2016-10-05",
         "questions": [
@@ -278900,44 +707477,44 @@
         ],
         "short_id": "T00295",
         "short_tools": [
-            "rna_star",
-            "join1",
-            "picard_MarkDuplicates",
+            "cat1",
             "ChangeCase",
-            "pygenomeTracks",
-            "length_and_gc_content",
-            "samtools_idxstats",
-            "collection_element_identifiers",
+            "rna_star",
             "deseq2",
-            "__MERGE_COLLECTION__",
-            "gtftobed12",
-            "fastqc",
-            "deg_annotate",
-            "dexseq",
-            "Grouping1",
-            "__EXTRACT_DATASET__",
             "pathview",
-            "table_compute",
-            "rseqc_geneBody_coverage",
-            "tp_cat",
+            "__EXTRACT_DATASET__",
+            "dexseq_count",
+            "rseqc_infer_experiment",
             "samtools_view",
-            "Filter1",
-            "ggplot2_heatmap2",
-            "tp_sort_header_tool",
+            "gtftobed12",
             "cutadapt",
-            "multiqc",
-            "goseq",
-            "Cut1",
             "__TAG_FROM_FILE__",
-            "rseqc_infer_experiment",
             "rseqc_read_distribution",
-            "tp_tail_tool",
-            "cat1",
+            "Filter1",
             "tp_replace_in_line",
-            "dexseq_count",
+            "collection_element_identifiers",
+            "tp_sort_header_tool",
+            "featurecounts",
+            "ggplot2_heatmap2",
+            "picard_MarkDuplicates",
+            "__MERGE_COLLECTION__",
+            "multiqc",
+            "dexseq",
             "Add_a_column1",
+            "Cut1",
+            "pygenomeTracks",
+            "deg_annotate",
+            "tp_cat",
             "__FLATTEN__",
-            "featurecounts"
+            "goseq",
+            "fastqc",
+            "join1",
+            "tp_tail_tool",
+            "rseqc_geneBody_coverage",
+            "table_compute",
+            "samtools_idxstats",
+            "Grouping1",
+            "length_and_gc_content"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -278949,11 +707526,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -278983,6 +707555,7690 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
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+                    "id": "ChangeCase",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Cut1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
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+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.6.4.1",
+                                "2.6.4",
+                                "2.4"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "5.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "5.0.3+galaxy0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "bulk",
@@ -279067,7 +715323,7 @@
         "video_versions": 2,
         "video_view": 0,
         "visit_duration": 176,
-        "visitors": 142889,
+        "visitors": 143559,
         "workflows": [
             {
                 "creators": [
@@ -279412,7 +715668,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nInput Dataset Collection\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nDrosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nheader\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nKEGG pathways to plot\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"Extract samples\u2019 name\"];\n  0 -->|output| 4;\n  5[\"Compute gene length\"];\n  1 -->|output| 5;\n  6[\"Extract groups\"];\n  4 -->|output| 6;\n  7[\"Change Case\"];\n  5 -->|length| 7;\n  8[\"Tag elements with groups\"];\n  0 -->|output| 8;\n  6 -->|outfile| 8;\n  9[\"Differential Analysis\"];\n  8 -->|output| 9;\n  c1ff3e9a-46d3-4862-adb6-076ea951be26[\"Output\\nDESeq2_plots\"];\n  9 --> c1ff3e9a-46d3-4862-adb6-076ea951be26;\n  style c1ff3e9a-46d3-4862-adb6-076ea951be26 stroke:#2c3143,stroke-width:4px;\n  b430e84e-cfa5-48e8-92a7-ef5630ced1e5[\"Output\\nDESeq2_normalized_counts\"];\n  9 --> b430e84e-cfa5-48e8-92a7-ef5630ced1e5;\n  style b430e84e-cfa5-48e8-92a7-ef5630ced1e5 stroke:#2c3143,stroke-width:4px;\n  10[\"Compute\"];\n  9 -->|deseq_out| 10;\n  11[\"Annotate DESeq2/DEXSeq output tables\"];\n  1 -->|output| 11;\n  9 -->|deseq_out| 11;\n  12[\"Table Compute\"];\n  9 -->|counts_out| 12;\n  13[\"Cut\"];\n  10 -->|out_file1| 13;\n  14[\"Concatenate datasets\"];\n  2 -->|output| 14;\n  11 -->|output| 14;\n  11f46837-7dbb-453b-962a-3c97cb0faad4[\"Output\\nDESeq2_annotated_results_with_header\"];\n  14 --> 11f46837-7dbb-453b-962a-3c97cb0faad4;\n  style 11f46837-7dbb-453b-962a-3c97cb0faad4 stroke:#2c3143,stroke-width:4px;\n  15[\"Table Compute\"];\n  9 -->|counts_out| 15;\n  12 -->|table| 15;\n  32004d23-7c99-4405-a65f-fd861b40c949[\"Output\\nz_score\"];\n  15 --> 32004d23-7c99-4405-a65f-fd861b40c949;\n  style 32004d23-7c99-4405-a65f-fd861b40c949 stroke:#2c3143,stroke-width:4px;\n  16[\"Change Case\"];\n  13 -->|out_file1| 16;\n  17[\"Filter\"];\n  14 -->|out_file1| 17;\n  18[\"goseq\"];\n  16 -->|out_file1| 18;\n  7 -->|out_file1| 18;\n  a0dd7397-7262-4336-abd6-a915ab6be36a[\"Output\\ngo_genes\"];\n  18 --> a0dd7397-7262-4336-abd6-a915ab6be36a;\n  style a0dd7397-7262-4336-abd6-a915ab6be36a stroke:#2c3143,stroke-width:4px;\n  659fec58-4ed5-4aee-9e50-7acce21113cb[\"Output\\ngo_plot\"];\n  18 --> 659fec58-4ed5-4aee-9e50-7acce21113cb;\n  style 659fec58-4ed5-4aee-9e50-7acce21113cb stroke:#2c3143,stroke-width:4px;\n  c06c58d4-ab5d-49da-b481-baf668c6fc29[\"Output\\ngo_terms\"];\n  18 --> c06c58d4-ab5d-49da-b481-baf668c6fc29;\n  style c06c58d4-ab5d-49da-b481-baf668c6fc29 stroke:#2c3143,stroke-width:4px;\n  19[\"goseq\"];\n  16 -->|out_file1| 19;\n  7 -->|out_file1| 19;\n  9872b017-9b39-4cd3-b232-a305979a782b[\"Output\\nkegg_genes\"];\n  19 --> 9872b017-9b39-4cd3-b232-a305979a782b;\n  style 9872b017-9b39-4cd3-b232-a305979a782b stroke:#2c3143,stroke-width:4px;\n  8d0ac5be-ac7d-4f10-85ac-d3461f561a50[\"Output\\nkegg_pathways\"];\n  19 --> 8d0ac5be-ac7d-4f10-85ac-d3461f561a50;\n  style 8d0ac5be-ac7d-4f10-85ac-d3461f561a50 stroke:#2c3143,stroke-width:4px;\n  20[\"Cut\"];\n  17 -->|out_file1| 20;\n  21[\"Filter\"];\n  17 -->|out_file1| 21;\n  22[\"Filter\"];\n  18 -->|wallenius_tab| 22;\n  ae762394-0e90-4b9a-a7b4-7cffeccc80a7[\"Output\\ngo_underrepresented\"];\n  22 --> ae762394-0e90-4b9a-a7b4-7cffeccc80a7;\n  style ae762394-0e90-4b9a-a7b4-7cffeccc80a7 stroke:#2c3143,stroke-width:4px;\n  23[\"Filter\"];\n  18 -->|wallenius_tab| 23;\n  b788d5b7-119c-418a-a12b-a97ef7ea5bf2[\"Output\\ngo_overrepresented\"];\n  23 --> b788d5b7-119c-418a-a12b-a97ef7ea5bf2;\n  style b788d5b7-119c-418a-a12b-a97ef7ea5bf2 stroke:#2c3143,stroke-width:4px;\n  24[\"Filter\"];\n  19 -->|wallenius_tab| 24;\n  69f80c89-fc7d-4bea-836f-34e68615abcd[\"Output\\nkegg_underrepresented\"];\n  24 --> 69f80c89-fc7d-4bea-836f-34e68615abcd;\n  style 69f80c89-fc7d-4bea-836f-34e68615abcd stroke:#2c3143,stroke-width:4px;\n  25[\"Filter\"];\n  19 -->|wallenius_tab| 25;\n  930f1461-0ade-4744-a83d-843108c4b597[\"Output\\nkegg_overrepresented\"];\n  25 --> 930f1461-0ade-4744-a83d-843108c4b597;\n  style 930f1461-0ade-4744-a83d-843108c4b597 stroke:#2c3143,stroke-width:4px;\n  26[\"Pathview\"];\n  20 -->|out_file1| 26;\n  3 -->|output| 26;\n  7cdd4475-6de3-4c02-be8d-d76e788980f6[\"Output\\npathview_plot\"];\n  26 --> 7cdd4475-6de3-4c02-be8d-d76e788980f6;\n  style 7cdd4475-6de3-4c02-be8d-d76e788980f6 stroke:#2c3143,stroke-width:4px;\n  27[\"Join two Datasets\"];\n  9 -->|counts_out| 27;\n  21 -->|out_file1| 27;\n  28[\"Group\"];\n  22 -->|out_file1| 28;\n  d1ae921d-2e2b-46d8-95a2-4443f5a1b3b4[\"Output\\ngo_underrepresented_categories\"];\n  28 --> d1ae921d-2e2b-46d8-95a2-4443f5a1b3b4;\n  style d1ae921d-2e2b-46d8-95a2-4443f5a1b3b4 stroke:#2c3143,stroke-width:4px;\n  29[\"Group\"];\n  23 -->|out_file1| 29;\n  4d2d01eb-15d2-4863-a522-9462c15eb51c[\"Output\\ngo_overrepresented_categories\"];\n  29 --> 4d2d01eb-15d2-4863-a522-9462c15eb51c;\n  style 4d2d01eb-15d2-4863-a522-9462c15eb51c stroke:#2c3143,stroke-width:4px;\n  30[\"Cut\"];\n  27 -->|out_file1| 30;\n  31[\"heatmap2\"];\n  30 -->|out_file1| 31;\n  42cb6b68-4ed6-4b6e-9312-744b9e0c1442[\"Output\\nheatmap_log\"];\n  31 --> 42cb6b68-4ed6-4b6e-9312-744b9e0c1442;\n  style 42cb6b68-4ed6-4b6e-9312-744b9e0c1442 stroke:#2c3143,stroke-width:4px;\n  32[\"heatmap2\"];\n  30 -->|out_file1| 32;\n  0ecef5aa-76ed-4fe7-9244-3b32d231e7f3[\"Output\\nheatmap_zscore\"];\n  32 --> 0ecef5aa-76ed-4fe7-9244-3b32d231e7f3;\n  style 0ecef5aa-76ed-4fe7-9244-3b32d231e7f3 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "DEG Part - Ref Based RNA Seq - Transcriptomics - GTN",
                 "outputs": [
                     {
@@ -280422,7 +716678,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nsingle fastqs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Collection\\npaired fastqs\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nDrosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Cutadapt: remove bad quality bp\"];\n  0 -->|output| 3;\n  4[\"Flatten paired collection for FastQC\"];\n  1 -->|output| 4;\n  5[\"Cutadapt\"];\n  1 -->|output| 5;\n  6[\"Get gene length\"];\n  2 -->|output| 6;\n  077640cc-edbb-4185-9eb1-d11b522774af[\"Output\\nGene length\"];\n  6 --> 077640cc-edbb-4185-9eb1-d11b522774af;\n  style 077640cc-edbb-4185-9eb1-d11b522774af stroke:#2c3143,stroke-width:4px;\n  7[\"convert gtf to bed12\"];\n  2 -->|output| 7;\n  8[\"STAR: map single reads\"];\n  2 -->|output| 8;\n  3 -->|out1| 8;\n  9[\"Merge fastqs for FastQC\"];\n  4 -->|output| 9;\n  0 -->|output| 9;\n  10[\"Merge Cutadapt reports\"];\n  5 -->|report| 10;\n  3 -->|report| 10;\n  11[\"STAR: map paired reads\"];\n  2 -->|output| 11;\n  5 -->|out_pairs| 11;\n  12[\"count reads per gene for SR\"];\n  8 -->|mapped_reads| 12;\n  2 -->|output| 12;\n  13[\"FastQC check read qualities\"];\n  9 -->|output| 13;\n  14[\"Combine cutadapt results\"];\n  10 -->|output| 14;\n  cab760db-5c9d-4a3c-b768-998bfbac6b57[\"Output\\nmultiqc_cutadapt_html\"];\n  14 --> cab760db-5c9d-4a3c-b768-998bfbac6b57;\n  style cab760db-5c9d-4a3c-b768-998bfbac6b57 stroke:#2c3143,stroke-width:4px;\n  15[\"Merge STAR logs\"];\n  11 -->|output_log| 15;\n  8 -->|output_log| 15;\n  16[\"Merge STAR counts\"];\n  8 -->|reads_per_gene| 16;\n  11 -->|reads_per_gene| 16;\n  17[\"count fragments per gene for PE\"];\n  11 -->|mapped_reads| 17;\n  2 -->|output| 17;\n  1527b5d7-1681-4934-9d9e-3a5f86ae0fee[\"Output\\nfeatureCounts_gene_length\"];\n  17 --> 1527b5d7-1681-4934-9d9e-3a5f86ae0fee;\n  style 1527b5d7-1681-4934-9d9e-3a5f86ae0fee stroke:#2c3143,stroke-width:4px;\n  18[\"Merge STAR BAM\"];\n  11 -->|mapped_reads| 18;\n  8 -->|mapped_reads| 18;\n  802017f4-fb1a-4243-b50d-2ed46f746f11[\"Output\\nSTAR_BAM\"];\n  18 --> 802017f4-fb1a-4243-b50d-2ed46f746f11;\n  style 802017f4-fb1a-4243-b50d-2ed46f746f11 stroke:#2c3143,stroke-width:4px;\n  19[\"merge coverage unique strand 1\"];\n  8 -->|signal_unique_str1| 19;\n  11 -->|signal_unique_str1| 19;\n  20[\"merge coverage unique strand 2\"];\n  8 -->|signal_unique_str2| 20;\n  11 -->|signal_unique_str2| 20;\n  21[\"Combine FastQC results\"];\n  13 -->|text_file| 21;\n  8d0ce9ee-e4e4-4c0c-8261-420ce756ecfd[\"Output\\nmultiqc_fastqc_html\"];\n  21 --> 8d0ce9ee-e4e4-4c0c-8261-420ce756ecfd;\n  style 8d0ce9ee-e4e4-4c0c-8261-420ce756ecfd stroke:#2c3143,stroke-width:4px;\n  22[\"Combine STAR Results\"];\n  15 -->|output| 22;\n  204e3f6c-6f54-46f0-b07c-1f31113265e7[\"Output\\nmultiqc_star_html\"];\n  22 --> 204e3f6c-6f54-46f0-b07c-1f31113265e7;\n  style 204e3f6c-6f54-46f0-b07c-1f31113265e7 stroke:#2c3143,stroke-width:4px;\n  23[\"Remove statistics from STAR counts\"];\n  16 -->|output| 23;\n  24[\"Determine library strandness with STAR\"];\n  16 -->|output| 24;\n  fe7b84dd-4466-4fe7-94a8-408f4ac7ed1a[\"Output\\nmultiqc_star_counts_html\"];\n  24 --> fe7b84dd-4466-4fe7-94a8-408f4ac7ed1a;\n  style fe7b84dd-4466-4fe7-94a8-408f4ac7ed1a stroke:#2c3143,stroke-width:4px;\n  25[\"merge counts from featureCounts\"];\n  12 -->|output_short| 25;\n  17 -->|output_short| 25;\n  c82388f8-cb09-4fdf-8a0e-03cdad579f37[\"Output\\nfeatureCounts\"];\n  25 --> c82388f8-cb09-4fdf-8a0e-03cdad579f37;\n  style c82388f8-cb09-4fdf-8a0e-03cdad579f37 stroke:#2c3143,stroke-width:4px;\n  26[\"merge featureCounts summary\"];\n  12 -->|output_summary| 26;\n  17 -->|output_summary| 26;\n  27[\"Determine library strandness with Infer Experiment\"];\n  18 -->|output| 27;\n  7 -->|bed_file| 27;\n  940ec3ec-dd2e-4d50-bbc4-756945eb16b2[\"Output\\ninferexperiment\"];\n  27 --> 940ec3ec-dd2e-4d50-bbc4-756945eb16b2;\n  style 940ec3ec-dd2e-4d50-bbc4-756945eb16b2 stroke:#2c3143,stroke-width:4px;\n  28[\"Read Distribution\"];\n  18 -->|output| 28;\n  7 -->|bed_file| 28;\n  29[\"Compute read distribution statistics\"];\n  18 -->|output| 29;\n  7 -->|bed_file| 29;\n  30[\"sample BAM\"];\n  18 -->|output| 30;\n  31[\"Get reads number per chromosome\"];\n  18 -->|output| 31;\n  32[\"Remove duplicates\"];\n  18 -->|output| 32;\n  33[\"Determine library strandness with STAR coverage\"];\n  19 -->|output| 33;\n  20 -->|output| 33;\n  2 -->|output| 33;\n  89e1b053-03c2-467a-95a0-d2dc404670ec[\"Output\\npgt\"];\n  33 --> 89e1b053-03c2-467a-95a0-d2dc404670ec;\n  style 89e1b053-03c2-467a-95a0-d2dc404670ec stroke:#2c3143,stroke-width:4px;\n  34[\"Select unstranded counts\"];\n  23 -->|outfile| 34;\n  bce755be-ac3b-4346-9ac5-1128a287bf00[\"Output\\ncounts_from_star\"];\n  34 --> bce755be-ac3b-4346-9ac5-1128a287bf00;\n  style bce755be-ac3b-4346-9ac5-1128a287bf00 stroke:#2c3143,stroke-width:4px;\n  35[\"Sort counts to get gene with highest count on feature Counts\"];\n  25 -->|output| 35;\n  6aeb4dd1-445f-4c66-b1ce-4bb8faac53db[\"Output\\nfeatureCounts_sorted\"];\n  35 --> 6aeb4dd1-445f-4c66-b1ce-4bb8faac53db;\n  style 6aeb4dd1-445f-4c66-b1ce-4bb8faac53db stroke:#2c3143,stroke-width:4px;\n  36[\"Combine read asignments statistics\"];\n  26 -->|output| 36;\n  fc72242a-f23c-4ceb-9a8b-5280343ea5d6[\"Output\\nmultiqc_featureCounts_html\"];\n  36 --> fc72242a-f23c-4ceb-9a8b-5280343ea5d6;\n  style fc72242a-f23c-4ceb-9a8b-5280343ea5d6 stroke:#2c3143,stroke-width:4px;\n  37[\"Combine read distribution on known features\"];\n  29 -->|output| 37;\n  07dca732-0ac7-432e-9e61-2b77f921a23b[\"Output\\nmultiqc_read_distrib\"];\n  37 --> 07dca732-0ac7-432e-9e61-2b77f921a23b;\n  style 07dca732-0ac7-432e-9e61-2b77f921a23b stroke:#2c3143,stroke-width:4px;\n  38[\"Get gene body coverage\"];\n  30 -->|outputsam| 38;\n  7 -->|bed_file| 38;\n  39[\"Combine results on reads per chromosome\"];\n  31 -->|output| 39;\n  7bfa8ae7-8ffd-46a1-a56e-815ed2c9f1cf[\"Output\\nmultiqc_reads_per_chrom\"];\n  39 --> 7bfa8ae7-8ffd-46a1-a56e-815ed2c9f1cf;\n  style 7bfa8ae7-8ffd-46a1-a56e-815ed2c9f1cf stroke:#2c3143,stroke-width:4px;\n  40[\"Combine results of duplicate reads\"];\n  32 -->|metrics_file| 40;\n  66553d0f-e851-458b-82c2-f9b30e394bac[\"Output\\nmultiqc_dup\"];\n  40 --> 66553d0f-e851-458b-82c2-f9b30e394bac;\n  style 66553d0f-e851-458b-82c2-f9b30e394bac stroke:#2c3143,stroke-width:4px;\n  41[\"Sort counts to get gene with highest count on STAR\"];\n  34 -->|out_file1| 41;\n  383df008-0ccb-4d67-98dd-33fa5e2db81e[\"Output\\ncounts_from_star_sorted\"];\n  41 --> 383df008-0ccb-4d67-98dd-33fa5e2db81e;\n  style 383df008-0ccb-4d67-98dd-33fa5e2db81e stroke:#2c3143,stroke-width:4px;\n  42[\"Combine gene body coverage\"];\n  38 -->|outputtxt| 42;\n  8544ea5c-faf2-44c9-85d6-40658fc9b9eb[\"Output\\nmultiqc_gene_body_cov\"];\n  42 --> 8544ea5c-faf2-44c9-85d6-40658fc9b9eb;\n  style 8544ea5c-faf2-44c9-85d6-40658fc9b9eb stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics - GTN",
                 "outputs": [
                     {
@@ -281749,7 +718005,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nPaired list collection with PE fastqs\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nDrosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\ud83d\udee0\ufe0f Subworkflow\\nFastQC\"];\n  style 2 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 2;\n  5f7652f1-e225-4ad1-8dbd-4d21544edb89[\"Output\\nmultiqc_fastqc_html\"];\n  2 --> 5f7652f1-e225-4ad1-8dbd-4d21544edb89;\n  style 5f7652f1-e225-4ad1-8dbd-4d21544edb89 stroke:#2c3143,stroke-width:4px;\n  3[\"\ud83d\udee0\ufe0f Subworkflow\\ncutadapt\"];\n  style 3 fill:#edd,stroke:#900,stroke-width:4px;\n  0 -->|output| 3;\n  41c7fbb5-655b-457c-8ba7-0e2eeab3d7ee[\"Output\\nmultiqc_cutadapt_html\"];\n  3 --> 41c7fbb5-655b-457c-8ba7-0e2eeab3d7ee;\n  style 41c7fbb5-655b-457c-8ba7-0e2eeab3d7ee stroke:#2c3143,stroke-width:4px;\n  4[\"\ud83d\udee0\ufe0f Subworkflow\\nSTAR + multiQC\"];\n  style 4 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 4;\n  3 -->|out_pairs| 4;\n  8aa5ef30-3f09-4a93-944d-0d89101c056a[\"Output\\nmultiqc_star_html\"];\n  4 --> 8aa5ef30-3f09-4a93-944d-0d89101c056a;\n  style 8aa5ef30-3f09-4a93-944d-0d89101c056a stroke:#2c3143,stroke-width:4px;\n  11af5c57-91b4-496c-9b0c-b02904963f81[\"Output\\nSTAR_BAM\"];\n  4 --> 11af5c57-91b4-496c-9b0c-b02904963f81;\n  style 11af5c57-91b4-496c-9b0c-b02904963f81 stroke:#2c3143,stroke-width:4px;\n  5[\"\ud83d\udee0\ufe0f Subworkflow\\nmore QC\"];\n  style 5 fill:#edd,stroke:#900,stroke-width:4px;\n  1 -->|output| 5;\n  4 -->|STAR_BAM| 5;\n  f2eed352-ca21-4d65-8810-f5a1d3c282b4[\"Output\\nmultiqc_read_distrib_html\"];\n  5 --> f2eed352-ca21-4d65-8810-f5a1d3c282b4;\n  style f2eed352-ca21-4d65-8810-f5a1d3c282b4 stroke:#2c3143,stroke-width:4px;\n  b306cb12-a275-4c6d-b609-47fdc208864b[\"Output\\nmultiqc_reads_per_chrom_html\"];\n  5 --> b306cb12-a275-4c6d-b609-47fdc208864b;\n  style 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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows",
                 "outputs": [
                     {
@@ -284669,19 +720925,19 @@
         "dir": "topics/transcriptomics/tutorials/minerva-pathways",
         "edam_operation": [
             "Data handling",
-            "Sequence alignment",
-            "Sequence trimming",
-            "Sequencing quality control",
-            "RNA-Seq analysis",
-            "Read summarisation",
-            "Statistical calculation",
             "RNA-Seq quantification",
-            "Validation",
+            "Gene functional annotation",
+            "Primer removal",
             "Annotation",
             "Sequence composition calculation",
+            "Validation",
+            "Sequencing quality control",
             "Read pre-processing",
-            "Primer removal",
-            "Gene functional annotation"
+            "Sequence trimming",
+            "Read summarisation",
+            "Statistical calculation",
+            "Sequence alignment",
+            "RNA-Seq analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -284695,7 +720951,6 @@
         "inexact_supported_servers": [
             "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)"
         ],
@@ -284716,7 +720971,7 @@
             "Perform an analysis using a workflow from WorkflowHub",
             "Visualise and interpret the results with MINERVA"
         ],
-        "pageviews": 210,
+        "pageviews": 213,
         "priority": 2,
         "pub_date": "2024-03-28",
         "questions": [
@@ -284725,26 +720980,26 @@
         ],
         "short_id": "T00437",
         "short_tools": [
-            "limma_voom",
-            "join1",
-            "collection_column_join",
-            "hisat2",
-            "fastqc",
-            "annotatemyids",
             "__EXTRACT_DATASET__",
-            "tp_sorted_uniq",
-            "rseqc_geneBody_coverage",
-            "tp_sort_header_tool",
+            "limma_voom",
             "cutadapt",
-            "multiqc",
-            "goseq",
-            "Grep1",
-            "Cut1",
-            "fasterq_dump",
+            "tp_sorted_uniq",
+            "hisat2",
             "rseqc_read_distribution",
             "tp_replace_in_line",
+            "tp_sort_header_tool",
+            "collection_column_join",
+            "featurecounts",
+            "Grep1",
+            "multiqc",
             "Add_a_column1",
-            "featurecounts"
+            "Cut1",
+            "goseq",
+            "annotatemyids",
+            "fastqc",
+            "join1",
+            "rseqc_geneBody_coverage",
+            "fasterq_dump"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -284774,10 +721029,136 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
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+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
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+                },
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+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
                 },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -284787,6 +721168,2982 @@
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
                     "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Cut1",
+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Grep1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
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+                        {
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+                            "state": "missing"
+                        },
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+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
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+                        {
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+                        {
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+                            "state": "missing"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "__EXTRACT_DATASET__",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
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+                            ]
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+                        {
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+                            "versions": [
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+                            ]
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "5.0.3+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.6.4.1",
+                                "2.4galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "5.0.1+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "5.0.1+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.6.4.1",
+                                "2.6.4",
+                                "2.4"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "5.0.1+galaxy2"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "5.0.1+galaxy2"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "5.0.1+galaxy2"
                 }
             ]
         },
@@ -284840,8 +724197,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 126,
-        "visitors": 176,
+        "visit_duration": 120,
+        "visitors": 179,
         "workflows": [
             {
                 "creators": [
@@ -284899,7 +724256,7 @@
                 ],
                 "license": "AGPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSample Table\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Cut\"];\n  0 -->|output| 1;\n  2[\"Select\"];\n  1 -->|out_file1| 2;\n  3[\"Faster Download and Extract Reads in FASTQ\"];\n  2 -->|out_file1| 3;\n  b7c7e59d-6a78-41af-ae59-e52fcc1fe2f6[\"Output\\noutput_collection\"];\n  3 --> b7c7e59d-6a78-41af-ae59-e52fcc1fe2f6;\n  style b7c7e59d-6a78-41af-ae59-e52fcc1fe2f6 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "BY-COVID: Data Download",
                 "outputs": [
                     {
@@ -285124,7 +724481,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nfeatureCounts: Counts\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nfactordata\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Collection\\nfeatureCounts: Lengths\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Column join\"];\n  0 -->|output| 3;\n  4[\"Extract dataset\"];\n  2 -->|output| 4;\n  5[\"countdata\"];\n  3 -->|tabular_output| 5;\n  e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5[\"Output\\ncount_data\"];\n  5 --> e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5;\n  style e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5 stroke:#2c3143,stroke-width:4px;\n  6[\"annodata\"];\n  3 -->|tabular_output| 6;\n  7[\"Replace Text\"];\n  5 -->|outfile| 7;\n  8[\"limma DEG analysis\"];\n  6 -->|out_tab| 8;\n  7 -->|outfile| 8;\n  1 -->|output| 8;\n  1c8d7950-1003-4c86-9986-c6ed1264cd8b[\"Output\\nlimma_report\"];\n  8 --> 1c8d7950-1003-4c86-9986-c6ed1264cd8b;\n  style 1c8d7950-1003-4c86-9986-c6ed1264cd8b stroke:#2c3143,stroke-width:4px;\n  9[\"Extract dataset\"];\n  8 -->|outTables| 9;\n  10[\"MINERVA Formatting\"];\n  9 -->|output| 10;\n  9ce4f48b-e742-4b7c-9bde-5d51f11068d3[\"Output\\nminerva_table\"];\n  10 --> 9ce4f48b-e742-4b7c-9bde-5d51f11068d3;\n  style 9ce4f48b-e742-4b7c-9bde-5d51f11068d3 stroke:#2c3143,stroke-width:4px;\n  11[\"Join two Datasets\"];\n  9 -->|output| 11;\n  4 -->|output| 11;\n  12[\"Compute\"];\n  11 -->|out_file1| 12;\n  13[\"Cut\"];\n  12 -->|out_file1| 13;\n  14[\"Unique\"];\n  13 -->|out_file1| 14;\n  15[\"Cut\"];\n  14 -->|outfile| 15;\n  16[\"Cut\"];\n  14 -->|outfile| 16;\n  17[\"goseq\"];\n  15 -->|out_file1| 17;\n  16 -->|out_file1| 17;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "mRNA-Seq BY-COVID Pipeline: Analysis",
                 "outputs": [
                     {
@@ -285413,7 +724770,7 @@
                 ],
                 "license": "GPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nmRNA-Seq Reads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nUCSC Genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"FastQC\"];\n  0 -->|output| 2;\n  3[\"Cutadapt\"];\n  0 -->|output| 3;\n  4[\"FastQC\"];\n  3 -->|out1| 4;\n  5[\"HISAT2\"];\n  3 -->|out1| 5;\n  6[\"featureCounts\"];\n  5 -->|output_alignments| 6;\n  5cb5bd5d-df81-4463-8002-e89551780f01[\"Output\\noutput_feature_lengths\"];\n  6 --> 5cb5bd5d-df81-4463-8002-e89551780f01;\n  style 5cb5bd5d-df81-4463-8002-e89551780f01 stroke:#2c3143,stroke-width:4px;\n  5dec13e1-0011-472c-a72d-6715fe55c23c[\"Output\\noutput_short\"];\n  6 --> 5dec13e1-0011-472c-a72d-6715fe55c23c;\n  style 5dec13e1-0011-472c-a72d-6715fe55c23c stroke:#2c3143,stroke-width:4px;\n  7[\"Read Distribution\"];\n  5 -->|output_alignments| 7;\n  1 -->|output| 7;\n  8[\"Gene Body Coverage BAM\"];\n  5 -->|output_alignments| 8;\n  1 -->|output| 8;\n  9[\"Multi QC raw reads\"];\n  2 -->|text_file| 9;\n  4 -->|text_file| 9;\n  3 -->|report| 9;\n  5 -->|summary_file| 9;\n  7 -->|output| 9;\n  8 -->|outputtxt| 9;\n  6 -->|output_summary| 9;\n  9217af4e-e34c-4a49-9d67-4b3df511ac2c[\"Output\\nhtml_report\"];\n  9 --> 9217af4e-e34c-4a49-9d67-4b3df511ac2c;\n  style 9217af4e-e34c-4a49-9d67-4b3df511ac2c stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "mRNA-Seq BY-COVID Pipeline: Counts",
                 "outputs": [
                     {
@@ -285712,22 +725069,21 @@
         ],
         "dir": "topics/transcriptomics/tutorials/de-novo",
         "edam_operation": [
-            "Sequence alignment",
+            "Transcriptome assembly",
+            "RNA-Seq quantification",
+            "Sequence composition calculation",
             "Differential gene expression analysis",
             "Sequencing quality control",
-            "RNA-Seq analysis",
             "Read summarisation",
+            "Sequence alignment",
             "Statistical calculation",
-            "RNA-Seq quantification",
             "Sequence annotation",
-            "Transcriptome assembly",
-            "Sequence composition calculation"
+            "RNA-Seq analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "Galaxy@AuBi",
             "UseGalaxy.be",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
@@ -285757,7 +725113,7 @@
             "Reconstruction of transcripts without reference transcriptome (de novo)",
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@@ -285780,16 +725136,16 @@
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@@ -285806,11 +725162,6 @@
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+                                "0.39+galaxy0",
+                                "0.36.4",
+                                "0.39+galaxy2",
+                                "0.36.5",
+                                "0.32.3",
+                                "0.32.1",
+                                "0.32.2",
+                                "0.36.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "0.38.1",
+                                "0.36.4",
+                                "0.36.5"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.38.0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
+                                "0.36.6",
+                                "0.36.5"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "0.38.0"
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+            ]
+        },
         "symlink": null,
         "time_estimation": "6h",
         "title": "De novo transcriptome reconstruction with RNA-Seq",
@@ -285875,7 +726884,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 151,
-        "visitors": 13418,
+        "visitors": 13476,
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@@ -286237,7 +727246,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nG1E_rep1_forward_read\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nG1E_rep1_reverse_read\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nG1E_rep2_forward_read\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nG1E_rep2_reverse_read\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_rep1_forward_read\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_rep1_reverse_read\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_rep2_forward_read\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\nMegakaryocyte_rep2_reverse_read\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\nRefSeq_reference_GTF\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"FastQC\"];\n  0 -->|output| 9;\n  10[\"FastQC\"];\n  1 -->|output| 10;\n  11[\"Trimmomatic\"];\n  0 -->|output| 11;\n  1 -->|output| 11;\n  12[\"FastQC\"];\n  2 -->|output| 12;\n  13[\"FastQC\"];\n  3 -->|output| 13;\n  14[\"Trimmomatic\"];\n  2 -->|output| 14;\n  3 -->|output| 14;\n  15[\"FastQC\"];\n  4 -->|output| 15;\n  16[\"FastQC\"];\n  5 -->|output| 16;\n  17[\"Trimmomatic\"];\n  4 -->|output| 17;\n  5 -->|output| 17;\n  18[\"FastQC\"];\n  6 -->|output| 18;\n  19[\"FastQC\"];\n  7 -->|output| 19;\n  20[\"Trimmomatic\"];\n  6 -->|output| 20;\n  7 -->|output| 20;\n  21[\"HISAT2\"];\n  11 -->|fastq_out_r1_paired| 21;\n  11 -->|fastq_out_r2_paired| 21;\n  22[\"FastQC\"];\n  11 -->|fastq_out_r1_paired| 22;\n  23[\"FastQC\"];\n  11 -->|fastq_out_r2_paired| 23;\n  24[\"HISAT2\"];\n  14 -->|fastq_out_r1_paired| 24;\n  14 -->|fastq_out_r2_paired| 24;\n  25[\"FastQC\"];\n  14 -->|fastq_out_r1_paired| 25;\n  26[\"FastQC\"];\n  14 -->|fastq_out_r2_paired| 26;\n  27[\"HISAT2\"];\n  17 -->|fastq_out_r1_paired| 27;\n  17 -->|fastq_out_r2_paired| 27;\n  28[\"FastQC\"];\n  17 -->|fastq_out_r1_paired| 28;\n  29[\"FastQC\"];\n  17 -->|fastq_out_r2_paired| 29;\n  30[\"HISAT2\"];\n  20 -->|fastq_out_r1_paired| 30;\n  20 -->|fastq_out_r2_paired| 30;\n  31[\"FastQC\"];\n  20 -->|fastq_out_r1_paired| 31;\n  32[\"FastQC\"];\n  20 -->|fastq_out_r2_paired| 32;\n  33[\"StringTie\"];\n  21 -->|output_alignments| 33;\n  34[\"bamCoverage\"];\n  21 -->|output_alignments| 34;\n  35[\"bamCoverage\"];\n  21 -->|output_alignments| 35;\n  36[\"StringTie\"];\n  24 -->|output_alignments| 36;\n  37[\"bamCoverage\"];\n  24 -->|output_alignments| 37;\n  38[\"bamCoverage\"];\n  24 -->|output_alignments| 38;\n  39[\"StringTie\"];\n  27 -->|output_alignments| 39;\n  40[\"bamCoverage\"];\n  27 -->|output_alignments| 40;\n  41[\"bamCoverage\"];\n  27 -->|output_alignments| 41;\n  42[\"StringTie\"];\n  30 -->|output_alignments| 42;\n  43[\"bamCoverage\"];\n  30 -->|output_alignments| 43;\n  44[\"bamCoverage\"];\n  30 -->|output_alignments| 44;\n  45[\"StringTie merge\"];\n  8 -->|output| 45;\n  33 -->|output_gtf| 45;\n  36 -->|output_gtf| 45;\n  42 -->|output_gtf| 45;\n  39 -->|output_gtf| 45;\n  46[\"GffCompare\"];\n  8 -->|output| 46;\n  45 -->|out_gtf| 46;\n  47[\"featureCounts\"];\n  21 -->|output_alignments| 47;\n  46 -->|transcripts_annotated| 47;\n  48[\"featureCounts\"];\n  24 -->|output_alignments| 48;\n  46 -->|transcripts_annotated| 48;\n  49[\"featureCounts\"];\n  27 -->|output_alignments| 49;\n  46 -->|transcripts_annotated| 49;\n  50[\"featureCounts\"];\n  30 -->|output_alignments| 50;\n  46 -->|transcripts_annotated| 50;\n  51[\"DESeq2\"];\n  47 -->|output_short| 51;\n  48 -->|output_short| 51;\n  49 -->|output_short| 51;\n  50 -->|output_short| 51;\n  52[\"Filter\"];\n  51 -->|deseq_out| 52;\n  53[\"Filter\"];\n  52 -->|out_file1| 53;\n  54[\"Filter\"];\n  52 -->|out_file1| 54;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "De novo transcriptome reconstruction with RNA-Seq",
                 "outputs": [
                     {
@@ -288372,7 +729381,7 @@
         "license": "CC-BY-4.0",
         "logo": "GTN",
         "mod_date": "2023-03-05",
-        "pageviews": 5897569,
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         "priority": 0,
         "pub_date": "2016-08-19",
         "redirect_from": [
@@ -288418,6 +729427,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
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+            "tools": []
+        },
         "symlink": null,
         "title": "Introduction to Variant analysis",
         "tools": [],
@@ -288441,7 +729454,7 @@
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         "video_view": 0,
         "visit_duration": 152,
-        "visitors": 2133613
+        "visitors": 2144539
     },
     {
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@@ -288559,17 +729572,17 @@
             "topic_0199"
         ],
         "edam_operation": [
+            "Variant calling",
             "Data handling",
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
             "Sequence alignment analysis",
-            "Generation",
-            "Statistical calculation",
-            "Variant calling",
-            "Sequence composition calculation",
+            "Genome indexing",
             "Formatting",
-            "Genome indexing"
+            "Sequence composition calculation",
+            "Generation",
+            "Sequencing quality control",
+            "Read mapping",
+            "Sequence alignment",
+            "Statistical calculation"
         ],
         "edam_topic": [
             "Genomics",
@@ -288582,7 +729595,6 @@
         "exact_supported_servers": [
             "UseGalaxy.be",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)"
         ],
@@ -288610,23 +729622,23 @@
         "objectives": [
             "Using Galaxy's main site we will see how to call variants in bacteria, viruses, and organelles."
         ],
-        "pageviews": 13577,
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         "questions": [
             "How does frequency of mitochondrial polymorphisms change from mother to child?"
         ],
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-            "bwa_mem",
-            "picard_MarkDuplicates",
-            "vcffilter2",
-            "bamFilter",
-            "picard_MergeSamFiles",
             "Cut1",
-            "bamleftalign",
+            "bamFilter",
             "fastqc",
+            "freebayes",
+            "picard_MergeSamFiles",
             "vcf2tsv",
-            "freebayes"
+            "bwa_mem",
+            "vcffilter2",
+            "picard_MarkDuplicates",
+            "bamleftalign"
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         "slides_recordings": false,
@@ -288643,11 +729655,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -288672,6 +729679,1896 @@
                 }
             ]
         },
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+                    "url": "http://apostl.moffitt.org/"
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
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+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
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+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
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+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
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+                },
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+                    "usegalaxy": false
+                },
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+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
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+                },
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+                    "url": "https://usegalaxy.no/",
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+                    "url": "https://usegalaxy.org.au",
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+                    "url": "https://viralvariant.anses.fr/"
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+                            "state": "local"
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+                            "state": "local"
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+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
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         "tags": [
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@@ -288713,7 +731610,7 @@
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         "video_view": 0,
         "visit_duration": 123,
-        "visitors": 7149,
+        "visitors": 7181,
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@@ -288918,7 +731815,7 @@
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Calling variants in non-diploid systems",
                 "outputs": [
                     {
@@ -289975,12 +732872,12 @@
         "dir": "topics/variant-analysis/tutorials/dunovo",
         "draft": true,
         "edam_operation": [
-            "Generation",
-            "Statistical calculation",
-            "Sequence alignment",
             "Variant calling",
+            "Genome indexing",
             "Read mapping",
-            "Genome indexing"
+            "Statistical calculation",
+            "Sequence alignment",
+            "Generation"
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         "edam_topic": [],
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@@ -290007,7 +732904,7 @@
             "Processing raw duplex sequencing data into consensus sequences",
             "Find rare variants without relying on diploid assumptions"
         ],
-        "pageviews": 2479,
+        "pageviews": 2481,
         "pub_date": "2017-02-22",
         "questions": [
             "What frequency of variants is so low that it is obscured by sequencing error rate?",
@@ -290015,16 +732912,16 @@
         ],
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+            "allele_counts_1",
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-            "allele_counts_1",
-            "bamleftalign",
             "sequence_content_trimmer",
-            "make_families"
+            "make_families",
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@@ -290044,6 +732941,1513 @@
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@@ -290082,7 +734486,7 @@
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-        "visitors": 1509,
+        "visitors": 1511,
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@@ -290185,7 +734589,7 @@
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Du Novo GTN Tutorial - Make Consensus Sequences",
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@@ -290532,7 +734936,7 @@
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Du Novo GTN Tutorial - Variant Calling",
                 "outputs": [
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@@ -290917,22 +735321,22 @@
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-            "Phylogenetic tree generation",
-            "Phylogenetic tree visualisation",
-            "Sequencing quality control",
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-            "Variant calling",
-            "Global alignment",
-            "Statistical calculation",
+            "Phylogenetic tree generation",
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             "Taxonomic classification",
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-            "Local alignment",
-            "Sequence composition calculation",
-            "Antimicrobial resistance prediction"
+            "Sequencing quality control",
+            "Global alignment",
+            "Sequence alignment",
+            "Sequence contamination filtering",
+            "Phylogenetic tree visualisation",
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         ],
         "edam_topic": [
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@@ -290967,7 +735371,7 @@
             "How can we predict drug resistance from those variants",
             "How do we annotate those variants"
         ],
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+        "pageviews": 9186,
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         "questions": [
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@@ -291002,26 +735406,26 @@
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@@ -291030,6 +735434,3583 @@
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+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
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+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "local"
+                        },
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+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
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+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "prokaryote",
@@ -291083,8 +739064,8 @@
         "video": false,
         "video_versions": 2,
         "video_view": 0,
-        "visit_duration": 177,
-        "visitors": 5788,
+        "visit_duration": 176,
+        "visitors": 5800,
         "workflows": [
             {
                 "creators": [
@@ -291343,7 +739324,7 @@
                 ],
                 "license": "AGPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Collection\\nReads\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference Genome\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Parameter\\nMinimum depth of coverage\"];\n  style 2 fill:#ded,stroke:#393,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Parameter\\nMinimum variant allele frequency\"];\n  style 3 fill:#ded,stroke:#393,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Parameter\\nAdditional BWA-MEM options\"];\n  style 4 fill:#ded,stroke:#393,stroke-width:4px;\n  5[\"fastp\"];\n  0 -->|output| 5;\n  6[\"seqret\"];\n  1 -->|output| 6;\n  7[\"snippy\"];\n  4 -->|output| 7;\n  2 -->|output| 7;\n  3 -->|output| 7;\n  5 -->|output_paired_coll| 7;\n  1 -->|output| 7;\n  8[\"Kraken2\"];\n  5 -->|output_paired_coll| 8;\n  c7abf2bf-ed4c-433e-a695-9eca61282bb5[\"Output\\nreport_output\"];\n  8 --> c7abf2bf-ed4c-433e-a695-9eca61282bb5;\n  style c7abf2bf-ed4c-433e-a695-9eca61282bb5 stroke:#2c3143,stroke-width:4px;\n  083a0e51-7780-4c91-a071-dc0e4641d060[\"Output\\noutput\"];\n  8 --> 083a0e51-7780-4c91-a071-dc0e4641d060;\n  style 083a0e51-7780-4c91-a071-dc0e4641d060 stroke:#2c3143,stroke-width:4px;\n  9[\"QualiMap BamQC\"];\n  7 -->|snpsbam| 9;\n  10[\"mosdepth\"];\n  2 -->|output| 10;\n  7 -->|snpsbam| 10;\n  11[\"TB Variant Filter\"];\n  7 -->|snpvcf| 11;\n  12[\"TB-Profiler Profile\"];\n  7 -->|snpsbam| 12;\n  335635b4-a4de-4980-ad02-68f0035daeaa[\"Output\\noutput_txt\"];\n  12 --> 335635b4-a4de-4980-ad02-68f0035daeaa;\n  style 335635b4-a4de-4980-ad02-68f0035daeaa stroke:#2c3143,stroke-width:4px;\n  13[\"TB Variant Filter\"];\n  7 -->|snpvcf| 13;\n  14[\"Flatten collection\"];\n  9 -->|raw_data| 14;\n  15[\"Text reformatting\"];\n  10 -->|output_quantized_bed| 15;\n  16[\"Text transformation\"];\n  11 -->|output1| 16;\n  007df8c2-bd13-495f-8904-abf31d4594d0[\"Output\\nFinal annotated VCF\"];\n  16 --> 007df8c2-bd13-495f-8904-abf31d4594d0;\n  style 007df8c2-bd13-495f-8904-abf31d4594d0 stroke:#2c3143,stroke-width:4px;\n  17[\"MultiQC\"];\n  5 -->|report_json| 17;\n  14 -->|output| 17;\n  59528235-7525-4ef9-8810-36f1ed0f01f6[\"Output\\nhtml_report\"];\n  17 --> 59528235-7525-4ef9-8810-36f1ed0f01f6;\n  style 59528235-7525-4ef9-8810-36f1ed0f01f6 stroke:#2c3143,stroke-width:4px;\n  18[\"bcftools consensus\"];\n  13 -->|output1| 18;\n  6 -->|out_file1| 18;\n  15 -->|outfile| 18;\n  c71b135d-35f9-44d0-a20e-f25528e518af[\"Output\\nconsensus_genome\"];\n  18 --> c71b135d-35f9-44d0-a20e-f25528e518af;\n  style c71b135d-35f9-44d0-a20e-f25528e518af stroke:#2c3143,stroke-width:4px;\n  19[\"TB Variant Report\"];\n  16 -->|output| 19;\n  12 -->|results_json| 19;\n  959528d2-f8f2-4440-99cf-44fddd6c5069[\"Output\\ndrug_resistance_report_html\"];\n  19 --> 959528d2-f8f2-4440-99cf-44fddd6c5069;\n  style 959528d2-f8f2-4440-99cf-44fddd6c5069 stroke:#2c3143,stroke-width:4px;\n  4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0[\"Output\\nvariants_report_html\"];\n  19 --> 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0;\n  style 4d9636eb-075b-4fd2-a1e4-1a7c37a17fc0 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "TB Variant Analysis v1.0",
                 "outputs": [
                     {
@@ -291980,15 +739961,15 @@
         "dir": "topics/variant-analysis/tutorials/sars-cov-2",
         "edam_operation": [
             "Data handling",
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
-            "Sequence contamination filtering",
+            "Genome indexing",
+            "Formatting",
             "Generation",
-            "Validation",
             "SNP detection",
-            "Formatting",
-            "Genome indexing"
+            "Validation",
+            "Sequencing quality control",
+            "Read mapping",
+            "Sequence contamination filtering",
+            "Sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -292003,7 +739984,6 @@
             "MISSISSIPPI",
             "UseGalaxy.be",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
@@ -292025,7 +740005,7 @@
             "Understand how collections enable processing of sequencing data in batches",
             "Understand the analysis steps required to identify and annotate genomic mutations from sequencing data of SARS-CoV-2 samples"
         ],
-        "pageviews": 18702,
+        "pageviews": 18745,
         "pub_date": "2020-06-24",
         "questions": [
             "How can you download public sequencing data deposited in the NCBI Sequence Read Archive (SRA) into a Galaxy history for analysis?",
@@ -292048,20 +740028,20 @@
         ],
         "short_id": "T00315",
         "short_tools": [
-            "bwa_mem",
-            "samtools_stats",
-            "picard_MarkDuplicates",
-            "fastp",
-            "Filter1",
-            "lofreq_viterbi",
+            "lofreq_call",
             "snpeff_sars_cov_2",
             "multiqc",
             "lofreq_indelqual",
+            "snpSift_extractFields",
+            "bwa_mem",
             "Grep1",
+            "picard_MarkDuplicates",
+            "samtools_stats",
+            "fastp",
+            "lofreq_viterbi",
             "fasterq_dump",
-            "lofreq_call",
             "tp_cut_tool",
-            "snpSift_extractFields"
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -292096,19 +740076,2338 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
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+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
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+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
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+                            "server": "https://www.immportgalaxy.org/",
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+                            ]
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+                            "state": "missing"
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+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
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+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.10.4",
+                                "2.11.0+galaxy0",
+                                "2.10.7+galaxy1",
+                                "2.10.4+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "3.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "3.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "2.11.0+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "3.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "3.0.3+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "3.0.3+galaxy0"
                 }
             ]
         },
@@ -292157,7 +742456,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 174,
-        "visitors": 12312,
+        "visitors": 12341,
         "workflows": [
             {
                 "creators": [],
@@ -292288,7 +742587,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nNC_045512.2 fasta file\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSRA Manifest\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Faster Download and Extract Reads in FASTQ\"];\n  1 -->|output| 2;\n  3[\"fastp\"];\n  2 -->|list_paired| 3;\n  4[\"Map with BWA-MEM\"];\n  3 -->|output_paired_coll| 4;\n  0 -->|output| 4;\n  5[\"MarkDuplicates\"];\n  4 -->|bam_output| 5;\n  6[\"Realign reads\"];\n  5 -->|outFile| 6;\n  0 -->|output| 6;\n  7[\"Samtools stats\"];\n  5 -->|outFile| 7;\n  8[\"Insert indel qualities\"];\n  6 -->|realigned| 8;\n  0 -->|output| 8;\n  2ca7c89b-999f-41dc-8037-e54e25959a7e[\"Output\\nRealigned Alignments with Indel Qualities\"];\n  8 --> 2ca7c89b-999f-41dc-8037-e54e25959a7e;\n  style 2ca7c89b-999f-41dc-8037-e54e25959a7e stroke:#2c3143,stroke-width:4px;\n  9[\"Call variants\"];\n  8 -->|output| 9;\n  0 -->|output| 9;\n  10[\"SnpEff eff:\"];\n  9 -->|variants| 10;\n  11[\"SnpSift Extract Fields\"];\n  10 -->|snpeff_output| 11;\n  06259137-eaa5-404a-923c-70ee5f1d89d4[\"Output\\nSnpSift tabular output\"];\n  11 --> 06259137-eaa5-404a-923c-70ee5f1d89d4;\n  style 06259137-eaa5-404a-923c-70ee5f1d89d4 stroke:#2c3143,stroke-width:4px;\n  12[\"MultiQC\"];\n  3 -->|report_json| 12;\n  7 -->|output| 12;\n  5 -->|metrics_file| 12;\n  10 -->|csvFile| 12;\n  758ffde5-7ddd-482a-88b2-1504f8335488[\"Output\\nMultiQC Report PE\"];\n  12 --> 758ffde5-7ddd-482a-88b2-1504f8335488;\n  style 758ffde5-7ddd-482a-88b2-1504f8335488 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Simple COVID-19 - PE Variation",
                 "outputs": [
                     {
@@ -292865,17 +743164,17 @@
         ],
         "dir": "topics/variant-analysis/tutorials/somatic-variants",
         "edam_operation": [
+            "Variant calling",
             "Data handling",
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
             "Sequence alignment analysis",
+            "Genome indexing",
+            "Sequence composition calculation",
             "Generation",
-            "Statistical calculation",
-            "Variant calling",
             "Validation",
-            "Sequence composition calculation",
-            "Genome indexing"
+            "Sequencing quality control",
+            "Read mapping",
+            "Sequence alignment",
+            "Statistical calculation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -292890,8 +743189,7 @@
         "hands_on": true,
         "id": "variant-analysis/somatic-variants",
         "inexact_supported_servers": [
-            "UseGalaxy.cz",
-            "UseGalaxy.fr"
+            "UseGalaxy.cz"
         ],
         "js_requirements": {
             "mathjax": null,
@@ -292912,7 +743210,7 @@
             "Annotate variants with a wealth of human genetic and cancer-specific information extracted from public databases",
             "Add gene-level annotations and generate reports of annotated somatic and germline variants, loss-of-heterozygosity (LOH) events, and affected genes, ready for interpretation by clinicians"
         ],
-        "pageviews": 22023,
+        "pageviews": 22070,
         "pub_date": "2019-03-13",
         "questions": [
             "What are the specific challenges in somatic variant calling that set it apart from regular diploid variant calling?",
@@ -292921,21 +743219,21 @@
         ],
         "short_id": "T00318",
         "short_tools": [
-            "bwa_mem",
-            "tp_easyjoin_tool",
-            "snpEff",
-            "gemini_annotate",
+            "bamFilter",
             "gemini_load",
-            "samtools_rmdup",
             "bg_column_arrange_by_header",
-            "bamFilter",
-            "multiqc",
-            "varscan_somatic",
-            "bamleftalign",
-            "fastqc",
             "trimmomatic",
             "gemini_query",
-            "samtools_calmd"
+            "samtools_calmd",
+            "tp_easyjoin_tool",
+            "fastqc",
+            "samtools_rmdup",
+            "bwa_mem",
+            "varscan_somatic",
+            "multiqc",
+            "snpEff",
+            "gemini_annotate",
+            "bamleftalign"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -292973,11 +743271,2316 @@
                     "name": "UseGalaxy.cz",
                     "url": "https://usegalaxy.cz/",
                     "usegalaxy": false
+                }
+            ]
+        },
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+            "servers": [
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+                    "url": "http://apostl.moffitt.org/"
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
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+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
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+                    "name": "ChemFlow",
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+                },
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+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
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+                },
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+                },
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+                    "name": "GASLINI",
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+                },
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+                    "url": "https://galaxy.mesocentre.uca.fr",
                     "usegalaxy": false
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+                    "url": "https://galaxy.pasteur.fr/",
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+                },
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+                    "usegalaxy": true
+                },
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+                    "url": "https://viralvariant.anses.fr/"
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                 "history": [
                     {
                         "hash": "caffacad4879c005f2c65ec0fce10bca42df9576",
@@ -293357,8 +745960,8 @@
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                 "license": null,
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nSLGFSK-N_231335_r1_chr5_12_17.fastq\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nSLGFSK-N_231335_r2_chr5_12_17.fastq\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\nSLGFSK-T_231336_r1_chr5_12_17.fastq\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"\u2139\ufe0f Input Dataset\\nSLGFSK-T_231336_r2_chr5_12_17.fastq\"];\n  style 3 stroke:#2c3143,stroke-width:4px;\n  4[\"\u2139\ufe0f Input Dataset\\nhg19.chr5_12_17.fa\"];\n  style 4 stroke:#2c3143,stroke-width:4px;\n  5[\"\u2139\ufe0f Input Dataset\\nhotspots.bed\"];\n  style 5 stroke:#2c3143,stroke-width:4px;\n  6[\"\u2139\ufe0f Input Dataset\\ncgi_variant_positions.bed\"];\n  style 6 stroke:#2c3143,stroke-width:4px;\n  7[\"\u2139\ufe0f Input Dataset\\n01-Feb-2019-CIVic.bed\"];\n  style 7 stroke:#2c3143,stroke-width:4px;\n  8[\"\u2139\ufe0f Input Dataset\\ndbsnp.b147.chr5_12_17.vcf.gz\"];\n  style 8 stroke:#2c3143,stroke-width:4px;\n  9[\"\u2139\ufe0f Input Dataset\\nUniprot_Cancer_Genes.13Feb2019.txt\"];\n  style 9 stroke:#2c3143,stroke-width:4px;\n  10[\"\u2139\ufe0f Input Dataset\\ncgi_genes.txt\"];\n  style 10 stroke:#2c3143,stroke-width:4px;\n  11[\"\u2139\ufe0f Input Dataset\\n01-Feb-2019-GeneSummaries.tsv\"];\n  style 11 stroke:#2c3143,stroke-width:4px;\n  12[\"FastQC\"];\n  0 -->|output| 12;\n  13[\"FastQC\"];\n  1 -->|output| 13;\n  14[\"Trimmomatic\"];\n  0 -->|output| 14;\n  1 -->|output| 14;\n  15[\"FastQC\"];\n  2 -->|output| 15;\n  16[\"FastQC\"];\n  3 -->|output| 16;\n  17[\"Trimmomatic\"];\n  2 -->|output| 17;\n  3 -->|output| 17;\n  18[\"FastQC\"];\n  14 -->|fastq_out_r2_paired| 18;\n  19[\"FastQC\"];\n  14 -->|fastq_out_r1_paired| 19;\n  20[\"Map with BWA-MEM\"];\n  14 -->|fastq_out_r1_paired| 20;\n  14 -->|fastq_out_r2_paired| 20;\n  21[\"MultiQC\"];\n  13 -->|text_file| 21;\n  15 -->|text_file| 21;\n  16 -->|text_file| 21;\n  12 -->|text_file| 21;\n  22[\"FastQC\"];\n  17 -->|fastq_out_r1_paired| 22;\n  23[\"FastQC\"];\n  17 -->|fastq_out_r2_paired| 23;\n  24[\"Map with BWA-MEM\"];\n  17 -->|fastq_out_r1_paired| 24;\n  17 -->|fastq_out_r2_paired| 24;\n  25[\"Filter\"];\n  20 -->|bam_output| 25;\n  26[\"MultiQC\"];\n  19 -->|text_file| 26;\n  22 -->|text_file| 26;\n  23 -->|text_file| 26;\n  18 -->|text_file| 26;\n  27[\"Filter\"];\n  24 -->|bam_output| 27;\n  28[\"RmDup\"];\n  25 -->|out_file1| 28;\n  29[\"RmDup\"];\n  27 -->|out_file1| 29;\n  30[\"BamLeftAlign\"];\n  28 -->|output1| 30;\n  31[\"BamLeftAlign\"];\n  29 -->|output1| 31;\n  32[\"CalMD\"];\n  30 -->|output_bam| 32;\n  33[\"CalMD\"];\n  31 -->|output_bam| 33;\n  34[\"Filter\"];\n  32 -->|calmd_output| 34;\n  35[\"Filter\"];\n  33 -->|calmd_output| 35;\n  36[\"VarScan somatic\"];\n  34 -->|out_file1| 36;\n  35 -->|out_file1| 36;\n  37[\"SnpEff eff:\"];\n  36 -->|output| 37;\n  38[\"GEMINI load\"];\n  37 -->|snpeff_output| 38;\n  39[\"GEMINI annotate\"];\n  36 -->|output| 39;\n  38 -->|outfile| 39;\n  40[\"GEMINI annotate\"];\n  8 -->|output| 40;\n  39 -->|outfile| 40;\n  41[\"GEMINI annotate\"];\n  5 -->|output| 41;\n  40 -->|outfile| 41;\n  42[\"GEMINI annotate\"];\n  7 -->|output| 42;\n  41 -->|outfile| 42;\n  43[\"GEMINI annotate\"];\n  6 -->|output| 43;\n  42 -->|outfile| 43;\n  44[\"GEMINI query\"];\n  43 -->|outfile| 44;\n  45[\"GEMINI query\"];\n  43 -->|outfile| 45;\n  46[\"GEMINI query\"];\n  43 -->|outfile| 46;\n  47[\"GEMINI query\"];\n  43 -->|outfile| 47;\n  48[\"Join\"];\n  47 -->|outfile| 48;\n  9 -->|output| 48;\n  49[\"Join\"];\n  48 -->|output| 49;\n  10 -->|output| 49;\n  50[\"Join\"];\n  49 -->|output| 50;\n  11 -->|output| 50;\n  51[\"Column arrange\"];\n  50 -->|output| 51;\n  d185756d-454a-4ce6-b986-20ad6a65ee03[\"Output\\ngene_report_output\"];\n  51 --> d185756d-454a-4ce6-b986-20ad6a65ee03;\n  style d185756d-454a-4ce6-b986-20ad6a65ee03 stroke:#2c3143,stroke-width:4px;",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Identification of somatic and germline variants from tumor and normal sample pairs tutorial",
                 "outputs": [
                     {
@@ -293401,7 +746004,7 @@
                             {
                                 "label": "gene_report_output",
                                 "output_name": "output",
-                                "uuid": "feb210a2-c095-4ebb-9446-68fccaa0cce7"
+                                "uuid": "d185756d-454a-4ce6-b986-20ad6a65ee03"
                             }
                         ]
                     }
@@ -293669,18 +746272,18 @@
         ],
         "dir": "topics/variant-analysis/tutorials/somatic-variant-discovery",
         "edam_operation": [
-            "Copy number estimation",
-            "Sequence alignment",
-            "Sequence visualisation",
-            "Read mapping",
-            "Sequencing quality control",
-            "Generation",
             "Variant calling",
-            "Statistical calculation",
+            "Genome indexing",
+            "Sequence composition calculation",
+            "Generation",
             "Validation",
+            "Sequencing quality control",
+            "Copy number estimation",
+            "Read mapping",
             "Genome alignment",
-            "Sequence composition calculation",
-            "Genome indexing"
+            "Sequence visualisation",
+            "Sequence alignment",
+            "Statistical calculation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [],
@@ -293709,7 +746312,7 @@
             "Use Control-Freec for hCNV Identefication in tumor tissue.",
             "Visualise the detected hCNVs in specific chromosomes."
         ],
-        "pageviews": 1535,
+        "pageviews": 1550,
         "pub_date": "2022-10-05",
         "questions": [
             "What are the specific challenges in locating human Copy Number Variances (hCNVs)?",
@@ -293719,22 +746322,22 @@
         ],
         "short_id": "T00317",
         "short_tools": [
-            "bwa_mem",
-            "__EXTRACT_DATASET__",
-            "circos",
             "samtools_view",
-            "samtools_rmdup",
             "tp_replace_in_line",
-            "__RELABEL_FROM_FILE__",
             "control_freec",
+            "trimmomatic",
             "multiqc",
+            "__RELABEL_FROM_FILE__",
+            "samtools_calmd",
+            "fastqc",
+            "samtools_rmdup",
+            "bwa_mem",
+            "circos",
             "Grep1",
             "__BUILD_LIST__",
+            "__EXTRACT_DATASET__",
             "bamleftalign",
-            "tp_text_file_with_recurring_lines",
-            "fastqc",
-            "trimmomatic",
-            "samtools_calmd"
+            "tp_text_file_with_recurring_lines"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -293769,6 +746372,3843 @@
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+                                "0.36.6",
+                                "0.38.0",
+                                "0.39+galaxy2",
+                                "0.36.5",
+                                "0.32.3",
+                                "0.36.2",
+                                "0.36.3"
+                            ]
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+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
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+                    ],
+                    "version": "0.39+galaxy0"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "3H",
         "title": "Somatic Variant Discovery from WES Data Using Control-FREEC",
@@ -293818,8 +750258,8 @@
         "video": false,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 119,
-        "visitors": 1167,
+        "visit_duration": 117,
+        "visitors": 1178,
         "workflows": [
             {
                 "creators": [
@@ -294009,7 +750449,7 @@
                 ],
                 "license": "AGPL-3.0-or-later",
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC",
                 "outputs": [
                     {
@@ -294412,8 +750852,8 @@
         ],
         "dir": "topics/variant-analysis/tutorials/trio-analysis",
         "edam_operation": [
-            "Genetic variation analysis",
-            "Sequence analysis"
+            "Sequence analysis",
+            "Genetic variation analysis"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -294445,7 +750885,7 @@
             "Pre-process VCFs using regular expressions.",
             "Use annotations and phenotype information to find the causative variant(s)."
         ],
-        "pageviews": 2787,
+        "pageviews": 2793,
         "pub_date": "2022-05-19",
         "questions": [
             "How do you import data from the EGA?",
@@ -294468,18 +750908,18 @@
         ],
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-            "CONVERTER_uncompressed_to_gz",
-            "Filter1",
-            "gemini_load",
-            "pyega3",
-            "tp_grep_tool",
             "bcftools_merge",
-            "gene_iobio_display_generation_iframe",
+            "bcftools_norm",
             "gemini_inheritance",
+            "gemini_load",
+            "gene_iobio_display_generation_iframe",
             "regexColumn1",
             "CONVERTER_gz_to_uncompressed",
+            "tp_grep_tool",
+            "pyega3",
             "snpEff",
-            "bcftools_norm"
+            "CONVERTER_uncompressed_to_gz",
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -294505,6 +750945,1810 @@
                 }
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "4.3+T.galaxy2"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "exact",
+                            "version": "4.3+T.galaxy1"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "4.3+T.galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "exact",
+                            "version": "4.3+T.galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "4.3+T.galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "4.3+T.galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "4.3+T.galaxy1"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "4.3+T.galaxy1"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "4.3+T.galaxy1"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "cyoa"
@@ -294544,8 +752788,8 @@
         "video": false,
         "video_versions": 1,
         "video_view": 0,
-        "visit_duration": 242,
-        "visitors": 1424,
+        "visit_duration": 241,
+        "visitors": 1430,
         "workflows": [
             {
                 "creators": [
@@ -294750,7 +752994,7 @@
                 ],
                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"EGA Download Client\"];\n  85672f3a-1556-49b6-be09-2e6c81721fb3[\"Output\\nEGA Download Client: authorized datasets\"];\n  0 --> 85672f3a-1556-49b6-be09-2e6c81721fb3;\n  style 85672f3a-1556-49b6-be09-2e6c81721fb3 stroke:#2c3143,stroke-width:4px;\n  1[\"EGA Download Client\"];\n  acd2bcf0-4b9d-4743-9034-716e73d4824f[\"Output\\nList of files in EGAD00001008392\"];\n  1 --> acd2bcf0-4b9d-4743-9034-716e73d4824f;\n  style acd2bcf0-4b9d-4743-9034-716e73d4824f stroke:#2c3143,stroke-width:4px;\n  2[\"\u2139\ufe0f Input Dataset\\npedigree\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"Search in textfiles\"];\n  1 -->|dataset_file_list| 3;\n  6d5d135e-a373-4938-9374-019a09f45a51[\"Output\\nList of Case 5 VCFs\"];\n  3 --> 6d5d135e-a373-4938-9374-019a09f45a51;\n  style 6d5d135e-a373-4938-9374-019a09f45a51 stroke:#2c3143,stroke-width:4px;\n  4[\"EGA Download Client\"];\n  3 -->|output| 4;\n  bdce7169-390b-4adb-9305-5550d5d70a73[\"Output\\nCase 5 VCFs.gz\"];\n  4 --> bdce7169-390b-4adb-9305-5550d5d70a73;\n  style bdce7169-390b-4adb-9305-5550d5d70a73 stroke:#2c3143,stroke-width:4px;\n  5[\"Convert compressed file to uncompressed.\"];\n  4 -->|downloaded_file_collection| 5;\n  82b71cdc-d813-4c77-8ff3-fa59e1725709[\"Output\\nCase 5 VCFs\"];\n  5 --> 82b71cdc-d813-4c77-8ff3-fa59e1725709;\n  style 82b71cdc-d813-4c77-8ff3-fa59e1725709 stroke:#2c3143,stroke-width:4px;\n  6[\"Column Regex Find And Replace\"];\n  5 -->|output1| 6;\n  5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27[\"Output\\nCase 5 VCFs (Fixed Header and Chr)\"];\n  6 --> 5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27;\n  style 5e1ff158-cf8a-4dc8-9c22-b987a9f5ac27 stroke:#2c3143,stroke-width:4px;\n  7[\"bcftools norm\"];\n  6 -->|out_file1| 7;\n  96b34c8d-fa92-48cb-b01f-c05364deba5d[\"Output\\nCase 5 Normalized VCFs\"];\n  7 --> 96b34c8d-fa92-48cb-b01f-c05364deba5d;\n  style 96b34c8d-fa92-48cb-b01f-c05364deba5d stroke:#2c3143,stroke-width:4px;\n  8[\"Filter\"];\n  7 -->|output_file| 8;\n  a8539eb9-8bc3-473b-a27f-201c3acf5539[\"Output\\nCase 5 Normalized VCFs (Removed <NON_REF>)\"];\n  8 --> a8539eb9-8bc3-473b-a27f-201c3acf5539;\n  style a8539eb9-8bc3-473b-a27f-201c3acf5539 stroke:#2c3143,stroke-width:4px;\n  9[\"bcftools merge\"];\n  8 -->|out_file1| 9;\n  b5c479b2-e58a-4fe2-b1cf-fc64476c8192[\"Output\\nCase 5 Merged VCF\"];\n  9 --> b5c479b2-e58a-4fe2-b1cf-fc64476c8192;\n  style b5c479b2-e58a-4fe2-b1cf-fc64476c8192 stroke:#2c3143,stroke-width:4px;\n  10[\"SnpEff eff:\"];\n  9 -->|output_file| 10;\n  cd7b4941-4f4c-4631-8ad5-3411e60fbbd9[\"Output\\nCase 5 SnpEff Annotated vcf\"];\n  10 --> cd7b4941-4f4c-4631-8ad5-3411e60fbbd9;\n  style cd7b4941-4f4c-4631-8ad5-3411e60fbbd9 stroke:#2c3143,stroke-width:4px;\n  11[\"Convert uncompressed file to compressed\"];\n  10 -->|snpeff_output| 11;\n  6e5e1084-b5e1-4daf-8f3b-bd3868a52a25[\"Output\\nSnpEff Annotated vcf_bgzip\"];\n  11 --> 6e5e1084-b5e1-4daf-8f3b-bd3868a52a25;\n  style 6e5e1084-b5e1-4daf-8f3b-bd3868a52a25 stroke:#2c3143,stroke-width:4px;\n  12[\"gene.iobio visualisation\"];\n  11 -->|output1| 12;\n  11 -->|output1| 12;\n  11 -->|output1| 12;\n  0b30f4e0-7328-4479-8a56-bbf828fcfdba[\"Output\\nCase 5 gene.iobio results\"];\n  12 --> 0b30f4e0-7328-4479-8a56-bbf828fcfdba;\n  style 0b30f4e0-7328-4479-8a56-bbf828fcfdba stroke:#2c3143,stroke-width:4px;\n  13[\"Case 5 GEMINI Database\"];\n  11 -->|output1| 13;\n  2 -->|output| 13;\n  8a1964d9-607c-4dd3-a2dc-0f9a68dbb681[\"Output\\nGEMINI Database\"];\n  13 --> 8a1964d9-607c-4dd3-a2dc-0f9a68dbb681;\n  style 8a1964d9-607c-4dd3-a2dc-0f9a68dbb681 stroke:#2c3143,stroke-width:4px;\n  14[\"Case 5 GEMINI Inheritance pattern\"];\n  13 -->|outfile| 14;\n  960ef978-089c-4292-81b5-731965c72a0d[\"Output\\nCase 5 GEMINI results\"];\n  14 --> 960ef978-089c-4292-81b5-731965c72a0d;\n  style 960ef978-089c-4292-81b5-731965c72a0d stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Trio Analysis Tutorial",
                 "outputs": [
                     {
@@ -295670,17 +753914,17 @@
         ],
         "dir": "topics/variant-analysis/tutorials/pox-tiled-amplicon",
         "edam_operation": [
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
             "Sequence alignment analysis",
+            "Genome indexing",
             "Sequence analysis",
-            "Multiple sequence alignment",
-            "Sequence contamination filtering",
             "Generation",
-            "Global alignment",
+            "Multiple sequence alignment",
+            "Sequencing quality control",
             "Local alignment",
-            "Genome indexing"
+            "Read mapping",
+            "Global alignment",
+            "Sequence contamination filtering",
+            "Sequence alignment"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
@@ -295711,7 +753955,7 @@
             "Construct a sample consensus genome from mapped reads",
             "Explore a recombinant pox virus genome via a multiple-sequence alignment of consensus genome and references and through lists of mutations derived from it"
         ],
-        "pageviews": 670,
+        "pageviews": 678,
         "pub_date": "2023-05-15",
         "questions": [
             "Which special challenges does one encounter during sequence data analysis of pox viruses?",
@@ -295730,28 +753974,28 @@
         ],
         "short_id": "T00347",
         "short_tools": [
-            "ivar_trim",
-            "upload1",
-            "compose_text_param",
             "qualimap_bamqc",
-            "param_value_from_file",
-            "__ZIP_COLLECTION__",
-            "mimodd_info",
-            "datamash_ops",
-            "bwa_mem",
-            "ivar_consensus",
             "fatovcf",
-            "EMBOSS: maskseq51",
-            "__APPLY_RULES__",
+            "fasta_regex_finder",
+            "fastp",
             "samtools_view",
             "rbc_mafft",
+            "bwa_mem",
+            "upload1",
+            "datamash_ops",
+            "ivar_trim",
+            "__APPLY_RULES__",
+            "compose_text_param",
+            "EMBOSS: maskseq51",
+            "ivar_consensus",
             "Grep1",
-            "Cut1",
-            "fasta_regex_finder",
             "samtools_merge",
-            "fastp",
             "fasta_compute_length",
-            "Add_a_column1"
+            "Add_a_column1",
+            "Cut1",
+            "mimodd_info",
+            "__ZIP_COLLECTION__",
+            "param_value_from_file"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -295772,6 +754016,3264 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Cut1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Grep1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
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                 "license": "MIT",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nPrimer Scheme\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nReference FASTA\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Select pool1 primers\"];\n  0 -->|output| 2;\n  3[\"Select pool2 primers\"];\n  0 -->|output| 3;\n  4[\"Compute sequence length\"];\n  1 -->|output| 4;\n  5[\"Datamash\"];\n  2 -->|out_file1| 5;\n  6[\"Datamash\"];\n  3 -->|out_file1| 6;\n  7[\"Cut\"];\n  4 -->|output| 7;\n  8[\"Compute\"];\n  5 -->|out_file| 8;\n  9[\"Get start position of Pool2\"];\n  6 -->|out_file| 9;\n  10[\"Get end position of sequence\"];\n  7 -->|out_file1| 10;\n  11[\"Get end position of Pool1\"];\n  8 -->|out_file1| 11;\n  12[\"Compose text parameter value\"];\n  9 -->|text_param| 12;\n  13[\"Compose text parameter value\"];\n  11 -->|text_param| 13;\n  10 -->|text_param| 13;\n  14[\"Mask Reference for Pool2\"];\n  1 -->|output| 14;\n  12 -->|out1| 14;\n  af755a5e-2b20-49bc-9d52-34781f937f48[\"Output\\nmasked_ref_pool2\"];\n  14 --> af755a5e-2b20-49bc-9d52-34781f937f48;\n  style af755a5e-2b20-49bc-9d52-34781f937f48 stroke:#2c3143,stroke-width:4px;\n  15[\"Mask Reference for Pool1\"];\n  1 -->|output| 15;\n  13 -->|out1| 15;\n  0c3b5b20-c426-428c-a08b-c835a82477c1[\"Output\\nmasked_ref_pool1\"];\n  15 --> 0c3b5b20-c426-428c-a08b-c835a82477c1;\n  style 0c3b5b20-c426-428c-a08b-c835a82477c1 stroke:#2c3143,stroke-width:4px;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "pox-virus-tiled-amplicon-ref-masking",
                 "outputs": [
                     {
@@ -296269,23 +757771,22 @@
         ],
         "dir": "topics/variant-analysis/tutorials/exome-seq",
         "edam_operation": [
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
+            "Variant calling",
+            "Genetic variation analysis",
+            "Genome indexing",
             "Sequence analysis",
+            "Sequence composition calculation",
             "Generation",
-            "Statistical calculation",
-            "Variant calling",
             "Validation",
-            "Sequence composition calculation",
-            "Genetic variation analysis",
-            "Genome indexing"
+            "Sequencing quality control",
+            "Read mapping",
+            "Sequence alignment",
+            "Statistical calculation"
         ],
         "edam_topic": [],
         "exact_supported_servers": [
             "UseGalaxy.cz",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
@@ -296313,7 +757814,7 @@
             "Jointly call variants and genotypes for a family trio from whole-exome sequencing data",
             "Use variant annotation and the observed inheritance pattern of a phenotype to identify candidate causative variants and to prioritize them"
         ],
-        "pageviews": 52086,
+        "pageviews": 52179,
         "pub_date": "2016-08-19",
         "questions": [
             "How do you identify genetic variants in samples based on exome sequencing data?",
@@ -296321,18 +757822,18 @@
         ],
         "short_id": "T00311",
         "short_tools": [
-            "bwa_mem",
-            "snpEff",
             "samtools_view",
+            "bcftools_norm",
+            "gemini_inheritance",
             "gemini_load",
-            "samtools_rmdup",
             "snpEff_download",
-            "multiqc",
-            "gemini_inheritance",
-            "fastqc",
             "trimmomatic",
+            "fastqc",
             "freebayes",
-            "bcftools_norm"
+            "samtools_rmdup",
+            "bwa_mem",
+            "multiqc",
+            "snpEff"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -296349,11 +757850,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -296378,6 +757874,1916 @@
                 }
             ]
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         "symlink": null,
         "time_estimation": "5h",
         "title": "Exome sequencing data analysis for diagnosing a genetic disease",
@@ -296415,7 +759821,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 168,
-        "visitors": 26968,
+        "visitors": 27046,
         "workflows": [
             {
                 "creators": [
@@ -296582,7 +759988,7 @@
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Exome Seq Training Pre-Mapped W Cached Ref",
                 "outputs": [
                     {
@@ -296968,7 +760374,7 @@
                 ],
                 "license": "MIT",
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Exome Seq Training Full W Cached Ref",
                 "outputs": [
                     {
@@ -297308,7 +760714,7 @@
             "Perform variant linkage analyses for phenotypically selected recombinant progeny",
             "Filter, annotate and report lists of variants"
         ],
-        "pageviews": 5499,
+        "pageviews": 5505,
         "pub_date": "2018-03-07",
         "questions": [
             "What is mapping-by-sequencing?",
@@ -297316,14 +760722,14 @@
         ],
         "short_id": "T00312",
         "short_tools": [
-            "mimodd_map",
-            "mimodd_varcall",
             "snpEff_download",
-            "tp_find_and_replace",
             "mimodd_varextract",
-            "mimodd_varreport",
+            "mimodd_vcf_filter",
+            "tp_find_and_replace",
+            "mimodd_map",
+            "mimodd_varcall",
             "snpEff",
-            "mimodd_vcf_filter"
+            "mimodd_varreport"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -297369,6 +760775,1342 @@
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             ]
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         "time_estimation": "2h",
         "title": "Mapping and molecular identification of phenotype-causing mutations",
@@ -297402,7 +762144,7 @@
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         "video_view": 0,
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@@ -297504,7 +762246,7 @@
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Mapping And Molecular Identification Of Phenotype Causing Mutations",
                 "outputs": [],
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@@ -297628,10 +762370,10 @@
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         "edam_operation": [
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-            "Genetic variation analysis",
             "Variant calling",
-            "Sequence analysis"
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@@ -297665,20 +762406,20 @@
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             "gemini_query",
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+            "freebayes",
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@@ -297703,19 +762444,1193 @@
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+                            "state": "exact",
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+                            "state": "inexact",
+                            "versions": [
+                                "4.3+T.galaxy2",
+                                "3.4"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "inexact",
+                            "versions": [
+                                "4.3+T.galaxy2",
+                                "4.1.0",
+                                "4.0.0"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "inexact",
+                            "versions": [
+                                "4.3+T.galaxy2",
+                                "4.3+T.galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "inexact",
+                            "versions": [
+                                "4.3+T.galaxy2",
+                                "4.3+T.galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "inexact",
+                            "versions": [
+                                "4.3+T.galaxy2",
+                                "4.3+T.galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "4.3r.1"
                 }
             ]
         },
@@ -297751,7 +763666,7 @@
         "video_versions": 0,
         "video_view": 0,
         "visit_duration": 192,
-        "visitors": 12589,
+        "visitors": 12611,
         "workflows": [
             {
                 "creators": [],
@@ -297854,7 +763769,7 @@
                 ],
                 "license": null,
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nGIAB-Ashkenazim-Trio-hg19.bam\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"SnpEff Download\"];\n  2[\"\u2139\ufe0f Input Dataset\\nGIAB-Ashkenazim-Trio.tabular\"];\n  style 2 stroke:#2c3143,stroke-width:4px;\n  3[\"FreeBayes\"];\n  0 -->|output| 3;\n  4[\"VcfAllelicPrimitives:\"];\n  3 -->|output_vcf| 4;\n  5[\"SnpEff eff:\"];\n  4 -->|out_file1| 5;\n  1 -->|snpeff_db| 5;\n  6[\"GEMINI load\"];\n  5 -->|snpeff_output| 6;\n  2 -->|output| 6;\n  7[\"GEMINI_db_info\"];\n  6 -->|outfile| 7;\n  8[\"GEMINI_query2\"];\n  6 -->|outfile| 8;\n  9[\"GEMINI_query1\"];\n  6 -->|outfile| 9;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Diploid",
                 "outputs": [
                     {
@@ -298166,9 +764081,9 @@
             "topic_0199"
         ],
         "edam_operation": [
-            "Genome visualisation",
             "Variant calling",
             "Phylogenetic tree visualisation",
+            "Genome visualisation",
             "Phylogenetic tree generation"
         ],
         "edam_topic": [
@@ -298191,7 +764106,6 @@
         "inexact_supported_servers": [
             "GalaxyTrakr",
             "UseGalaxy.cz",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org.au"
         ],
@@ -298213,7 +764127,7 @@
             "Determine the effect of those variants on genomic features",
             "Understand if the SNP is potentially affecting the phenotype"
         ],
-        "pageviews": 20693,
+        "pageviews": 20722,
         "pub_date": "2018-02-26",
         "questions": [
             "How do we detect differences between a set of reads from a microorganism and a reference genome"
@@ -298256,19 +764170,459 @@
                     "usegalaxy": false
                 },
                 {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                }
+            ]
+        },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
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@@ -298305,7 +764659,7 @@
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@@ -298575,12 +764929,12 @@
                             {
                                 "label": "snippy_fasta",
                                 "output_name": "snpconsensus",
-                                "uuid": "419ad933-d100-406b-bd61-a70885eec0f8"
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                                 "output_name": "snpsum",
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@@ -298636,7 +764990,7 @@
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@@ -298802,10 +765156,10 @@
         ],
         "dir": "topics/variant-analysis/tutorials/sars-cov-2-variant-discovery",
         "edam_operation": [
-            "Tree-based sequence alignment",
             "Variant calling",
+            "Methylation analysis",
             "Variant classification",
-            "Methylation analysis"
+            "Tree-based sequence alignment"
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@@ -298840,7 +765194,7 @@
             "Know different SARS-CoV-2 lineage classification systems, and use pangolin and Nextclade to assign samples to predefined lineages",
             "Combine information from different analysis steps to be able to draw appropriate conclusions about individual samples and batches of viral data"
         ],
-        "pageviews": 12061,
+        "pageviews": 12082,
         "pub_date": "2021-06-30",
         "questions": [
             "How can a complete analysis, including viral consensus sequence reconstruction and lineage assignment be performed?",
@@ -298904,11 +765258,11 @@
         "short_id": "T00316",
         "short_tools": [
             "pangolin",
-            "Filter1",
+            "nextclade",
             "upload1",
+            "datamash_ops",
             "fasta_regex_finder",
-            "nextclade",
-            "datamash_ops"
+            "Filter1"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -298934,6 +765288,987 @@
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             ]
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+                },
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+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
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+                    "name": "ChemFlow",
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+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
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+                },
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+                    "url": "http://dintor.eurac.edu/"
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+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
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+                    "url": "https://galaxy.mesocentre.uca.fr",
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+                            "state": "local"
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+                    "version": "local"
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         "tags": [
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@@ -298970,7 +766305,7 @@
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         "video_view": 0,
         "visit_duration": 208,
-        "visitors": 6502
+        "visitors": 6513
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@@ -298981,42 +766316,42 @@
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                     "owner": "bgruening",
-                    "revisions": "d698c222f354",
+                    "revisions": "86755160afbf",
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                 },
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                     "owner": "devteam",
-                    "revisions": "e188dc7a68e6",
+                    "revisions": "2477830927ec",
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                 },
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                     "owner": "iuc",
-                    "revisions": "9b520009db81",
+                    "revisions": "9b8feb118f9e",
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                 },
                 {
                     "name": "fastp",
                     "owner": "iuc",
-                    "revisions": "65b93b623c77",
+                    "revisions": "d60c3f704da0",
                     "tool_panel_section_label": "FASTA/FASTQ",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
                     "name": "iqtree",
                     "owner": "iuc",
-                    "revisions": "24d024316465",
+                    "revisions": "0878b7fd5260",
                     "tool_panel_section_label": "Evolution",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
                 },
                 {
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                     "owner": "iuc",
-                    "revisions": "40737febe339",
+                    "revisions": "3a72fede57ce",
                     "tool_panel_section_label": "Virology",
                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
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@@ -299030,14 +766365,14 @@
                 {
                     "name": "samtools_view",
                     "owner": "iuc",
-                    "revisions": "5826298f6a73",
+                    "revisions": "32dc5f781059",
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                 },
                 {
                     "name": "seqtk",
                     "owner": "iuc",
-                    "revisions": "3da72230c066",
+                    "revisions": "4b494533146a",
                     "tool_panel_section_label": "FASTA/FASTQ",
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@@ -299058,13 +766393,13 @@
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                     "owner": "rnateam",
-                    "revisions": "bf28a8cff401",
+                    "revisions": "8e649f27aa0d",
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                     "tool_shed_url": "https://toolshed.g2.bx.psu.edu/"
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@@ -299087,20 +766422,20 @@
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         "dir": "topics/variant-analysis/tutorials/aiv-analysis",
         "edam_operation": [
+            "Sequence file editing",
             "Data handling",
-            "Sequence alignment",
-            "Read mapping",
-            "Sequencing quality control",
-            "De-novo assembly",
             "Sequence alignment analysis",
-            "Phylogenetic analysis",
-            "Sequence contamination filtering",
+            "Genome indexing",
+            "De-novo assembly",
+            "Data retrieval",
             "Sequence analysis",
-            "Multiple sequence alignment",
             "Generation",
-            "Sequence file editing",
-            "Data retrieval",
-            "Genome indexing"
+            "Multiple sequence alignment",
+            "Sequencing quality control",
+            "Read mapping",
+            "Phylogenetic analysis",
+            "Sequence contamination filtering",
+            "Sequence alignment"
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         "edam_topic": [],
         "exact_supported_servers": [
@@ -299114,6 +766449,16 @@
         "inexact_supported_servers": [
             "UseGalaxy.cz"
         ],
+        "input_histories": [
+            {
+                "history": "https://usegalaxy.eu/published/history?id=0fc6b637aadbc8a2",
+                "label": "UseGalaxy.eu"
+            },
+            {
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+                "label": "UseGalaxy.org"
+            }
+        ],
         "js_requirements": {
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@@ -299127,14 +766472,14 @@
         "layout": "tutorial_hands_on",
         "level": "Intermediate",
         "license": "CC-BY-4.0",
-        "mod_date": "2024-03-20",
+        "mod_date": "2024-10-04",
         "objectives": [
             "Determine how reassortment impacts reference-based mapping approaches",
             "Use a collection of per-segment reference sequences to construct a hybrid reference genome that is sufficiently close to a sequenced sample to be useful as a reference for mapping",
             "Construct a sample consensus genome from mapped reads",
             "Generate per-segment phylogenetic trees of AIV consensus sequences"
         ],
-        "pageviews": 1887,
+        "pageviews": 1903,
         "pub_date": "2022-11-21",
         "questions": [
             "With reassortment of gene segments being a common event in avian influenza virus (AIV) evolution, does it make sense to use a reference-based mapping approach for constructing consensus genome sequences for AIV samples?",
@@ -299143,22 +766488,22 @@
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         "short_id": "T00308",
         "short_tools": [
-            "bwa_mem",
-            "fastp",
+            "qualimap_bamqc",
             "samtools_view",
-            "vapor",
-            "upload1",
-            "Show beginning1",
+            "collapse_dataset",
+            "rbc_mafft",
+            "seqtk_subseq",
             "__RELABEL_FROM_FILE__",
+            "iqtree",
+            "Show beginning1",
             "tp_find_and_replace",
             "ivar_consensus",
-            "qualimap_bamqc",
-            "seqtk_subseq",
+            "bwa_mem",
             "Grep1",
+            "upload1",
+            "fastp",
             "bamtools_split_ref",
-            "iqtree",
-            "rbc_mafft",
-            "collapse_dataset"
+            "vapor"
         ],
         "slides": false,
         "slides_recordings": false,
@@ -299184,6 +766529,2511 @@
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             ]
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+                    "url": "http://apostl.moffitt.org/"
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+                    "url": "http://smile.hku.hk/SARGs"
+                },
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+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
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+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
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+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
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+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
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+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
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+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
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+                    "url": "http://galaxy.inf.ethz.ch"
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+                    "url": "https://viralvariant.anses.fr/"
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         "time_estimation": "2H",
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@@ -299715,7 +770649,7 @@
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@@ -299753,24 +770687,155 @@
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+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
                 {
                     "name": "MISSISSIPPI",
                     "url": "https://mississippi.sorbonne-universite.fr",
                     "usegalaxy": false
                 },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
                 {
                     "name": "UseGalaxy.be",
                     "url": "https://usegalaxy.be/",
                     "usegalaxy": false
                 },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -299785,6 +770850,1272 @@
                     "name": "UseGalaxy.org.au",
                     "url": "https://usegalaxy.org.au",
                     "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
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+                    "id": "Cut1",
+                    "servers": [
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+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
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+                            "state": "local"
+                        },
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+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
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+                        },
+                        {
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+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
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@@ -299820,8 +772151,8 @@
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@@ -300014,7 +772345,7 @@
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-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:46 +0000",
                 "name": "Circos for E. Coli",
                 "outputs": [
                     {
@@ -300244,7 +772575,6 @@
             "Galaxy@Pasteur",
             "MISSISSIPPI",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.org (Main)"
         ],
         "feedback_mean_note": null,
@@ -300272,7 +772602,7 @@
             "Create a number of Circos plots using the Galaxy tool",
             "Familiarise yourself with the various different track types"
         ],
-        "pageviews": 5939927,
+        "pageviews": 5972066,
         "pub_date": "2020-01-10",
         "questions": [
             "What can the Circos Galaxy tool be used for?",
@@ -300297,11 +772627,11 @@
         ],
         "short_id": "T00321",
         "short_tools": [
-            "circos",
-            "upload1",
+            "Cut1",
             "random_lines1",
+            "circos",
             "Grep1",
-            "Cut1",
+            "upload1",
             "Remove beginning1"
         ],
         "slides": true,
@@ -300337,11 +772667,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.org (Main)",
                     "url": "https://usegalaxy.org",
@@ -300366,6 +772691,953 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
+                    "name": "HyPhy HIV NGS Tools",
+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "Cut1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Grep1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "Remove beginning1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "random_lines1",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                },
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy12",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "exact",
+                            "version": "0.69.8+galaxy12"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
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+                            "server": "http://galaxy.inf.ethz.ch",
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+                        {
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+                        {
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+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
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+                                "0.69.8+galaxy7",
+                                "0.69.8+galaxy9",
+                                "0.69.8+galaxy10",
+                                "0.69.8+galaxy8"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "0.69.8+galaxy12"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "0.69.8+galaxy12"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
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+                    "version": "0.69.8+galaxy12"
+                },
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+                    "servers": [
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+                            "server": "http://apostl.moffitt.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "local"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "local"
+                        }
+                    ],
+                    "version": "local"
+                }
+            ]
+        },
         "symlink": null,
         "time_estimation": "2h",
         "title": "Visualisation with Circos",
@@ -300397,7 +773669,7 @@
         "video_versions": 1,
         "video_view": 0,
         "visit_duration": 256,
-        "visitors": 2159100,
+        "visitors": 2170120,
         "workflows": [
             {
                 "creators": [
@@ -300522,7 +773794,7 @@
                 ],
                 "license": "AGPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"Remove beginning\"];\n  2[\"Remove beginning\"];\n  3[\"Select\"];\n  4[\"Circos\"];\n  5[\"Cut\"];\n  1 -->|out_file1| 5;\n  6[\"Select random lines\"];\n  2 -->|out_file1| 6;\n  7[\"Cut\"];\n  3 -->|out_file1| 7;\n  8[\"Select random lines\"];\n  5 -->|out_file1| 8;\n  9[\"Circos\"];\n  0 -->|output| 9;\n  7 -->|out_file1| 9;\n  10[\"Circos\"];\n  0 -->|output| 10;\n  7 -->|out_file1| 10;\n  11[\"Circos\"];\n  0 -->|output| 11;\n  7 -->|out_file1| 11;\n  8 -->|out_file1| 11;\n  12[\"Circos\"];\n  0 -->|output| 12;\n  7 -->|out_file1| 12;\n  8 -->|out_file1| 12;\n  13[\"Circos\"];\n  0 -->|output| 13;\n  7 -->|out_file1| 13;\n  8 -->|out_file1| 13;\n  14[\"Circos\"];\n  0 -->|output| 14;\n  7 -->|out_file1| 14;\n  8 -->|out_file1| 14;\n  15[\"Circos\"];\n  0 -->|output| 15;\n  7 -->|out_file1| 15;\n  8 -->|out_file1| 15;\n  6 -->|out_file1| 15;\n  16[\"Circos\"];\n  0 -->|output| 16;\n  7 -->|out_file1| 16;\n  8 -->|out_file1| 16;\n  6 -->|out_file1| 16;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:47 +0000",
                 "name": "Circos tutorial",
                 "outputs": [],
                 "parent_id": "visualisation/circos",
@@ -300665,7 +773937,7 @@
                 ],
                 "license": "AGPL-3.0-or-later",
                 "mermaid": "flowchart TD\n  0[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 0 stroke:#2c3143,stroke-width:4px;\n  1[\"\u2139\ufe0f Input Dataset\\nInput dataset\"];\n  style 1 stroke:#2c3143,stroke-width:4px;\n  2[\"Circos\"];\n  0 -->|output| 2;\n  1 -->|output| 2;\n  1 -->|output| 2;\n  1 -->|output| 2;\n  3[\"Circos\"];\n  0 -->|output| 3;\n  1 -->|output| 3;\n  1 -->|output| 3;\n  1 -->|output| 3;",
-                "modified": "2024-10-02 12:08:11 +0000",
+                "modified": "2024-10-08 10:05:47 +0000",
                 "name": "Circos: Nature workflow",
                 "outputs": [],
                 "parent_id": "visualisation/circos",
@@ -300771,7 +774043,7 @@
         "license": "MIT",
         "logo": "GTN",
         "mod_date": "2023-11-20",
-        "pageviews": 1179269,
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         "short_id": "S00112",
         "short_tools": [],
@@ -300810,6 +774082,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [],
+            "tools": []
+        },
         "symlink": null,
         "title": "Friends Don't Let Friends Make Bad Graphs",
         "tools": [],
@@ -300832,8 +774108,8 @@
         "video": true,
         "video_versions": 0,
         "video_view": 0,
-        "visit_duration": 149,
-        "visitors": 494809,
+        "visit_duration": 151,
+        "visitors": 505382,
         "voice": {
             "id": "Brian",
             "lang": "en-GB",
@@ -300953,7 +774229,6 @@
             "Galaxy@AuBi",
             "UseGalaxy.be",
             "UseGalaxy.eu",
-            "UseGalaxy.fr",
             "UseGalaxy.no",
             "UseGalaxy.org (Main)",
             "UseGalaxy.org.au"
@@ -300985,7 +774260,7 @@
             "Build several visualisations in JBrowse",
             "Have basic familiarity with moving around JBrowse, and loading several data tracks"
         ],
-        "pageviews": 5902923,
+        "pageviews": 5934951,
         "pub_date": "2020-01-10",
         "questions": [
             "How can I visualise features or blast data?",
@@ -301014,11 +774289,6 @@
                     "url": "https://usegalaxy.eu",
                     "usegalaxy": true
                 },
-                {
-                    "name": "UseGalaxy.fr",
-                    "url": "https://usegalaxy.fr/",
-                    "usegalaxy": false
-                },
                 {
                     "name": "UseGalaxy.no",
                     "url": "https://usegalaxy.no/",
@@ -301058,6 +774328,297 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
+            "servers": [
+                {
+                    "name": "APOSTL",
+                    "url": "http://apostl.moffitt.org/"
+                },
+                {
+                    "name": "ARGs-OAP",
+                    "url": "http://smile.hku.hk/SARGs"
+                },
+                {
+                    "name": "CIRM-CFBP",
+                    "url": "https://iris.angers.inra.fr/galaxypub-cfbp"
+                },
+                {
+                    "name": "ChemFlow",
+                    "url": "https://vm-chemflow-francegrille.eu/"
+                },
+                {
+                    "name": "Coloc-stats",
+                    "url": "https://hyperbrowser.uio.no/coloc-stats"
+                },
+                {
+                    "name": "CoralSNP",
+                    "url": "https://coralsnp.science.psu.edu/galaxy/"
+                },
+                {
+                    "name": "CropGalaxy",
+                    "url": "http://cropgalaxy.excellenceinbreeding.org/"
+                },
+                {
+                    "name": "Dintor",
+                    "url": "http://dintor.eurac.edu/"
+                },
+                {
+                    "name": "GASLINI",
+                    "url": "http://igg.cloud.ba.infn.it/galaxy"
+                },
+                {
+                    "name": "Galaxy@AuBi",
+                    "url": "https://galaxy.mesocentre.uca.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Galaxy@Pasteur",
+                    "url": "https://galaxy.pasteur.fr/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "GalaxyTrakr",
+                    "url": "https://galaxytrakr.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Genomic Hyperbrowser",
+                    "url": "http://hyperbrowser.uio.no/hb/"
+                },
+                {
+                    "name": "GigaGalaxy",
+                    "url": "http://gigagalaxy.net/"
+                },
+                {
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+                    "url": "https://galaxy.hyphy.org/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "IPK Galaxy Blast Suite",
+                    "url": "https://galaxy-web.ipk-gatersleben.de"
+                },
+                {
+                    "name": "ImmPort Galaxy",
+                    "url": "https://www.immportgalaxy.org/"
+                },
+                {
+                    "name": "InteractoMIX",
+                    "url": "http://galaxy.interactomix.com/"
+                },
+                {
+                    "name": "MISSISSIPPI",
+                    "url": "https://mississippi.sorbonne-universite.fr",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "Mandoiu Lab",
+                    "url": "https://neo.engr.uconn.edu/"
+                },
+                {
+                    "name": "MiModD NacreousMap",
+                    "url": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/"
+                },
+                {
+                    "name": "Oqtans",
+                    "url": "http://galaxy.inf.ethz.ch"
+                },
+                {
+                    "name": "Palfinder",
+                    "url": "https://palfinder.ls.manchester.ac.uk/"
+                },
+                {
+                    "name": "PepSimili",
+                    "url": "http://pepsimili.e-nios.com:8080/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.be",
+                    "url": "https://usegalaxy.be/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.cz",
+                    "url": "https://usegalaxy.cz/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.eu",
+                    "url": "https://usegalaxy.eu",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.no",
+                    "url": "https://usegalaxy.no/",
+                    "usegalaxy": false
+                },
+                {
+                    "name": "UseGalaxy.org (Main)",
+                    "url": "https://usegalaxy.org",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "UseGalaxy.org.au",
+                    "url": "https://usegalaxy.org.au",
+                    "usegalaxy": true
+                },
+                {
+                    "name": "Viral Variant Visualizer (VVV)",
+                    "url": "https://viralvariant.anses.fr/"
+                }
+            ],
+            "tools": [
+                {
+                    "id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0",
+                    "servers": [
+                        {
+                            "server": "http://apostl.moffitt.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://smile.hku.hk/SARGs",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://iris.angers.inra.fr/galaxypub-cfbp",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://vm-chemflow-francegrille.eu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://hyperbrowser.uio.no/coloc-stats",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://coralsnp.science.psu.edu/galaxy/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://cropgalaxy.excellenceinbreeding.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://dintor.eurac.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://igg.cloud.ba.infn.it/galaxy",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.mesocentre.uca.fr",
+                            "state": "exact",
+                            "version": "1.16.9+galaxy0"
+                        },
+                        {
+                            "server": "https://galaxy.pasteur.fr/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.16.11+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://galaxytrakr.org/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.16.11+galaxy1",
+                                "1.16.10+galaxy0"
+                            ]
+                        },
+                        {
+                            "server": "http://hyperbrowser.uio.no/hb/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://gigagalaxy.net/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy.hyphy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://galaxy-web.ipk-gatersleben.de",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://www.immportgalaxy.org/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.interactomix.com/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://mississippi.sorbonne-universite.fr",
+                            "state": "inexact",
+                            "versions": [
+                                "1.16.11+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://neo.engr.uconn.edu/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://mapping-by-sequencing.vm.uni-freiburg.de:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://galaxy.inf.ethz.ch",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://palfinder.ls.manchester.ac.uk/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "http://pepsimili.e-nios.com:8080/",
+                            "state": "missing"
+                        },
+                        {
+                            "server": "https://usegalaxy.be/",
+                            "state": "exact",
+                            "version": "1.16.9+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.cz/",
+                            "state": "inexact",
+                            "versions": [
+                                "1.16.11+galaxy1"
+                            ]
+                        },
+                        {
+                            "server": "https://usegalaxy.eu",
+                            "state": "exact",
+                            "version": "1.16.9+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.no/",
+                            "state": "exact",
+                            "version": "1.16.9+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org",
+                            "state": "exact",
+                            "version": "1.16.9+galaxy0"
+                        },
+                        {
+                            "server": "https://usegalaxy.org.au",
+                            "state": "exact",
+                            "version": "1.16.9+galaxy0"
+                        },
+                        {
+                            "server": "https://viralvariant.anses.fr/",
+                            "state": "missing"
+                        }
+                    ],
+                    "version": "1.16.9+galaxy0"
+                }
+            ]
+        },
         "symlink": null,
         "tags": [
             "gmod",
@@ -301088,7 +774649,7 @@
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         "video_view": 0,
         "visit_duration": 287,
-        "visitors": 2137540,
+        "visitors": 2148473,
         "zenodo_link": "https://doi.org/10.5281/zenodo.3591856"
     },
     {
@@ -301187,7 +774748,7 @@
         "license": "CC-BY-4.0",
         "logo": "GTN",
         "mod_date": "2023-01-12",
-        "pageviews": 5897571,
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         "priority": 1,
         "pub_date": "2020-01-10",
         "redirect_from": [
@@ -301232,6 +774793,10 @@
                 }
             ]
         },
+        "supported_servers_matrix": {
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+            "tools": []
+        },
         "symlink": null,
         "title": "Visualisations in Galaxy",
         "tools": [],
@@ -301255,6 +774820,6 @@
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-        "visitors": 2133613
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 ]
\ No newline at end of file
diff --git a/communities/assembly/resources/tools.html b/communities/assembly/resources/tools.html
index 0953ee76..10449d8c 100644
--- a/communities/assembly/resources/tools.html
+++ b/communities/assembly/resources/tools.html
@@ -95,7 +95,6 @@
       <th>Tools available on CoralSNP</th>
       <th>Tools available on CropGalaxy</th>
       <th>Tools available on Dintor</th>
-      <th>Tools available on FreeBioinfo</th>
       <th>Tools available on GASLINI</th>
       <th>Tools available on Galaxy@AuBi</th>
       <th>Tools available on Galaxy@Pasteur</th>
@@ -112,12 +111,27 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
+      <th>Tools available on PhagePromotor</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
       <th>Tools available on Viral Variant Visualizer (VVV)</th>
-      <th>No. of tool users (2022-2023) (usegalaxy.eu)</th>
-      <th>Total tool usage (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.eu)</th>
+      <th>No. of tool users (all time) (usegalaxy.eu)</th>
+      <th>Tool usage (5 years) (usegalaxy.eu)</th>
+      <th>Tool usage (all time) (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org)</th>
+      <th>No. of tool users (all time) (usegalaxy.org)</th>
+      <th>Tool usage (5 years) (usegalaxy.org)</th>
+      <th>Tool usage (all time) (usegalaxy.org)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org.au)</th>
+      <th>No. of tool users (all time) (usegalaxy.org.au)</th>
+      <th>Tool usage (5 years) (usegalaxy.org.au)</th>
+      <th>Tool usage (all time) (usegalaxy.org.au)</th>
+      <th>No. of tool users (5 years) - all main servers</th>
+      <th>No. of tool users (all time) - all main servers</th>
+      <th>Tool usage (5 years) - all main servers</th>
+      <th>Tool usage (all time) - all main servers</th>
       <th>Deprecated</th>
     </tr>
   </thead>
@@ -183,8 +197,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
-      <td>42</td>
+      <td>43</td>
+      <td>43</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>20</td>
+      <td>20</td>
       <td></td>
     </tr>
     <tr>
@@ -214,11 +242,10 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -250,6 +277,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -279,9 +321,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -309,12 +350,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>391</td>
-      <td>4278</td>
+      <td>5543</td>
+      <td>5543</td>
+      <td>1042</td>
+      <td>1042</td>
+      <td>1301</td>
+      <td>1305</td>
+      <td>413</td>
+      <td>414</td>
+      <td>2030</td>
+      <td>2030</td>
+      <td>299</td>
+      <td>299</td>
+      <td>8874</td>
+      <td>8878</td>
+      <td>1754</td>
+      <td>1755</td>
       <td></td>
     </tr>
     <tr>
@@ -378,8 +434,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>37</td>
-      <td>217</td>
+      <td>348</td>
+      <td>348</td>
+      <td>62</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>348</td>
+      <td>348</td>
+      <td>62</td>
+      <td>62</td>
       <td></td>
     </tr>
     <tr>
@@ -409,11 +479,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -443,8 +513,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>42</td>
-      <td>481</td>
+      <td>1436</td>
+      <td>1436</td>
+      <td>244</td>
+      <td>244</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>119</td>
+      <td>10</td>
+      <td>10</td>
+      <td>1555</td>
+      <td>1555</td>
+      <td>254</td>
+      <td>254</td>
       <td></td>
     </tr>
     <tr>
@@ -508,8 +592,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>11</td>
-      <td>329</td>
+      <td>511</td>
+      <td>541</td>
+      <td>32</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>511</td>
+      <td>541</td>
+      <td>32</td>
+      <td>35</td>
       <td></td>
     </tr>
     <tr>
@@ -539,11 +637,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -620,7 +732,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -640,6 +751,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -703,8 +829,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>26</td>
-      <td>257</td>
+      <td>232</td>
+      <td>279</td>
+      <td>62</td>
+      <td>72</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>232</td>
+      <td>279</td>
+      <td>62</td>
+      <td>72</td>
       <td></td>
     </tr>
     <tr>
@@ -770,6 +910,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -835,6 +989,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -900,6 +1068,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>617</td>
+      <td>617</td>
+      <td>63</td>
+      <td>63</td>
+      <td>617</td>
+      <td>617</td>
+      <td>63</td>
+      <td>63</td>
       <td></td>
     </tr>
     <tr>
@@ -963,8 +1145,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>112</td>
-      <td>531</td>
+      <td>547</td>
+      <td>547</td>
+      <td>151</td>
+      <td>151</td>
+      <td>143</td>
+      <td>143</td>
+      <td>43</td>
+      <td>43</td>
+      <td>596</td>
+      <td>596</td>
+      <td>22</td>
+      <td>22</td>
+      <td>1286</td>
+      <td>1286</td>
+      <td>216</td>
+      <td>216</td>
       <td></td>
     </tr>
     <tr>
@@ -1028,8 +1224,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1</td>
       <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>3</td>
+      <td>3</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -1075,7 +1285,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1090,11 +1299,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>121</td>
-      <td>22499</td>
+      <td>24916</td>
+      <td>27120</td>
+      <td>283</td>
+      <td>347</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24916</td>
+      <td>27120</td>
+      <td>283</td>
+      <td>347</td>
       <td></td>
     </tr>
     <tr>
@@ -1139,7 +1363,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1160,6 +1383,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -1205,7 +1443,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1225,6 +1462,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1269,7 +1521,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1290,6 +1541,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -1335,7 +1601,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1355,6 +1620,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1418,8 +1698,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>21</td>
-      <td>685</td>
+      <td>1527</td>
+      <td>1527</td>
+      <td>79</td>
+      <td>79</td>
+      <td>6</td>
+      <td>6</td>
+      <td>1</td>
+      <td>1</td>
+      <td>317</td>
+      <td>317</td>
+      <td>26</td>
+      <td>26</td>
+      <td>1850</td>
+      <td>1850</td>
+      <td>106</td>
+      <td>106</td>
       <td></td>
     </tr>
     <tr>
@@ -1464,7 +1758,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1480,11 +1773,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>101</td>
-      <td>7766</td>
+      <td>9869</td>
+      <td>9869</td>
+      <td>158</td>
+      <td>158</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6886</td>
+      <td>6886</td>
+      <td>146</td>
+      <td>146</td>
+      <td>16755</td>
+      <td>16755</td>
+      <td>304</td>
+      <td>304</td>
       <td></td>
     </tr>
     <tr>
@@ -1514,10 +1822,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1545,11 +1852,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>280</td>
-      <td>4474</td>
+      <td>10414</td>
+      <td>10414</td>
+      <td>510</td>
+      <td>510</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>10418</td>
+      <td>10418</td>
+      <td>512</td>
+      <td>512</td>
       <td></td>
     </tr>
     <tr>
@@ -1594,7 +1916,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1615,6 +1936,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1678,8 +2014,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>16</td>
-      <td>269</td>
+      <td>524</td>
+      <td>524</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>524</td>
+      <td>524</td>
+      <td>32</td>
+      <td>32</td>
       <td></td>
     </tr>
     <tr>
@@ -1745,6 +2095,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1810,6 +2174,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1875,6 +2253,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1920,7 +2312,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1940,6 +2331,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1985,7 +2391,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2005,6 +2410,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2034,8 +2454,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2067,9 +2486,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>5090</td>
-      <td>232004</td>
+      <td>259754</td>
+      <td>272370</td>
+      <td>11716</td>
+      <td>12601</td>
+      <td>334550</td>
+      <td>362356</td>
+      <td>18618</td>
+      <td>20162</td>
+      <td>64377</td>
+      <td>65986</td>
+      <td>3507</td>
+      <td>3627</td>
+      <td>658681</td>
+      <td>700712</td>
+      <td>33841</td>
+      <td>36390</td>
       <td></td>
     </tr>
     <tr>
@@ -2115,7 +2549,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2129,12 +2562,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>42</td>
-      <td>369</td>
+      <td>358</td>
+      <td>406</td>
+      <td>124</td>
+      <td>139</td>
+      <td>1361</td>
+      <td>1361</td>
+      <td>384</td>
+      <td>384</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1719</td>
+      <td>1767</td>
+      <td>508</td>
+      <td>523</td>
       <td></td>
     </tr>
     <tr>
@@ -2198,8 +2646,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>28</td>
+      <td>28</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>28</td>
+      <td>28</td>
+      <td>2</td>
+      <td>2</td>
       <td></td>
     </tr>
     <tr>
@@ -2229,8 +2691,7 @@
       <td>107</td>
       <td>107</td>
       <td>107</td>
-      <td>107</td>
-      <td>107</td>
+      <td>0</td>
       <td>107</td>
       <td>107</td>
       <td>107</td>
@@ -2259,12 +2720,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>107</td>
       <td>107</td>
       <td>107</td>
       <td>0</td>
-      <td>1816</td>
-      <td>89530</td>
+      <td>143762</td>
+      <td>148864</td>
+      <td>4481</td>
+      <td>5039</td>
+      <td>151989</td>
+      <td>296028</td>
+      <td>13224</td>
+      <td>31140</td>
+      <td>24955</td>
+      <td>27001</td>
+      <td>2397</td>
+      <td>2705</td>
+      <td>320706</td>
+      <td>471893</td>
+      <td>20102</td>
+      <td>38884</td>
       <td></td>
     </tr>
     <tr>
@@ -2294,8 +2770,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2324,12 +2799,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>242</td>
-      <td>2644</td>
+      <td>3278</td>
+      <td>3361</td>
+      <td>460</td>
+      <td>478</td>
+      <td>6144</td>
+      <td>6144</td>
+      <td>595</td>
+      <td>595</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>183</td>
+      <td>183</td>
+      <td>10561</td>
+      <td>10644</td>
+      <td>1238</td>
+      <td>1256</td>
       <td></td>
     </tr>
     <tr>
@@ -2375,7 +2865,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2395,6 +2884,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5191</td>
+      <td>5367</td>
+      <td>104</td>
+      <td>130</td>
+      <td>5191</td>
+      <td>5367</td>
+      <td>104</td>
+      <td>130</td>
       <td></td>
     </tr>
     <tr>
@@ -2410,13 +2914,13 @@
       <td></td>
       <td></td>
       <td>To update</td>
-      <td></td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length</td>
       <td>Fasta Manipulation</td>
       <td>fasta_compute_length</td>
       <td>devteam</td>
       <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length</td>
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length</td>
-      <td>1.0.3</td>
+      <td>1.0.4</td>
       <td>python</td>
       <td></td>
       <td></td>
@@ -2424,8 +2928,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2454,12 +2957,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>380</td>
-      <td>7758</td>
+      <td>8547</td>
+      <td>9136</td>
+      <td>978</td>
+      <td>1129</td>
+      <td>17748</td>
+      <td>51150</td>
+      <td>1404</td>
+      <td>5670</td>
+      <td>4239</td>
+      <td>4404</td>
+      <td>162</td>
+      <td>190</td>
+      <td>30534</td>
+      <td>64690</td>
+      <td>2544</td>
+      <td>6989</td>
       <td></td>
     </tr>
     <tr>
@@ -2489,8 +3007,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2519,12 +3036,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>88</td>
-      <td>35793</td>
+      <td>39695</td>
+      <td>39742</td>
+      <td>242</td>
+      <td>255</td>
+      <td>13660</td>
+      <td>19007</td>
+      <td>600</td>
+      <td>1398</td>
+      <td>1521</td>
+      <td>1603</td>
+      <td>92</td>
+      <td>112</td>
+      <td>54876</td>
+      <td>60352</td>
+      <td>934</td>
+      <td>1765</td>
       <td></td>
     </tr>
     <tr>
@@ -2548,7 +3080,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id</td>
       <td>0.0.7</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -2590,6 +3122,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2619,8 +3165,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2649,12 +3194,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>350</td>
-      <td>48649</td>
+      <td>47494</td>
+      <td>51924</td>
+      <td>889</td>
+      <td>997</td>
+      <td>50663</td>
+      <td>101663</td>
+      <td>1488</td>
+      <td>3742</td>
+      <td>3919</td>
+      <td>5601</td>
+      <td>241</td>
+      <td>276</td>
+      <td>102076</td>
+      <td>159188</td>
+      <td>2618</td>
+      <td>5015</td>
       <td></td>
     </tr>
     <tr>
@@ -2684,8 +3244,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2714,12 +3273,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>68</td>
-      <td>2912</td>
+      <td>5235</td>
+      <td>5486</td>
+      <td>237</td>
+      <td>288</td>
+      <td>4060</td>
+      <td>25609</td>
+      <td>480</td>
+      <td>2039</td>
+      <td>816</td>
+      <td>1093</td>
+      <td>73</td>
+      <td>89</td>
+      <td>10111</td>
+      <td>32188</td>
+      <td>790</td>
+      <td>2416</td>
       <td></td>
     </tr>
     <tr>
@@ -2749,8 +3323,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2779,12 +3352,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>461</td>
-      <td>29886</td>
+      <td>30917</td>
+      <td>32191</td>
+      <td>1142</td>
+      <td>1257</td>
+      <td>36869</td>
+      <td>36869</td>
+      <td>1346</td>
+      <td>1346</td>
+      <td>5236</td>
+      <td>5236</td>
+      <td>230</td>
+      <td>230</td>
+      <td>73022</td>
+      <td>74296</td>
+      <td>2718</td>
+      <td>2833</td>
       <td></td>
     </tr>
     <tr>
@@ -2814,8 +3402,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2844,12 +3431,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>29</td>
-      <td>774</td>
+      <td>497</td>
+      <td>808</td>
+      <td>71</td>
+      <td>108</td>
+      <td>2249</td>
+      <td>5479</td>
+      <td>216</td>
+      <td>703</td>
+      <td>415</td>
+      <td>437</td>
+      <td>18</td>
+      <td>20</td>
+      <td>3161</td>
+      <td>6724</td>
+      <td>305</td>
+      <td>831</td>
       <td></td>
     </tr>
     <tr>
@@ -2879,8 +3481,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2909,12 +3510,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>622</td>
-      <td>105935</td>
+      <td>108876</td>
+      <td>113638</td>
+      <td>1572</td>
+      <td>1793</td>
+      <td>82527</td>
+      <td>192112</td>
+      <td>2209</td>
+      <td>8565</td>
+      <td>5711</td>
+      <td>7649</td>
+      <td>275</td>
+      <td>334</td>
+      <td>197114</td>
+      <td>313399</td>
+      <td>4056</td>
+      <td>10692</td>
       <td></td>
     </tr>
     <tr>
@@ -2978,8 +3594,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>136</td>
+      <td>136</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>136</td>
+      <td>136</td>
+      <td>11</td>
+      <td>11</td>
       <td></td>
     </tr>
     <tr>
@@ -2994,7 +3624,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation, Fasta Manipulation</td>
       <td>fastq_combiner</td>
@@ -3003,14 +3633,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3039,12 +3668,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>66</td>
-      <td>8676</td>
+      <td>8604</td>
+      <td>8799</td>
+      <td>215</td>
+      <td>240</td>
+      <td>54200</td>
+      <td>75329</td>
+      <td>919</td>
+      <td>2957</td>
+      <td>1562</td>
+      <td>1680</td>
+      <td>76</td>
+      <td>85</td>
+      <td>64366</td>
+      <td>85808</td>
+      <td>1210</td>
+      <td>3282</td>
       <td></td>
     </tr>
     <tr>
@@ -3059,7 +3703,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_filter</td>
@@ -3068,14 +3712,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3104,12 +3747,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>266</td>
-      <td>14222</td>
+      <td>15582</td>
+      <td>18350</td>
+      <td>690</td>
+      <td>771</td>
+      <td>40489</td>
+      <td>121585</td>
+      <td>2715</td>
+      <td>9239</td>
+      <td>4657</td>
+      <td>5793</td>
+      <td>214</td>
+      <td>287</td>
+      <td>60728</td>
+      <td>145728</td>
+      <td>3619</td>
+      <td>10297</td>
       <td></td>
     </tr>
     <tr>
@@ -3133,7 +3791,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id</td>
       <td>0.0.7</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -3175,6 +3833,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3189,7 +3861,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_groomer</td>
@@ -3198,14 +3870,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3234,12 +3905,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1028</td>
-      <td>94802</td>
+      <td>92594</td>
+      <td>102535</td>
+      <td>2576</td>
+      <td>2995</td>
+      <td>179461</td>
+      <td>897457</td>
+      <td>9437</td>
+      <td>44701</td>
+      <td>15434</td>
+      <td>25533</td>
+      <td>664</td>
+      <td>1073</td>
+      <td>287489</td>
+      <td>1025525</td>
+      <td>12677</td>
+      <td>48769</td>
       <td></td>
     </tr>
     <tr>
@@ -3285,7 +3971,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3300,11 +3985,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>679</td>
-      <td>5765</td>
+      <td>7560</td>
+      <td>7560</td>
+      <td>1266</td>
+      <td>1266</td>
+      <td>6539</td>
+      <td>6539</td>
+      <td>1581</td>
+      <td>1581</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14099</td>
+      <td>14099</td>
+      <td>2847</td>
+      <td>2847</td>
       <td></td>
     </tr>
     <tr>
@@ -3319,7 +4019,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_manipulation</td>
@@ -3328,17 +4028,17 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3368,8 +4068,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>69</td>
-      <td>2503</td>
+      <td>2488</td>
+      <td>3132</td>
+      <td>215</td>
+      <td>267</td>
+      <td>6241</td>
+      <td>14508</td>
+      <td>834</td>
+      <td>2121</td>
+      <td>4121</td>
+      <td>4592</td>
+      <td>131</td>
+      <td>158</td>
+      <td>12850</td>
+      <td>22232</td>
+      <td>1180</td>
+      <td>2546</td>
       <td></td>
     </tr>
     <tr>
@@ -3384,7 +4098,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_masker_by_quality</td>
@@ -3393,14 +4107,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3429,12 +4142,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>16</td>
-      <td>170</td>
+      <td>234</td>
+      <td>249</td>
+      <td>43</td>
+      <td>44</td>
+      <td>2648</td>
+      <td>8092</td>
+      <td>288</td>
+      <td>983</td>
+      <td>442</td>
+      <td>466</td>
+      <td>12</td>
+      <td>17</td>
+      <td>3324</td>
+      <td>8807</td>
+      <td>343</td>
+      <td>1044</td>
       <td></td>
     </tr>
     <tr>
@@ -3500,6 +4228,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3514,7 +4256,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_paired_end_deinterlacer</td>
@@ -3523,14 +4265,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3559,12 +4300,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>122</td>
-      <td>8410</td>
+      <td>5873</td>
+      <td>8936</td>
+      <td>532</td>
+      <td>657</td>
+      <td>14738</td>
+      <td>20229</td>
+      <td>1889</td>
+      <td>2366</td>
+      <td>2316</td>
+      <td>2711</td>
+      <td>225</td>
+      <td>261</td>
+      <td>22927</td>
+      <td>31876</td>
+      <td>2646</td>
+      <td>3284</td>
       <td></td>
     </tr>
     <tr>
@@ -3579,7 +4335,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_paired_end_interlacer</td>
@@ -3588,14 +4344,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3624,12 +4379,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1087</td>
-      <td>17024</td>
+      <td>18216</td>
+      <td>19573</td>
+      <td>2348</td>
+      <td>2492</td>
+      <td>23484</td>
+      <td>25936</td>
+      <td>3482</td>
+      <td>3851</td>
+      <td>6207</td>
+      <td>6551</td>
+      <td>1402</td>
+      <td>1442</td>
+      <td>47907</td>
+      <td>52060</td>
+      <td>7232</td>
+      <td>7785</td>
       <td></td>
     </tr>
     <tr>
@@ -3644,7 +4414,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_paired_end_joiner</td>
@@ -3653,14 +4423,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3689,12 +4458,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>245</td>
-      <td>16635</td>
+      <td>15628</td>
+      <td>17130</td>
+      <td>536</td>
+      <td>679</td>
+      <td>24157</td>
+      <td>58368</td>
+      <td>1954</td>
+      <td>5716</td>
+      <td>1941</td>
+      <td>2266</td>
+      <td>172</td>
+      <td>214</td>
+      <td>41726</td>
+      <td>77764</td>
+      <td>2662</td>
+      <td>6609</td>
       <td></td>
     </tr>
     <tr>
@@ -3709,7 +4493,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_paired_end_splitter</td>
@@ -3718,17 +4502,17 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3758,8 +4542,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>196</td>
-      <td>3092</td>
+      <td>3169</td>
+      <td>3521</td>
+      <td>459</td>
+      <td>535</td>
+      <td>19309</td>
+      <td>30747</td>
+      <td>1410</td>
+      <td>3441</td>
+      <td>807</td>
+      <td>1023</td>
+      <td>219</td>
+      <td>247</td>
+      <td>23285</td>
+      <td>35291</td>
+      <td>2088</td>
+      <td>4223</td>
       <td></td>
     </tr>
     <tr>
@@ -3789,8 +4587,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3819,12 +4616,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>1271</td>
+      <td>1393</td>
+      <td>131</td>
+      <td>176</td>
+      <td>12763</td>
+      <td>58819</td>
+      <td>2073</td>
+      <td>8850</td>
+      <td>430</td>
+      <td>479</td>
+      <td>32</td>
       <td>51</td>
-      <td>1178</td>
+      <td>14464</td>
+      <td>60691</td>
+      <td>2236</td>
+      <td>9077</td>
       <td></td>
     </tr>
     <tr>
@@ -3854,8 +4666,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3884,12 +4695,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>11</td>
-      <td>220</td>
+      <td>335</td>
+      <td>352</td>
+      <td>44</td>
+      <td>47</td>
+      <td>1583</td>
+      <td>9696</td>
+      <td>269</td>
+      <td>2229</td>
+      <td>1131</td>
+      <td>1254</td>
+      <td>15</td>
+      <td>27</td>
+      <td>3049</td>
+      <td>11302</td>
+      <td>328</td>
+      <td>2303</td>
       <td></td>
     </tr>
     <tr>
@@ -3919,8 +4745,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3949,12 +4774,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1509</td>
-      <td>15172</td>
+      <td>17279</td>
+      <td>18386</td>
+      <td>3826</td>
+      <td>4062</td>
+      <td>55268</td>
+      <td>136888</td>
+      <td>6055</td>
+      <td>12590</td>
+      <td>7685</td>
+      <td>9356</td>
+      <td>1854</td>
+      <td>2043</td>
+      <td>80232</td>
+      <td>164630</td>
+      <td>11735</td>
+      <td>18695</td>
       <td></td>
     </tr>
     <tr>
@@ -4020,6 +4860,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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       <td></td>
     </tr>
     <tr>
@@ -4034,7 +4888,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_stats</td>
@@ -4043,14 +4897,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4079,12 +4932,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>221</td>
-      <td>4246</td>
+      <td>3858</td>
+      <td>4595</td>
+      <td>680</td>
+      <td>815</td>
+      <td>15213</td>
+      <td>81513</td>
+      <td>3159</td>
+      <td>14109</td>
+      <td>3855</td>
+      <td>4163</td>
+      <td>184</td>
+      <td>256</td>
+      <td>22926</td>
+      <td>90271</td>
+      <td>4023</td>
+      <td>15180</td>
       <td></td>
     </tr>
     <tr>
@@ -4114,8 +4982,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4144,12 +5011,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>419</td>
-      <td>13599</td>
+      <td>36069</td>
+      <td>37805</td>
+      <td>1151</td>
+      <td>1234</td>
+      <td>45213</td>
+      <td>99852</td>
+      <td>2691</td>
+      <td>6370</td>
+      <td>8457</td>
+      <td>13335</td>
+      <td>408</td>
+      <td>609</td>
+      <td>89739</td>
+      <td>150992</td>
+      <td>4250</td>
+      <td>8213</td>
       <td></td>
     </tr>
     <tr>
@@ -4164,7 +5046,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_to_tabular</td>
@@ -4173,14 +5055,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4209,12 +5090,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>93</td>
-      <td>12593</td>
+      <td>12895</td>
+      <td>14110</td>
+      <td>269</td>
+      <td>297</td>
+      <td>13315</td>
+      <td>30673</td>
+      <td>612</td>
+      <td>1810</td>
+      <td>5125</td>
+      <td>5373</td>
+      <td>64</td>
+      <td>87</td>
+      <td>31335</td>
+      <td>50156</td>
+      <td>945</td>
+      <td>2194</td>
       <td></td>
     </tr>
     <tr>
@@ -4229,7 +5125,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastq_trimmer</td>
@@ -4238,14 +5134,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4274,12 +5169,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>210</td>
-      <td>9757</td>
+      <td>10114</td>
+      <td>11383</td>
+      <td>582</td>
+      <td>665</td>
+      <td>23906</td>
+      <td>92351</td>
+      <td>1986</td>
+      <td>8818</td>
+      <td>1588</td>
+      <td>2607</td>
+      <td>108</td>
+      <td>212</td>
+      <td>35608</td>
+      <td>106341</td>
+      <td>2676</td>
+      <td>9695</td>
       <td></td>
     </tr>
     <tr>
@@ -4294,7 +5204,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td></td>
       <td>Fastq Manipulation</td>
       <td>fastq_trimmer_by_quality</td>
@@ -4303,17 +5213,17 @@
       <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4343,8 +5253,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>459</td>
-      <td>5676</td>
+      <td>4881</td>
+      <td>6165</td>
+      <td>859</td>
+      <td>967</td>
+      <td>29458</td>
+      <td>99179</td>
+      <td>3455</td>
+      <td>11369</td>
+      <td>2171</td>
+      <td>2678</td>
+      <td>259</td>
+      <td>338</td>
+      <td>36510</td>
+      <td>108022</td>
+      <td>4573</td>
+      <td>12674</td>
       <td></td>
     </tr>
     <tr>
@@ -4374,8 +5298,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4407,9 +5330,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>17447</td>
-      <td>1556625</td>
+      <td>1784056</td>
+      <td>1913280</td>
+      <td>41344</td>
+      <td>43940</td>
+      <td>2269843</td>
+      <td>3195869</td>
+      <td>90828</td>
+      <td>140008</td>
+      <td>410004</td>
+      <td>445555</td>
+      <td>14195</td>
+      <td>16026</td>
+      <td>4463903</td>
+      <td>5554704</td>
+      <td>146367</td>
+      <td>199974</td>
       <td></td>
     </tr>
     <tr>
@@ -4475,6 +5413,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>3</td>
       <td></td>
     </tr>
     <tr>
@@ -4489,7 +5441,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>fastqtofasta</td>
@@ -4498,7 +5450,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
@@ -4520,7 +5472,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4534,12 +5485,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1371</td>
-      <td>178178</td>
+      <td>208349</td>
+      <td>217568</td>
+      <td>3421</td>
+      <td>3732</td>
+      <td>131388</td>
+      <td>245005</td>
+      <td>5108</td>
+      <td>13227</td>
+      <td>18655</td>
+      <td>18655</td>
+      <td>679</td>
+      <td>679</td>
+      <td>358392</td>
+      <td>481228</td>
+      <td>9208</td>
+      <td>17638</td>
       <td></td>
     </tr>
     <tr>
@@ -4569,8 +5535,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4599,12 +5564,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>27</td>
-      <td>1810</td>
+      <td>1769</td>
+      <td>2020</td>
+      <td>88</td>
+      <td>101</td>
+      <td>6948</td>
+      <td>24960</td>
+      <td>358</td>
+      <td>2424</td>
+      <td>623</td>
+      <td>998</td>
+      <td>32</td>
+      <td>50</td>
+      <td>9340</td>
+      <td>27978</td>
+      <td>478</td>
+      <td>2575</td>
       <td></td>
     </tr>
     <tr>
@@ -4634,8 +5614,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4664,12 +5643,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>128</td>
-      <td>16591</td>
+      <td>16957</td>
+      <td>18124</td>
+      <td>225</td>
+      <td>260</td>
+      <td>37001</td>
+      <td>89126</td>
+      <td>919</td>
+      <td>2720</td>
+      <td>863</td>
+      <td>989</td>
+      <td>56</td>
+      <td>68</td>
+      <td>54821</td>
+      <td>108239</td>
+      <td>1200</td>
+      <td>3048</td>
       <td></td>
     </tr>
     <tr>
@@ -4699,8 +5693,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4729,12 +5722,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>96</td>
-      <td>3333</td>
+      <td>3140</td>
+      <td>3520</td>
+      <td>178</td>
+      <td>212</td>
+      <td>13975</td>
+      <td>117900</td>
+      <td>1198</td>
+      <td>6006</td>
+      <td>409</td>
+      <td>712</td>
+      <td>36</td>
+      <td>55</td>
+      <td>17524</td>
+      <td>122132</td>
+      <td>1412</td>
+      <td>6273</td>
       <td></td>
     </tr>
     <tr>
@@ -4764,8 +5772,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4794,12 +5801,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>114</td>
-      <td>61218</td>
+      <td>64187</td>
+      <td>67981</td>
+      <td>326</td>
+      <td>349</td>
+      <td>87477</td>
+      <td>185555</td>
+      <td>781</td>
+      <td>3067</td>
+      <td>16563</td>
+      <td>17125</td>
+      <td>58</td>
+      <td>78</td>
+      <td>168227</td>
+      <td>270661</td>
+      <td>1165</td>
+      <td>3494</td>
       <td></td>
     </tr>
     <tr>
@@ -4829,8 +5851,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4859,12 +5880,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>25</td>
-      <td>249</td>
+      <td>174</td>
+      <td>272</td>
+      <td>61</td>
+      <td>92</td>
+      <td>4295</td>
+      <td>25068</td>
+      <td>1056</td>
+      <td>4180</td>
+      <td>1127</td>
+      <td>1171</td>
+      <td>70</td>
+      <td>89</td>
+      <td>5596</td>
+      <td>26511</td>
+      <td>1187</td>
+      <td>4361</td>
       <td></td>
     </tr>
     <tr>
@@ -4894,8 +5930,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4924,12 +5959,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>63</td>
-      <td>2176</td>
+      <td>2218</td>
+      <td>2344</td>
+      <td>168</td>
+      <td>206</td>
+      <td>20551</td>
+      <td>60032</td>
+      <td>3784</td>
+      <td>9866</td>
+      <td>2347</td>
+      <td>2460</td>
+      <td>234</td>
+      <td>256</td>
+      <td>25116</td>
+      <td>64836</td>
+      <td>4186</td>
+      <td>10328</td>
       <td></td>
     </tr>
     <tr>
@@ -4959,8 +6009,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4989,12 +6038,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>68</td>
-      <td>2280</td>
+      <td>2364</td>
+      <td>2526</td>
+      <td>180</td>
+      <td>214</td>
+      <td>6572</td>
+      <td>11745</td>
+      <td>303</td>
+      <td>1024</td>
+      <td>462</td>
+      <td>696</td>
+      <td>49</td>
+      <td>64</td>
+      <td>9398</td>
+      <td>14967</td>
+      <td>532</td>
+      <td>1302</td>
       <td></td>
     </tr>
     <tr>
@@ -5024,8 +6088,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -5054,12 +6117,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>156</td>
-      <td>10832</td>
+      <td>10707</td>
+      <td>12597</td>
+      <td>356</td>
+      <td>415</td>
+      <td>21568</td>
+      <td>67304</td>
+      <td>574</td>
+      <td>1527</td>
+      <td>719</td>
+      <td>861</td>
+      <td>61</td>
+      <td>78</td>
+      <td>32994</td>
+      <td>80762</td>
+      <td>991</td>
+      <td>2020</td>
       <td></td>
     </tr>
     <tr>
@@ -5089,8 +6167,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -5119,12 +6196,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>205</td>
-      <td>13149</td>
+      <td>13584</td>
+      <td>14557</td>
+      <td>550</td>
+      <td>641</td>
+      <td>123676</td>
+      <td>206733</td>
+      <td>2034</td>
+      <td>8390</td>
+      <td>2819</td>
+      <td>4757</td>
+      <td>229</td>
+      <td>267</td>
+      <td>140079</td>
+      <td>226047</td>
+      <td>2813</td>
+      <td>9298</td>
       <td></td>
     </tr>
     <tr>
@@ -5190,6 +6282,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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       <td></td>
     </tr>
     <tr>
@@ -5234,7 +6340,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5255,6 +6360,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -5284,8 +6404,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -5315,11 +6434,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>426</td>
-      <td>26274</td>
+      <td>26717</td>
+      <td>29932</td>
+      <td>1026</td>
+      <td>1072</td>
+      <td>42990</td>
+      <td>42990</td>
+      <td>1176</td>
+      <td>1176</td>
+      <td>9619</td>
+      <td>9619</td>
+      <td>230</td>
+      <td>230</td>
+      <td>79326</td>
+      <td>82541</td>
+      <td>2432</td>
+      <td>2478</td>
       <td></td>
     </tr>
     <tr>
@@ -5365,7 +6499,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5385,6 +6518,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5414,8 +6562,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -5444,12 +6591,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>617</td>
-      <td>30483</td>
+      <td>53310</td>
+      <td>53944</td>
+      <td>1499</td>
+      <td>1575</td>
+      <td>25043</td>
+      <td>25043</td>
+      <td>726</td>
+      <td>726</td>
+      <td>10824</td>
+      <td>10824</td>
+      <td>593</td>
+      <td>593</td>
+      <td>89177</td>
+      <td>89811</td>
+      <td>2818</td>
+      <td>2894</td>
       <td></td>
     </tr>
     <tr>
@@ -5513,8 +6675,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>14</td>
-      <td>331</td>
+      <td>1985</td>
+      <td>1985</td>
+      <td>41</td>
+      <td>41</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1985</td>
+      <td>1985</td>
+      <td>41</td>
+      <td>41</td>
       <td></td>
     </tr>
     <tr>
@@ -5560,7 +6736,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5574,12 +6749,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>74</td>
-      <td>13759</td>
+      <td>22017</td>
+      <td>22304</td>
+      <td>239</td>
+      <td>255</td>
+      <td>9399</td>
+      <td>14886</td>
+      <td>462</td>
+      <td>709</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>31420</td>
+      <td>37194</td>
+      <td>702</td>
+      <td>965</td>
       <td></td>
     </tr>
     <tr>
@@ -5609,8 +6799,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -5639,12 +6828,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1499</td>
-      <td>20904</td>
+      <td>32514</td>
+      <td>32675</td>
+      <td>3379</td>
+      <td>3422</td>
+      <td>19434</td>
+      <td>19434</td>
+      <td>2537</td>
+      <td>2537</td>
+      <td>9843</td>
+      <td>9843</td>
+      <td>1624</td>
+      <td>1624</td>
+      <td>61791</td>
+      <td>61952</td>
+      <td>7540</td>
+      <td>7583</td>
       <td></td>
     </tr>
     <tr>
@@ -5708,8 +6912,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>20</td>
-      <td>166</td>
+      <td>189</td>
+      <td>203</td>
+      <td>57</td>
+      <td>60</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>189</td>
+      <td>203</td>
+      <td>57</td>
+      <td>60</td>
       <td></td>
     </tr>
     <tr>
@@ -5775,6 +6993,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5820,7 +7052,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5840,6 +7071,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5903,8 +7149,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>18</td>
-      <td>495</td>
+      <td>1542</td>
+      <td>1542</td>
+      <td>159</td>
+      <td>159</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>587</td>
+      <td>587</td>
+      <td>64</td>
+      <td>64</td>
+      <td>2129</td>
+      <td>2129</td>
+      <td>223</td>
+      <td>223</td>
       <td></td>
     </tr>
     <tr>
@@ -5950,7 +7210,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -5964,12 +7223,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>136</td>
-      <td>6651</td>
+      <td>7012</td>
+      <td>7344</td>
+      <td>323</td>
+      <td>338</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7012</td>
+      <td>7344</td>
+      <td>323</td>
+      <td>338</td>
       <td></td>
     </tr>
     <tr>
@@ -6015,7 +7289,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6035,6 +7308,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1</td>
+      <td>1</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -6100,6 +7388,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>103</td>
+      <td>103</td>
+      <td>4</td>
+      <td>4</td>
+      <td>103</td>
+      <td>103</td>
+      <td>4</td>
+      <td>4</td>
       <td></td>
     </tr>
     <tr>
@@ -6129,11 +7431,11 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6163,8 +7465,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>36</td>
-      <td>295</td>
+      <td>502</td>
+      <td>502</td>
+      <td>66</td>
+      <td>66</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>502</td>
+      <td>502</td>
+      <td>66</td>
+      <td>66</td>
       <td></td>
     </tr>
     <tr>
@@ -6194,8 +7510,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -6225,11 +7540,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>297</td>
-      <td>1410</td>
+      <td>1819</td>
+      <td>1819</td>
+      <td>539</td>
+      <td>539</td>
+      <td>1334</td>
+      <td>1334</td>
+      <td>389</td>
+      <td>389</td>
+      <td>2472</td>
+      <td>2472</td>
+      <td>137</td>
+      <td>137</td>
+      <td>5625</td>
+      <td>5625</td>
+      <td>1065</td>
+      <td>1065</td>
       <td></td>
     </tr>
     <tr>
@@ -6275,8 +7605,16 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6286,6 +7624,10 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>228</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6295,6 +7637,8 @@
       <td>0</td>
       <td>0</td>
       <td>228</td>
+      <td>0</td>
+      <td>12</td>
       <td></td>
     </tr>
     <tr>
@@ -6324,8 +7668,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -6354,12 +7697,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>4183</td>
-      <td>299104</td>
+      <td>337151</td>
+      <td>353499</td>
+      <td>10046</td>
+      <td>10719</td>
+      <td>699868</td>
+      <td>896164</td>
+      <td>26656</td>
+      <td>34018</td>
+      <td>87016</td>
+      <td>94859</td>
+      <td>5302</td>
+      <td>5695</td>
+      <td>1124035</td>
+      <td>1344522</td>
+      <td>42004</td>
+      <td>50432</td>
       <td></td>
     </tr>
     <tr>
@@ -6423,8 +7781,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>39</td>
-      <td>354</td>
+      <td>473</td>
+      <td>473</td>
+      <td>93</td>
+      <td>93</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>473</td>
+      <td>93</td>
+      <td>93</td>
       <td></td>
     </tr>
     <tr>
@@ -6454,10 +7826,9 @@
       <td>3</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
       <td>0</td>
       <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -6484,12 +7855,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>69</td>
-      <td>1127</td>
+      <td>1200</td>
+      <td>1220</td>
+      <td>187</td>
+      <td>195</td>
+      <td>1588</td>
+      <td>1588</td>
+      <td>267</td>
+      <td>267</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2788</td>
+      <td>2808</td>
+      <td>454</td>
+      <td>462</td>
       <td></td>
     </tr>
     <tr>
@@ -6553,8 +7939,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>157</td>
+      <td>157</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>157</td>
+      <td>157</td>
+      <td>14</td>
       <td>14</td>
-      <td>139</td>
       <td></td>
     </tr>
     <tr>
@@ -6584,9 +7984,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6615,11 +8014,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>91</td>
-      <td>1138</td>
+      <td>1825</td>
+      <td>1825</td>
+      <td>237</td>
+      <td>237</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>971</td>
+      <td>971</td>
+      <td>56</td>
+      <td>56</td>
+      <td>2796</td>
+      <td>2796</td>
+      <td>293</td>
+      <td>293</td>
       <td></td>
     </tr>
     <tr>
@@ -6664,7 +8078,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6679,12 +8092,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
-      <td>63</td>
-      <td>2022</td>
+      <td>1995</td>
+      <td>2091</td>
+      <td>174</td>
+      <td>193</td>
+      <td>1430</td>
+      <td>1430</td>
+      <td>389</td>
+      <td>389</td>
+      <td>1580</td>
+      <td>1580</td>
+      <td>56</td>
+      <td>56</td>
+      <td>5005</td>
+      <td>5101</td>
+      <td>619</td>
+      <td>638</td>
       <td></td>
     </tr>
     <tr>
@@ -6714,8 +8142,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -6744,12 +8171,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>322</td>
-      <td>4090</td>
+      <td>4349</td>
+      <td>4466</td>
+      <td>666</td>
+      <td>698</td>
+      <td>2093</td>
+      <td>2286</td>
+      <td>928</td>
+      <td>998</td>
+      <td>201</td>
+      <td>201</td>
+      <td>77</td>
+      <td>77</td>
+      <td>6643</td>
+      <td>6953</td>
+      <td>1671</td>
+      <td>1773</td>
       <td></td>
     </tr>
     <tr>
@@ -6813,8 +8255,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>9</td>
-      <td>152</td>
+      <td>149</td>
+      <td>171</td>
+      <td>27</td>
+      <td>30</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>149</td>
+      <td>171</td>
+      <td>27</td>
+      <td>30</td>
       <td></td>
     </tr>
     <tr>
@@ -6860,7 +8316,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6875,11 +8330,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>77</td>
-      <td>405</td>
+      <td>512</td>
+      <td>512</td>
+      <td>126</td>
+      <td>126</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>480</td>
+      <td>480</td>
+      <td>65</td>
+      <td>65</td>
+      <td>992</td>
+      <td>992</td>
+      <td>191</td>
+      <td>191</td>
       <td></td>
     </tr>
     <tr>
@@ -6945,6 +8415,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -6974,8 +8458,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -7004,12 +8487,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>548</td>
-      <td>9530</td>
+      <td>12692</td>
+      <td>13292</td>
+      <td>1349</td>
+      <td>1400</td>
+      <td>16645</td>
+      <td>16645</td>
+      <td>2140</td>
+      <td>2140</td>
+      <td>6214</td>
+      <td>6214</td>
+      <td>431</td>
+      <td>431</td>
+      <td>35551</td>
+      <td>36151</td>
+      <td>3920</td>
+      <td>3971</td>
       <td></td>
     </tr>
     <tr>
@@ -7039,8 +8537,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -7070,11 +8567,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>54</td>
-      <td>475</td>
+      <td>513</td>
+      <td>557</td>
+      <td>152</td>
+      <td>155</td>
+      <td>74</td>
+      <td>74</td>
+      <td>35</td>
+      <td>35</td>
+      <td>10</td>
+      <td>10</td>
+      <td>4</td>
+      <td>4</td>
+      <td>597</td>
+      <td>641</td>
+      <td>191</td>
+      <td>194</td>
       <td></td>
     </tr>
     <tr>
@@ -7104,8 +8616,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -7135,11 +8646,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>244</td>
-      <td>2483</td>
+      <td>3150</td>
+      <td>3150</td>
+      <td>477</td>
+      <td>477</td>
+      <td>730</td>
+      <td>730</td>
+      <td>196</td>
+      <td>196</td>
+      <td>1183</td>
+      <td>1183</td>
+      <td>151</td>
+      <td>151</td>
+      <td>5063</td>
+      <td>5063</td>
+      <td>824</td>
+      <td>824</td>
       <td></td>
     </tr>
     <tr>
@@ -7205,6 +8731,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -7268,8 +8808,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>573</td>
+      <td>573</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>573</td>
+      <td>573</td>
+      <td>3</td>
+      <td>3</td>
       <td></td>
     </tr>
     <tr>
@@ -7315,7 +8869,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7329,12 +8882,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>109</td>
-      <td>2206</td>
+      <td>7116</td>
+      <td>7116</td>
+      <td>256</td>
+      <td>256</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>278</td>
+      <td>278</td>
+      <td>60</td>
+      <td>60</td>
+      <td>7394</td>
+      <td>7394</td>
+      <td>316</td>
+      <td>316</td>
       <td></td>
     </tr>
     <tr>
@@ -7364,8 +8932,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -7394,12 +8961,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>178</td>
-      <td>11938</td>
+      <td>13357</td>
+      <td>13479</td>
+      <td>554</td>
+      <td>562</td>
+      <td>8416</td>
+      <td>8416</td>
+      <td>448</td>
+      <td>448</td>
+      <td>898</td>
+      <td>898</td>
+      <td>85</td>
+      <td>85</td>
+      <td>22671</td>
+      <td>22793</td>
+      <td>1087</td>
+      <td>1095</td>
       <td></td>
     </tr>
     <tr>
@@ -7445,7 +9027,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7460,11 +9041,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>66</td>
-      <td>881</td>
+      <td>1117</td>
+      <td>1117</td>
+      <td>116</td>
+      <td>116</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>295</td>
+      <td>295</td>
+      <td>25</td>
+      <td>25</td>
+      <td>1412</td>
+      <td>1412</td>
+      <td>141</td>
+      <td>141</td>
       <td></td>
     </tr>
     <tr>
@@ -7510,7 +9106,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7525,11 +9120,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>56</td>
-      <td>613</td>
+      <td>1020</td>
+      <td>1020</td>
+      <td>176</td>
+      <td>176</td>
+      <td>414</td>
+      <td>414</td>
+      <td>73</td>
+      <td>73</td>
+      <td>277</td>
+      <td>277</td>
+      <td>20</td>
+      <td>20</td>
+      <td>1711</td>
+      <td>1711</td>
+      <td>269</td>
+      <td>269</td>
       <td></td>
     </tr>
     <tr>
@@ -7593,8 +9203,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>34</td>
-      <td>803</td>
+      <td>864</td>
+      <td>929</td>
+      <td>91</td>
+      <td>101</td>
+      <td>1100</td>
+      <td>1100</td>
+      <td>175</td>
+      <td>175</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1964</td>
+      <td>2029</td>
+      <td>266</td>
+      <td>276</td>
       <td></td>
     </tr>
     <tr>
@@ -7624,8 +9248,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -7657,9 +9280,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>8320</td>
-      <td>162790</td>
+      <td>182221</td>
+      <td>192389</td>
+      <td>19343</td>
+      <td>20494</td>
+      <td>163961</td>
+      <td>182413</td>
+      <td>26449</td>
+      <td>29758</td>
+      <td>40663</td>
+      <td>41855</td>
+      <td>5974</td>
+      <td>6157</td>
+      <td>386845</td>
+      <td>416657</td>
+      <td>51766</td>
+      <td>56409</td>
       <td></td>
     </tr>
     <tr>
@@ -7723,8 +9361,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>95</td>
-      <td>667</td>
+      <td>790</td>
+      <td>790</td>
+      <td>160</td>
+      <td>160</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>790</td>
+      <td>790</td>
+      <td>160</td>
+      <td>160</td>
       <td></td>
     </tr>
     <tr>
@@ -7751,11 +9403,11 @@
       <td>2.5.2</td>
       <td>De-novo assembly, Genome assembly</td>
       <td>Sequencing, Sequence assembly</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>0</td>
@@ -7788,8 +9440,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>84</td>
-      <td>268</td>
+      <td>391</td>
+      <td>391</td>
+      <td>158</td>
+      <td>158</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>391</td>
+      <td>391</td>
+      <td>158</td>
+      <td>158</td>
       <td></td>
     </tr>
     <tr>
@@ -7855,6 +9521,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -7884,9 +9564,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7914,12 +9593,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>162</td>
-      <td>6384</td>
+      <td>7780</td>
+      <td>7780</td>
+      <td>337</td>
+      <td>337</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2323</td>
+      <td>2323</td>
+      <td>99</td>
+      <td>99</td>
+      <td>10104</td>
+      <td>10104</td>
+      <td>437</td>
+      <td>437</td>
       <td></td>
     </tr>
     <tr>
@@ -7964,16 +9658,30 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8030,7 +9738,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8044,12 +9751,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
-      <td>39</td>
-      <td>2654</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>87</td>
+      <td>87</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>87</td>
+      <td>87</td>
       <td></td>
     </tr>
     <tr>
@@ -8113,8 +9835,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>22</td>
+      <td>22</td>
+      <td>109</td>
+      <td>109</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>167</td>
+      <td>167</td>
+      <td>41</td>
+      <td>41</td>
       <td></td>
     </tr>
     <tr>
@@ -8159,7 +9895,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8174,12 +9909,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>150</td>
-      <td>4305</td>
+      <td>6269</td>
+      <td>6866</td>
+      <td>260</td>
+      <td>292</td>
+      <td>5530</td>
+      <td>20068</td>
+      <td>467</td>
+      <td>1664</td>
+      <td>5647</td>
+      <td>8471</td>
+      <td>198</td>
+      <td>300</td>
+      <td>17446</td>
+      <td>35405</td>
+      <td>925</td>
+      <td>2256</td>
       <td></td>
     </tr>
     <tr>
@@ -8224,7 +9974,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8245,6 +9994,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -8289,7 +10053,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8304,12 +10067,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1046</td>
-      <td>185468</td>
+      <td>262015</td>
+      <td>262852</td>
+      <td>2627</td>
+      <td>2711</td>
+      <td>83623</td>
+      <td>83623</td>
+      <td>1918</td>
+      <td>1918</td>
+      <td>52558</td>
+      <td>52558</td>
+      <td>1037</td>
+      <td>1037</td>
+      <td>398196</td>
+      <td>399033</td>
+      <td>5582</td>
+      <td>5666</td>
       <td></td>
     </tr>
     <tr>
@@ -8355,7 +10133,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>13</td>
       <td>0</td>
       <td>0</td>
@@ -8370,11 +10147,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>6</td>
       <td>13</td>
       <td>0</td>
-      <td>409</td>
-      <td>18773</td>
+      <td>19942</td>
+      <td>20587</td>
+      <td>1055</td>
+      <td>1245</td>
+      <td>33619</td>
+      <td>40808</td>
+      <td>2183</td>
+      <td>2594</td>
+      <td>9261</td>
+      <td>9261</td>
+      <td>365</td>
+      <td>365</td>
+      <td>62822</td>
+      <td>70656</td>
+      <td>3603</td>
+      <td>4204</td>
       <td></td>
     </tr>
     <tr>
@@ -8404,10 +10196,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8434,12 +10225,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>70</td>
-      <td>7881</td>
+      <td>10152</td>
+      <td>10626</td>
+      <td>253</td>
+      <td>281</td>
+      <td>10581</td>
+      <td>10581</td>
+      <td>1240</td>
+      <td>1240</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20733</td>
+      <td>21207</td>
+      <td>1493</td>
+      <td>1521</td>
       <td></td>
     </tr>
     <tr>
@@ -8505,6 +10311,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -8568,8 +10388,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>167</td>
-      <td>16800</td>
+      <td>17782</td>
+      <td>17782</td>
+      <td>287</td>
+      <td>287</td>
+      <td>853</td>
+      <td>853</td>
+      <td>65</td>
+      <td>65</td>
+      <td>2224</td>
+      <td>2224</td>
+      <td>65</td>
+      <td>65</td>
+      <td>20859</td>
+      <td>20859</td>
+      <td>417</td>
+      <td>417</td>
       <td></td>
     </tr>
     <tr>
@@ -8599,8 +10433,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -8630,11 +10463,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>350</td>
-      <td>21123</td>
+      <td>22742</td>
+      <td>22742</td>
+      <td>557</td>
+      <td>557</td>
+      <td>2159</td>
+      <td>2159</td>
+      <td>716</td>
+      <td>716</td>
+      <td>776</td>
+      <td>776</td>
+      <td>448</td>
+      <td>448</td>
+      <td>25677</td>
+      <td>25677</td>
+      <td>1721</td>
+      <td>1721</td>
       <td></td>
     </tr>
     <tr>
@@ -8700,6 +10548,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -8729,8 +10591,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -8759,12 +10620,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3567</td>
-      <td>51567</td>
+      <td>67737</td>
+      <td>69738</td>
+      <td>7787</td>
+      <td>7971</td>
+      <td>51925</td>
+      <td>56602</td>
+      <td>9692</td>
+      <td>10646</td>
+      <td>32003</td>
+      <td>34145</td>
+      <td>3890</td>
+      <td>4127</td>
+      <td>151665</td>
+      <td>160485</td>
+      <td>21369</td>
+      <td>22744</td>
       <td></td>
     </tr>
     <tr>
@@ -8783,7 +10659,7 @@
       <td>https://github.com/mahulchak/quickmerge</td>
       <td>Assembly</td>
       <td>quickmerge</td>
-      <td>galaxy-australia</td>
+      <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge</td>
       <td>0.3</td>
@@ -8830,6 +10706,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -8859,9 +10749,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8890,11 +10779,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>237</td>
-      <td>2833</td>
+      <td>4844</td>
+      <td>4844</td>
+      <td>480</td>
+      <td>480</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>3</td>
+      <td>3</td>
+      <td>4851</td>
+      <td>4851</td>
+      <td>483</td>
+      <td>483</td>
       <td></td>
     </tr>
     <tr>
@@ -8924,9 +10828,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8955,11 +10858,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>262</td>
-      <td>6902</td>
+      <td>9477</td>
+      <td>9477</td>
+      <td>438</td>
+      <td>438</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10585</td>
+      <td>10585</td>
+      <td>182</td>
+      <td>182</td>
+      <td>20062</td>
+      <td>20062</td>
+      <td>620</td>
+      <td>620</td>
       <td></td>
     </tr>
     <tr>
@@ -9023,8 +10941,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>30</td>
-      <td>569</td>
+      <td>655</td>
+      <td>655</td>
+      <td>57</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>655</td>
+      <td>655</td>
+      <td>57</td>
+      <td>57</td>
       <td></td>
     </tr>
     <tr>
@@ -9054,11 +10986,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -9088,8 +11020,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>109</td>
-      <td>1110</td>
+      <td>1522</td>
+      <td>1522</td>
+      <td>254</td>
+      <td>254</td>
+      <td>372</td>
+      <td>372</td>
+      <td>75</td>
+      <td>75</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1899</td>
+      <td>1899</td>
+      <td>330</td>
+      <td>330</td>
       <td></td>
     </tr>
     <tr>
@@ -9135,7 +11081,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9149,12 +11094,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>84</td>
-      <td>454</td>
+      <td>463</td>
+      <td>463</td>
+      <td>119</td>
+      <td>119</td>
+      <td>1038</td>
+      <td>1038</td>
+      <td>87</td>
+      <td>87</td>
+      <td>410</td>
+      <td>410</td>
+      <td>24</td>
+      <td>24</td>
+      <td>1911</td>
+      <td>1911</td>
+      <td>230</td>
+      <td>230</td>
       <td></td>
     </tr>
     <tr>
@@ -9169,14 +11129,14 @@
       <td>A tool to mark duplicates and extract discordant and split reads from SAM files.</td>
       <td>Split read mapping</td>
       <td>DNA, Sequencing, Mapping</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/GregoryFaust/samblaster</td>
       <td>SAM, Fastq Manipulation, Variant Analysis</td>
       <td>samblaster</td>
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster</td>
-      <td>0.1.24</td>
+      <td>0.1.26</td>
       <td>samblaster</td>
       <td>0.1.26</td>
       <td>Split read mapping</td>
@@ -9220,6 +11180,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -9249,8 +11223,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -9280,11 +11253,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>149</td>
-      <td>3765</td>
+      <td>3421</td>
+      <td>3859</td>
+      <td>340</td>
+      <td>382</td>
+      <td>883</td>
+      <td>883</td>
+      <td>109</td>
+      <td>109</td>
+      <td>1138</td>
+      <td>1138</td>
+      <td>15</td>
+      <td>15</td>
+      <td>5442</td>
+      <td>5880</td>
+      <td>464</td>
+      <td>506</td>
       <td></td>
     </tr>
     <tr>
@@ -9350,6 +11338,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -9379,8 +11381,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -9409,12 +11410,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>296</td>
-      <td>4948</td>
+      <td>6485</td>
+      <td>6549</td>
+      <td>720</td>
+      <td>726</td>
+      <td>10127</td>
+      <td>10127</td>
+      <td>1518</td>
+      <td>1518</td>
+      <td>238</td>
+      <td>238</td>
+      <td>37</td>
+      <td>37</td>
+      <td>16850</td>
+      <td>16914</td>
+      <td>2275</td>
+      <td>2281</td>
       <td></td>
     </tr>
     <tr>
@@ -9444,8 +11460,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -9474,12 +11489,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1450</td>
-      <td>48426</td>
+      <td>52099</td>
+      <td>55110</td>
+      <td>4053</td>
+      <td>4497</td>
+      <td>73194</td>
+      <td>108684</td>
+      <td>6930</td>
+      <td>9936</td>
+      <td>14771</td>
+      <td>15714</td>
+      <td>1222</td>
+      <td>1419</td>
+      <td>140064</td>
+      <td>179508</td>
+      <td>12205</td>
+      <td>15852</td>
       <td></td>
     </tr>
     <tr>
@@ -9509,8 +11539,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -9540,11 +11569,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>306</td>
-      <td>25302</td>
+      <td>30300</td>
+      <td>32553</td>
+      <td>732</td>
+      <td>799</td>
+      <td>21726</td>
+      <td>31891</td>
+      <td>619</td>
+      <td>621</td>
+      <td>2886</td>
+      <td>2886</td>
+      <td>144</td>
+      <td>144</td>
+      <td>54912</td>
+      <td>67330</td>
+      <td>1495</td>
+      <td>1564</td>
       <td></td>
     </tr>
     <tr>
@@ -9590,7 +11634,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9605,11 +11648,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>82</td>
-      <td>3784</td>
+      <td>4322</td>
+      <td>4714</td>
+      <td>180</td>
+      <td>205</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4322</td>
+      <td>4714</td>
+      <td>180</td>
+      <td>205</td>
       <td></td>
     </tr>
     <tr>
@@ -9655,7 +11713,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9675,6 +11732,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -9698,7 +11770,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip</td>
       <td>0.0.18</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -9740,6 +11812,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -9763,7 +11849,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename</td>
       <td>0.0.10</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -9785,7 +11871,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9801,10 +11886,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -9850,7 +11950,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9870,6 +11969,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2196</td>
+      <td>3529</td>
+      <td>260</td>
+      <td>289</td>
+      <td>2196</td>
+      <td>3529</td>
+      <td>260</td>
+      <td>289</td>
       <td></td>
     </tr>
     <tr>
@@ -9933,8 +12047,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>2424</td>
+      <td>2424</td>
+      <td>102</td>
+      <td>102</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2424</td>
+      <td>2424</td>
+      <td>102</td>
+      <td>102</td>
       <td></td>
     </tr>
     <tr>
@@ -9980,7 +12108,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10000,6 +12127,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -10045,7 +12187,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10059,12 +12200,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>154</td>
-      <td>763</td>
+      <td>913</td>
+      <td>913</td>
+      <td>308</td>
+      <td>308</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>568</td>
+      <td>568</td>
+      <td>73</td>
+      <td>73</td>
+      <td>1481</td>
+      <td>1481</td>
+      <td>381</td>
+      <td>381</td>
       <td></td>
     </tr>
     <tr>
@@ -10128,8 +12284,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>21</td>
+      <td>175</td>
       <td>220</td>
+      <td>51</td>
+      <td>60</td>
+      <td>350</td>
+      <td>6657</td>
+      <td>85</td>
+      <td>1602</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>525</td>
+      <td>6877</td>
+      <td>136</td>
+      <td>1662</td>
       <td></td>
     </tr>
     <tr>
@@ -10159,8 +12329,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -10189,12 +12358,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1008</td>
-      <td>41600</td>
+      <td>46125</td>
+      <td>47376</td>
+      <td>2273</td>
+      <td>2356</td>
+      <td>40577</td>
+      <td>40577</td>
+      <td>3971</td>
+      <td>3971</td>
+      <td>19960</td>
+      <td>21130</td>
+      <td>1085</td>
+      <td>1199</td>
+      <td>106662</td>
+      <td>109083</td>
+      <td>7329</td>
+      <td>7526</td>
       <td></td>
     </tr>
     <tr>
@@ -10224,10 +12408,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10257,9 +12440,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>269</td>
-      <td>14982</td>
+      <td>18184</td>
+      <td>18937</td>
+      <td>555</td>
+      <td>608</td>
+      <td>10514</td>
+      <td>10514</td>
+      <td>1063</td>
+      <td>1063</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>28698</td>
+      <td>29451</td>
+      <td>1618</td>
+      <td>1671</td>
       <td></td>
     </tr>
     <tr>
@@ -10323,8 +12521,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>22</td>
-      <td>203</td>
+      <td>325</td>
+      <td>325</td>
+      <td>61</td>
+      <td>61</td>
+      <td>137</td>
+      <td>137</td>
+      <td>54</td>
+      <td>54</td>
+      <td>843</td>
+      <td>843</td>
+      <td>63</td>
+      <td>63</td>
+      <td>1305</td>
+      <td>1305</td>
+      <td>178</td>
+      <td>178</td>
       <td></td>
     </tr>
     <tr>
@@ -10333,7 +12545,7 @@
       <td>spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades</td>
       <td>SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.</td>
       <td>spades</td>
-      <td>spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades</td>
+      <td>spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades</td>
       <td></td>
       <td>SPAdes</td>
       <td>St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.</td>
@@ -10354,8 +12566,7 @@
       <td>9</td>
       <td>9</td>
       <td>9</td>
-      <td>9</td>
-      <td>9</td>
+      <td>0</td>
       <td>9</td>
       <td>9</td>
       <td>9</td>
@@ -10384,12 +12595,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>9</td>
       <td>3</td>
       <td>0</td>
-      <td>3547</td>
-      <td>72953</td>
+      <td>82716</td>
+      <td>87113</td>
+      <td>8209</td>
+      <td>8526</td>
+      <td>120471</td>
+      <td>120475</td>
+      <td>14787</td>
+      <td>14790</td>
+      <td>54067</td>
+      <td>61541</td>
+      <td>5817</td>
+      <td>6653</td>
+      <td>257254</td>
+      <td>269129</td>
+      <td>28813</td>
+      <td>29969</td>
       <td></td>
     </tr>
     <tr>
@@ -10455,6 +12681,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -10500,7 +12740,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10520,6 +12759,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>0</td>
+      <td>3</td>
+      <td>200</td>
+      <td>384</td>
+      <td>31</td>
+      <td>66</td>
+      <td>200</td>
+      <td>397</td>
+      <td>31</td>
+      <td>69</td>
       <td></td>
     </tr>
     <tr>
@@ -10549,8 +12803,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -10579,12 +12832,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>6247</td>
-      <td>350032</td>
+      <td>364871</td>
+      <td>376580</td>
+      <td>16710</td>
+      <td>17342</td>
+      <td>583675</td>
+      <td>678448</td>
+      <td>53271</td>
+      <td>59638</td>
+      <td>48131</td>
+      <td>50455</td>
+      <td>5910</td>
+      <td>6181</td>
+      <td>996677</td>
+      <td>1105483</td>
+      <td>75891</td>
+      <td>83161</td>
       <td></td>
     </tr>
     <tr>
@@ -10599,7 +12867,7 @@
       <td></td>
       <td></td>
       <td></td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/galaxyproject/sequence_utils</td>
       <td>Fastq Manipulation</td>
       <td>tabular_to_fastq</td>
@@ -10608,14 +12876,13 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq</td>
       <td>1.1.5</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -10644,12 +12911,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>200</td>
-      <td>7388</td>
+      <td>7011</td>
+      <td>8135</td>
+      <td>449</td>
+      <td>482</td>
+      <td>9473</td>
+      <td>28494</td>
+      <td>626</td>
+      <td>2183</td>
+      <td>850</td>
+      <td>1090</td>
+      <td>80</td>
+      <td>104</td>
+      <td>17334</td>
+      <td>37719</td>
+      <td>1155</td>
+      <td>2769</td>
       <td></td>
     </tr>
     <tr>
@@ -10715,6 +12997,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -10744,8 +13040,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -10774,12 +13069,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1801</td>
-      <td>27426</td>
+      <td>36069</td>
+      <td>36922</td>
+      <td>5257</td>
+      <td>5431</td>
+      <td>25255</td>
+      <td>30822</td>
+      <td>5066</td>
+      <td>5826</td>
+      <td>7949</td>
+      <td>7949</td>
+      <td>1584</td>
+      <td>1584</td>
+      <td>69273</td>
+      <td>75693</td>
+      <td>11907</td>
+      <td>12841</td>
       <td></td>
     </tr>
     <tr>
@@ -10843,8 +13153,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>36</td>
-      <td>460</td>
+      <td>547</td>
+      <td>547</td>
+      <td>51</td>
+      <td>51</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>547</td>
+      <td>547</td>
+      <td>51</td>
+      <td>51</td>
       <td></td>
     </tr>
     <tr>
@@ -10874,8 +13198,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -10904,12 +13227,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2334</td>
-      <td>238699</td>
+      <td>229489</td>
+      <td>275008</td>
+      <td>5733</td>
+      <td>6500</td>
+      <td>228708</td>
+      <td>324716</td>
+      <td>11708</td>
+      <td>16638</td>
+      <td>22644</td>
+      <td>23869</td>
+      <td>1439</td>
+      <td>1527</td>
+      <td>480841</td>
+      <td>623593</td>
+      <td>18880</td>
+      <td>24665</td>
       <td></td>
     </tr>
     <tr>
@@ -10939,8 +13277,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -10969,12 +13306,27 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5862</td>
-      <td>305866</td>
+      <td>352353</td>
+      <td>383014</td>
+      <td>14547</td>
+      <td>15408</td>
+      <td>632385</td>
+      <td>839058</td>
+      <td>39323</td>
+      <td>49850</td>
+      <td>125340</td>
+      <td>139097</td>
+      <td>5268</td>
+      <td>5975</td>
+      <td>1110078</td>
+      <td>1361169</td>
+      <td>59138</td>
+      <td>71233</td>
       <td></td>
     </tr>
     <tr>
@@ -11004,9 +13356,8 @@
       <td>0</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
       <td>0</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -11035,11 +13386,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
+      <td>14681</td>
+      <td>14681</td>
+      <td>265</td>
+      <td>265</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4488</td>
+      <td>4488</td>
       <td>147</td>
-      <td>8942</td>
+      <td>147</td>
+      <td>19169</td>
+      <td>19169</td>
+      <td>412</td>
+      <td>412</td>
       <td></td>
     </tr>
     <tr>
@@ -11069,8 +13435,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -11099,12 +13464,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1558</td>
-      <td>65732</td>
+      <td>74120</td>
+      <td>77648</td>
+      <td>3798</td>
+      <td>3963</td>
+      <td>64946</td>
+      <td>90075</td>
+      <td>5451</td>
+      <td>7380</td>
+      <td>19516</td>
+      <td>20422</td>
+      <td>2010</td>
+      <td>2080</td>
+      <td>158582</td>
+      <td>188145</td>
+      <td>11259</td>
+      <td>13423</td>
       <td></td>
     </tr>
     <tr>
@@ -11168,8 +13548,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>25</td>
-      <td>86</td>
+      <td>112</td>
+      <td>112</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>112</td>
+      <td>112</td>
+      <td>38</td>
+      <td>38</td>
       <td></td>
     </tr>
     <tr>
@@ -11199,8 +13593,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -11229,12 +13622,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2083</td>
-      <td>25420</td>
+      <td>25171</td>
+      <td>27943</td>
+      <td>3899</td>
+      <td>4270</td>
+      <td>51187</td>
+      <td>51187</td>
+      <td>7557</td>
+      <td>7557</td>
+      <td>28546</td>
+      <td>28619</td>
+      <td>3585</td>
+      <td>3613</td>
+      <td>104904</td>
+      <td>107749</td>
+      <td>15041</td>
+      <td>15440</td>
       <td></td>
     </tr>
     <tr>
@@ -11278,7 +13686,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -11294,12 +13701,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>255</td>
-      <td>4741</td>
+      <td>4715</td>
+      <td>5343</td>
+      <td>888</td>
+      <td>965</td>
+      <td>9575</td>
+      <td>9576</td>
+      <td>2117</td>
+      <td>2117</td>
+      <td>3271</td>
+      <td>5524</td>
+      <td>1050</td>
+      <td>1397</td>
+      <td>17561</td>
+      <td>20443</td>
+      <td>4055</td>
+      <td>4479</td>
       <td></td>
     </tr>
     <tr>
@@ -11323,7 +13745,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko</td>
       <td>1.3.1</td>
       <td>verkko</td>
-      <td>2.2</td>
+      <td>2.2.1</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -11363,8 +13785,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
-      <td>22</td>
+      <td>48</td>
+      <td>48</td>
+      <td>25</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>25</td>
+      <td>25</td>
       <td></td>
     </tr>
     <tr>
@@ -11394,10 +13830,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -11425,11 +13860,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>116</td>
-      <td>1660</td>
+      <td>1619</td>
+      <td>1715</td>
+      <td>337</td>
+      <td>376</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1619</td>
+      <td>1715</td>
+      <td>337</td>
+      <td>376</td>
       <td></td>
     </tr>
     <tr>
@@ -11495,6 +13945,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -11539,7 +14003,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -11560,6 +14023,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -11623,8 +14101,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>64</td>
-      <td>344</td>
+      <td>618</td>
+      <td>618</td>
+      <td>176</td>
+      <td>176</td>
+      <td>336</td>
+      <td>336</td>
+      <td>62</td>
+      <td>62</td>
+      <td>588</td>
+      <td>588</td>
+      <td>25</td>
+      <td>25</td>
+      <td>1542</td>
+      <td>1542</td>
+      <td>263</td>
+      <td>263</td>
       <td></td>
     </tr>
   </tbody>
diff --git a/communities/assembly/resources/tools.tsv b/communities/assembly/resources/tools.tsv
index 95725e88..ace928af 100644
--- a/communities/assembly/resources/tools.tsv
+++ b/communities/assembly/resources/tools.tsv
@@ -1,178 +1,178 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	False		
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278	False		
-adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	37	217	False		
-agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	42	481	False		
-align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	329	False		
-assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	26	257	False		
-bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	False		
-biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	False		
-blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499	False		
-blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	False		
-cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	101	7766	False		
-cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474	False		
-cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	False		
-clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	5090	232004	False		
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369	False		
-ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	107	107	107	0	1816	89530	False		
-fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	469	ucsc-fasplit	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	242	2644	False		
-fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-fasta_compute_length	fasta_compute_length	Compute sequence length								To update		Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	380	7758	False		
-fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	35793	False		
-fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	350	48649	False		
-fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	68	2912	False		
-fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	461	29886	False		
-fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	29	774	False		
-fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	622	105935	False		
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	66	8676	False		
-fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	266	14222	False		
-fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1028	94802	False		
-fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	679	5765	False		
-fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	69	2503	False		
-fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	170	False		
-fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	122	8410	False		
-fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1087	17024	False		
-fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	245	16635	False		
-fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	196	3092	False		
-fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	51	1178	False		
-fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	11	220	False		
-fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1509	15172	False		
-fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_stats	fastq_stats	FASTQ Summary Statistics by column								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	221	4246	False		
-fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	419	13599	False		
-fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	93	12593	False		
-fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	210	9757	False		
-fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								Up-to-date		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	459	5676	False		
-fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	0	17447	1556625	False		
-fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1371	178178	False		
-fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	27	1810	False		
-fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	128	16591	False		
-fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	96	3333	False		
-fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	114	61218	False		
-fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	25	249	False		
-fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	63	2176	False		
-fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	68	2280	False		
-fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	156	10832	False		
-fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	205	13149	False		
-fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	426	26274	False		
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	617	30483	False		
-flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	14	331	False		
-flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	74	13759	False		
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904	False		
-format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	166	False		
-get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	False		
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651	False		
-guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	False		
-hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	False		
-hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	False		
-hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	4183	299104	False		
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	False		
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127	False		
-instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	False		
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	False		
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022	False		
-length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	322	4090	False		
-lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152	False		
-links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	False		
-make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530	False		
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475	False		
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	False		
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206	False		
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938	False		
-mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	False		
-mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	False		
-msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	803	False		
-multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	8320	162790	False		
-necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	False		
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	False		
-nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	162	6384	False		
-oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	39	2654	False		
-pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	150	4305	False		
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1046	185468	False		
-poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	6	13	0	409	18773	False		
-prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	70	7881	False		
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	False		
-pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123	False		
-qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567	False		
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
-ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	False		
-raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	False		
-rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	569	False		
-rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	109	1110	False		
-salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	84	454	False		
-samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	To update	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.24	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	False		
-samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	296	4948	False		
-samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1450	48426	False		
-seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	25302	False		
-seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	False		
-seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
-seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	154	763	False		
-short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	21	220	False		
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600	False		
-sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	269	14982	False		
-smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	False		
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953	False		
-spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	3	3	3	0	6247	350032	False		
-tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	200	7388	False		
-tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426	False		
-tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	False		
-trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	2334	238699	False		
-trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	1	1	1	0	5862	305866	False		
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	False		
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732	False		
-validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	86	False		
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420	False		
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741	False		
-verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	False		
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	False		
-xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	43	43	20	20	0	0	0	0	0	0	0	0	43	43	20	20	False		
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5543	5543	1042	1042	1301	1305	413	414	2030	2030	299	299	8874	8878	1754	1755	False		
+adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	348	348	62	62	0	0	0	0	0	0	0	0	348	348	62	62	False		
+agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	244	244	0	0	0	0	119	119	10	10	1555	1555	254	254	False		
+align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	511	541	32	35	0	0	0	0	0	0	0	0	511	541	32	35	False		
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	232	279	62	72	0	0	0	0	0	0	0	0	232	279	62	72	False		
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	617	617	63	63	617	617	63	63	False		
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	151	151	143	143	43	43	596	596	22	22	1286	1286	216	216	False		
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	3	1	1	0	0	0	0	0	0	0	0	3	3	1	1	False		
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24916	27120	283	347	0	0	0	0	0	0	0	0	24916	27120	283	347	False		
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1527	1527	79	79	6	6	1	1	317	317	26	26	1850	1850	106	106	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	9869	9869	158	158	0	0	0	0	6886	6886	146	146	16755	16755	304	304	False		
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10414	10414	510	510	2	2	1	1	2	2	1	1	10418	10418	512	512	False		
+cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	524	524	32	32	0	0	0	0	0	0	0	0	524	524	32	32	False		
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	259754	272370	11716	12601	334550	362356	18618	20162	64377	65986	3507	3627	658681	700712	33841	36390	False		
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	358	406	124	139	1361	1361	384	384	0	0	0	0	1719	1767	508	523	False		
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	28	28	2	2	0	0	0	0	0	0	0	0	28	28	2	2	False		
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	0	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	107	107	107	0	143762	148864	4481	5039	151989	296028	13224	31140	24955	27001	2397	2705	320706	471893	20102	38884	False		
+fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	469	ucsc-fasplit	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3278	3361	460	478	6144	6144	595	595	1139	1139	183	183	10561	10644	1238	1256	False		
+fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5191	5367	104	130	5191	5367	104	130	False		
+fasta_compute_length	fasta_compute_length	Compute sequence length								To update	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.4	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	8547	9136	978	1129	17748	51150	1404	5670	4239	4404	162	190	30534	64690	2544	6989	False		
+fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39695	39742	242	255	13660	19007	600	1398	1521	1603	92	112	54876	60352	934	1765	False		
+fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	47494	51924	889	997	50663	101663	1488	3742	3919	5601	241	276	102076	159188	2618	5015	False		
+fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	1	5235	5486	237	288	4060	25609	480	2039	816	1093	73	89	10111	32188	790	2416	False		
+fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	30917	32191	1142	1257	36869	36869	1346	1346	5236	5236	230	230	73022	74296	2718	2833	False		
+fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	497	808	71	108	2249	5479	216	703	415	437	18	20	3161	6724	305	831	False		
+fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	108876	113638	1572	1793	82527	192112	2209	8565	5711	7649	275	334	197114	313399	4056	10692	False		
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	136	11	11	0	0	0	0	0	0	0	0	136	136	11	11	False		
+fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8604	8799	215	240	54200	75329	919	2957	1562	1680	76	85	64366	85808	1210	3282	False		
+fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15582	18350	690	771	40489	121585	2715	9239	4657	5793	214	287	60728	145728	3619	10297	False		
+fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	92594	102535	2576	2995	179461	897457	9437	44701	15434	25533	664	1073	287489	1025525	12677	48769	False		
+fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7560	7560	1266	1266	6539	6539	1581	1581	0	0	0	0	14099	14099	2847	2847	False		
+fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2488	3132	215	267	6241	14508	834	2121	4121	4592	131	158	12850	22232	1180	2546	False		
+fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	234	249	43	44	2648	8092	288	983	442	466	12	17	3324	8807	343	1044	False		
+fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5873	8936	532	657	14738	20229	1889	2366	2316	2711	225	261	22927	31876	2646	3284	False		
+fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18216	19573	2348	2492	23484	25936	3482	3851	6207	6551	1402	1442	47907	52060	7232	7785	False		
+fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15628	17130	536	679	24157	58368	1954	5716	1941	2266	172	214	41726	77764	2662	6609	False		
+fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3169	3521	459	535	19309	30747	1410	3441	807	1023	219	247	23285	35291	2088	4223	False		
+fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1271	1393	131	176	12763	58819	2073	8850	430	479	32	51	14464	60691	2236	9077	False		
+fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	335	352	44	47	1583	9696	269	2229	1131	1254	15	27	3049	11302	328	2303	False		
+fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	17279	18386	3826	4062	55268	136888	6055	12590	7685	9356	1854	2043	80232	164630	11735	18695	False		
+fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_stats	fastq_stats	FASTQ Summary Statistics by column								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3858	4595	680	815	15213	81513	3159	14109	3855	4163	184	256	22926	90271	4023	15180	False		
+fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	36069	37805	1151	1234	45213	99852	2691	6370	8457	13335	408	609	89739	150992	4250	8213	False		
+fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	12895	14110	269	297	13315	30673	612	1810	5125	5373	64	87	31335	50156	945	2194	False		
+fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10114	11383	582	665	23906	92351	1986	8818	1588	2607	108	212	35608	106341	2676	9695	False		
+fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								To update		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4881	6165	859	967	29458	99179	3455	11369	2171	2678	259	338	36510	108022	4573	12674	False		
+fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	1	0	1784056	1913280	41344	43940	2269843	3195869	90828	140008	410004	445555	14195	16026	4463903	5554704	146367	199974	False		
+fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	3	0	0	0	0	0	8	0	3	False		
+fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	208349	217568	3421	3732	131388	245005	5108	13227	18655	18655	679	679	358392	481228	9208	17638	False		
+fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1769	2020	88	101	6948	24960	358	2424	623	998	32	50	9340	27978	478	2575	False		
+fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	16957	18124	225	260	37001	89126	919	2720	863	989	56	68	54821	108239	1200	3048	False		
+fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3140	3520	178	212	13975	117900	1198	6006	409	712	36	55	17524	122132	1412	6273	False		
+fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	64187	67981	326	349	87477	185555	781	3067	16563	17125	58	78	168227	270661	1165	3494	False		
+fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	174	272	61	92	4295	25068	1056	4180	1127	1171	70	89	5596	26511	1187	4361	False		
+fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2218	2344	168	206	20551	60032	3784	9866	2347	2460	234	256	25116	64836	4186	10328	False		
+fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2364	2526	180	214	6572	11745	303	1024	462	696	49	64	9398	14967	532	1302	False		
+fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10707	12597	356	415	21568	67304	574	1527	719	861	61	78	32994	80762	991	2020	False		
+fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	13584	14557	550	641	123676	206733	2034	8390	2819	4757	229	267	140079	226047	2813	9298	False		
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	1	1	1	1	False		
+filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	26717	29932	1026	1072	42990	42990	1176	1176	9619	9619	230	230	79326	82541	2432	2478	False		
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	53310	53944	1499	1575	25043	25043	726	726	10824	10824	593	593	89177	89811	2818	2894	False		
+flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	1985	1985	41	41	0	0	0	0	0	0	0	0	1985	1985	41	41	False		
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22017	22304	239	255	9399	14886	462	709	4	4	1	1	31420	37194	702	965	False		
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32514	32675	3379	3422	19434	19434	2537	2537	9843	9843	1624	1624	61791	61952	7540	7583	False		
+format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	189	203	57	60	0	0	0	0	0	0	0	0	189	203	57	60	False		
+get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1542	1542	159	159	0	0	0	0	587	587	64	64	2129	2129	223	223	False		
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	7012	7344	323	338	0	0	0	0	0	0	0	0	7012	7344	323	338	False		
+guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	1	1	7	7	1	1	False		
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	103	103	4	4	103	103	4	4	False		
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	502	502	66	66	0	0	0	0	0	0	0	0	502	502	66	66	False		
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1819	1819	539	539	1334	1334	389	389	2472	2472	137	137	5625	5625	1065	1065	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	0	12	0	0	0	0	0	0	0	0	0	228	0	12	False		
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	337151	353499	10046	10719	699868	896164	26656	34018	87016	94859	5302	5695	1124035	1344522	42004	50432	False		
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	473	473	93	93	0	0	0	0	0	0	0	0	473	473	93	93	False		
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	1200	1220	187	195	1588	1588	267	267	0	0	0	0	2788	2808	454	462	False		
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	157	157	14	14	0	0	0	0	0	0	0	0	157	157	14	14	False		
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1825	1825	237	237	0	0	0	0	971	971	56	56	2796	2796	293	293	False		
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	8	8	8	0	1995	2091	174	193	1430	1430	389	389	1580	1580	56	56	5005	5101	619	638	False		
+length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	4349	4466	666	698	2093	2286	928	998	201	201	77	77	6643	6953	1671	1773	False		
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	171	27	30	0	0	0	0	0	0	0	0	149	171	27	30	False		
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	512	512	126	126	0	0	0	0	480	480	65	65	992	992	191	191	False		
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	12692	13292	1349	1400	16645	16645	2140	2140	6214	6214	431	431	35551	36151	3920	3971	False		
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	513	557	152	155	74	74	35	35	10	10	4	4	597	641	191	194	False		
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3150	3150	477	477	730	730	196	196	1183	1183	151	151	5063	5063	824	824	False		
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	573	573	3	3	0	0	0	0	0	0	0	0	573	573	3	3	False		
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7116	7116	256	256	0	0	0	0	278	278	60	60	7394	7394	316	316	False		
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13357	13479	554	562	8416	8416	448	448	898	898	85	85	22671	22793	1087	1095	False		
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1117	1117	116	116	0	0	0	0	295	295	25	25	1412	1412	141	141	False		
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1020	1020	176	176	414	414	73	73	277	277	20	20	1711	1711	269	269	False		
+msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	864	929	91	101	1100	1100	175	175	0	0	0	0	1964	2029	266	276	False		
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	182221	192389	19343	20494	163961	182413	26449	29758	40663	41855	5974	6157	386845	416657	51766	56409	False		
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	790	790	160	160	0	0	0	0	0	0	0	0	790	790	160	160	False		
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	391	391	158	158	0	0	0	0	0	0	0	0	391	391	158	158	False		
+nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	7780	7780	337	337	1	1	1	1	2323	2323	99	99	10104	10104	437	437	False		
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	3051	3051	87	87	0	0	0	0	0	0	0	0	3051	3051	87	87	False		
+pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	22	22	109	109	19	19	0	0	0	0	167	167	41	41	False		
+pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	6269	6866	260	292	5530	20068	467	1664	5647	8471	198	300	17446	35405	925	2256	False		
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	262015	262852	2627	2711	83623	83623	1918	1918	52558	52558	1037	1037	398196	399033	5582	5666	False		
+poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	13	0	19942	20587	1055	1245	33619	40808	2183	2594	9261	9261	365	365	62822	70656	3603	4204	False		
+prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10152	10626	253	281	10581	10581	1240	1240	0	0	0	0	20733	21207	1493	1521	False		
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17782	17782	287	287	853	853	65	65	2224	2224	65	65	20859	20859	417	417	False		
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22742	22742	557	557	2159	2159	716	716	776	776	448	448	25677	25677	1721	1721	False		
+qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	67737	69738	7787	7971	51925	56602	9692	10646	32003	34145	3890	4127	151665	160485	21369	22744	False		
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4844	4844	480	480	0	0	0	0	7	7	3	3	4851	4851	483	483	False		
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9477	9477	438	438	0	0	0	0	10585	10585	182	182	20062	20062	620	620	False		
+rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	655	655	57	57	0	0	0	0	0	0	0	0	655	655	57	57	False		
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1522	1522	254	254	372	372	75	75	5	5	1	1	1899	1899	330	330	False		
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	463	463	119	119	1038	1038	87	87	410	410	24	24	1911	1911	230	230	False		
+samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	Up-to-date	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.26	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3421	3859	340	382	883	883	109	109	1138	1138	15	15	5442	5880	464	506	False		
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6485	6549	720	726	10127	10127	1518	1518	238	238	37	37	16850	16914	2275	2281	False		
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	52099	55110	4053	4497	73194	108684	6930	9936	14771	15714	1222	1419	140064	179508	12205	15852	False		
+seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30300	32553	732	799	21726	31891	619	621	2886	2886	144	144	54912	67330	1495	1564	False		
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4322	4714	180	205	0	0	0	0	0	0	0	0	4322	4714	180	205	False		
+seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2196	3529	260	289	2196	3529	260	289	False		
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2424	2424	102	102	0	0	0	0	0	0	0	0	2424	2424	102	102	False		
+sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	913	913	308	308	0	0	0	0	568	568	73	73	1481	1481	381	381	False		
+short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	175	220	51	60	350	6657	85	1602	0	0	0	0	525	6877	136	1662	False		
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46125	47376	2273	2356	40577	40577	3971	3971	19960	21130	1085	1199	106662	109083	7329	7526	False		
+sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	0	18184	18937	555	608	10514	10514	1063	1063	0	0	0	0	28698	29451	1618	1671	False		
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	325	325	61	61	137	137	54	54	843	843	63	63	1305	1305	178	178	False		
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	3	9	3	0	82716	87113	8209	8526	120471	120475	14787	14790	54067	61541	5817	6653	257254	269129	28813	29969	False		
+spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	3	200	384	31	66	200	397	31	69	False		
+sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	0	3	3	3	0	364871	376580	16710	17342	583675	678448	53271	59638	48131	50455	5910	6181	996677	1105483	75891	83161	False		
+tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7011	8135	449	482	9473	28494	626	2183	850	1090	80	104	17334	37719	1155	2769	False		
+tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	36069	36922	5257	5431	25255	30822	5066	5826	7949	7949	1584	1584	69273	75693	11907	12841	False		
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	51	51	0	0	0	0	0	0	0	0	547	547	51	51	False		
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	229489	275008	5733	6500	228708	324716	11708	16638	22644	23869	1439	1527	480841	623593	18880	24665	False		
+trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	1	1	1	0	352353	383014	14547	15408	632385	839058	39323	49850	125340	139097	5268	5975	1110078	1361169	59138	71233	False		
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	14681	14681	265	265	0	0	0	0	4488	4488	147	147	19169	19169	412	412	False		
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	74120	77648	3798	3963	64946	90075	5451	7380	19516	20422	2010	2080	158582	188145	11259	13423	False		
+validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	112	38	38	0	0	0	0	0	0	0	0	112	112	38	38	False		
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	25171	27943	3899	4270	51187	51187	7557	7557	28546	28619	3585	3613	104904	107749	15041	15440	False		
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4715	5343	888	965	9575	9576	2117	2117	3271	5524	1050	1397	17561	20443	4055	4479	False		
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	48	25	25	0	0	0	0	0	0	0	0	48	48	25	25	False		
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1619	1715	337	376	0	0	0	0	0	0	0	0	1619	1715	337	376	False		
+xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	618	618	176	176	336	336	62	62	588	588	25	25	1542	1542	263	263	False		
diff --git a/communities/assembly/resources/tools_filtered_by_ts_categories.tsv b/communities/assembly/resources/tools_filtered_by_ts_categories.tsv
index 95725e88..ace928af 100644
--- a/communities/assembly/resources/tools_filtered_by_ts_categories.tsv
+++ b/communities/assembly/resources/tools_filtered_by_ts_categories.tsv
@@ -1,178 +1,178 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	False		
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278	False		
-adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	37	217	False		
-agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	42	481	False		
-align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	329	False		
-assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	26	257	False		
-bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	False		
-biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	False		
-blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499	False		
-blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	False		
-cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	101	7766	False		
-cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474	False		
-cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	False		
-clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	5090	232004	False		
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369	False		
-ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	107	107	107	0	1816	89530	False		
-fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	469	ucsc-fasplit	469		Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	242	2644	False		
-fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-fasta_compute_length	fasta_compute_length	Compute sequence length								To update		Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	380	7758	False		
-fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.13.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	35793	False		
-fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	350	48649	False		
-fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	68	2912	False		
-fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	461	29886	False		
-fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	29	774	False		
-fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	622	105935	False		
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	66	8676	False		
-fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	266	14222	False		
-fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1028	94802	False		
-fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	679	5765	False		
-fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	69	2503	False		
-fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	170	False		
-fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	122	8410	False		
-fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1087	17024	False		
-fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	245	16635	False		
-fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	196	3092	False		
-fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	51	1178	False		
-fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	11	220	False		
-fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1509	15172	False		
-fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastq_stats	fastq_stats	FASTQ Summary Statistics by column								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	221	4246	False		
-fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	419	13599	False		
-fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	93	12593	False		
-fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	210	9757	False		
-fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								Up-to-date		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	459	5676	False		
-fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	0	17447	1556625	False		
-fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1371	178178	False		
-fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	27	1810	False		
-fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	128	16591	False		
-fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	96	3333	False		
-fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	114	61218	False		
-fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	25	249	False		
-fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	63	2176	False		
-fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	68	2280	False		
-fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	156	10832	False		
-fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	205	13149	False		
-fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	426	26274	False		
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	617	30483	False		
-flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	14	331	False		
-flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	74	13759	False		
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904	False		
-format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	166	False		
-get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	False		
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651	False		
-guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	False		
-hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	False		
-hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	False		
-hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	4183	299104	False		
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	False		
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127	False		
-instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	False		
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	False		
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022	False		
-length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	322	4090	False		
-lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152	False		
-links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	False		
-make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530	False		
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475	False		
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	False		
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206	False		
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938	False		
-mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	False		
-mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	False		
-msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	803	False		
-multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	8320	162790	False		
-necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	False		
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	False		
-nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	162	6384	False		
-oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	39	2654	False		
-pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	150	4305	False		
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1046	185468	False		
-poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	6	13	0	409	18773	False		
-prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	70	7881	False		
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	False		
-pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123	False		
-qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567	False		
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
-ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	False		
-raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	False		
-rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	569	False		
-rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	109	1110	False		
-salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	84	454	False		
-samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	To update	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.24	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	False		
-samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	296	4948	False		
-samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1450	48426	False		
-seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	25302	False		
-seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	False		
-seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
-seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	154	763	False		
-short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	21	220	False		
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600	False		
-sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	269	14982	False		
-smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	False		
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953	False		
-spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	3	3	3	0	6247	350032	False		
-tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	200	7388	False		
-tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426	False		
-tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	False		
-trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	2334	238699	False		
-trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	1	1	1	0	5862	305866	False		
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	False		
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732	False		
-validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	86	False		
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420	False		
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741	False		
-verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	False		
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	False		
-xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	43	43	20	20	0	0	0	0	0	0	0	0	43	43	20	20	False		
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5543	5543	1042	1042	1301	1305	413	414	2030	2030	299	299	8874	8878	1754	1755	False		
+adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	348	348	62	62	0	0	0	0	0	0	0	0	348	348	62	62	False		
+agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	244	244	0	0	0	0	119	119	10	10	1555	1555	254	254	False		
+align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	511	541	32	35	0	0	0	0	0	0	0	0	511	541	32	35	False		
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	232	279	62	72	0	0	0	0	0	0	0	0	232	279	62	72	False		
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	617	617	63	63	617	617	63	63	False		
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	151	151	143	143	43	43	596	596	22	22	1286	1286	216	216	False		
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	3	1	1	0	0	0	0	0	0	0	0	3	3	1	1	False		
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24916	27120	283	347	0	0	0	0	0	0	0	0	24916	27120	283	347	False		
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1527	1527	79	79	6	6	1	1	317	317	26	26	1850	1850	106	106	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	9869	9869	158	158	0	0	0	0	6886	6886	146	146	16755	16755	304	304	False		
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10414	10414	510	510	2	2	1	1	2	2	1	1	10418	10418	512	512	False		
+cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	524	524	32	32	0	0	0	0	0	0	0	0	524	524	32	32	False		
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	259754	272370	11716	12601	334550	362356	18618	20162	64377	65986	3507	3627	658681	700712	33841	36390	False		
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	358	406	124	139	1361	1361	384	384	0	0	0	0	1719	1767	508	523	False		
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	28	28	2	2	0	0	0	0	0	0	0	0	28	28	2	2	False		
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	0	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	107	107	107	0	143762	148864	4481	5039	151989	296028	13224	31140	24955	27001	2397	2705	320706	471893	20102	38884	False		
+fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	469	ucsc-fasplit	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3278	3361	460	478	6144	6144	595	595	1139	1139	183	183	10561	10644	1238	1256	False		
+fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5191	5367	104	130	5191	5367	104	130	False		
+fasta_compute_length	fasta_compute_length	Compute sequence length								To update	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.4	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	8547	9136	978	1129	17748	51150	1404	5670	4239	4404	162	190	30534	64690	2544	6989	False		
+fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39695	39742	242	255	13660	19007	600	1398	1521	1603	92	112	54876	60352	934	1765	False		
+fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	47494	51924	889	997	50663	101663	1488	3742	3919	5601	241	276	102076	159188	2618	5015	False		
+fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	1	5235	5486	237	288	4060	25609	480	2039	816	1093	73	89	10111	32188	790	2416	False		
+fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	30917	32191	1142	1257	36869	36869	1346	1346	5236	5236	230	230	73022	74296	2718	2833	False		
+fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	497	808	71	108	2249	5479	216	703	415	437	18	20	3161	6724	305	831	False		
+fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	108876	113638	1572	1793	82527	192112	2209	8565	5711	7649	275	334	197114	313399	4056	10692	False		
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	136	11	11	0	0	0	0	0	0	0	0	136	136	11	11	False		
+fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8604	8799	215	240	54200	75329	919	2957	1562	1680	76	85	64366	85808	1210	3282	False		
+fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15582	18350	690	771	40489	121585	2715	9239	4657	5793	214	287	60728	145728	3619	10297	False		
+fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	92594	102535	2576	2995	179461	897457	9437	44701	15434	25533	664	1073	287489	1025525	12677	48769	False		
+fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7560	7560	1266	1266	6539	6539	1581	1581	0	0	0	0	14099	14099	2847	2847	False		
+fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2488	3132	215	267	6241	14508	834	2121	4121	4592	131	158	12850	22232	1180	2546	False		
+fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	234	249	43	44	2648	8092	288	983	442	466	12	17	3324	8807	343	1044	False		
+fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5873	8936	532	657	14738	20229	1889	2366	2316	2711	225	261	22927	31876	2646	3284	False		
+fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18216	19573	2348	2492	23484	25936	3482	3851	6207	6551	1402	1442	47907	52060	7232	7785	False		
+fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15628	17130	536	679	24157	58368	1954	5716	1941	2266	172	214	41726	77764	2662	6609	False		
+fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3169	3521	459	535	19309	30747	1410	3441	807	1023	219	247	23285	35291	2088	4223	False		
+fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1271	1393	131	176	12763	58819	2073	8850	430	479	32	51	14464	60691	2236	9077	False		
+fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	335	352	44	47	1583	9696	269	2229	1131	1254	15	27	3049	11302	328	2303	False		
+fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	17279	18386	3826	4062	55268	136888	6055	12590	7685	9356	1854	2043	80232	164630	11735	18695	False		
+fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_stats	fastq_stats	FASTQ Summary Statistics by column								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3858	4595	680	815	15213	81513	3159	14109	3855	4163	184	256	22926	90271	4023	15180	False		
+fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	36069	37805	1151	1234	45213	99852	2691	6370	8457	13335	408	609	89739	150992	4250	8213	False		
+fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	12895	14110	269	297	13315	30673	612	1810	5125	5373	64	87	31335	50156	945	2194	False		
+fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10114	11383	582	665	23906	92351	1986	8818	1588	2607	108	212	35608	106341	2676	9695	False		
+fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								To update		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4881	6165	859	967	29458	99179	3455	11369	2171	2678	259	338	36510	108022	4573	12674	False		
+fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	1	0	1784056	1913280	41344	43940	2269843	3195869	90828	140008	410004	445555	14195	16026	4463903	5554704	146367	199974	False		
+fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	3	0	0	0	0	0	8	0	3	False		
+fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	208349	217568	3421	3732	131388	245005	5108	13227	18655	18655	679	679	358392	481228	9208	17638	False		
+fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1769	2020	88	101	6948	24960	358	2424	623	998	32	50	9340	27978	478	2575	False		
+fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	16957	18124	225	260	37001	89126	919	2720	863	989	56	68	54821	108239	1200	3048	False		
+fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3140	3520	178	212	13975	117900	1198	6006	409	712	36	55	17524	122132	1412	6273	False		
+fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	64187	67981	326	349	87477	185555	781	3067	16563	17125	58	78	168227	270661	1165	3494	False		
+fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	174	272	61	92	4295	25068	1056	4180	1127	1171	70	89	5596	26511	1187	4361	False		
+fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2218	2344	168	206	20551	60032	3784	9866	2347	2460	234	256	25116	64836	4186	10328	False		
+fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2364	2526	180	214	6572	11745	303	1024	462	696	49	64	9398	14967	532	1302	False		
+fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10707	12597	356	415	21568	67304	574	1527	719	861	61	78	32994	80762	991	2020	False		
+fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	13584	14557	550	641	123676	206733	2034	8390	2819	4757	229	267	140079	226047	2813	9298	False		
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	1	1	1	1	False		
+filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	26717	29932	1026	1072	42990	42990	1176	1176	9619	9619	230	230	79326	82541	2432	2478	False		
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	53310	53944	1499	1575	25043	25043	726	726	10824	10824	593	593	89177	89811	2818	2894	False		
+flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	1985	1985	41	41	0	0	0	0	0	0	0	0	1985	1985	41	41	False		
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22017	22304	239	255	9399	14886	462	709	4	4	1	1	31420	37194	702	965	False		
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32514	32675	3379	3422	19434	19434	2537	2537	9843	9843	1624	1624	61791	61952	7540	7583	False		
+format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	189	203	57	60	0	0	0	0	0	0	0	0	189	203	57	60	False		
+get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1542	1542	159	159	0	0	0	0	587	587	64	64	2129	2129	223	223	False		
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	7012	7344	323	338	0	0	0	0	0	0	0	0	7012	7344	323	338	False		
+guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	1	1	7	7	1	1	False		
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	103	103	4	4	103	103	4	4	False		
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	502	502	66	66	0	0	0	0	0	0	0	0	502	502	66	66	False		
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1819	1819	539	539	1334	1334	389	389	2472	2472	137	137	5625	5625	1065	1065	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	0	12	0	0	0	0	0	0	0	0	0	228	0	12	False		
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	337151	353499	10046	10719	699868	896164	26656	34018	87016	94859	5302	5695	1124035	1344522	42004	50432	False		
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	473	473	93	93	0	0	0	0	0	0	0	0	473	473	93	93	False		
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	1200	1220	187	195	1588	1588	267	267	0	0	0	0	2788	2808	454	462	False		
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	157	157	14	14	0	0	0	0	0	0	0	0	157	157	14	14	False		
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1825	1825	237	237	0	0	0	0	971	971	56	56	2796	2796	293	293	False		
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	8	8	8	0	1995	2091	174	193	1430	1430	389	389	1580	1580	56	56	5005	5101	619	638	False		
+length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	4349	4466	666	698	2093	2286	928	998	201	201	77	77	6643	6953	1671	1773	False		
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	171	27	30	0	0	0	0	0	0	0	0	149	171	27	30	False		
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	512	512	126	126	0	0	0	0	480	480	65	65	992	992	191	191	False		
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	12692	13292	1349	1400	16645	16645	2140	2140	6214	6214	431	431	35551	36151	3920	3971	False		
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	513	557	152	155	74	74	35	35	10	10	4	4	597	641	191	194	False		
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3150	3150	477	477	730	730	196	196	1183	1183	151	151	5063	5063	824	824	False		
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	573	573	3	3	0	0	0	0	0	0	0	0	573	573	3	3	False		
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7116	7116	256	256	0	0	0	0	278	278	60	60	7394	7394	316	316	False		
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13357	13479	554	562	8416	8416	448	448	898	898	85	85	22671	22793	1087	1095	False		
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1117	1117	116	116	0	0	0	0	295	295	25	25	1412	1412	141	141	False		
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1020	1020	176	176	414	414	73	73	277	277	20	20	1711	1711	269	269	False		
+msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	864	929	91	101	1100	1100	175	175	0	0	0	0	1964	2029	266	276	False		
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	182221	192389	19343	20494	163961	182413	26449	29758	40663	41855	5974	6157	386845	416657	51766	56409	False		
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	790	790	160	160	0	0	0	0	0	0	0	0	790	790	160	160	False		
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	391	391	158	158	0	0	0	0	0	0	0	0	391	391	158	158	False		
+nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	7780	7780	337	337	1	1	1	1	2323	2323	99	99	10104	10104	437	437	False		
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	3051	3051	87	87	0	0	0	0	0	0	0	0	3051	3051	87	87	False		
+pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	22	22	109	109	19	19	0	0	0	0	167	167	41	41	False		
+pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	6269	6866	260	292	5530	20068	467	1664	5647	8471	198	300	17446	35405	925	2256	False		
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	262015	262852	2627	2711	83623	83623	1918	1918	52558	52558	1037	1037	398196	399033	5582	5666	False		
+poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	13	0	19942	20587	1055	1245	33619	40808	2183	2594	9261	9261	365	365	62822	70656	3603	4204	False		
+prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10152	10626	253	281	10581	10581	1240	1240	0	0	0	0	20733	21207	1493	1521	False		
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17782	17782	287	287	853	853	65	65	2224	2224	65	65	20859	20859	417	417	False		
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22742	22742	557	557	2159	2159	716	716	776	776	448	448	25677	25677	1721	1721	False		
+qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	67737	69738	7787	7971	51925	56602	9692	10646	32003	34145	3890	4127	151665	160485	21369	22744	False		
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4844	4844	480	480	0	0	0	0	7	7	3	3	4851	4851	483	483	False		
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9477	9477	438	438	0	0	0	0	10585	10585	182	182	20062	20062	620	620	False		
+rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	655	655	57	57	0	0	0	0	0	0	0	0	655	655	57	57	False		
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1522	1522	254	254	372	372	75	75	5	5	1	1	1899	1899	330	330	False		
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	463	463	119	119	1038	1038	87	87	410	410	24	24	1911	1911	230	230	False		
+samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	Up-to-date	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.26	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3421	3859	340	382	883	883	109	109	1138	1138	15	15	5442	5880	464	506	False		
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6485	6549	720	726	10127	10127	1518	1518	238	238	37	37	16850	16914	2275	2281	False		
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	52099	55110	4053	4497	73194	108684	6930	9936	14771	15714	1222	1419	140064	179508	12205	15852	False		
+seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30300	32553	732	799	21726	31891	619	621	2886	2886	144	144	54912	67330	1495	1564	False		
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4322	4714	180	205	0	0	0	0	0	0	0	0	4322	4714	180	205	False		
+seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2196	3529	260	289	2196	3529	260	289	False		
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2424	2424	102	102	0	0	0	0	0	0	0	0	2424	2424	102	102	False		
+sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	913	913	308	308	0	0	0	0	568	568	73	73	1481	1481	381	381	False		
+short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	175	220	51	60	350	6657	85	1602	0	0	0	0	525	6877	136	1662	False		
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46125	47376	2273	2356	40577	40577	3971	3971	19960	21130	1085	1199	106662	109083	7329	7526	False		
+sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	0	18184	18937	555	608	10514	10514	1063	1063	0	0	0	0	28698	29451	1618	1671	False		
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	325	325	61	61	137	137	54	54	843	843	63	63	1305	1305	178	178	False		
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	3	9	3	0	82716	87113	8209	8526	120471	120475	14787	14790	54067	61541	5817	6653	257254	269129	28813	29969	False		
+spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	3	200	384	31	66	200	397	31	69	False		
+sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	0	3	3	3	0	364871	376580	16710	17342	583675	678448	53271	59638	48131	50455	5910	6181	996677	1105483	75891	83161	False		
+tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7011	8135	449	482	9473	28494	626	2183	850	1090	80	104	17334	37719	1155	2769	False		
+tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	36069	36922	5257	5431	25255	30822	5066	5826	7949	7949	1584	1584	69273	75693	11907	12841	False		
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	51	51	0	0	0	0	0	0	0	0	547	547	51	51	False		
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	229489	275008	5733	6500	228708	324716	11708	16638	22644	23869	1439	1527	480841	623593	18880	24665	False		
+trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	1	1	1	0	352353	383014	14547	15408	632385	839058	39323	49850	125340	139097	5268	5975	1110078	1361169	59138	71233	False		
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	14681	14681	265	265	0	0	0	0	4488	4488	147	147	19169	19169	412	412	False		
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	74120	77648	3798	3963	64946	90075	5451	7380	19516	20422	2010	2080	158582	188145	11259	13423	False		
+validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	112	38	38	0	0	0	0	0	0	0	0	112	112	38	38	False		
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	25171	27943	3899	4270	51187	51187	7557	7557	28546	28619	3585	3613	104904	107749	15041	15440	False		
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4715	5343	888	965	9575	9576	2117	2117	3271	5524	1050	1397	17561	20443	4055	4479	False		
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	48	25	25	0	0	0	0	0	0	0	0	48	48	25	25	False		
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1619	1715	337	376	0	0	0	0	0	0	0	0	1619	1715	337	376	False		
+xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	618	618	176	176	336	336	62	62	588	588	25	25	1542	1542	263	263	False		
diff --git a/communities/assembly/resources/tools_wordcloud.png b/communities/assembly/resources/tools_wordcloud.png
index 21d4135e..648842f5 100644
Binary files a/communities/assembly/resources/tools_wordcloud.png and b/communities/assembly/resources/tools_wordcloud.png differ
diff --git a/communities/biodiversity/resources/tools.html b/communities/biodiversity/resources/tools.html
index ce8795c7..1bff9ccd 100644
--- a/communities/biodiversity/resources/tools.html
+++ b/communities/biodiversity/resources/tools.html
@@ -95,7 +95,6 @@
       <th>Tools available on CoralSNP</th>
       <th>Tools available on CropGalaxy</th>
       <th>Tools available on Dintor</th>
-      <th>Tools available on FreeBioinfo</th>
       <th>Tools available on GASLINI</th>
       <th>Tools available on Galaxy@AuBi</th>
       <th>Tools available on Galaxy@Pasteur</th>
@@ -112,12 +111,27 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
+      <th>Tools available on PhagePromotor</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
       <th>Tools available on Viral Variant Visualizer (VVV)</th>
-      <th>No. of tool users (2022-2023) (usegalaxy.eu)</th>
-      <th>Total tool usage (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.eu)</th>
+      <th>No. of tool users (all time) (usegalaxy.eu)</th>
+      <th>Tool usage (5 years) (usegalaxy.eu)</th>
+      <th>Tool usage (all time) (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org)</th>
+      <th>No. of tool users (all time) (usegalaxy.org)</th>
+      <th>Tool usage (5 years) (usegalaxy.org)</th>
+      <th>Tool usage (all time) (usegalaxy.org)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org.au)</th>
+      <th>No. of tool users (all time) (usegalaxy.org.au)</th>
+      <th>Tool usage (5 years) (usegalaxy.org.au)</th>
+      <th>Tool usage (all time) (usegalaxy.org.au)</th>
+      <th>No. of tool users (5 years) - all main servers</th>
+      <th>No. of tool users (all time) - all main servers</th>
+      <th>Tool usage (5 years) - all main servers</th>
+      <th>Tool usage (all time) - all main servers</th>
       <th>Deprecated</th>
     </tr>
   </thead>
@@ -149,11 +163,11 @@
       <td>0</td>
       <td>0</td>
       <td>11</td>
-      <td>9</td>
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@@ -183,8 +197,22 @@
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-      <td>5</td>
-      <td>102</td>
+      <td>516</td>
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+      <td>516</td>
+      <td>128</td>
+      <td>128</td>
       <td></td>
     </tr>
     <tr>
@@ -214,11 +242,11 @@
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       <td>0</td>
       <td>6</td>
-      <td>5</td>
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       <td>6</td>
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@@ -248,8 +276,22 @@
       <td>5</td>
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       <td>0</td>
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+      <td>352</td>
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       <td></td>
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@@ -279,11 +321,10 @@
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@@ -314,7 +355,22 @@
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+      <td>53</td>
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+      <td>18</td>
       <td></td>
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@@ -344,11 +400,11 @@
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@@ -378,8 +434,22 @@
       <td>5</td>
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-      <td>73</td>
-      <td>1004</td>
+      <td>1038</td>
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+      <td>184</td>
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       <td></td>
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@@ -443,8 +513,22 @@
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-      <td>8</td>
-      <td>42</td>
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       <td></td>
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@@ -474,11 +558,10 @@
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@@ -510,6 +593,21 @@
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@@ -539,9 +637,8 @@
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-      <td>1</td>
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@@ -569,12 +666,27 @@
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-      <td>391</td>
-      <td>4278</td>
+      <td>5543</td>
+      <td>5543</td>
+      <td>1042</td>
+      <td>1042</td>
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+      <td>2030</td>
+      <td>2030</td>
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+      <td>8874</td>
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+      <td>1754</td>
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@@ -604,8 +716,7 @@
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@@ -634,12 +745,27 @@
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@@ -703,8 +829,22 @@
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@@ -799,11 +953,25 @@
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@@ -880,7 +1048,6 @@
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-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -900,6 +1067,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -965,6 +1147,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1030,6 +1226,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1093,8 +1303,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>112</td>
-      <td>531</td>
+      <td>547</td>
+      <td>547</td>
+      <td>151</td>
+      <td>151</td>
+      <td>143</td>
+      <td>143</td>
+      <td>43</td>
+      <td>43</td>
+      <td>596</td>
+      <td>596</td>
+      <td>22</td>
+      <td>22</td>
+      <td>1286</td>
+      <td>1286</td>
+      <td>216</td>
+      <td>216</td>
       <td></td>
     </tr>
     <tr>
@@ -1160,6 +1384,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6243</td>
+      <td>6243</td>
+      <td>375</td>
+      <td>375</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6243</td>
+      <td>6243</td>
+      <td>375</td>
+      <td>375</td>
       <td></td>
     </tr>
     <tr>
@@ -1223,8 +1461,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>3</td>
+      <td>3</td>
       <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
       <td>3</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -1269,7 +1521,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1290,6 +1541,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -1334,7 +1600,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1355,6 +1620,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -1400,7 +1680,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1420,6 +1699,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1483,8 +1777,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>21</td>
-      <td>685</td>
+      <td>1527</td>
+      <td>1527</td>
+      <td>79</td>
+      <td>79</td>
+      <td>6</td>
+      <td>6</td>
+      <td>1</td>
+      <td>1</td>
+      <td>317</td>
+      <td>317</td>
+      <td>26</td>
+      <td>26</td>
+      <td>1850</td>
+      <td>1850</td>
+      <td>106</td>
+      <td>106</td>
       <td></td>
     </tr>
     <tr>
@@ -1548,8 +1856,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>17</td>
-      <td>109</td>
+      <td>165</td>
+      <td>165</td>
+      <td>48</td>
+      <td>48</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>165</td>
+      <td>165</td>
+      <td>48</td>
+      <td>48</td>
       <td></td>
     </tr>
     <tr>
@@ -1579,11 +1901,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -1613,8 +1935,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>10</td>
-      <td>567</td>
+      <td>1938</td>
+      <td>1938</td>
+      <td>294</td>
+      <td>294</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>412</td>
+      <td>412</td>
+      <td>71</td>
+      <td>71</td>
+      <td>2350</td>
+      <td>2350</td>
+      <td>365</td>
+      <td>365</td>
       <td></td>
     </tr>
     <tr>
@@ -1659,7 +1995,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -1675,11 +2010,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>101</td>
-      <td>7766</td>
+      <td>9869</td>
+      <td>9869</td>
+      <td>158</td>
+      <td>158</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6886</td>
+      <td>6886</td>
+      <td>146</td>
+      <td>146</td>
+      <td>16755</td>
+      <td>16755</td>
+      <td>304</td>
+      <td>304</td>
       <td></td>
     </tr>
     <tr>
@@ -1709,11 +2059,11 @@
       <td>0</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -1743,8 +2093,22 @@
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>19</td>
-      <td>174</td>
+      <td>183</td>
+      <td>183</td>
+      <td>20</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>183</td>
+      <td>183</td>
+      <td>20</td>
+      <td>20</td>
       <td></td>
     </tr>
     <tr>
@@ -1797,7 +2161,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1805,11 +2168,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>418</td>
-      <td>15690</td>
+      <td>16468</td>
+      <td>18344</td>
+      <td>956</td>
+      <td>991</td>
+      <td>33692</td>
+      <td>34453</td>
+      <td>2559</td>
+      <td>2625</td>
+      <td>2948</td>
+      <td>2948</td>
+      <td>104</td>
+      <td>104</td>
+      <td>53108</td>
+      <td>55745</td>
+      <td>3619</td>
+      <td>3720</td>
       <td></td>
     </tr>
     <tr>
@@ -1873,8 +2251,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>16</td>
-      <td>269</td>
+      <td>524</td>
+      <td>524</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>524</td>
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+      <td>32</td>
+      <td>32</td>
       <td></td>
     </tr>
     <tr>
@@ -1940,6 +2332,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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       <td></td>
     </tr>
     <tr>
@@ -2005,6 +2411,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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       <td></td>
     </tr>
     <tr>
@@ -2050,7 +2470,6 @@
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       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2070,6 +2489,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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       <td></td>
     </tr>
     <tr>
@@ -2115,7 +2549,6 @@
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       <td>0</td>
-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -2135,6 +2568,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
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       <td></td>
     </tr>
     <tr>
@@ -2164,11 +2612,11 @@
       <td>0</td>
       <td>0</td>
       <td>6</td>
-      <td>6</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>6</td>
-      <td>6</td>
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       <td>0</td>
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@@ -2198,8 +2646,22 @@
       <td>6</td>
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       <td>0</td>
-      <td>146</td>
-      <td>658</td>
+      <td>967</td>
+      <td>967</td>
+      <td>308</td>
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+      <td>0</td>
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+      <td>967</td>
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+      <td>308</td>
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       <td></td>
     </tr>
     <tr>
@@ -2229,10 +2691,9 @@
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       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
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@@ -2264,7 +2725,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
+      <td>65</td>
+      <td>65</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
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+      <td>65</td>
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+      <td>37</td>
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       <td></td>
     </tr>
     <tr>
@@ -2310,7 +2786,6 @@
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-      <td>0</td>
       <td>1</td>
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       <td>0</td>
@@ -2324,12 +2799,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>42</td>
-      <td>369</td>
+      <td>358</td>
+      <td>406</td>
+      <td>124</td>
+      <td>139</td>
+      <td>1361</td>
+      <td>1361</td>
+      <td>384</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>1719</td>
+      <td>1767</td>
+      <td>508</td>
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       <td></td>
     </tr>
     <tr>
@@ -2395,6 +2885,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td></td>
     </tr>
     <tr>
@@ -2458,8 +2962,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>28</td>
+      <td>28</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
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+      <td>0</td>
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       <td>0</td>
+      <td>0</td>
+      <td>28</td>
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       <td></td>
     </tr>
     <tr>
@@ -2525,6 +3043,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td></td>
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     <tr>
@@ -2588,8 +3120,22 @@
       <td>0</td>
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       <td>0</td>
+      <td>136</td>
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       <td></td>
     </tr>
     <tr>
@@ -2655,6 +3201,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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     <tr>
@@ -2700,7 +3260,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2720,6 +3279,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2765,7 +3339,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2779,12 +3352,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>74</td>
-      <td>13759</td>
+      <td>22017</td>
+      <td>22304</td>
+      <td>239</td>
+      <td>255</td>
+      <td>9399</td>
+      <td>14886</td>
+      <td>462</td>
+      <td>709</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>31420</td>
+      <td>37194</td>
+      <td>702</td>
+      <td>965</td>
       <td></td>
     </tr>
     <tr>
@@ -2814,8 +3402,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2844,12 +3431,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1499</td>
-      <td>20904</td>
+      <td>32514</td>
+      <td>32675</td>
+      <td>3379</td>
+      <td>3422</td>
+      <td>19434</td>
+      <td>19434</td>
+      <td>2537</td>
+      <td>2537</td>
+      <td>9843</td>
+      <td>9843</td>
+      <td>1624</td>
+      <td>1624</td>
+      <td>61791</td>
+      <td>61952</td>
+      <td>7540</td>
+      <td>7583</td>
       <td></td>
     </tr>
     <tr>
@@ -2879,11 +3481,11 @@
       <td>3</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>3</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2913,8 +3515,22 @@
       <td>5</td>
       <td>0</td>
       <td>0</td>
-      <td>900</td>
-      <td>5906</td>
+      <td>8648</td>
+      <td>8648</td>
+      <td>1408</td>
+      <td>1408</td>
+      <td>32</td>
+      <td>32</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6406</td>
+      <td>6406</td>
+      <td>597</td>
+      <td>597</td>
+      <td>15086</td>
+      <td>15086</td>
+      <td>2011</td>
+      <td>2011</td>
       <td></td>
     </tr>
     <tr>
@@ -2944,11 +3560,11 @@
       <td>0</td>
       <td>0</td>
       <td>8</td>
-      <td>8</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>8</td>
-      <td>8</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -2978,8 +3594,22 @@
       <td>8</td>
       <td>8</td>
       <td>0</td>
-      <td>10</td>
-      <td>1475</td>
+      <td>1409</td>
+      <td>1498</td>
+      <td>39</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1409</td>
+      <td>1498</td>
+      <td>39</td>
+      <td>42</td>
       <td></td>
     </tr>
     <tr>
@@ -3043,8 +3673,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>18</td>
-      <td>495</td>
+      <td>1542</td>
+      <td>1542</td>
+      <td>159</td>
+      <td>159</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>587</td>
+      <td>587</td>
+      <td>64</td>
+      <td>64</td>
+      <td>2129</td>
+      <td>2129</td>
+      <td>223</td>
+      <td>223</td>
       <td></td>
     </tr>
     <tr>
@@ -3074,8 +3718,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -3104,12 +3747,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>408</td>
-      <td>5484</td>
+      <td>5800</td>
+      <td>6212</td>
+      <td>826</td>
+      <td>871</td>
+      <td>7756</td>
+      <td>7756</td>
+      <td>1048</td>
+      <td>1048</td>
+      <td>1149</td>
+      <td>1149</td>
+      <td>215</td>
+      <td>215</td>
+      <td>14705</td>
+      <td>15117</td>
+      <td>2089</td>
+      <td>2134</td>
       <td></td>
     </tr>
     <tr>
@@ -3155,7 +3813,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -3169,12 +3826,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>136</td>
-      <td>6651</td>
+      <td>7012</td>
+      <td>7344</td>
+      <td>323</td>
+      <td>338</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7012</td>
+      <td>7344</td>
+      <td>323</td>
+      <td>338</td>
       <td></td>
     </tr>
     <tr>
@@ -3240,6 +3912,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>103</td>
+      <td>103</td>
+      <td>4</td>
+      <td>4</td>
+      <td>103</td>
+      <td>103</td>
+      <td>4</td>
+      <td>4</td>
       <td></td>
     </tr>
     <tr>
@@ -3269,11 +3955,11 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3303,8 +3989,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>36</td>
-      <td>295</td>
+      <td>502</td>
+      <td>502</td>
+      <td>66</td>
+      <td>66</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>502</td>
+      <td>502</td>
+      <td>66</td>
+      <td>66</td>
       <td></td>
     </tr>
     <tr>
@@ -3334,9 +4034,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -3365,11 +4064,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>93</td>
+      <td>267</td>
+      <td>267</td>
+      <td>39</td>
+      <td>39</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>80</td>
+      <td>80</td>
+      <td>7</td>
+      <td>7</td>
+      <td>347</td>
+      <td>347</td>
+      <td>46</td>
+      <td>46</td>
       <td></td>
     </tr>
     <tr>
@@ -3399,8 +4113,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3430,11 +4143,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>297</td>
-      <td>1410</td>
+      <td>1819</td>
+      <td>1819</td>
+      <td>539</td>
+      <td>539</td>
+      <td>1334</td>
+      <td>1334</td>
+      <td>389</td>
+      <td>389</td>
+      <td>2472</td>
+      <td>2472</td>
+      <td>137</td>
+      <td>137</td>
+      <td>5625</td>
+      <td>5625</td>
+      <td>1065</td>
+      <td>1065</td>
       <td></td>
     </tr>
     <tr>
@@ -3498,8 +4226,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>2</td>
+      <td>2</td>
       <td></td>
     </tr>
     <tr>
@@ -3545,7 +4287,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3564,7 +4305,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>228</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>228</td>
+      <td>0</td>
+      <td>12</td>
       <td></td>
     </tr>
     <tr>
@@ -3594,8 +4350,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3624,12 +4379,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>4183</td>
-      <td>299104</td>
+      <td>337151</td>
+      <td>353499</td>
+      <td>10046</td>
+      <td>10719</td>
+      <td>699868</td>
+      <td>896164</td>
+      <td>26656</td>
+      <td>34018</td>
+      <td>87016</td>
+      <td>94859</td>
+      <td>5302</td>
+      <td>5695</td>
+      <td>1124035</td>
+      <td>1344522</td>
+      <td>42004</td>
+      <td>50432</td>
       <td></td>
     </tr>
     <tr>
@@ -3693,8 +4463,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>39</td>
-      <td>354</td>
+      <td>473</td>
+      <td>473</td>
+      <td>93</td>
+      <td>93</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>473</td>
+      <td>93</td>
+      <td>93</td>
       <td></td>
     </tr>
     <tr>
@@ -3740,7 +4524,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3760,6 +4543,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3789,10 +4587,9 @@
       <td>3</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
       <td>0</td>
       <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -3819,12 +4616,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>69</td>
-      <td>1127</td>
+      <td>1200</td>
+      <td>1220</td>
+      <td>187</td>
+      <td>195</td>
+      <td>1588</td>
+      <td>1588</td>
+      <td>267</td>
+      <td>267</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2788</td>
+      <td>2808</td>
+      <td>454</td>
+      <td>462</td>
       <td></td>
     </tr>
     <tr>
@@ -3888,8 +4700,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>157</td>
+      <td>157</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>157</td>
+      <td>157</td>
+      <td>14</td>
       <td>14</td>
-      <td>139</td>
       <td></td>
     </tr>
     <tr>
@@ -3953,8 +4779,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>7</td>
+      <td>7</td>
       <td></td>
     </tr>
     <tr>
@@ -3984,9 +4824,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4015,11 +4854,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>91</td>
-      <td>1138</td>
+      <td>1825</td>
+      <td>1825</td>
+      <td>237</td>
+      <td>237</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>971</td>
+      <td>971</td>
+      <td>56</td>
+      <td>56</td>
+      <td>2796</td>
+      <td>2796</td>
+      <td>293</td>
+      <td>293</td>
       <td></td>
     </tr>
     <tr>
@@ -4064,7 +4918,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4079,12 +4932,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
-      <td>63</td>
-      <td>2022</td>
+      <td>1995</td>
+      <td>2091</td>
+      <td>174</td>
+      <td>193</td>
+      <td>1430</td>
+      <td>1430</td>
+      <td>389</td>
+      <td>389</td>
+      <td>1580</td>
+      <td>1580</td>
+      <td>56</td>
+      <td>56</td>
+      <td>5005</td>
+      <td>5101</td>
+      <td>619</td>
+      <td>638</td>
       <td></td>
     </tr>
     <tr>
@@ -4130,7 +4998,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4145,11 +5012,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>77</td>
-      <td>405</td>
+      <td>512</td>
+      <td>512</td>
+      <td>126</td>
+      <td>126</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>480</td>
+      <td>480</td>
+      <td>65</td>
+      <td>65</td>
+      <td>992</td>
+      <td>992</td>
+      <td>191</td>
+      <td>191</td>
       <td></td>
     </tr>
     <tr>
@@ -4213,8 +5095,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>51</td>
+      <td>51</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>51</td>
+      <td>51</td>
+      <td>4</td>
+      <td>4</td>
       <td></td>
     </tr>
     <tr>
@@ -4252,7 +5148,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4278,8 +5174,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>20</td>
+      <td>25</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
       <td>0</td>
-      <td>24</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>25</td>
+      <td>3</td>
+      <td>3</td>
       <td></td>
     </tr>
     <tr>
@@ -4343,8 +5253,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>9</td>
+      <td>9</td>
       <td></td>
     </tr>
     <tr>
@@ -4374,8 +5298,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4404,12 +5327,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>548</td>
-      <td>9530</td>
+      <td>12692</td>
+      <td>13292</td>
+      <td>1349</td>
+      <td>1400</td>
+      <td>16645</td>
+      <td>16645</td>
+      <td>2140</td>
+      <td>2140</td>
+      <td>6214</td>
+      <td>6214</td>
+      <td>431</td>
+      <td>431</td>
+      <td>35551</td>
+      <td>36151</td>
+      <td>3920</td>
+      <td>3971</td>
       <td></td>
     </tr>
     <tr>
@@ -4439,8 +5377,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4470,11 +5407,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>54</td>
-      <td>475</td>
+      <td>513</td>
+      <td>557</td>
+      <td>152</td>
+      <td>155</td>
+      <td>74</td>
+      <td>74</td>
+      <td>35</td>
+      <td>35</td>
+      <td>10</td>
+      <td>10</td>
+      <td>4</td>
+      <td>4</td>
+      <td>597</td>
+      <td>641</td>
+      <td>191</td>
+      <td>194</td>
       <td></td>
     </tr>
     <tr>
@@ -4504,11 +5456,11 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -4538,8 +5490,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>244</td>
-      <td>2483</td>
+      <td>3150</td>
+      <td>3150</td>
+      <td>477</td>
+      <td>477</td>
+      <td>730</td>
+      <td>730</td>
+      <td>196</td>
+      <td>196</td>
+      <td>1183</td>
+      <td>1183</td>
+      <td>151</td>
+      <td>151</td>
+      <td>5063</td>
+      <td>5063</td>
+      <td>824</td>
+      <td>824</td>
       <td></td>
     </tr>
     <tr>
@@ -4605,6 +5571,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -4626,7 +5606,7 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk</td>
-      <td>5.34c21f2</td>
+      <td>7.bba0d80</td>
       <td>metaeuk</td>
       <td>6.a5d39d9</td>
       <td>Homology-based gene prediction</td>
@@ -4668,8 +5648,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>16</td>
-      <td>184</td>
+      <td>312</td>
+      <td>312</td>
+      <td>40</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>312</td>
+      <td>312</td>
+      <td>40</td>
+      <td>40</td>
       <td></td>
     </tr>
     <tr>
@@ -4715,7 +5709,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4729,12 +5722,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>109</td>
-      <td>2206</td>
+      <td>7116</td>
+      <td>7116</td>
+      <td>256</td>
+      <td>256</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>278</td>
+      <td>278</td>
+      <td>60</td>
+      <td>60</td>
+      <td>7394</td>
+      <td>7394</td>
+      <td>316</td>
+      <td>316</td>
       <td></td>
     </tr>
     <tr>
@@ -4764,8 +5772,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4794,12 +5801,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>178</td>
-      <td>11938</td>
+      <td>13357</td>
+      <td>13479</td>
+      <td>554</td>
+      <td>562</td>
+      <td>8416</td>
+      <td>8416</td>
+      <td>448</td>
+      <td>448</td>
+      <td>898</td>
+      <td>898</td>
+      <td>85</td>
+      <td>85</td>
+      <td>22671</td>
+      <td>22793</td>
+      <td>1087</td>
+      <td>1095</td>
       <td></td>
     </tr>
     <tr>
@@ -4845,7 +5867,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4860,11 +5881,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>66</td>
-      <td>881</td>
+      <td>1117</td>
+      <td>1117</td>
+      <td>116</td>
+      <td>116</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>295</td>
+      <td>295</td>
+      <td>25</td>
+      <td>25</td>
+      <td>1412</td>
+      <td>1412</td>
+      <td>141</td>
+      <td>141</td>
       <td></td>
     </tr>
     <tr>
@@ -4910,7 +5946,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4925,11 +5960,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>56</td>
-      <td>613</td>
+      <td>1020</td>
+      <td>1020</td>
+      <td>176</td>
+      <td>176</td>
+      <td>414</td>
+      <td>414</td>
+      <td>73</td>
+      <td>73</td>
+      <td>277</td>
+      <td>277</td>
+      <td>20</td>
+      <td>20</td>
+      <td>1711</td>
+      <td>1711</td>
+      <td>269</td>
+      <td>269</td>
       <td></td>
     </tr>
     <tr>
@@ -4995,6 +6045,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>6</td>
+      <td>6</td>
       <td></td>
     </tr>
     <tr>
@@ -5058,8 +6122,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>95</td>
-      <td>667</td>
+      <td>790</td>
+      <td>790</td>
+      <td>160</td>
+      <td>160</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>790</td>
+      <td>790</td>
+      <td>160</td>
+      <td>160</td>
       <td></td>
     </tr>
     <tr>
@@ -5086,13 +6164,21 @@
       <td>2.5.2</td>
       <td>De-novo assembly, Genome assembly</td>
       <td>Sequencing, Sequence assembly</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5112,19 +6198,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>391</td>
+      <td>391</td>
+      <td>158</td>
+      <td>158</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>84</td>
-      <td>268</td>
+      <td>391</td>
+      <td>391</td>
+      <td>158</td>
+      <td>158</td>
       <td></td>
     </tr>
     <tr>
@@ -5154,9 +6246,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5184,12 +6275,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>162</td>
-      <td>6384</td>
+      <td>7780</td>
+      <td>7780</td>
+      <td>337</td>
+      <td>337</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2323</td>
+      <td>2323</td>
+      <td>99</td>
+      <td>99</td>
+      <td>10104</td>
+      <td>10104</td>
+      <td>437</td>
+      <td>437</td>
       <td></td>
     </tr>
     <tr>
@@ -5234,7 +6340,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5255,6 +6360,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5284,11 +6404,11 @@
       <td>1</td>
       <td>0</td>
       <td>2</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>2</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5318,8 +6438,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
-      <td>45</td>
+      <td>352</td>
+      <td>352</td>
+      <td>42</td>
+      <td>42</td>
+      <td>8</td>
+      <td>8</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>360</td>
+      <td>360</td>
+      <td>48</td>
+      <td>48</td>
       <td></td>
     </tr>
     <tr>
@@ -5383,7 +6517,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
       <td>6</td>
       <td></td>
     </tr>
@@ -5448,8 +6596,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>98</td>
+      <td>98</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>98</td>
+      <td>6</td>
+      <td>6</td>
       <td></td>
     </tr>
     <tr>
@@ -5513,8 +6675,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>4</td>
+      <td>4</td>
       <td></td>
     </tr>
     <tr>
@@ -5560,7 +6736,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5575,11 +6750,26 @@
       <td>0</td>
       <td>1</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>74</td>
-      <td>2565</td>
+      <td>5462</td>
+      <td>5462</td>
+      <td>334</td>
+      <td>334</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>309</td>
+      <td>309</td>
+      <td>52</td>
+      <td>52</td>
+      <td>5771</td>
+      <td>5771</td>
+      <td>386</td>
+      <td>386</td>
       <td></td>
     </tr>
     <tr>
@@ -5624,7 +6814,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5645,6 +6834,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5674,9 +6878,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5687,7 +6890,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5709,7 +6912,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1902</td>
+      <td>1902</td>
+      <td>167</td>
+      <td>167</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>1902</td>
+      <td>1902</td>
+      <td>167</td>
+      <td>167</td>
       <td></td>
     </tr>
     <tr>
@@ -5775,6 +6993,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5838,8 +7070,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>167</td>
-      <td>16800</td>
+      <td>17782</td>
+      <td>17782</td>
+      <td>287</td>
+      <td>287</td>
+      <td>853</td>
+      <td>853</td>
+      <td>65</td>
+      <td>65</td>
+      <td>2224</td>
+      <td>2224</td>
+      <td>65</td>
+      <td>65</td>
+      <td>20859</td>
+      <td>20859</td>
+      <td>417</td>
+      <td>417</td>
       <td></td>
     </tr>
     <tr>
@@ -5869,8 +7115,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -5899,12 +7144,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3567</td>
-      <td>51567</td>
+      <td>67737</td>
+      <td>69738</td>
+      <td>7787</td>
+      <td>7971</td>
+      <td>51925</td>
+      <td>56602</td>
+      <td>9692</td>
+      <td>10646</td>
+      <td>32003</td>
+      <td>34145</td>
+      <td>3890</td>
+      <td>4127</td>
+      <td>151665</td>
+      <td>160485</td>
+      <td>21369</td>
+      <td>22744</td>
       <td></td>
     </tr>
     <tr>
@@ -5923,7 +7183,7 @@
       <td>https://github.com/mahulchak/quickmerge</td>
       <td>Assembly</td>
       <td>quickmerge</td>
-      <td>galaxy-australia</td>
+      <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge</td>
       <td>0.3</td>
@@ -5970,6 +7230,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -5999,9 +7273,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6030,11 +7303,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>237</td>
-      <td>2833</td>
+      <td>4844</td>
+      <td>4844</td>
+      <td>480</td>
+      <td>480</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>3</td>
+      <td>3</td>
+      <td>4851</td>
+      <td>4851</td>
+      <td>483</td>
+      <td>483</td>
       <td></td>
     </tr>
     <tr>
@@ -6064,9 +7352,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -6095,11 +7382,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>262</td>
-      <td>6902</td>
+      <td>9477</td>
+      <td>9477</td>
+      <td>438</td>
+      <td>438</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10585</td>
+      <td>10585</td>
+      <td>182</td>
+      <td>182</td>
+      <td>20062</td>
+      <td>20062</td>
+      <td>620</td>
+      <td>620</td>
       <td></td>
     </tr>
     <tr>
@@ -6129,11 +7431,11 @@
       <td>0</td>
       <td>0</td>
       <td>7</td>
-      <td>7</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>7</td>
-      <td>7</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6163,8 +7465,22 @@
       <td>7</td>
       <td>7</td>
       <td>0</td>
-      <td>22</td>
-      <td>526</td>
+      <td>438</td>
+      <td>542</td>
+      <td>128</td>
+      <td>157</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>438</td>
+      <td>542</td>
+      <td>128</td>
+      <td>157</td>
       <td></td>
     </tr>
     <tr>
@@ -6228,8 +7544,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>95</td>
+      <td>95</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
-      <td>16</td>
+      <td>95</td>
+      <td>95</td>
+      <td>38</td>
+      <td>38</td>
       <td></td>
     </tr>
     <tr>
@@ -6259,8 +7589,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -6290,11 +7619,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>217</td>
-      <td>1177</td>
+      <td>7963</td>
+      <td>7963</td>
+      <td>413</td>
+      <td>413</td>
+      <td>1485</td>
+      <td>1485</td>
+      <td>220</td>
+      <td>220</td>
+      <td>8402</td>
+      <td>8402</td>
+      <td>168</td>
+      <td>168</td>
+      <td>17850</td>
+      <td>17850</td>
+      <td>801</td>
+      <td>801</td>
       <td></td>
     </tr>
     <tr>
@@ -6358,8 +7702,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -6389,11 +7747,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6423,8 +7781,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>109</td>
-      <td>1110</td>
+      <td>1522</td>
+      <td>1522</td>
+      <td>254</td>
+      <td>254</td>
+      <td>372</td>
+      <td>372</td>
+      <td>75</td>
+      <td>75</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1899</td>
+      <td>1899</td>
+      <td>330</td>
+      <td>330</td>
       <td></td>
     </tr>
     <tr>
@@ -6470,7 +7842,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6484,12 +7855,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>84</td>
-      <td>454</td>
+      <td>463</td>
+      <td>463</td>
+      <td>119</td>
+      <td>119</td>
+      <td>1038</td>
+      <td>1038</td>
+      <td>87</td>
+      <td>87</td>
+      <td>410</td>
+      <td>410</td>
+      <td>24</td>
+      <td>24</td>
+      <td>1911</td>
+      <td>1911</td>
+      <td>230</td>
+      <td>230</td>
       <td></td>
     </tr>
     <tr>
@@ -6519,8 +7905,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -6550,11 +7935,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>149</td>
-      <td>3765</td>
+      <td>3421</td>
+      <td>3859</td>
+      <td>340</td>
+      <td>382</td>
+      <td>883</td>
+      <td>883</td>
+      <td>109</td>
+      <td>109</td>
+      <td>1138</td>
+      <td>1138</td>
+      <td>15</td>
+      <td>15</td>
+      <td>5442</td>
+      <td>5880</td>
+      <td>464</td>
+      <td>506</td>
       <td></td>
     </tr>
     <tr>
@@ -6620,6 +8020,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -6649,8 +8063,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -6679,12 +8092,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>296</td>
-      <td>4948</td>
+      <td>6485</td>
+      <td>6549</td>
+      <td>720</td>
+      <td>726</td>
+      <td>10127</td>
+      <td>10127</td>
+      <td>1518</td>
+      <td>1518</td>
+      <td>238</td>
+      <td>238</td>
+      <td>37</td>
+      <td>37</td>
+      <td>16850</td>
+      <td>16914</td>
+      <td>2275</td>
+      <td>2281</td>
       <td></td>
     </tr>
     <tr>
@@ -6714,8 +8142,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -6744,12 +8171,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1450</td>
-      <td>48426</td>
+      <td>52099</td>
+      <td>55110</td>
+      <td>4053</td>
+      <td>4497</td>
+      <td>73194</td>
+      <td>108684</td>
+      <td>6930</td>
+      <td>9936</td>
+      <td>14771</td>
+      <td>15714</td>
+      <td>1222</td>
+      <td>1419</td>
+      <td>140064</td>
+      <td>179508</td>
+      <td>12205</td>
+      <td>15852</td>
       <td></td>
     </tr>
     <tr>
@@ -6813,8 +8255,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -6860,7 +8316,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6875,11 +8330,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>82</td>
-      <td>3784</td>
+      <td>4322</td>
+      <td>4714</td>
+      <td>180</td>
+      <td>205</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4322</td>
+      <td>4714</td>
+      <td>180</td>
+      <td>205</td>
       <td></td>
     </tr>
     <tr>
@@ -6903,7 +8373,7 @@
       <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip</td>
       <td>0.0.18</td>
       <td>galaxy_sequence_utils</td>
-      <td>1.1.5</td>
+      <td>1.2.0</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -6945,6 +8415,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -6990,7 +8474,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7004,12 +8487,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>154</td>
-      <td>763</td>
+      <td>913</td>
+      <td>913</td>
+      <td>308</td>
+      <td>308</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>568</td>
+      <td>568</td>
+      <td>73</td>
+      <td>73</td>
+      <td>1481</td>
+      <td>1481</td>
+      <td>381</td>
+      <td>381</td>
       <td></td>
     </tr>
     <tr>
@@ -7039,8 +8537,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -7069,12 +8566,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1008</td>
-      <td>41600</td>
+      <td>46125</td>
+      <td>47376</td>
+      <td>2273</td>
+      <td>2356</td>
+      <td>40577</td>
+      <td>40577</td>
+      <td>3971</td>
+      <td>3971</td>
+      <td>19960</td>
+      <td>21130</td>
+      <td>1085</td>
+      <td>1199</td>
+      <td>106662</td>
+      <td>109083</td>
+      <td>7329</td>
+      <td>7526</td>
       <td></td>
     </tr>
     <tr>
@@ -7138,8 +8650,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>22</td>
-      <td>203</td>
+      <td>325</td>
+      <td>325</td>
+      <td>61</td>
+      <td>61</td>
+      <td>137</td>
+      <td>137</td>
+      <td>54</td>
+      <td>54</td>
+      <td>843</td>
+      <td>843</td>
+      <td>63</td>
+      <td>63</td>
+      <td>1305</td>
+      <td>1305</td>
+      <td>178</td>
+      <td>178</td>
       <td></td>
     </tr>
     <tr>
@@ -7148,7 +8674,7 @@
       <td>spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades</td>
       <td>SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.</td>
       <td>spades</td>
-      <td>spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades</td>
+      <td>spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades</td>
       <td></td>
       <td>SPAdes</td>
       <td>St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.</td>
@@ -7169,8 +8695,7 @@
       <td>9</td>
       <td>9</td>
       <td>9</td>
-      <td>9</td>
-      <td>9</td>
+      <td>0</td>
       <td>9</td>
       <td>9</td>
       <td>9</td>
@@ -7199,12 +8724,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>9</td>
       <td>3</td>
       <td>0</td>
-      <td>3547</td>
-      <td>72953</td>
+      <td>82716</td>
+      <td>87113</td>
+      <td>8209</td>
+      <td>8526</td>
+      <td>120471</td>
+      <td>120475</td>
+      <td>14787</td>
+      <td>14790</td>
+      <td>54067</td>
+      <td>61541</td>
+      <td>5817</td>
+      <td>6653</td>
+      <td>257254</td>
+      <td>269129</td>
+      <td>28813</td>
+      <td>29969</td>
       <td></td>
     </tr>
     <tr>
@@ -7250,7 +8790,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -7264,12 +8803,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>34</td>
-      <td>446</td>
+      <td>450</td>
+      <td>491</td>
+      <td>91</td>
+      <td>100</td>
+      <td>4270</td>
+      <td>4270</td>
+      <td>288</td>
+      <td>288</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4720</td>
+      <td>4761</td>
+      <td>379</td>
+      <td>388</td>
       <td></td>
     </tr>
     <tr>
@@ -7299,10 +8853,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7329,12 +8882,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>56</td>
-      <td>769</td>
+      <td>789</td>
+      <td>840</td>
+      <td>130</td>
+      <td>134</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>789</td>
+      <td>840</td>
+      <td>130</td>
+      <td>134</td>
       <td></td>
     </tr>
     <tr>
@@ -7364,11 +8932,11 @@
       <td>4</td>
       <td>0</td>
       <td>7</td>
-      <td>7</td>
+      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>7</td>
-      <td>7</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7398,8 +8966,22 @@
       <td>7</td>
       <td>0</td>
       <td>0</td>
-      <td>21</td>
-      <td>225</td>
+      <td>239</td>
+      <td>239</td>
+      <td>34</td>
+      <td>34</td>
+      <td>44</td>
+      <td>44</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>283</td>
+      <td>283</td>
+      <td>47</td>
+      <td>47</td>
       <td></td>
     </tr>
     <tr>
@@ -7429,11 +9011,11 @@
       <td>0</td>
       <td>0</td>
       <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -7463,8 +9045,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>10</td>
-      <td>325</td>
+      <td>328</td>
+      <td>328</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>328</td>
+      <td>328</td>
+      <td>38</td>
+      <td>38</td>
       <td></td>
     </tr>
     <tr>
@@ -7510,7 +9106,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7530,6 +9125,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -7559,8 +9169,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -7589,12 +9198,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1801</td>
-      <td>27426</td>
+      <td>36069</td>
+      <td>36922</td>
+      <td>5257</td>
+      <td>5431</td>
+      <td>25255</td>
+      <td>30822</td>
+      <td>5066</td>
+      <td>5826</td>
+      <td>7949</td>
+      <td>7949</td>
+      <td>1584</td>
+      <td>1584</td>
+      <td>69273</td>
+      <td>75693</td>
+      <td>11907</td>
+      <td>12841</td>
       <td></td>
     </tr>
     <tr>
@@ -7660,6 +9284,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -7723,8 +9361,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>36</td>
-      <td>460</td>
+      <td>547</td>
+      <td>547</td>
+      <td>51</td>
+      <td>51</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>547</td>
+      <td>547</td>
+      <td>51</td>
+      <td>51</td>
       <td></td>
     </tr>
     <tr>
@@ -7788,8 +9440,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>84</td>
-      <td>907</td>
+      <td>1039</td>
+      <td>1039</td>
+      <td>189</td>
+      <td>189</td>
+      <td>2672</td>
+      <td>3349</td>
+      <td>467</td>
+      <td>485</td>
+      <td>358</td>
+      <td>358</td>
+      <td>47</td>
+      <td>47</td>
+      <td>4069</td>
+      <td>4746</td>
+      <td>703</td>
+      <td>721</td>
       <td></td>
     </tr>
     <tr>
@@ -7819,9 +9485,8 @@
       <td>0</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
       <td>0</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -7850,11 +9515,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
+      <td>14681</td>
+      <td>14681</td>
+      <td>265</td>
+      <td>265</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4488</td>
+      <td>4488</td>
+      <td>147</td>
       <td>147</td>
-      <td>8942</td>
+      <td>19169</td>
+      <td>19169</td>
+      <td>412</td>
+      <td>412</td>
       <td></td>
     </tr>
     <tr>
@@ -7884,10 +9564,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7919,7 +9598,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
+      <td>17</td>
+      <td>17</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>7</td>
+      <td>7</td>
       <td></td>
     </tr>
     <tr>
@@ -7949,8 +9643,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -7979,12 +9672,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1558</td>
-      <td>65732</td>
+      <td>74120</td>
+      <td>77648</td>
+      <td>3798</td>
+      <td>3963</td>
+      <td>64946</td>
+      <td>90075</td>
+      <td>5451</td>
+      <td>7380</td>
+      <td>19516</td>
+      <td>20422</td>
+      <td>2010</td>
+      <td>2080</td>
+      <td>158582</td>
+      <td>188145</td>
+      <td>11259</td>
+      <td>13423</td>
       <td></td>
     </tr>
     <tr>
@@ -8014,8 +9722,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -8044,12 +9751,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2083</td>
-      <td>25420</td>
+      <td>25171</td>
+      <td>27943</td>
+      <td>3899</td>
+      <td>4270</td>
+      <td>51187</td>
+      <td>51187</td>
+      <td>7557</td>
+      <td>7557</td>
+      <td>28546</td>
+      <td>28619</td>
+      <td>3585</td>
+      <td>3613</td>
+      <td>104904</td>
+      <td>107749</td>
+      <td>15041</td>
+      <td>15440</td>
       <td></td>
     </tr>
     <tr>
@@ -8093,7 +9815,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -8109,12 +9830,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>255</td>
-      <td>4741</td>
+      <td>4715</td>
+      <td>5343</td>
+      <td>888</td>
+      <td>965</td>
+      <td>9575</td>
+      <td>9576</td>
+      <td>2117</td>
+      <td>2117</td>
+      <td>3271</td>
+      <td>5524</td>
+      <td>1050</td>
+      <td>1397</td>
+      <td>17561</td>
+      <td>20443</td>
+      <td>4055</td>
+      <td>4479</td>
       <td></td>
     </tr>
     <tr>
@@ -8138,7 +9874,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko</td>
       <td>1.3.1</td>
       <td>verkko</td>
-      <td>2.2</td>
+      <td>2.2.1</td>
       <td></td>
       <td></td>
       <td>0</td>
@@ -8178,8 +9914,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
-      <td>22</td>
+      <td>48</td>
+      <td>48</td>
+      <td>25</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>25</td>
+      <td>25</td>
       <td></td>
     </tr>
     <tr>
@@ -8209,11 +9959,11 @@
       <td>0</td>
       <td>0</td>
       <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8243,8 +9993,22 @@
       <td>4</td>
       <td>4</td>
       <td>0</td>
-      <td>351</td>
-      <td>12203</td>
+      <td>14412</td>
+      <td>14590</td>
+      <td>722</td>
+      <td>732</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14412</td>
+      <td>14590</td>
+      <td>722</td>
+      <td>732</td>
       <td></td>
     </tr>
     <tr>
@@ -8274,10 +10038,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8305,11 +10068,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>116</td>
-      <td>1660</td>
+      <td>1619</td>
+      <td>1715</td>
+      <td>337</td>
+      <td>376</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1619</td>
+      <td>1715</td>
+      <td>337</td>
+      <td>376</td>
       <td></td>
     </tr>
     <tr>
@@ -8339,11 +10117,11 @@
       <td>5</td>
       <td>2</td>
       <td>6</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>2</td>
       <td>6</td>
-      <td>5</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8373,8 +10151,22 @@
       <td>6</td>
       <td>2</td>
       <td>0</td>
-      <td>175</td>
-      <td>5876</td>
+      <td>5995</td>
+      <td>5995</td>
+      <td>275</td>
+      <td>275</td>
+      <td>66</td>
+      <td>66</td>
+      <td>23</td>
+      <td>23</td>
+      <td>295</td>
+      <td>295</td>
+      <td>3</td>
+      <td>3</td>
+      <td>6356</td>
+      <td>6356</td>
+      <td>301</td>
+      <td>301</td>
       <td></td>
     </tr>
     <tr>
@@ -8438,8 +10230,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>64</td>
-      <td>344</td>
+      <td>618</td>
+      <td>618</td>
+      <td>176</td>
+      <td>176</td>
+      <td>336</td>
+      <td>336</td>
+      <td>62</td>
+      <td>62</td>
+      <td>588</td>
+      <td>588</td>
+      <td>25</td>
+      <td>25</td>
+      <td>1542</td>
+      <td>1542</td>
+      <td>263</td>
+      <td>263</td>
       <td></td>
     </tr>
     <tr>
@@ -8503,8 +10309,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>4</td>
+      <td>4</td>
       <td></td>
     </tr>
   </tbody>
diff --git a/communities/biodiversity/resources/tools.tsv b/communities/biodiversity/resources/tools.tsv
index 64b21831..933aed9e 100644
--- a/communities/biodiversity/resources/tools.tsv
+++ b/communities/biodiversity/resources/tools.tsv
@@ -1,132 +1,132 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	9	0	0	11	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	102	False		
-Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	82	False		
-Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004	False		
-TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	False		
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278	False		
-annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1175	25975	False		
-aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	False		
-biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	False		
-blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	False		
-braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	17	109	False		
-braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	567	False		
-cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	101	7766	False		
-champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	19	174	False		
-chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	418	15690	False		
-circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	False		
-clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	146	658	False		
-deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	False		
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369	False		
-dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	74	13759	False		
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904	False		
-funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	900	5906	False		
-gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	10	1475	False		
-getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	False		
-goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	408	5484	False		
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651	False		
-hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	False		
-helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	93	False		
-hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	False		
-hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	False		
-hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	4183	299104	False		
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	False		
-icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127	False		
-instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	False		
-interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	False		
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022	False		
-links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	False		
-marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	24	False		
-medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530	False		
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475	False		
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	False		
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	184	False		
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206	False		
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938	False		
-mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	False		
-mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	False		
-ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	False		
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	False		
-novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	162	6384	False		
-oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45	False		
-ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	False		
-ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	516	516	128	128	0	0	0	0	0	0	0	0	516	516	128	128	False		
+Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	352	352	36	36	0	0	0	0	0	0	0	0	352	352	36	36	False		
+Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	53	53	18	18	0	0	0	0	0	0	0	0	53	53	18	18	False		
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	1038	1038	146	146	0	0	0	0	849	849	38	38	1887	1887	184	184	False		
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	43	43	20	20	0	0	0	0	0	0	0	0	43	43	20	20	False		
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5543	5543	1042	1042	1301	1305	413	414	2030	2030	299	299	8874	8878	1754	1755	False		
+annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	29266	30655	2849	2973	59299	66180	5917	6355	5644	5644	1049	1049	94209	102479	9815	10377	False		
+aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	75	75	9	9	0	0	0	0	0	0	0	0	75	75	9	9	False		
+argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	151	151	143	143	43	43	596	596	22	22	1286	1286	216	216	False		
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6243	6243	375	375	0	0	0	0	6243	6243	375	375	False		
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	3	1	1	0	0	0	0	0	0	0	0	3	3	1	1	False		
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1527	1527	79	79	6	6	1	1	317	317	26	26	1850	1850	106	106	False		
+braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	165	165	48	48	0	0	0	0	0	0	0	0	165	165	48	48	False		
+braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1938	1938	294	294	0	0	0	0	412	412	71	71	2350	2350	365	365	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	9869	9869	158	158	0	0	0	0	6886	6886	146	146	16755	16755	304	304	False		
+champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	183	183	20	20	0	0	0	0	0	0	0	0	183	183	20	20	False		
+chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	16468	18344	956	991	33692	34453	2559	2625	2948	2948	104	104	53108	55745	3619	3720	False		
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	524	524	32	32	0	0	0	0	0	0	0	0	524	524	32	32	False		
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	967	967	308	308	0	0	0	0	0	0	0	0	967	967	308	308	False		
+deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	37	37	0	0	0	0	0	0	0	0	65	65	37	37	False		
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	358	406	124	139	1361	1361	384	384	0	0	0	0	1719	1767	508	523	False		
+dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	28	28	2	2	0	0	0	0	0	0	0	0	28	28	2	2	False		
+evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	136	11	11	0	0	0	0	0	0	0	0	136	136	11	11	False		
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22017	22304	239	255	9399	14886	462	709	4	4	1	1	31420	37194	702	965	False		
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32514	32675	3379	3422	19434	19434	2537	2537	9843	9843	1624	1624	61791	61952	7540	7583	False		
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	8648	8648	1408	1408	32	32	6	6	6406	6406	597	597	15086	15086	2011	2011	False		
+gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	1409	1498	39	42	0	0	0	0	0	0	0	0	1409	1498	39	42	False		
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1542	1542	159	159	0	0	0	0	587	587	64	64	2129	2129	223	223	False		
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	5800	6212	826	871	7756	7756	1048	1048	1149	1149	215	215	14705	15117	2089	2134	False		
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	7012	7344	323	338	0	0	0	0	0	0	0	0	7012	7344	323	338	False		
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	103	103	4	4	103	103	4	4	False		
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	502	502	66	66	0	0	0	0	0	0	0	0	502	502	66	66	False		
+helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	267	267	39	39	0	0	0	0	80	80	7	7	347	347	46	46	False		
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1819	1819	539	539	1334	1334	389	389	2472	2472	137	137	5625	5625	1065	1065	False		
+hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	2	2	0	0	0	0	0	0	0	0	18	18	2	2	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	0	12	0	0	0	0	0	0	0	0	0	228	0	12	False		
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	337151	353499	10046	10719	699868	896164	26656	34018	87016	94859	5302	5695	1124035	1344522	42004	50432	False		
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	473	473	93	93	0	0	0	0	0	0	0	0	473	473	93	93	False		
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	1200	1220	187	195	1588	1588	267	267	0	0	0	0	2788	2808	454	462	False		
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	157	157	14	14	0	0	0	0	0	0	0	0	157	157	14	14	False		
+interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	70	7	7	0	0	0	0	0	0	0	0	70	70	7	7	False		
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1825	1825	237	237	0	0	0	0	971	971	56	56	2796	2796	293	293	False		
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	8	8	8	0	1995	2091	174	193	1430	1430	389	389	1580	1580	56	56	5005	5101	619	638	False		
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	512	512	126	126	0	0	0	0	480	480	65	65	992	992	191	191	False		
+marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	51	51	4	4	0	0	0	0	0	0	0	0	51	51	4	4	False		
+mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	3	3	0	0	0	0	0	0	0	0	20	25	3	3	False		
+medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	9	9	0	0	0	0	0	0	0	0	27	27	9	9	False		
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	12692	13292	1349	1400	16645	16645	2140	2140	6214	6214	431	431	35551	36151	3920	3971	False		
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	513	557	152	155	74	74	35	35	10	10	4	4	597	641	191	194	False		
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3150	3150	477	477	730	730	196	196	1183	1183	151	151	5063	5063	824	824	False		
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	7.bba0d80	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	312	312	40	40	0	0	0	0	0	0	0	0	312	312	40	40	False		
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7116	7116	256	256	0	0	0	0	278	278	60	60	7394	7394	316	316	False		
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13357	13479	554	562	8416	8416	448	448	898	898	85	85	22671	22793	1087	1095	False		
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1117	1117	116	116	0	0	0	0	295	295	25	25	1412	1412	141	141	False		
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1020	1020	176	176	414	414	73	73	277	277	20	20	1711	1711	269	269	False		
+ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	6	6	0	0	0	0	15	15	6	6	False		
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	790	790	160	160	0	0	0	0	0	0	0	0	790	790	160	160	False		
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	391	391	158	158	0	0	0	0	0	0	0	0	391	391	158	158	False		
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	7780	7780	337	337	1	1	1	1	2323	2323	99	99	10104	10104	437	437	False		
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	352	352	42	42	8	8	6	6	0	0	0	0	360	360	48	48	False		
+ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	54	6	6	0	0	0	0	0	0	0	0	54	54	6	6	False		
+ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	98	6	6	0	0	0	0	0	0	0	0	98	98	6	6	False		
+ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	57	57	4	4	0	0	0	0	0	0	0	0	57	57	4	4	False		
 pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
                 pharokka
-            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	74	2565	False		
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	False		
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567	False		
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
-ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	False		
-raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	False		
-regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	22	526	False		
-repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	False		
-repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	217	1177	False		
-retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	109	1110	False		
-salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	84	454	False		
-sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	False		
-samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	296	4948	False		
-samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1450	48426	False		
-sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	False		
-seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	154	763	False		
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600	False		
-smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	False		
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953	False		
-spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	34	446	False		
-spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	56	769	False		
-srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	7	4	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	21	225	False		
-stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	10	325	False		
-taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426	False		
-telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	False		
-transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	84	907	False		
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	False		
-tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	False		
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732	False		
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420	False		
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741	False		
-verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	False		
-vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	351	12203	False		
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	False		
-xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	5	5	2	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	175	5876	False		
-yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	False		
-zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	5462	5462	334	334	0	0	0	0	309	309	52	52	5771	5771	386	386	False		
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1902	1902	167	167	0	0	0	0	0	0	0	0	1902	1902	167	167	False		
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17782	17782	287	287	853	853	65	65	2224	2224	65	65	20859	20859	417	417	False		
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	67737	69738	7787	7971	51925	56602	9692	10646	32003	34145	3890	4127	151665	160485	21369	22744	False		
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4844	4844	480	480	0	0	0	0	7	7	3	3	4851	4851	483	483	False		
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9477	9477	438	438	0	0	0	0	10585	10585	182	182	20062	20062	620	620	False		
+regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	438	542	128	157	0	0	0	0	0	0	0	0	438	542	128	157	False		
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	95	38	38	0	0	0	0	0	0	0	0	95	95	38	38	False		
+repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7963	7963	413	413	1485	1485	220	220	8402	8402	168	168	17850	17850	801	801	False		
+retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1522	1522	254	254	372	372	75	75	5	5	1	1	1899	1899	330	330	False		
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	463	463	119	119	1038	1038	87	87	410	410	24	24	1911	1911	230	230	False		
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3421	3859	340	382	883	883	109	109	1138	1138	15	15	5442	5880	464	506	False		
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6485	6549	720	726	10127	10127	1518	1518	238	238	37	37	16850	16914	2275	2281	False		
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	52099	55110	4053	4497	73194	108684	6930	9936	14771	15714	1222	1419	140064	179508	12205	15852	False		
+sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4322	4714	180	205	0	0	0	0	0	0	0	0	4322	4714	180	205	False		
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	913	913	308	308	0	0	0	0	568	568	73	73	1481	1481	381	381	False		
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46125	47376	2273	2356	40577	40577	3971	3971	19960	21130	1085	1199	106662	109083	7329	7526	False		
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	325	325	61	61	137	137	54	54	843	843	63	63	1305	1305	178	178	False		
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	3	9	3	0	82716	87113	8209	8526	120471	120475	14787	14790	54067	61541	5817	6653	257254	269129	28813	29969	False		
+spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	450	491	91	100	4270	4270	288	288	0	0	0	0	4720	4761	379	388	False		
+spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	789	840	130	134	0	0	0	0	0	0	0	0	789	840	130	134	False		
+srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	0	4	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	239	239	34	34	44	44	13	13	0	0	0	0	283	283	47	47	False		
+stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	328	328	38	38	0	0	0	0	0	0	0	0	328	328	38	38	False		
+taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	36069	36922	5257	5431	25255	30822	5066	5826	7949	7949	1584	1584	69273	75693	11907	12841	False		
+telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	51	51	0	0	0	0	0	0	0	0	547	547	51	51	False		
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	1039	1039	189	189	2672	3349	467	485	358	358	47	47	4069	4746	703	721	False		
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	14681	14681	265	265	0	0	0	0	4488	4488	147	147	19169	19169	412	412	False		
+tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	7	7	0	0	0	0	0	0	0	0	17	17	7	7	False		
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	74120	77648	3798	3963	64946	90075	5451	7380	19516	20422	2010	2080	158582	188145	11259	13423	False		
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	25171	27943	3899	4270	51187	51187	7557	7557	28546	28619	3585	3613	104904	107749	15041	15440	False		
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4715	5343	888	965	9575	9576	2117	2117	3271	5524	1050	1397	17561	20443	4055	4479	False		
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	48	25	25	0	0	0	0	0	0	0	0	48	48	25	25	False		
+vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	14412	14590	722	732	0	0	0	0	0	0	0	0	14412	14590	722	732	False		
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1619	1715	337	376	0	0	0	0	0	0	0	0	1619	1715	337	376	False		
+xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	0	5	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	5995	5995	275	275	66	66	23	23	295	295	3	3	6356	6356	301	301	False		
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	618	618	176	176	336	336	62	62	588	588	25	25	1542	1542	263	263	False		
+zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	4	4	0	0	0	0	0	0	0	0	26	26	4	4	False		
diff --git a/communities/biodiversity/resources/tools_filtered_by_ts_categories.tsv b/communities/biodiversity/resources/tools_filtered_by_ts_categories.tsv
index 64b21831..933aed9e 100644
--- a/communities/biodiversity/resources/tools_filtered_by_ts_categories.tsv
+++ b/communities/biodiversity/resources/tools_filtered_by_ts_categories.tsv
@@ -1,132 +1,132 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	9	0	0	11	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	102	False		
-Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	82	False		
-Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004	False		
-TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	False		
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278	False		
-annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1175	25975	False		
-aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	False		
-biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	False		
-blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	False		
-braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	17	109	False		
-braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	567	False		
-cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	101	7766	False		
-champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	19	174	False		
-chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	418	15690	False		
-circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	False		
-clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	146	658	False		
-deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	False		
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369	False		
-dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	74	13759	False		
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904	False		
-funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	900	5906	False		
-gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	10	1475	False		
-getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	False		
-goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	408	5484	False		
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651	False		
-hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	False		
-helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	93	False		
-hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	False		
-hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	False		
-hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	4183	299104	False		
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	False		
-icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127	False		
-instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	False		
-interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	False		
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022	False		
-links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	False		
-marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	24	False		
-medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530	False		
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475	False		
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	False		
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	184	False		
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206	False		
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938	False		
-mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	False		
-mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	False		
-ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	False		
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	False		
-novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	162	6384	False		
-oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	False		
-obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45	False		
-ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	False		
-ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	516	516	128	128	0	0	0	0	0	0	0	0	516	516	128	128	False		
+Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	352	352	36	36	0	0	0	0	0	0	0	0	352	352	36	36	False		
+Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	53	53	18	18	0	0	0	0	0	0	0	0	53	53	18	18	False		
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	1038	1038	146	146	0	0	0	0	849	849	38	38	1887	1887	184	184	False		
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	43	43	20	20	0	0	0	0	0	0	0	0	43	43	20	20	False		
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5543	5543	1042	1042	1301	1305	413	414	2030	2030	299	299	8874	8878	1754	1755	False		
+annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	29266	30655	2849	2973	59299	66180	5917	6355	5644	5644	1049	1049	94209	102479	9815	10377	False		
+aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	75	75	9	9	0	0	0	0	0	0	0	0	75	75	9	9	False		
+argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	151	151	143	143	43	43	596	596	22	22	1286	1286	216	216	False		
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6243	6243	375	375	0	0	0	0	6243	6243	375	375	False		
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	3	1	1	0	0	0	0	0	0	0	0	3	3	1	1	False		
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1527	1527	79	79	6	6	1	1	317	317	26	26	1850	1850	106	106	False		
+braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	165	165	48	48	0	0	0	0	0	0	0	0	165	165	48	48	False		
+braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1938	1938	294	294	0	0	0	0	412	412	71	71	2350	2350	365	365	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	9869	9869	158	158	0	0	0	0	6886	6886	146	146	16755	16755	304	304	False		
+champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	183	183	20	20	0	0	0	0	0	0	0	0	183	183	20	20	False		
+chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	16468	18344	956	991	33692	34453	2559	2625	2948	2948	104	104	53108	55745	3619	3720	False		
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	524	524	32	32	0	0	0	0	0	0	0	0	524	524	32	32	False		
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	967	967	308	308	0	0	0	0	0	0	0	0	967	967	308	308	False		
+deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	37	37	0	0	0	0	0	0	0	0	65	65	37	37	False		
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	358	406	124	139	1361	1361	384	384	0	0	0	0	1719	1767	508	523	False		
+dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	28	28	2	2	0	0	0	0	0	0	0	0	28	28	2	2	False		
+evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	136	11	11	0	0	0	0	0	0	0	0	136	136	11	11	False		
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22017	22304	239	255	9399	14886	462	709	4	4	1	1	31420	37194	702	965	False		
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32514	32675	3379	3422	19434	19434	2537	2537	9843	9843	1624	1624	61791	61952	7540	7583	False		
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	8648	8648	1408	1408	32	32	6	6	6406	6406	597	597	15086	15086	2011	2011	False		
+gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	1409	1498	39	42	0	0	0	0	0	0	0	0	1409	1498	39	42	False		
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1542	1542	159	159	0	0	0	0	587	587	64	64	2129	2129	223	223	False		
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	5800	6212	826	871	7756	7756	1048	1048	1149	1149	215	215	14705	15117	2089	2134	False		
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	7012	7344	323	338	0	0	0	0	0	0	0	0	7012	7344	323	338	False		
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	103	103	4	4	103	103	4	4	False		
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	502	502	66	66	0	0	0	0	0	0	0	0	502	502	66	66	False		
+helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	267	267	39	39	0	0	0	0	80	80	7	7	347	347	46	46	False		
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1819	1819	539	539	1334	1334	389	389	2472	2472	137	137	5625	5625	1065	1065	False		
+hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	2	2	0	0	0	0	0	0	0	0	18	18	2	2	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	0	12	0	0	0	0	0	0	0	0	0	228	0	12	False		
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	337151	353499	10046	10719	699868	896164	26656	34018	87016	94859	5302	5695	1124035	1344522	42004	50432	False		
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	473	473	93	93	0	0	0	0	0	0	0	0	473	473	93	93	False		
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	1200	1220	187	195	1588	1588	267	267	0	0	0	0	2788	2808	454	462	False		
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	157	157	14	14	0	0	0	0	0	0	0	0	157	157	14	14	False		
+interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	70	7	7	0	0	0	0	0	0	0	0	70	70	7	7	False		
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1825	1825	237	237	0	0	0	0	971	971	56	56	2796	2796	293	293	False		
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	8	8	8	0	1995	2091	174	193	1430	1430	389	389	1580	1580	56	56	5005	5101	619	638	False		
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	512	512	126	126	0	0	0	0	480	480	65	65	992	992	191	191	False		
+marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	51	51	4	4	0	0	0	0	0	0	0	0	51	51	4	4	False		
+mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	3	3	0	0	0	0	0	0	0	0	20	25	3	3	False		
+medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	9	9	0	0	0	0	0	0	0	0	27	27	9	9	False		
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	12692	13292	1349	1400	16645	16645	2140	2140	6214	6214	431	431	35551	36151	3920	3971	False		
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	513	557	152	155	74	74	35	35	10	10	4	4	597	641	191	194	False		
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3150	3150	477	477	730	730	196	196	1183	1183	151	151	5063	5063	824	824	False		
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	7.bba0d80	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	312	312	40	40	0	0	0	0	0	0	0	0	312	312	40	40	False		
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7116	7116	256	256	0	0	0	0	278	278	60	60	7394	7394	316	316	False		
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13357	13479	554	562	8416	8416	448	448	898	898	85	85	22671	22793	1087	1095	False		
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1117	1117	116	116	0	0	0	0	295	295	25	25	1412	1412	141	141	False		
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1020	1020	176	176	414	414	73	73	277	277	20	20	1711	1711	269	269	False		
+ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	6	6	0	0	0	0	15	15	6	6	False		
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	790	790	160	160	0	0	0	0	0	0	0	0	790	790	160	160	False		
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	391	391	158	158	0	0	0	0	0	0	0	0	391	391	158	158	False		
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	7780	7780	337	337	1	1	1	1	2323	2323	99	99	10104	10104	437	437	False		
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	352	352	42	42	8	8	6	6	0	0	0	0	360	360	48	48	False		
+ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	54	6	6	0	0	0	0	0	0	0	0	54	54	6	6	False		
+ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	98	6	6	0	0	0	0	0	0	0	0	98	98	6	6	False		
+ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	57	57	4	4	0	0	0	0	0	0	0	0	57	57	4	4	False		
 pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
                 pharokka
-            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	74	2565	False		
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	False		
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567	False		
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	False		
-ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	False		
-raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	False		
-regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	22	526	False		
-repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	False		
-repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	217	1177	False		
-retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	109	1110	False		
-salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	84	454	False		
-sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	False		
-samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	296	4948	False		
-samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1450	48426	False		
-sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	False		
-seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	154	763	False		
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600	False		
-smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	False		
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953	False		
-spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	34	446	False		
-spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	56	769	False		
-srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	7	4	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	21	225	False		
-stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	10	325	False		
-taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426	False		
-telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	False		
-transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	84	907	False		
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	False		
-tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	False		
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732	False		
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420	False		
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741	False		
-verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	False		
-vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	351	12203	False		
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	False		
-xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	5	5	2	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	175	5876	False		
-yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	False		
-zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	5462	5462	334	334	0	0	0	0	309	309	52	52	5771	5771	386	386	False		
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1902	1902	167	167	0	0	0	0	0	0	0	0	1902	1902	167	167	False		
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17782	17782	287	287	853	853	65	65	2224	2224	65	65	20859	20859	417	417	False		
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	67737	69738	7787	7971	51925	56602	9692	10646	32003	34145	3890	4127	151665	160485	21369	22744	False		
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4844	4844	480	480	0	0	0	0	7	7	3	3	4851	4851	483	483	False		
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9477	9477	438	438	0	0	0	0	10585	10585	182	182	20062	20062	620	620	False		
+regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	438	542	128	157	0	0	0	0	0	0	0	0	438	542	128	157	False		
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	95	38	38	0	0	0	0	0	0	0	0	95	95	38	38	False		
+repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7963	7963	413	413	1485	1485	220	220	8402	8402	168	168	17850	17850	801	801	False		
+retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1522	1522	254	254	372	372	75	75	5	5	1	1	1899	1899	330	330	False		
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	463	463	119	119	1038	1038	87	87	410	410	24	24	1911	1911	230	230	False		
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3421	3859	340	382	883	883	109	109	1138	1138	15	15	5442	5880	464	506	False		
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6485	6549	720	726	10127	10127	1518	1518	238	238	37	37	16850	16914	2275	2281	False		
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	52099	55110	4053	4497	73194	108684	6930	9936	14771	15714	1222	1419	140064	179508	12205	15852	False		
+sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4322	4714	180	205	0	0	0	0	0	0	0	0	4322	4714	180	205	False		
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	913	913	308	308	0	0	0	0	568	568	73	73	1481	1481	381	381	False		
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46125	47376	2273	2356	40577	40577	3971	3971	19960	21130	1085	1199	106662	109083	7329	7526	False		
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	325	325	61	61	137	137	54	54	843	843	63	63	1305	1305	178	178	False		
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	3	9	3	0	82716	87113	8209	8526	120471	120475	14787	14790	54067	61541	5817	6653	257254	269129	28813	29969	False		
+spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	450	491	91	100	4270	4270	288	288	0	0	0	0	4720	4761	379	388	False		
+spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	789	840	130	134	0	0	0	0	0	0	0	0	789	840	130	134	False		
+srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	0	4	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	239	239	34	34	44	44	13	13	0	0	0	0	283	283	47	47	False		
+stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	328	328	38	38	0	0	0	0	0	0	0	0	328	328	38	38	False		
+taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	36069	36922	5257	5431	25255	30822	5066	5826	7949	7949	1584	1584	69273	75693	11907	12841	False		
+telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	51	51	0	0	0	0	0	0	0	0	547	547	51	51	False		
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	1039	1039	189	189	2672	3349	467	485	358	358	47	47	4069	4746	703	721	False		
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	14681	14681	265	265	0	0	0	0	4488	4488	147	147	19169	19169	412	412	False		
+tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	7	7	0	0	0	0	0	0	0	0	17	17	7	7	False		
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	74120	77648	3798	3963	64946	90075	5451	7380	19516	20422	2010	2080	158582	188145	11259	13423	False		
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	25171	27943	3899	4270	51187	51187	7557	7557	28546	28619	3585	3613	104904	107749	15041	15440	False		
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4715	5343	888	965	9575	9576	2117	2117	3271	5524	1050	1397	17561	20443	4055	4479	False		
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	48	25	25	0	0	0	0	0	0	0	0	48	48	25	25	False		
+vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	14412	14590	722	732	0	0	0	0	0	0	0	0	14412	14590	722	732	False		
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1619	1715	337	376	0	0	0	0	0	0	0	0	1619	1715	337	376	False		
+xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	0	5	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	5995	5995	275	275	66	66	23	23	295	295	3	3	6356	6356	301	301	False		
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	618	618	176	176	336	336	62	62	588	588	25	25	1542	1542	263	263	False		
+zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	4	4	0	0	0	0	0	0	0	0	26	26	4	4	False		
diff --git a/communities/biodiversity/resources/tools_wordcloud.png b/communities/biodiversity/resources/tools_wordcloud.png
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+
+<div class="display nowrap" style="width:80%" width="100%">
+
+<table class="dataframe display nowrap" id="dataframe">
+  <thead>
+    <tr style="text-align: right;">
+      <th>Expand</th>
+      <th>Galaxy wrapper id</th>
+      <th>Galaxy tool ids</th>
+      <th>Description</th>
+      <th>bio.tool id</th>
+      <th>bio.tool ids</th>
+      <th>biii</th>
+      <th>bio.tool name</th>
+      <th>bio.tool description</th>
+      <th>EDAM operation</th>
+      <th>EDAM topic</th>
+      <th>Status</th>
+      <th>Source</th>
+      <th>ToolShed categories</th>
+      <th>ToolShed id</th>
+      <th>Galaxy wrapper owner</th>
+      <th>Galaxy wrapper source</th>
+      <th>Galaxy wrapper parsed folder</th>
+      <th>Galaxy wrapper version</th>
+      <th>Conda id</th>
+      <th>Conda version</th>
+      <th>EDAM operation (no superclasses)</th>
+      <th>EDAM topic (no superclasses)</th>
+      <th>Available on UseGalaxy.org (Main)</th>
+      <th>Available on UseGalaxy.org.au</th>
+      <th>Available on UseGalaxy.eu</th>
+      <th>Available on UseGalaxy.fr</th>
+      <th>Tools available on UseGalaxy.org (Main)</th>
+      <th>Tools available on UseGalaxy.org.au</th>
+      <th>Tools available on UseGalaxy.eu</th>
+      <th>Tools available on UseGalaxy.fr</th>
+      <th>Tools available on APOSTL</th>
+      <th>Tools available on ARGs-OAP</th>
+      <th>Tools available on CIRM-CFBP</th>
+      <th>Tools available on ChemFlow</th>
+      <th>Tools available on Coloc-stats</th>
+      <th>Tools available on CoralSNP</th>
+      <th>Tools available on CropGalaxy</th>
+      <th>Tools available on Dintor</th>
+      <th>Tools available on GASLINI</th>
+      <th>Tools available on Galaxy@AuBi</th>
+      <th>Tools available on Galaxy@Pasteur</th>
+      <th>Tools available on GalaxyTrakr</th>
+      <th>Tools available on Genomic Hyperbrowser</th>
+      <th>Tools available on GigaGalaxy</th>
+      <th>Tools available on HyPhy HIV NGS Tools</th>
+      <th>Tools available on IPK Galaxy Blast Suite</th>
+      <th>Tools available on ImmPort Galaxy</th>
+      <th>Tools available on InteractoMIX</th>
+      <th>Tools available on MISSISSIPPI</th>
+      <th>Tools available on Mandoiu Lab</th>
+      <th>Tools available on MiModD NacreousMap</th>
+      <th>Tools available on Oqtans</th>
+      <th>Tools available on Palfinder</th>
+      <th>Tools available on PepSimili</th>
+      <th>Tools available on PhagePromotor</th>
+      <th>Tools available on UseGalaxy.be</th>
+      <th>Tools available on UseGalaxy.cz</th>
+      <th>Tools available on UseGalaxy.no</th>
+      <th>Tools available on Viral Variant Visualizer (VVV)</th>
+      <th>No. of tool users (5 years) (usegalaxy.eu)</th>
+      <th>No. of tool users (all time) (usegalaxy.eu)</th>
+      <th>Tool usage (5 years) (usegalaxy.eu)</th>
+      <th>Tool usage (all time) (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org)</th>
+      <th>No. of tool users (all time) (usegalaxy.org)</th>
+      <th>Tool usage (5 years) (usegalaxy.org)</th>
+      <th>Tool usage (all time) (usegalaxy.org)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org.au)</th>
+      <th>No. of tool users (all time) (usegalaxy.org.au)</th>
+      <th>Tool usage (5 years) (usegalaxy.org.au)</th>
+      <th>Tool usage (all time) (usegalaxy.org.au)</th>
+      <th>No. of tool users (5 years) - all main servers</th>
+      <th>No. of tool users (all time) - all main servers</th>
+      <th>Tool usage (5 years) - all main servers</th>
+      <th>Tool usage (all time) - all main servers</th>
+      <th>Deprecated</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <td></td>
+      <td>10x_bamtofastq</td>
+      <td>10x_bamtofastq</td>
+      <td>Converts 10x Genomics BAM to FASTQ</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/10XGenomics/bamtofastq</td>
+      <td>Convert Formats</td>
+      <td>10x_bamtofastq</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq</td>
+      <td>1.4.1</td>
+      <td>10x_bamtofastq</td>
+      <td>1.4.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>307</td>
+      <td>307</td>
+      <td>80</td>
+      <td>80</td>
+      <td>8</td>
+      <td>8</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1</td>
+      <td>1</td>
+      <td>318</td>
+      <td>318</td>
+      <td>84</td>
+      <td>84</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>2d_auto_threshold</td>
+      <td>ip_threshold</td>
+      <td>Automatic thresholding</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.</td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>2d_auto_threshold</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold</td>
+      <td>0.18.1</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1434</td>
+      <td>6746</td>
+      <td>120</td>
+      <td>122</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>305</td>
+      <td>305</td>
+      <td>11</td>
+      <td>11</td>
+      <td>1739</td>
+      <td>7051</td>
+      <td>131</td>
+      <td>133</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>2d_feature_extraction</td>
+      <td>ip_2d_feature_extraction</td>
+      <td>2D feature extraction</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.</td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>2d_feature_extraction</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction</td>
+      <td>0.18.1</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1156</td>
+      <td>13842</td>
+      <td>40</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1277</td>
+      <td>13963</td>
+      <td>44</td>
+      <td>46</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>2d_filter_segmentation_by_features</td>
+      <td>ip_2d_filter_segmentation_by_features</td>
+      <td>filter segmentation by rules</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>2d_filter_segmentation_by_features</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features</td>
+      <td>0.0.1-4</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>591</td>
+      <td>6863</td>
+      <td>38</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>119</td>
+      <td>3</td>
+      <td>3</td>
+      <td>710</td>
+      <td>6982</td>
+      <td>41</td>
+      <td>43</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>2d_histogram_equalization</td>
+      <td>ip_histogram_equalization</td>
+      <td>2d histogram equalization</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.</td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>2d_histogram_equalization</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization</td>
+      <td>0.18.1</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>762</td>
+      <td>782</td>
+      <td>100</td>
+      <td>101</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>230</td>
+      <td>230</td>
+      <td>14</td>
+      <td>14</td>
+      <td>992</td>
+      <td>1012</td>
+      <td>114</td>
+      <td>115</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>2d_simple_filter</td>
+      <td>ip_filter_standard</td>
+      <td>2d simple filter</td>
+      <td></td>
+      <td></td>
+      <td>scipy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>2d_simple_filter</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter</td>
+      <td>1.12.0</td>
+      <td>scipy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>948</td>
+      <td>6261</td>
+      <td>98</td>
+      <td>100</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>153</td>
+      <td>153</td>
+      <td>13</td>
+      <td>13</td>
+      <td>1101</td>
+      <td>6414</td>
+      <td>111</td>
+      <td>113</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>AggregateAlignments</td>
+      <td>graphclust_aggregate_alignments</td>
+      <td>Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_aggregate_alignments</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments</td>
+      <td>0.6.0</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>45</td>
+      <td>119</td>
+      <td>14</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45</td>
+      <td>119</td>
+      <td>14</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>AlignCluster</td>
+      <td>graphclust_align_cluster</td>
+      <td>Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_align_cluster</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster</td>
+      <td>0.1</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>189</td>
+      <td>3094</td>
+      <td>23</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>189</td>
+      <td>3094</td>
+      <td>23</td>
+      <td>25</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>CMFinder</td>
+      <td>cmFinder</td>
+      <td>Determines consensus motives for sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_cmfinder</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder</td>
+      <td>0.4</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>25532</td>
+      <td>50045</td>
+      <td>45</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25532</td>
+      <td>50045</td>
+      <td>45</td>
+      <td>57</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>CollectResults</td>
+      <td>glob_report</td>
+      <td>Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_postprocessing</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults</td>
+      <td>0.5</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1119</td>
+      <td>2115</td>
+      <td>50</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1119</td>
+      <td>2115</td>
+      <td>50</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>CollectResultsNoAlign</td>
+      <td>graphclust_glob_report_no_align</td>
+      <td>Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_postprocessing_no_align</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign</td>
+      <td>0.5</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>37</td>
+      <td>108</td>
+      <td>1</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>108</td>
+      <td>1</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>EMLassemblyline</td>
+      <td>annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template</td>
+      <td>Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/EDIorg/EMLassemblyline</td>
+      <td>Ecology</td>
+      <td>emlassemblyline</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline</td>
+      <td>0.1.0+galaxy0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>516</td>
+      <td>516</td>
+      <td>128</td>
+      <td>128</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>516</td>
+      <td>516</td>
+      <td>128</td>
+      <td>128</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>Ecoregionalization_workflow</td>
+      <td>ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker</td>
+      <td>Tools to compute ecoregionalization with BRT model predictions and clustering.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/PaulineSGN/Workflow_Galaxy</td>
+      <td>Ecology</td>
+      <td>ecoregionalization</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow</td>
+      <td>0.1.0+galaxy0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>352</td>
+      <td>352</td>
+      <td>36</td>
+      <td>36</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>352</td>
+      <td>352</td>
+      <td>36</td>
+      <td>36</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>Ensembl-REST</td>
+      <td>get_feature_info, get_genetree, get_sequences</td>
+      <td>A suite of Galaxy tools designed to work with Ensembl REST API.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://rest.ensembl.org</td>
+      <td>Data Source</td>
+      <td></td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST</td>
+      <td>0.1.2</td>
+      <td>requests</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>474</td>
+      <td>2914</td>
+      <td>132</td>
+      <td>163</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>474</td>
+      <td>2914</td>
+      <td>132</td>
+      <td>163</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>GAFA</td>
+      <td>gafa</td>
+      <td>Gene Align and Family Aggregator</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://aequatus.tgac.ac.uk</td>
+      <td>Visualization</td>
+      <td>gafa</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA</td>
+      <td>0.3.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>40</td>
+      <td>47</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>47</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>GSPAN</td>
+      <td>gspan</td>
+      <td>Second step of GraphClust</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_fasta_to_gspan</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN</td>
+      <td>0.4</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>80</td>
+      <td>150</td>
+      <td>18</td>
+      <td>23</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>80</td>
+      <td>150</td>
+      <td>18</td>
+      <td>23</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>Geom_mean_workflow</td>
+      <td>Map_shp, Mean_geom, bar_plot</td>
+      <td>Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom</td>
+      <td>Ecology</td>
+      <td>Geometric means (Dead wood)</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow</td>
+      <td>0.1.0+galaxy0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>53</td>
+      <td>53</td>
+      <td>18</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>53</td>
+      <td>53</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>LocARNAGraphClust</td>
+      <td>locarna_best_subtree</td>
+      <td>MLocARNA computes a multiple sequence-structure alignment of RNA sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_mlocarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust</td>
+      <td>0.4</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>25572</td>
+      <td>50177</td>
+      <td>45</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25572</td>
+      <td>50177</td>
+      <td>45</td>
+      <td>57</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>NSPDK</td>
+      <td>NSPDK_candidateClust, nspdk_sparse</td>
+      <td>Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_nspdk</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK</td>
+      <td>9.2.3.1</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>3210</td>
+      <td>62854</td>
+      <td>96</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3210</td>
+      <td>62854</td>
+      <td>96</td>
+      <td>124</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>PAMPA</td>
+      <td>pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm</td>
+      <td>Tools to compute and analyse biodiversity metrics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Ecology</td>
+      <td>pampa</td>
+      <td>ecology</td>
+      <td>https://github.com/ColineRoyaux/PAMPA-Galaxy</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA</td>
+      <td>0.0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>4</td>
+      <td>0</td>
+      <td>1038</td>
+      <td>1038</td>
+      <td>146</td>
+      <td>146</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>849</td>
+      <td>849</td>
+      <td>38</td>
+      <td>38</td>
+      <td>1887</td>
+      <td>1887</td>
+      <td>184</td>
+      <td>184</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>Plotting</td>
+      <td>motifFinderPlot</td>
+      <td>Plotting results for GraphClust</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_motif_finder_plot</td>
+      <td>rnateam</td>
+      <td>https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting</td>
+      <td>0.4</td>
+      <td>seaborn</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>45</td>
+      <td>71</td>
+      <td>9</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45</td>
+      <td>71</td>
+      <td>9</td>
+      <td>10</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>PrepareForMlocarna</td>
+      <td>preMloc</td>
+      <td>This tool prepares files for locarna step.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_prepocessing_for_mlocarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna</td>
+      <td>0.4</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1202</td>
+      <td>2121</td>
+      <td>48</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1202</td>
+      <td>2121</td>
+      <td>48</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>Preprocessing</td>
+      <td>preproc</td>
+      <td>Preprocessing input for GraphClust</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_preprocessing</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing</td>
+      <td>0.5</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1116</td>
+      <td>1897</td>
+      <td>57</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1116</td>
+      <td>1897</td>
+      <td>57</td>
+      <td>71</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>Structure_GSPAN</td>
+      <td>structure_to_gspan</td>
+      <td>Convert RNA structure to GSPAN graphs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>structure_to_gspan</td>
+      <td>rnateam</td>
+      <td>https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN</td>
+      <td>0.4</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>991</td>
+      <td>3060</td>
+      <td>50</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>991</td>
+      <td>3060</td>
+      <td>50</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ThermoRawFileParser</td>
+      <td>thermo_raw_file_converter</td>
+      <td>Thermo RAW file converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/compomics/ThermoRawFileParser</td>
+      <td>Proteomics</td>
+      <td>thermo_raw_file_converter</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser</td>
+      <td>1.3.4</td>
+      <td>thermorawfileparser</td>
+      <td>1.4.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2467</td>
+      <td>2959</td>
+      <td>88</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1097</td>
+      <td>1097</td>
+      <td>18</td>
+      <td>18</td>
+      <td>3564</td>
+      <td>4056</td>
+      <td>106</td>
+      <td>142</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>TreeBest</td>
+      <td>treebest_best</td>
+      <td>TreeBeST best</td>
+      <td>treebest</td>
+      <td>treebest</td>
+      <td></td>
+      <td>TreeBeST</td>
+      <td>TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.</td>
+      <td>Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)</td>
+      <td>Phylogenetics</td>
+      <td>To update</td>
+      <td>http://treesoft.sourceforge.net/treebest.shtml</td>
+      <td>Phylogenetics</td>
+      <td>treebest_best</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest</td>
+      <td>1.9.2.post0</td>
+      <td>treebest</td>
+      <td>1.9.2.post1</td>
+      <td>Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)</td>
+      <td>Phylogenetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1003</td>
+      <td>1022</td>
+      <td>48</td>
+      <td>52</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1003</td>
+      <td>1022</td>
+      <td>48</td>
+      <td>52</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>TrimNs</td>
+      <td>trimns</td>
+      <td>TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs</td>
+      <td>Assembly</td>
+      <td>trimns</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs</td>
+      <td>0.1.0</td>
+      <td>trimns_vgp</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ab1_fastq</td>
+      <td>ab1_fastq_converter</td>
+      <td>Tool to convert ab1 files into FASTQ files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats</td>
+      <td>ab1fastq</td>
+      <td>ecology</td>
+      <td>https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq</td>
+      <td>1.20.0</td>
+      <td>bioconductor-sangerseqr</td>
+      <td>1.38.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>49465</td>
+      <td>49465</td>
+      <td>281</td>
+      <td>281</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>49465</td>
+      <td>49465</td>
+      <td>281</td>
+      <td>281</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>abacas</td>
+      <td>abacas</td>
+      <td>Order and Orientate Contigs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/abacas</td>
+      <td>Assembly</td>
+      <td>abacas</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/abacas</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas</td>
+      <td>1.1</td>
+      <td>mummer</td>
+      <td>3.23</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>abricate</td>
+      <td>abricate, abricate_list, abricate_summary</td>
+      <td>Mass screening of contigs for antiobiotic resistance genes</td>
+      <td>ABRicate</td>
+      <td>ABRicate</td>
+      <td></td>
+      <td>ABRicate</td>
+      <td>Mass screening of contigs for antimicrobial resistance or virulence genes.</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Genomics, Microbiology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tseemann/abricate</td>
+      <td>Sequence Analysis</td>
+      <td>abricate</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate</td>
+      <td>1.0.1</td>
+      <td>abricate</td>
+      <td>1.0.1</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Genomics, Microbiology</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>619817</td>
+      <td>622353</td>
+      <td>4097</td>
+      <td>4130</td>
+      <td>320454</td>
+      <td>320454</td>
+      <td>2915</td>
+      <td>2915</td>
+      <td>496156</td>
+      <td>503743</td>
+      <td>2012</td>
+      <td>2227</td>
+      <td>1436427</td>
+      <td>1446550</td>
+      <td>9024</td>
+      <td>9272</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>abritamr</td>
+      <td>abritamr</td>
+      <td>A pipeline for running AMRfinderPlus and collating results into functional classes</td>
+      <td>abritamr</td>
+      <td>abritamr</td>
+      <td></td>
+      <td>abriTAMR</td>
+      <td>an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Microbiology, Public health and epidemiology, Infectious disease</td>
+      <td>Up-to-date</td>
+      <td>https://zenodo.org/record/7370628</td>
+      <td>Sequence Analysis</td>
+      <td>abritamr</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr</td>
+      <td>1.0.19</td>
+      <td>abritamr</td>
+      <td>1.0.19</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Microbiology, Public health and epidemiology, Infectious disease</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>109</td>
+      <td>109</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>109</td>
+      <td>109</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>abyss</td>
+      <td>abyss-pe</td>
+      <td>Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler</td>
+      <td>abyss</td>
+      <td>abyss</td>
+      <td></td>
+      <td>ABySS</td>
+      <td>De novo genome sequence assembler using short reads.</td>
+      <td>Genome assembly, De-novo assembly, Scaffolding</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>http://www.bcgsc.ca/platform/bioinfo/software/abyss</td>
+      <td>Assembly</td>
+      <td>abyss</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss</td>
+      <td>2.3.9</td>
+      <td>abyss</td>
+      <td>2.3.9</td>
+      <td>Genome assembly, De-novo assembly, Scaffolding</td>
+      <td>Sequence assembly</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5543</td>
+      <td>5543</td>
+      <td>1042</td>
+      <td>1042</td>
+      <td>1301</td>
+      <td>1305</td>
+      <td>413</td>
+      <td>414</td>
+      <td>2030</td>
+      <td>2030</td>
+      <td>299</td>
+      <td>299</td>
+      <td>8874</td>
+      <td>8878</td>
+      <td>1754</td>
+      <td>1755</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>adapter_removal</td>
+      <td>adapter_removal</td>
+      <td>Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.</td>
+      <td>adapterremoval</td>
+      <td>adapterremoval</td>
+      <td></td>
+      <td>AdapterRemoval</td>
+      <td>AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.</td>
+      <td>Sequence trimming, Sequence merging, Primer removal</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/MikkelSchubert/adapterremoval</td>
+      <td>Fasta Manipulation, Sequence Analysis</td>
+      <td>adapter_removal</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal</td>
+      <td>2.3.4</td>
+      <td>adapterremoval</td>
+      <td>2.3.4</td>
+      <td>Sequence trimming, Sequence merging, Primer removal</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>348</td>
+      <td>348</td>
+      <td>62</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>348</td>
+      <td>348</td>
+      <td>62</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>add_input_name_as_column</td>
+      <td>addName</td>
+      <td>Add input name as column on an existing tabular file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column</td>
+      <td>Text Manipulation</td>
+      <td>add_input_name_as_column</td>
+      <td>mvdbeek</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column</td>
+      <td>0.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>76834</td>
+      <td>86002</td>
+      <td>227</td>
+      <td>246</td>
+      <td>20174</td>
+      <td>20953</td>
+      <td>312</td>
+      <td>395</td>
+      <td>11</td>
+      <td>11</td>
+      <td>2</td>
+      <td>2</td>
+      <td>97019</td>
+      <td>106966</td>
+      <td>541</td>
+      <td>643</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>add_line_to_file</td>
+      <td>add_line_to_file</td>
+      <td>Adds a text line to the beginning or end of a file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>add_line_to_file</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file</td>
+      <td>0.1.0</td>
+      <td>coreutils</td>
+      <td>8.25</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15933</td>
+      <td>15933</td>
+      <td>378</td>
+      <td>378</td>
+      <td>1736</td>
+      <td>1736</td>
+      <td>214</td>
+      <td>214</td>
+      <td>380</td>
+      <td>380</td>
+      <td>28</td>
+      <td>28</td>
+      <td>18049</td>
+      <td>18049</td>
+      <td>620</td>
+      <td>620</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>add_value</td>
+      <td>addValue</td>
+      <td>Add a value as a new column.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>add_value</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value</td>
+      <td>1.0.1</td>
+      <td>perl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>37860</td>
+      <td>374587</td>
+      <td>1293</td>
+      <td>1610</td>
+      <td>17588</td>
+      <td>293713</td>
+      <td>1243</td>
+      <td>6197</td>
+      <td>3873</td>
+      <td>4397</td>
+      <td>202</td>
+      <td>229</td>
+      <td>59321</td>
+      <td>672697</td>
+      <td>2738</td>
+      <td>8036</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>aegean</td>
+      <td>aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval</td>
+      <td>AEGeAn toolkit wrappers</td>
+      <td>gaeval</td>
+      <td>gaeval</td>
+      <td></td>
+      <td>GAEVAL</td>
+      <td>Gene Annotation EVAluation.</td>
+      <td>Sequence annotation</td>
+      <td>Sequence analysis, Gene structure</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BrendelGroup/AEGeAn</td>
+      <td>Transcriptomics, Sequence Analysis</td>
+      <td>aegean</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean</td>
+      <td>0.16.0</td>
+      <td>aegean</td>
+      <td>0.16.0</td>
+      <td>Sequence annotation</td>
+      <td>Sequence analysis, Gene structure</td>
+      <td>1</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>1</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>200</td>
+      <td>200</td>
+      <td>77</td>
+      <td>77</td>
+      <td>83</td>
+      <td>83</td>
+      <td>39</td>
+      <td>39</td>
+      <td>1747</td>
+      <td>1747</td>
+      <td>44</td>
+      <td>44</td>
+      <td>2030</td>
+      <td>2030</td>
+      <td>160</td>
+      <td>160</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>agat</td>
+      <td>agat</td>
+      <td>GTF/GFF analysis toolkit</td>
+      <td>agat</td>
+      <td>agat</td>
+      <td></td>
+      <td>AGAT</td>
+      <td>Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.</td>
+      <td>Data handling, Genome annotation</td>
+      <td>Genomics</td>
+      <td>To update</td>
+      <td>https://github.com/NBISweden/AGAT</td>
+      <td>Convert Formats, Statistics, Fasta Manipulation</td>
+      <td>agat</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/agat</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/agat</td>
+      <td>1.4.0</td>
+      <td>agat</td>
+      <td>1.4.1</td>
+      <td>Data handling, Genome annotation</td>
+      <td>Genomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1436</td>
+      <td>1436</td>
+      <td>244</td>
+      <td>244</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>119</td>
+      <td>10</td>
+      <td>10</td>
+      <td>1555</td>
+      <td>1555</td>
+      <td>254</td>
+      <td>254</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>aldex2</td>
+      <td>aldex2</td>
+      <td>Performs analysis Of differential abundance taking sample variation into account</td>
+      <td>aldex2</td>
+      <td>aldex2</td>
+      <td></td>
+      <td>ALDEx2</td>
+      <td>A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.</td>
+      <td>Statistical inference</td>
+      <td>Gene expression, Statistics and probability</td>
+      <td>To update</td>
+      <td>https://github.com/ggloor/ALDEx_bioc</td>
+      <td>Metagenomics</td>
+      <td>aldex2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2</td>
+      <td>1.26.0</td>
+      <td>bioconductor-aldex2</td>
+      <td>1.34.0</td>
+      <td>Statistical inference</td>
+      <td>Gene expression, Statistics and probability</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>262</td>
+      <td>262</td>
+      <td>36</td>
+      <td>36</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>262</td>
+      <td>262</td>
+      <td>36</td>
+      <td>36</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>align_back_trans</td>
+      <td>align_back_trans</td>
+      <td>Thread nucleotides onto a protein alignment (back-translation)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans</td>
+      <td>Fasta Manipulation, Sequence Analysis</td>
+      <td>align_back_trans</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans</td>
+      <td>0.0.10</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>511</td>
+      <td>541</td>
+      <td>32</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>511</td>
+      <td>541</td>
+      <td>32</td>
+      <td>35</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>allegro</td>
+      <td>allegro</td>
+      <td>Linkage and haplotype analysis from deCODE</td>
+      <td>allegro</td>
+      <td>allegro</td>
+      <td></td>
+      <td>Allegro</td>
+      <td>It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.</td>
+      <td>Sequence motif discovery</td>
+      <td>Sequence analysis, Transcription factors and regulatory sites, DNA</td>
+      <td>To update</td>
+      <td>http://www.decode.com/software/</td>
+      <td>Variant Analysis</td>
+      <td>allegro</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro</td>
+      <td>@VER@.0</td>
+      <td>allegro</td>
+      <td>3</td>
+      <td>Sequence motif discovery</td>
+      <td>Sequence analysis, Transcription factors and regulatory sites, DNA</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ambertools</td>
+      <td>ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap</td>
+      <td>Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://ambermd.org/AmberTools.php</td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>ambertools</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools</td>
+      <td>21.10</td>
+      <td>ambertools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>7</td>
+      <td>2</td>
+      <td>7</td>
+      <td>0</td>
+      <td>7</td>
+      <td>2</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>7</td>
+      <td>5</td>
+      <td>0</td>
+      <td>41793</td>
+      <td>41881</td>
+      <td>510</td>
+      <td>511</td>
+      <td>1126</td>
+      <td>1126</td>
+      <td>159</td>
+      <td>159</td>
+      <td>1552</td>
+      <td>1552</td>
+      <td>85</td>
+      <td>85</td>
+      <td>44471</td>
+      <td>44559</td>
+      <td>754</td>
+      <td>755</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>amplican</td>
+      <td>amplican</td>
+      <td>AmpliCan is an analysis tool for genome editing.</td>
+      <td>amplican</td>
+      <td>amplican</td>
+      <td></td>
+      <td>amplican</td>
+      <td>It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.</td>
+      <td>Alignment, Standardisation and normalisation</td>
+      <td>PCR experiment, Statistics and probability</td>
+      <td>To update</td>
+      <td>https://github.com/valenlab/amplican</td>
+      <td>Sequence Analysis</td>
+      <td>amplican</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican</td>
+      <td>1.14.0</td>
+      <td>bioconductor-amplican</td>
+      <td>1.24.0</td>
+      <td>Alignment, Standardisation and normalisation</td>
+      <td>PCR experiment, Statistics and probability</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>81</td>
+      <td>81</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>81</td>
+      <td>81</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ampvis2</td>
+      <td>ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn</td>
+      <td>ampvis2</td>
+      <td>ampvis</td>
+      <td>ampvis</td>
+      <td></td>
+      <td>ampvis</td>
+      <td>ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.</td>
+      <td>Analysis, Visualisation</td>
+      <td>Biodiversity</td>
+      <td>To update</td>
+      <td>https://github.com/MadsAlbertsen/ampvis2/</td>
+      <td>Metagenomics</td>
+      <td>ampvis2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2</td>
+      <td>2.8.9</td>
+      <td></td>
+      <td></td>
+      <td>Analysis, Visualisation</td>
+      <td>Biodiversity</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1213</td>
+      <td>1213</td>
+      <td>155</td>
+      <td>155</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1213</td>
+      <td>1213</td>
+      <td>155</td>
+      <td>155</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>amrfinderplus</td>
+      <td>amrfinderplus</td>
+      <td>"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms.</td>
+      <td>amrfinderplus</td>
+      <td>amrfinderplus</td>
+      <td></td>
+      <td>AMRFinderPlus</td>
+      <td>AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Microbiology, Public health and epidemiology, Infectious disease</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/ncbi/amr</td>
+      <td>Sequence Analysis</td>
+      <td>AMRFinderPlus</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus</td>
+      <td>3.12.8</td>
+      <td>ncbi-amrfinderplus</td>
+      <td>3.12.8</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Microbiology, Public health and epidemiology, Infectious disease</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5734</td>
+      <td>5734</td>
+      <td>334</td>
+      <td>334</td>
+      <td>1035</td>
+      <td>1035</td>
+      <td>106</td>
+      <td>106</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6769</td>
+      <td>6769</td>
+      <td>440</td>
+      <td>440</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ancombc</td>
+      <td>ancombc</td>
+      <td>Performs analysis of compositions of microbiomes with bias correction.</td>
+      <td>ancombc</td>
+      <td>ancombc</td>
+      <td></td>
+      <td>ANCOMBC</td>
+      <td>Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.</td>
+      <td>DNA barcoding</td>
+      <td>Microbial ecology, Metagenomics, Taxonomy</td>
+      <td>To update</td>
+      <td>https://github.com/FrederickHuangLin/ANCOMBC</td>
+      <td>Metagenomics</td>
+      <td>ancombc</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc</td>
+      <td>1.4.0</td>
+      <td>bioconductor-ancombc</td>
+      <td>2.4.0</td>
+      <td>DNA barcoding</td>
+      <td>Microbial ecology, Metagenomics, Taxonomy</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>anisotropic_diffusion</td>
+      <td>ip_anisotropic_diffusion</td>
+      <td>Anisotropic image diffusion</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>anisotropic_diffusion</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion</td>
+      <td>0.4.0</td>
+      <td>medpy</td>
+      <td>0.4.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>36</td>
+      <td>41</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>36</td>
+      <td>41</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>anndata</td>
+      <td>anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom</td>
+      <td>Import, Export, Inspect and Manipulate Anndata and Loom objects</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://anndata.readthedocs.io</td>
+      <td>Single Cell, Spatial Omics</td>
+      <td>anndata</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata</td>
+      <td>0.10.9</td>
+      <td>anndata</td>
+      <td>0.6.22.post1</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>43047</td>
+      <td>43139</td>
+      <td>1826</td>
+      <td>1827</td>
+      <td>17240</td>
+      <td>17240</td>
+      <td>878</td>
+      <td>878</td>
+      <td>9309</td>
+      <td>9309</td>
+      <td>298</td>
+      <td>298</td>
+      <td>69596</td>
+      <td>69688</td>
+      <td>3002</td>
+      <td>3003</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>annotatemyids</td>
+      <td>annotatemyids</td>
+      <td>annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages</td>
+      <td>annotatemyids</td>
+      <td>annotatemyids</td>
+      <td></td>
+      <td>annotatemyids</td>
+      <td>This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.</td>
+      <td>Annotation</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids</td>
+      <td>Genome annotation</td>
+      <td>annotatemyids</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids</td>
+      <td>3.18.0</td>
+      <td>bioconductor-org.hs.eg.db</td>
+      <td>3.18.0</td>
+      <td>Annotation</td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>29266</td>
+      <td>30655</td>
+      <td>2849</td>
+      <td>2973</td>
+      <td>59299</td>
+      <td>66180</td>
+      <td>5917</td>
+      <td>6355</td>
+      <td>5644</td>
+      <td>5644</td>
+      <td>1049</td>
+      <td>1049</td>
+      <td>94209</td>
+      <td>102479</td>
+      <td>9815</td>
+      <td>10377</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>antarna</td>
+      <td>antarna</td>
+      <td>antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>antarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna</td>
+      <td>1.1</td>
+      <td>antarna</td>
+      <td>2.0.1.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>292</td>
+      <td>306</td>
+      <td>5</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>292</td>
+      <td>306</td>
+      <td>5</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>antismash</td>
+      <td>antismash</td>
+      <td>Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters</td>
+      <td>antismash</td>
+      <td>antismash</td>
+      <td></td>
+      <td>antiSMASH</td>
+      <td>Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.</td>
+      <td>Sequence clustering, Gene prediction, Differential gene expression analysis</td>
+      <td>Molecular interactions, pathways and networks, Gene and protein families</td>
+      <td>To update</td>
+      <td>https://antismash.secondarymetabolites.org</td>
+      <td>Sequence Analysis</td>
+      <td>antismash</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/antismash</td>
+      <td>6.1.1</td>
+      <td>antismash</td>
+      <td>7.1.0</td>
+      <td>Sequence clustering, Gene prediction, Differential gene expression analysis</td>
+      <td>Molecular interactions, pathways and networks, Gene and protein families</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15949</td>
+      <td>16490</td>
+      <td>726</td>
+      <td>811</td>
+      <td>5113</td>
+      <td>5113</td>
+      <td>649</td>
+      <td>649</td>
+      <td>6043</td>
+      <td>6043</td>
+      <td>169</td>
+      <td>169</td>
+      <td>27105</td>
+      <td>27646</td>
+      <td>1544</td>
+      <td>1629</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>apoc</td>
+      <td>apoc</td>
+      <td>Large-scale structural comparison of protein pockets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://cssb.biology.gatech.edu/APoc</td>
+      <td>Computational chemistry</td>
+      <td>apoc</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc</td>
+      <td>1.0+galaxy1</td>
+      <td>apoc</td>
+      <td>1b16</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>apollo</td>
+      <td>create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism</td>
+      <td>Access an Apollo instance from Galaxy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxy-genome-annotation/python-apollo</td>
+      <td>Web Services</td>
+      <td></td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo</td>
+      <td></td>
+      <td>apollo</td>
+      <td>4.2.13</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>3600</td>
+      <td>3760</td>
+      <td>883</td>
+      <td>911</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3606</td>
+      <td>3766</td>
+      <td>887</td>
+      <td>915</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>appendfdr</td>
+      <td>append_fdr</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>appendfdr</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>aquainfra_importer</td>
+      <td>aquainfra_importer</td>
+      <td>A data source tool for downloading datasets via the AquaINFRA Interaction Platform.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AquaINFRA/galaxy</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>75</td>
+      <td>75</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>75</td>
+      <td>75</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>aresite2</td>
+      <td>AREsite2_REST</td>
+      <td>AREsite2 REST Interface</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rna.tbi.univie.ac.at/AREsite</td>
+      <td>RNA, Data Source, Sequence Analysis</td>
+      <td>aresite2</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2</td>
+      <td>0.1.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>59</td>
+      <td>74</td>
+      <td>10</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59</td>
+      <td>74</td>
+      <td>10</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>argnorm</td>
+      <td>argnorm</td>
+      <td>argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database</td>
+      <td>argnorm</td>
+      <td>argnorm</td>
+      <td></td>
+      <td>argNorm</td>
+      <td>argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.</td>
+      <td>Gene functional annotation</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BigDataBiology/argNorm</td>
+      <td>Genome annotation</td>
+      <td>argnorm</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm</td>
+      <td>0.6.0</td>
+      <td>argnorm</td>
+      <td>0.6.0</td>
+      <td>Gene functional annotation</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>arriba</td>
+      <td>arriba, arriba_draw_fusions, arriba_get_filters</td>
+      <td>Arriba detects fusion genes in RNA-Seq data after running RNA-STAR</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/suhrig/arriba</td>
+      <td>Sequence Analysis, Transcriptomics</td>
+      <td>arriba</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba</td>
+      <td>2.4.0</td>
+      <td>arriba</td>
+      <td>2.4.0</td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3670</td>
+      <td>3670</td>
+      <td>71</td>
+      <td>71</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>234</td>
+      <td>234</td>
+      <td>10</td>
+      <td>10</td>
+      <td>3907</td>
+      <td>3907</td>
+      <td>83</td>
+      <td>83</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>art</td>
+      <td>art_454, art_illumina, art_solid</td>
+      <td>Simulator for Illumina, 454, and SOLiD sequencing data</td>
+      <td>art</td>
+      <td>art</td>
+      <td></td>
+      <td>ART</td>
+      <td>ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD</td>
+      <td>Conversion</td>
+      <td>Bioinformatics</td>
+      <td>To update</td>
+      <td>http://www.niehs.nih.gov/research/resources/software/biostatistics/art/</td>
+      <td>Sequence Analysis, Data Source</td>
+      <td>art</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/art</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/art</td>
+      <td>2014.11.03.0</td>
+      <td>art</td>
+      <td>2016.06.05</td>
+      <td>Conversion</td>
+      <td>Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>140</td>
+      <td>140</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>140</td>
+      <td>140</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>artbio_bam_cleaning</td>
+      <td>artbio_bam_cleaning</td>
+      <td>filter bam files before somatic-varscan or lumpy-smoove analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>SAM, Variant Analysis</td>
+      <td>artbio_bam_cleaning</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning</td>
+      <td>1.10+galaxy0</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>artic</td>
+      <td>artic_guppyplex, artic_minion</td>
+      <td>The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building</td>
+      <td>artic</td>
+      <td>artic</td>
+      <td></td>
+      <td>ARTIC</td>
+      <td>A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore</td>
+      <td>Sequence alignment</td>
+      <td>Genomics</td>
+      <td>To update</td>
+      <td>https://github.com/artic-network/fieldbioinformatics</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic</td>
+      <td></td>
+      <td>artic</td>
+      <td>1.2.4</td>
+      <td>Sequence alignment</td>
+      <td>Genomics</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9021</td>
+      <td>9021</td>
+      <td>238</td>
+      <td>238</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9021</td>
+      <td>9021</td>
+      <td>238</td>
+      <td>238</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>askomics</td>
+      <td>askomics_integrate</td>
+      <td>Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/askomics/</td>
+      <td>Web Services</td>
+      <td></td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics</td>
+      <td></td>
+      <td>askocli</td>
+      <td>0.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>askor</td>
+      <td>askor_de</td>
+      <td>AskoR links EdgeR and AskOmics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/askomics/askoR</td>
+      <td>Transcriptomics</td>
+      <td>askor_de</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/askor</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/askor</td>
+      <td>0.2</td>
+      <td>bioconductor-limma</td>
+      <td>3.58.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>assembly-stats</td>
+      <td>assembly_stats</td>
+      <td>Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/rjchallis/assembly-stats</td>
+      <td>Assembly</td>
+      <td>assembly_stats</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats</td>
+      <td>17.02</td>
+      <td>rjchallis-assembly-stats</td>
+      <td>17.02</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>assemblystats</td>
+      <td>assemblystats</td>
+      <td>Summarise an assembly (e.g. N50 metrics)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Assembly</td>
+      <td>assemblystats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats</td>
+      <td>1.1.0</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>astral</td>
+      <td>astral</td>
+      <td>Tool for estimating an unrooted species tree given a set of unrooted gene trees</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/smirarab/ASTRAL</td>
+      <td>Phylogenetics</td>
+      <td>astral</td>
+      <td>iuc</td>
+      <td>https://github.com/usegalaxy-be/galaxytools/tree/main/astral</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral</td>
+      <td>5.7.8</td>
+      <td>astral-tree</td>
+      <td>5.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>151</td>
+      <td>151</td>
+      <td>5</td>
+      <td>5</td>
+      <td>151</td>
+      <td>151</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>astropytools</td>
+      <td>astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo</td>
+      <td>AstropyTools library contains Galaxy tools for elementary Astrophysical operations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/astropy/astropy</td>
+      <td>Astronomy</td>
+      <td>astropytools</td>
+      <td>volodymyrss</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools</td>
+      <td>0.1.0+galaxy0</td>
+      <td>astropy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>atactk_trim_adapters</td>
+      <td>atactk_trim_adapters</td>
+      <td>Trim adapters from paired-end HTS reads.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ParkerLab/atactk/</td>
+      <td>Fastq Manipulation</td>
+      <td>atactk_trim_adapters</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters</td>
+      <td>0.1.6</td>
+      <td>atactk</td>
+      <td>0.1.9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>232</td>
+      <td>279</td>
+      <td>62</td>
+      <td>72</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>232</td>
+      <td>279</td>
+      <td>62</td>
+      <td>72</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>augustus</td>
+      <td>augustus, augustus_training</td>
+      <td>AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.</td>
+      <td>augustus</td>
+      <td>augustus</td>
+      <td></td>
+      <td>AUGUSTUS</td>
+      <td>AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.</td>
+      <td>Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation</td>
+      <td>Gene transcripts, Gene and protein families</td>
+      <td>To update</td>
+      <td>http://bioinf.uni-greifswald.de/augustus/</td>
+      <td>Sequence Analysis</td>
+      <td>augustus</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus</td>
+      <td>3.4.0</td>
+      <td>augustus</td>
+      <td>3.5.0</td>
+      <td>Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation</td>
+      <td>Gene transcripts, Gene and protein families</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>12890</td>
+      <td>13988</td>
+      <td>1826</td>
+      <td>1988</td>
+      <td>14901</td>
+      <td>14901</td>
+      <td>2633</td>
+      <td>2633</td>
+      <td>6187</td>
+      <td>6187</td>
+      <td>511</td>
+      <td>511</td>
+      <td>33978</td>
+      <td>35076</td>
+      <td>4970</td>
+      <td>5132</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>augustus</td>
+      <td>augustus</td>
+      <td>AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://bioinf.uni-greifswald.de/augustus/</td>
+      <td>Sequence Analysis</td>
+      <td>augustus</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/augustus</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/augustus</td>
+      <td>3.1.0</td>
+      <td>augustus</td>
+      <td>3.5.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>10109</td>
+      <td>11052</td>
+      <td>1378</td>
+      <td>1509</td>
+      <td>12573</td>
+      <td>12573</td>
+      <td>2206</td>
+      <td>2206</td>
+      <td>5274</td>
+      <td>5274</td>
+      <td>369</td>
+      <td>369</td>
+      <td>27956</td>
+      <td>28899</td>
+      <td>3953</td>
+      <td>4084</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>b2btools</td>
+      <td>b2btools_single_sequence</td>
+      <td>This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.</td>
+      <td>b2btools</td>
+      <td>b2btools</td>
+      <td></td>
+      <td>b2bTools</td>
+      <td>The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA</td>
+      <td>Protein disorder prediction, Protein secondary structure prediction, Protein feature detection</td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bio2byte.be</td>
+      <td>Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools</td>
+      <td>3.0.5+galaxy0</td>
+      <td>b2btools</td>
+      <td>3.0.7</td>
+      <td>Protein disorder prediction, Protein secondary structure prediction</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>369</td>
+      <td>369</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>369</td>
+      <td>369</td>
+      <td>19</td>
+      <td>19</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>background_removal</td>
+      <td>background_removal</td>
+      <td>Background removal filters using scikit-image</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>background_removal</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tools/background_removal</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal</td>
+      <td>0.24.0</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bakta</td>
+      <td>bakta</td>
+      <td>"Bakta is a tool for the rapid &amp; standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON &amp; bioinformatics standard file formats for automatic downstream analysis."</td>
+      <td>bakta</td>
+      <td>bakta</td>
+      <td></td>
+      <td>Bakta</td>
+      <td>Rapid &amp; standardized annotation of bacterial genomes, MAGs &amp; plasmids</td>
+      <td>Genome annotation</td>
+      <td>Genomics, Data submission, annotation and curation, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/oschwengers/bakta</td>
+      <td>Sequence Analysis</td>
+      <td>bakta</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta</td>
+      <td>1.9.4</td>
+      <td>bakta</td>
+      <td>1.9.4</td>
+      <td>Genome annotation</td>
+      <td>Genomics, Data submission, annotation and curation, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>11117</td>
+      <td>11117</td>
+      <td>534</td>
+      <td>534</td>
+      <td>19</td>
+      <td>19</td>
+      <td>1</td>
+      <td>1</td>
+      <td>9601</td>
+      <td>9601</td>
+      <td>167</td>
+      <td>167</td>
+      <td>20737</td>
+      <td>20737</td>
+      <td>702</td>
+      <td>702</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bam2mappingstats</td>
+      <td>bam2mappingstats</td>
+      <td>Generates mapping stats from a bam file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Assembly</td>
+      <td>bam2mappingstats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats</td>
+      <td>1.1.0</td>
+      <td>perl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bam_to_scidx</td>
+      <td>bam_to_scidx</td>
+      <td>Contains a tool that converts a BAM file to an ScIdx file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx</td>
+      <td>Convert Formats</td>
+      <td>bam_to_scidx</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx</td>
+      <td>1.0.1</td>
+      <td>openjdk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>83</td>
+      <td>131</td>
+      <td>15</td>
+      <td>20</td>
+      <td>329</td>
+      <td>785</td>
+      <td>50</td>
+      <td>210</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>412</td>
+      <td>916</td>
+      <td>65</td>
+      <td>230</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamclipper</td>
+      <td>bamclipper</td>
+      <td>Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tommyau/bamclipper</td>
+      <td>Sequence Analysis</td>
+      <td>bamclipper</td>
+      <td>nml</td>
+      <td>https://github.com/tommyau/bamclipper</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper</td>
+      <td>1.0.0</td>
+      <td>bamclipper</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamhash</td>
+      <td>bamhash</td>
+      <td>Hash BAM and FASTQ files to verify data integrity</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/DecodeGenetics/BamHash</td>
+      <td>Sequence Analysis</td>
+      <td>bamhash</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bamhash</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bamhash</td>
+      <td>1.1</td>
+      <td>bamhash</td>
+      <td>1.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>158</td>
+      <td>181</td>
+      <td>40</td>
+      <td>44</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>181</td>
+      <td>40</td>
+      <td>44</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamparse</td>
+      <td>bamparse</td>
+      <td>Generates hit count lists from bam alignments.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Transcriptomics</td>
+      <td>bamparse</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse</td>
+      <td>4.1.1</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamtools</td>
+      <td>bamtools</td>
+      <td>Operate on and transform BAM datasets in various ways using bamtools</td>
+      <td>bamtools</td>
+      <td>bamtools</td>
+      <td></td>
+      <td>BamTools</td>
+      <td>BamTools provides a fast, flexible C++ API &amp; toolkit for reading, writing, and managing BAM files.</td>
+      <td>Data handling, Sequence alignment analysis</td>
+      <td>Sequencing, Data management, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pezmaster31/bamtools</td>
+      <td>Sequence Analysis, SAM</td>
+      <td>bamtools</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools</td>
+      <td>2.5.2</td>
+      <td>bamtools</td>
+      <td>2.5.2</td>
+      <td>Data handling, Sequence alignment analysis</td>
+      <td>Sequencing, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>14693</td>
+      <td>15620</td>
+      <td>653</td>
+      <td>721</td>
+      <td>61872</td>
+      <td>101400</td>
+      <td>1656</td>
+      <td>5678</td>
+      <td>39</td>
+      <td>39</td>
+      <td>3</td>
+      <td>3</td>
+      <td>76604</td>
+      <td>117059</td>
+      <td>2312</td>
+      <td>6402</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamtools_filter</td>
+      <td>bamFilter</td>
+      <td>Filter BAM datasets on various attributes using bamtools filter</td>
+      <td>bamtools</td>
+      <td>bamtools</td>
+      <td></td>
+      <td>BamTools</td>
+      <td>BamTools provides a fast, flexible C++ API &amp; toolkit for reading, writing, and managing BAM files.</td>
+      <td>Data handling, Sequence alignment analysis</td>
+      <td>Sequencing, Data management, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pezmaster31/bamtools</td>
+      <td>Sequence Analysis, SAM</td>
+      <td>bamtools_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter</td>
+      <td>2.5.2</td>
+      <td>bamtools</td>
+      <td>2.5.2</td>
+      <td>Data handling, Sequence alignment analysis</td>
+      <td>Sequencing, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>115954</td>
+      <td>124795</td>
+      <td>2994</td>
+      <td>3180</td>
+      <td>95433</td>
+      <td>142254</td>
+      <td>6712</td>
+      <td>10660</td>
+      <td>5793</td>
+      <td>5793</td>
+      <td>497</td>
+      <td>497</td>
+      <td>217180</td>
+      <td>272842</td>
+      <td>10203</td>
+      <td>14337</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamtools_split</td>
+      <td>bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag</td>
+      <td>Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.</td>
+      <td>bamtools</td>
+      <td>bamtools</td>
+      <td></td>
+      <td>BamTools</td>
+      <td>BamTools provides a fast, flexible C++ API &amp; toolkit for reading, writing, and managing BAM files.</td>
+      <td>Data handling, Sequence alignment analysis</td>
+      <td>Sequencing, Data management, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pezmaster31/bamtools</td>
+      <td>Sequence Analysis, SAM</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split</td>
+      <td>2.5.2</td>
+      <td>bamtools</td>
+      <td>2.5.2</td>
+      <td>Data handling, Sequence alignment analysis</td>
+      <td>Sequencing, Sequence analysis</td>
+      <td>4</td>
+      <td>3</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>3</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9073</td>
+      <td>9073</td>
+      <td>401</td>
+      <td>401</td>
+      <td>2746</td>
+      <td>2746</td>
+      <td>224</td>
+      <td>224</td>
+      <td>103</td>
+      <td>103</td>
+      <td>10</td>
+      <td>10</td>
+      <td>11922</td>
+      <td>11922</td>
+      <td>635</td>
+      <td>635</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamutil</td>
+      <td>bamutil_clip_overlap, bamutil_diff</td>
+      <td>bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/statgen/bamUtil</td>
+      <td>Sequence Analysis</td>
+      <td>bamutil</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil</td>
+      <td></td>
+      <td>bamutil</td>
+      <td>1.0.15</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45</td>
+      <td>45</td>
+      <td>20</td>
+      <td>20</td>
+      <td>69</td>
+      <td>69</td>
+      <td>21</td>
+      <td>21</td>
+      <td>258</td>
+      <td>258</td>
+      <td>1</td>
+      <td>1</td>
+      <td>372</td>
+      <td>372</td>
+      <td>42</td>
+      <td>42</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bandage</td>
+      <td>bandage_image, bandage_info</td>
+      <td>Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily</td>
+      <td>bandage</td>
+      <td>bandage</td>
+      <td></td>
+      <td>Bandage</td>
+      <td>GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.</td>
+      <td>Sequence assembly visualisation</td>
+      <td>Genomics, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/rrwick/Bandage</td>
+      <td>Visualization</td>
+      <td>bandage</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage</td>
+      <td>2022.09</td>
+      <td>bandage_ng</td>
+      <td>2022.09</td>
+      <td>Sequence assembly visualisation</td>
+      <td>Genomics, Sequence assembly</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>55392</td>
+      <td>56095</td>
+      <td>4951</td>
+      <td>5035</td>
+      <td>47603</td>
+      <td>47603</td>
+      <td>4916</td>
+      <td>4916</td>
+      <td>18089</td>
+      <td>18089</td>
+      <td>3121</td>
+      <td>3121</td>
+      <td>121084</td>
+      <td>121787</td>
+      <td>12988</td>
+      <td>13072</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>barcode_collapse</td>
+      <td>barcode_collapse</td>
+      <td>Paired End randomer aware duplicate removal algorithm</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/YeoLab/gscripts</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>barcode_collapse</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse</td>
+      <td>0.1.0</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>barcode_splitter</td>
+      <td>barcode_splitter</td>
+      <td>A utility to split sequence files using multiple sets of barcodes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/princeton_genomics/barcode_splitter/</td>
+      <td>Fastq Manipulation</td>
+      <td>barcode_splitter</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter</td>
+      <td>0.18.4.0</td>
+      <td>barcode_splitter</td>
+      <td>0.18.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>baredsc</td>
+      <td>baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d</td>
+      <td>baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.</td>
+      <td>baredsc</td>
+      <td>baredsc</td>
+      <td></td>
+      <td>baredSC</td>
+      <td>The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.</td>
+      <td>Data retrieval, Expression correlation analysis, Differential gene expression profiling</td>
+      <td>RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lldelisle/baredSC</td>
+      <td>Single Cell, Transcriptomics, Visualization</td>
+      <td>baredsc</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc</td>
+      <td>1.1.3</td>
+      <td>baredsc</td>
+      <td>1.1.3</td>
+      <td>Data retrieval, Expression correlation analysis, Differential gene expression profiling</td>
+      <td>RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>111</td>
+      <td>111</td>
+      <td>8</td>
+      <td>8</td>
+      <td>29</td>
+      <td>29</td>
+      <td>10</td>
+      <td>10</td>
+      <td>21</td>
+      <td>21</td>
+      <td>4</td>
+      <td>4</td>
+      <td>161</td>
+      <td>161</td>
+      <td>22</td>
+      <td>22</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>baric_archive</td>
+      <td>baric_archive_rennes, baric_archive_toulouse</td>
+      <td>A data source tool to fetch data from a BARIC Archive server.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.cesgo.org/catibaric/</td>
+      <td>Data Source</td>
+      <td></td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>barrnap</td>
+      <td>barrnap</td>
+      <td>Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.</td>
+      <td>barrnap</td>
+      <td>barrnap</td>
+      <td></td>
+      <td>Barrnap</td>
+      <td>Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).</td>
+      <td>Gene prediction</td>
+      <td>Genomics, Model organisms, Model organisms</td>
+      <td>To update</td>
+      <td>https://github.com/tseemann/barrnap</td>
+      <td>Sequence Analysis</td>
+      <td>barrnap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap</td>
+      <td>1.2.2</td>
+      <td>barrnap</td>
+      <td>0.9</td>
+      <td>Gene prediction</td>
+      <td>Genomics, Model organisms, Model organisms</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6041</td>
+      <td>6041</td>
+      <td>316</td>
+      <td>316</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6723</td>
+      <td>7273</td>
+      <td>240</td>
+      <td>322</td>
+      <td>12764</td>
+      <td>13314</td>
+      <td>556</td>
+      <td>638</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>basecoverage</td>
+      <td>gops_basecoverage_1</td>
+      <td>Base Coverage of all intervals</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>basecoverage</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>226</td>
+      <td>308</td>
+      <td>27</td>
+      <td>35</td>
+      <td>2615</td>
+      <td>45557</td>
+      <td>302</td>
+      <td>2284</td>
+      <td>482</td>
+      <td>522</td>
+      <td>32</td>
+      <td>36</td>
+      <td>3323</td>
+      <td>46387</td>
+      <td>361</td>
+      <td>2355</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>baseline_calculator</td>
+      <td>tt_baseline</td>
+      <td>Toxicity prediction using QSAR models</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools</td>
+      <td>Ecology, Text Manipulation</td>
+      <td>baseline_toxicity_calculator</td>
+      <td>mbernt</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator</td>
+      <td>0.1.0+galaxy0</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>basil</td>
+      <td>basil</td>
+      <td>Breakpoint detection, including large insertions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/seqan/anise_basil</td>
+      <td>Variant Analysis</td>
+      <td>basil</td>
+      <td>iuc</td>
+      <td></td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil</td>
+      <td>1.2.0</td>
+      <td>anise_basil</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>306</td>
+      <td>311</td>
+      <td>82</td>
+      <td>83</td>
+      <td>467</td>
+      <td>467</td>
+      <td>99</td>
+      <td>99</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>773</td>
+      <td>778</td>
+      <td>181</td>
+      <td>182</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>batched_lastz</td>
+      <td>batched_lastz</td>
+      <td>Galaxy wrapper for the batching Lastz runs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/galaxyproject/KegAlign</td>
+      <td>Next Gen Mappers</td>
+      <td>batched_lastz</td>
+      <td>richard-burhans</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz</td>
+      <td>1.04.22</td>
+      <td>lastz</td>
+      <td>1.04.22</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>123</td>
+      <td>123</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>123</td>
+      <td>123</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bax2bam</td>
+      <td>bax2bam</td>
+      <td>BAX to BAM converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pacificbiosciences/bax2bam/</td>
+      <td>Convert Formats, Sequence Analysis</td>
+      <td>bax2bam</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam</td>
+      <td>0.0.11</td>
+      <td>bax2bam</td>
+      <td>0.0.11</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>208</td>
+      <td>208</td>
+      <td>26</td>
+      <td>26</td>
+      <td>210</td>
+      <td>210</td>
+      <td>30</td>
+      <td>30</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>418</td>
+      <td>418</td>
+      <td>56</td>
+      <td>56</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bayescan</td>
+      <td>BayeScan</td>
+      <td>Detecting natural selection from population-based genetic data</td>
+      <td>bayescan</td>
+      <td>bayescan</td>
+      <td></td>
+      <td>BayeScan</td>
+      <td>BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.</td>
+      <td>Statistical inference</td>
+      <td>Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism</td>
+      <td>To update</td>
+      <td>http://cmpg.unibe.ch/software/BayeScan/index.html</td>
+      <td>Sequence Analysis</td>
+      <td>bayescan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan</td>
+      <td>2.1</td>
+      <td>bayescan</td>
+      <td>2.0.1</td>
+      <td>Statistical inference</td>
+      <td>Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>90</td>
+      <td>90</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>90</td>
+      <td>90</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bbgbigwig</td>
+      <td>bbgtobigwig</td>
+      <td>Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file.</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://www.encodeproject.org/software/bedgraphtobigwig/</td>
+      <td>Convert Formats</td>
+      <td>bbgbigwig</td>
+      <td>iuc</td>
+      <td>https://www.encodeproject.org/software/bedgraphtobigwig/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig</td>
+      <td>0.1</td>
+      <td>ucsc-bedgraphtobigwig</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>7</td>
+      <td>7</td>
+      <td>175</td>
+      <td>175</td>
+      <td>26</td>
+      <td>26</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>217</td>
+      <td>217</td>
+      <td>33</td>
+      <td>33</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bbtools</td>
+      <td>bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole</td>
+      <td>BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.</td>
+      <td>bbmap</td>
+      <td>bbtools, bbmap</td>
+      <td></td>
+      <td>BBMap</td>
+      <td>BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.</td>
+      <td>RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment</td>
+      <td>Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq</td>
+      <td>To update</td>
+      <td>https://jgi.doe.gov/data-and-tools/bbtools/</td>
+      <td>Sequence Analysis</td>
+      <td>bbtools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools</td>
+      <td>39.08</td>
+      <td>bbmap</td>
+      <td>39.09</td>
+      <td>RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment</td>
+      <td>RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq</td>
+      <td>6</td>
+      <td>3</td>
+      <td>5</td>
+      <td>0</td>
+      <td>6</td>
+      <td>3</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11989</td>
+      <td>11989</td>
+      <td>768</td>
+      <td>768</td>
+      <td>4458</td>
+      <td>4458</td>
+      <td>652</td>
+      <td>652</td>
+      <td>2507</td>
+      <td>2507</td>
+      <td>80</td>
+      <td>80</td>
+      <td>18954</td>
+      <td>18954</td>
+      <td>1500</td>
+      <td>1500</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bcftools</td>
+      <td>bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@</td>
+      <td>BCFtools toolkit wrappers</td>
+      <td>bcftools</td>
+      <td>bcftools</td>
+      <td></td>
+      <td>BCFtools</td>
+      <td>BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</td>
+      <td>Data handling, Variant calling</td>
+      <td>Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment</td>
+      <td>To update</td>
+      <td>https://samtools.github.io/bcftools/</td>
+      <td>Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools</td>
+      <td>1.15.1</td>
+      <td>bcftools</td>
+      <td>1.21</td>
+      <td>Data handling, Variant calling</td>
+      <td>DNA polymorphism, GWAS study, Genotyping experiment</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bctools</td>
+      <td>bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events</td>
+      <td>bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/dmaticzka/bctools</td>
+      <td>Sequence Analysis, Transcriptomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools</td>
+      <td>0.2.2</td>
+      <td>bctools</td>
+      <td>0.2.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>2352</td>
+      <td>3092</td>
+      <td>234</td>
+      <td>265</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2352</td>
+      <td>3092</td>
+      <td>234</td>
+      <td>265</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>beacon2</td>
+      <td>beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff</td>
+      <td>beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).</td>
+      <td>ga4gh_beacon</td>
+      <td>ga4gh_beacon</td>
+      <td></td>
+      <td>GA4GH Beacon</td>
+      <td>A global search engine for genetic mutations.</td>
+      <td>Service discovery, Database search, Genetic variation analysis</td>
+      <td>Genetic variation, Population genetics, Data security, Rare diseases</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/EGA-archive/beacon2-ri-tools/tree/main</td>
+      <td>Variant Analysis</td>
+      <td>beacon2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2</td>
+      <td>2.0.0</td>
+      <td>beacon2-ri-tools</td>
+      <td>2.0.0</td>
+      <td>Service discovery, Database search, Genetic variation analysis</td>
+      <td>Genetic variation, Population genetics, Data security, Rare diseases</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>beacon2-import</td>
+      <td>beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence</td>
+      <td>Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants.</td>
+      <td>ga4gh_beacon</td>
+      <td>ga4gh_beacon</td>
+      <td></td>
+      <td>GA4GH Beacon</td>
+      <td>A global search engine for genetic mutations.</td>
+      <td>Service discovery, Database search, Genetic variation analysis</td>
+      <td>Genetic variation, Population genetics, Data security, Rare diseases</td>
+      <td>Up-to-date</td>
+      <td>https://pypi.org/project/beacon2-import/</td>
+      <td>Variant Analysis</td>
+      <td>Beacon2_Import</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import</td>
+      <td>2.2.4</td>
+      <td>beacon2-import</td>
+      <td>2.2.4</td>
+      <td>Service discovery, Database search, Genetic variation analysis</td>
+      <td>Genetic variation, Population genetics, Data security, Rare diseases</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22</td>
+      <td>22</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22</td>
+      <td>22</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>beagle</td>
+      <td>beagle</td>
+      <td>Beagle is a program for phasing and imputing missing genotypes.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://faculty.washington.edu/browning/beagle/beagle.html</td>
+      <td>Variant Analysis</td>
+      <td>beagle</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle</td>
+      <td>5.2_21Apr21.304</td>
+      <td>beagle</td>
+      <td>5.4_22Jul22.46e</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>88</td>
+      <td>88</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>88</td>
+      <td>88</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bed_to_protein_map</td>
+      <td>bed_to_protein_map</td>
+      <td>Converts a BED file to a tabular list of exon locations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>bed_to_protein_map</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map</td>
+      <td>0.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>410</td>
+      <td>419</td>
+      <td>134</td>
+      <td>137</td>
+      <td>363</td>
+      <td>363</td>
+      <td>99</td>
+      <td>99</td>
+      <td>158</td>
+      <td>158</td>
+      <td>13</td>
+      <td>13</td>
+      <td>931</td>
+      <td>940</td>
+      <td>246</td>
+      <td>249</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bedops</td>
+      <td>bedops-sort-bed</td>
+      <td>BEDOPS: high-performance genomic feature operations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://bedops.readthedocs.io/en/latest/</td>
+      <td>Genomic Interval Operations</td>
+      <td>bedops_sortbed</td>
+      <td>iuc</td>
+      <td>https://bedops.readthedocs.io/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops</td>
+      <td>2.4.41</td>
+      <td>bedops</td>
+      <td>2.4.41</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>93</td>
+      <td>93</td>
+      <td>36</td>
+      <td>36</td>
+      <td>181</td>
+      <td>181</td>
+      <td>62</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>274</td>
+      <td>274</td>
+      <td>98</td>
+      <td>98</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bedtools</td>
+      <td>bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed</td>
+      <td>bedtools is a powerful toolset for genome arithmetic</td>
+      <td>bedtools</td>
+      <td>bedtools</td>
+      <td></td>
+      <td>BEDTools</td>
+      <td>BEDTools is an extensive suite of utilities for comparing genomic features in BED format.</td>
+      <td>Mapping</td>
+      <td>Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/arq5x/bedtools2</td>
+      <td>Genomic Interval Operations, Text Manipulation</td>
+      <td>bedtools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools</td>
+      <td>2.31.1</td>
+      <td>bedtools</td>
+      <td>2.31.1</td>
+      <td>Mapping</td>
+      <td>Genomics</td>
+      <td>37</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>37</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>6</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>916111</td>
+      <td>962278</td>
+      <td>13235</td>
+      <td>14525</td>
+      <td>407944</td>
+      <td>647621</td>
+      <td>25849</td>
+      <td>41751</td>
+      <td>84008</td>
+      <td>89233</td>
+      <td>2486</td>
+      <td>2832</td>
+      <td>1408063</td>
+      <td>1699132</td>
+      <td>41570</td>
+      <td>59108</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bellerophon</td>
+      <td>bellerophon</td>
+      <td>Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/davebx/bellerophon</td>
+      <td>Sequence Analysis</td>
+      <td>bellerophon</td>
+      <td>iuc</td>
+      <td>https://github.com/davebx/bellerophon</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon</td>
+      <td>1.0</td>
+      <td>bellerophon</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1611</td>
+      <td>1611</td>
+      <td>262</td>
+      <td>262</td>
+      <td>763</td>
+      <td>763</td>
+      <td>67</td>
+      <td>67</td>
+      <td>543</td>
+      <td>543</td>
+      <td>30</td>
+      <td>30</td>
+      <td>2917</td>
+      <td>2917</td>
+      <td>359</td>
+      <td>359</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>berokka</td>
+      <td>berokka</td>
+      <td>Berokka is used to trim, circularise, orient &amp; filter long read bacterial genome assemblies.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tseemann/berokka</td>
+      <td>Fasta Manipulation</td>
+      <td>berokka</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka</td>
+      <td>0.2.3</td>
+      <td>berokka</td>
+      <td>0.2.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>617</td>
+      <td>617</td>
+      <td>63</td>
+      <td>63</td>
+      <td>617</td>
+      <td>617</td>
+      <td>63</td>
+      <td>63</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>best_regression_subsets</td>
+      <td>BestSubsetsRegression1</td>
+      <td>Perform Best-subsets Regression</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>best_regression_subsets</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets</td>
+      <td>1.0.0</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3</td>
+      <td>4</td>
+      <td>3</td>
+      <td>4</td>
+      <td>14</td>
+      <td>253</td>
+      <td>7</td>
+      <td>72</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>257</td>
+      <td>10</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bfconvert</td>
+      <td>ip_convertimage</td>
+      <td>Convert image</td>
+      <td></td>
+      <td></td>
+      <td>python-bioformats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging, Convert Formats</td>
+      <td>bfconvert</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert</td>
+      <td>6.7.0</td>
+      <td>bftools</td>
+      <td>6.7.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1635</td>
+      <td>1671</td>
+      <td>123</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>334</td>
+      <td>334</td>
+      <td>21</td>
+      <td>21</td>
+      <td>1969</td>
+      <td>2005</td>
+      <td>144</td>
+      <td>145</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bia-ftplinks</td>
+      <td>bia_download</td>
+      <td>Tool to query ftp links for study from bioimage archive</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>bia_download</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks</td>
+      <td>0.1.0</td>
+      <td>wget</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bigscape</td>
+      <td>bigscape</td>
+      <td>Construct sequence similarity networks of BGCs and groups them into GCF</td>
+      <td>BiG-SCAPE</td>
+      <td>BiG-SCAPE</td>
+      <td></td>
+      <td>BiG-SCAPE</td>
+      <td>A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.</td>
+      <td>Clustering, Global alignment, Fold recognition</td>
+      <td>Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/medema-group/BiG-SCAPE</td>
+      <td>Metagenomics</td>
+      <td>bigscape</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape</td>
+      <td>1.1.9</td>
+      <td>bigscape</td>
+      <td>1.1.9</td>
+      <td>Clustering, Global alignment, Fold recognition</td>
+      <td>Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>544</td>
+      <td>544</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>544</td>
+      <td>544</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bigwig_outlier_bed</td>
+      <td>bigwig_outlier_bed</td>
+      <td>pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files</td>
+      <td>bigtools</td>
+      <td>bigtools</td>
+      <td></td>
+      <td>bigtools</td>
+      <td>Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.</td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed</td>
+      <td>Sequence Analysis</td>
+      <td>bigwig_outlier_bed</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed</td>
+      <td>0.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bigwig_to_bedgraph</td>
+      <td>bigwig_to_bedgraph</td>
+      <td>Convert from bigWig to bedGraph format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats</td>
+      <td>bigwig_to_bedgraph</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph</td>
+      <td>0.1.0</td>
+      <td>ucsc_tools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5769</td>
+      <td>6802</td>
+      <td>567</td>
+      <td>650</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1</td>
+      <td>5769</td>
+      <td>6805</td>
+      <td>567</td>
+      <td>651</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bigwig_to_bedgraph</td>
+      <td>bigwig_to_bedgraph</td>
+      <td>Converts a bigWig file to bedGraph format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Convert Formats</td>
+      <td>bigwig_to_bedgraph</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph</td>
+      <td>377+galaxy1</td>
+      <td>ucsc-bigwigtobedgraph</td>
+      <td>469</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5769</td>
+      <td>6802</td>
+      <td>567</td>
+      <td>650</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1</td>
+      <td>5769</td>
+      <td>6805</td>
+      <td>567</td>
+      <td>651</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bigwig_to_wig</td>
+      <td>bigwig_to_wig</td>
+      <td>Converts a bigWig file to Wiggle (WIG) format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://artbio.fr</td>
+      <td>Convert Formats</td>
+      <td>bigwig_to_wig</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig</td>
+      <td>3+galaxy0</td>
+      <td>ucsc-bigwiginfo</td>
+      <td>469</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>binary2labelimage</td>
+      <td>ip_binary_to_labelimage</td>
+      <td>Binary 2 label image</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>binary2labelimage</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage</td>
+      <td>0.5</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>401</td>
+      <td>1385</td>
+      <td>87</td>
+      <td>88</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>188</td>
+      <td>188</td>
+      <td>9</td>
+      <td>9</td>
+      <td>589</td>
+      <td>1573</td>
+      <td>96</td>
+      <td>97</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>binaryimage2points</td>
+      <td>ip_binaryimage_to_points</td>
+      <td>Binary Image to Points</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>binaryimage2points</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points</td>
+      <td>0.1-2</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>24</td>
+      <td>29</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>29</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>binning_refiner</td>
+      <td>bin_refiner</td>
+      <td>Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.</td>
+      <td>binning_refiner</td>
+      <td>binning_refiner</td>
+      <td></td>
+      <td>Binning_refiner</td>
+      <td>Improving genome bins through the combination of different binning programs</td>
+      <td>Read binning, Sequence clustering</td>
+      <td>Metagenomics, Sequence assembly, Microbial ecology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/songweizhi/Binning_refiner</td>
+      <td>Metagenomics</td>
+      <td>binning_refiner</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner</td>
+      <td>1.4.3</td>
+      <td>binning_refiner</td>
+      <td>1.4.3</td>
+      <td>Read binning, Sequence clustering</td>
+      <td>Metagenomics, Sequence assembly, Microbial ecology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>126</td>
+      <td>126</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>126</td>
+      <td>126</td>
+      <td>42</td>
+      <td>42</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bio3d</td>
+      <td>bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize</td>
+      <td>Bio3d is a program that can be used to analyse molecular dynamics trajectories.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://thegrantlab.org/bio3d/index.php</td>
+      <td>Computational chemistry</td>
+      <td>bio3d</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d</td>
+      <td>2.4_1</td>
+      <td>r-bio3d</td>
+      <td>2.3_3</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>4</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>4</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>10600</td>
+      <td>10729</td>
+      <td>1150</td>
+      <td>1159</td>
+      <td>1042</td>
+      <td>1042</td>
+      <td>255</td>
+      <td>255</td>
+      <td>2756</td>
+      <td>2756</td>
+      <td>215</td>
+      <td>215</td>
+      <td>14398</td>
+      <td>14527</td>
+      <td>1620</td>
+      <td>1629</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bioext</td>
+      <td>bioext_bam2msa, bioext_bealign</td>
+      <td>A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://pypi.python.org/pypi/biopython-extensions/</td>
+      <td>Next Gen Mappers</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/davebx/bioext-gx/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext</td>
+      <td>0.21.9</td>
+      <td>python-bioext</td>
+      <td>0.21.9</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17413</td>
+      <td>17413</td>
+      <td>822</td>
+      <td>822</td>
+      <td>15349</td>
+      <td>15349</td>
+      <td>2020</td>
+      <td>2020</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>32764</td>
+      <td>32764</td>
+      <td>2843</td>
+      <td>2843</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bioformats2raw</td>
+      <td>bf2raw</td>
+      <td>Convert image to OME-Zarr</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/Euro-BioImaging</td>
+      <td>Imaging, Convert Formats</td>
+      <td>bioformats2raw</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw</td>
+      <td>0.7.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>61</td>
+      <td>61</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>61</td>
+      <td>61</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biohansel</td>
+      <td>biohansel</td>
+      <td>Heidelberg and Enteritidis SNP Elucidation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/biohansel</td>
+      <td>Sequence Analysis</td>
+      <td>biohansel</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/biohansel</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel</td>
+      <td>2.4.0</td>
+      <td>bio_hansel</td>
+      <td>2.6.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biohansel_bionumeric_converter</td>
+      <td>bionumeric_convert</td>
+      <td>Convert BioHansel output data to a Bionumerics friendly form</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Text Manipulation</td>
+      <td>biohansel_bionumeric_converter</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter</td>
+      <td>0.2.0</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bioimaging</td>
+      <td>bioimage_inference</td>
+      <td>Load model from BioImage.IO and make inferences</td>
+      <td>pytorch</td>
+      <td>pytorch</td>
+      <td>pytorch</td>
+      <td>PyTorch</td>
+      <td>PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.</td>
+      <td></td>
+      <td>Machine learning, Computer science</td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools</td>
+      <td>Imaging</td>
+      <td>bioimage_inference</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging</td>
+      <td>2.4.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td>Machine learning</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bioinformatics_cafe</td>
+      <td>fasta_regex_finder</td>
+      <td>Miscellanea of scripts for bioinformatics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/dariober/bioinformatics-cafe/</td>
+      <td>Sequence Analysis</td>
+      <td>bioinformatics_cafe</td>
+      <td>mbernt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe</td>
+      <td>0.1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1137</td>
+      <td>1137</td>
+      <td>97</td>
+      <td>97</td>
+      <td>1029</td>
+      <td>1029</td>
+      <td>71</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2166</td>
+      <td>2166</td>
+      <td>168</td>
+      <td>168</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biom_format</td>
+      <td>biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table</td>
+      <td>The biom-format package provides a command line interface and Python API for working with BIOM files.</td>
+      <td>biomformat</td>
+      <td>biomformat</td>
+      <td></td>
+      <td>biomformat</td>
+      <td>This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.</td>
+      <td>Formatting</td>
+      <td>Laboratory information management, Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/biocore/biom-format</td>
+      <td>Metagenomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format</td>
+      <td>2.1.15</td>
+      <td>biom-format</td>
+      <td>2.1.7</td>
+      <td>Formatting</td>
+      <td>Laboratory information management, Sequence analysis</td>
+      <td>2</td>
+      <td>2</td>
+      <td>6</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>12725</td>
+      <td>12725</td>
+      <td>297</td>
+      <td>297</td>
+      <td>2851</td>
+      <td>5049</td>
+      <td>450</td>
+      <td>638</td>
+      <td>2171</td>
+      <td>2371</td>
+      <td>214</td>
+      <td>239</td>
+      <td>17747</td>
+      <td>20145</td>
+      <td>961</td>
+      <td>1174</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biomodelsML</td>
+      <td>biomodels_biomd0000001066, biomodels_biomd0000001076</td>
+      <td>Wrappers for tools to bring BioModels AI models into Galaxy.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.ebi.ac.uk/biomodels/</td>
+      <td>Machine Learning</td>
+      <td>biomodels</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML</td>
+      <td>1.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25</td>
+      <td>25</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25</td>
+      <td>25</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biomoldyn</td>
+      <td>biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering</td>
+      <td>Tools for MD analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/moldyn/</td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>biomoldyn</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn</td>
+      <td>1.5.2</td>
+      <td>scipy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>3</td>
+      <td>0</td>
+      <td>493</td>
+      <td>493</td>
+      <td>119</td>
+      <td>119</td>
+      <td>441</td>
+      <td>441</td>
+      <td>148</td>
+      <td>148</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>934</td>
+      <td>934</td>
+      <td>267</td>
+      <td>267</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bionano</td>
+      <td>bionano_scaffold</td>
+      <td>Bionano Solve is a set of tools for analyzing Bionano data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bionanogenomics.com/</td>
+      <td>Assembly</td>
+      <td>bionano</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bionano</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bionano</td>
+      <td>3.7.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>547</td>
+      <td>547</td>
+      <td>151</td>
+      <td>151</td>
+      <td>143</td>
+      <td>143</td>
+      <td>43</td>
+      <td>43</td>
+      <td>596</td>
+      <td>596</td>
+      <td>22</td>
+      <td>22</td>
+      <td>1286</td>
+      <td>1286</td>
+      <td>216</td>
+      <td>216</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bioperl</td>
+      <td>bp_genbank2gff3</td>
+      <td>Converts GenBank format files to GFF3</td>
+      <td>bioperl</td>
+      <td>bioperl</td>
+      <td></td>
+      <td>BioPerl</td>
+      <td>A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.</td>
+      <td>Data handling, Service invocation</td>
+      <td>Genomics, Software engineering, Data management</td>
+      <td>To update</td>
+      <td>https://bioperl.org/</td>
+      <td>Sequence Analysis</td>
+      <td>bp_genbank2gff3</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl</td>
+      <td>1.1</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td>Data handling, Service invocation</td>
+      <td>Genomics, Software engineering</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7738</td>
+      <td>7931</td>
+      <td>478</td>
+      <td>508</td>
+      <td>8301</td>
+      <td>8301</td>
+      <td>849</td>
+      <td>849</td>
+      <td>1369</td>
+      <td>1369</td>
+      <td>154</td>
+      <td>154</td>
+      <td>17408</td>
+      <td>17601</td>
+      <td>1481</td>
+      <td>1511</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biotradis</td>
+      <td>bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites</td>
+      <td>Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.</td>
+      <td>biotradis</td>
+      <td>biotradis</td>
+      <td></td>
+      <td>biotradis</td>
+      <td>The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.</td>
+      <td>Sequence analysis</td>
+      <td>Mobile genetic elements, Workflows</td>
+      <td>Up-to-date</td>
+      <td>https://www.sanger.ac.uk/science/tools/bio-tradis</td>
+      <td>Genome annotation</td>
+      <td>biotradis</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis</td>
+      <td>1.4.5</td>
+      <td>biotradis</td>
+      <td>1.4.5</td>
+      <td>Sequence analysis</td>
+      <td>Mobile genetic elements, Workflows</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6243</td>
+      <td>6243</td>
+      <td>375</td>
+      <td>375</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6243</td>
+      <td>6243</td>
+      <td>375</td>
+      <td>375</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biotransformer</td>
+      <td>biotransformer</td>
+      <td>BioTransformer is a tool for prediction of small molecule metabolism in mammals.</td>
+      <td>biotransformer</td>
+      <td>biotransformer</td>
+      <td></td>
+      <td>BioTransformer</td>
+      <td>BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.</td>
+      <td>Metabolic pathway prediction, PTM site prediction, Natural product identification</td>
+      <td>Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR</td>
+      <td>Up-to-date</td>
+      <td>https://bitbucket.org/djoumbou/biotransformerjar/src/master/</td>
+      <td>Metabolomics</td>
+      <td>biotransformer</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer</td>
+      <td>3.0.20230403</td>
+      <td>biotransformer</td>
+      <td>3.0.20230403</td>
+      <td>Metabolic pathway prediction, PTM site prediction, Natural product identification</td>
+      <td>Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biscot</td>
+      <td>biscot</td>
+      <td>Bionano scaffolding correction tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/institut-de-genomique/biscot</td>
+      <td>Assembly</td>
+      <td>biscot</td>
+      <td>iuc</td>
+      <td>https://github.com/bgruening/iuc/tree/master/tools/biscot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot</td>
+      <td>2.3.3</td>
+      <td>biscot</td>
+      <td>2.3.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bismark</td>
+      <td>bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor</td>
+      <td>A tool to map bisulfite converted sequence reads and determine cytosine methylation states</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.bioinformatics.babraham.ac.uk/projects/bismark/</td>
+      <td>Sequence Analysis, Next Gen Mappers</td>
+      <td>bismark</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bismark</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bismark</td>
+      <td>0.22.1</td>
+      <td>bismark</td>
+      <td>0.24.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>13715</td>
+      <td>14997</td>
+      <td>992</td>
+      <td>1099</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>197</td>
+      <td>197</td>
+      <td>22</td>
+      <td>22</td>
+      <td>13912</td>
+      <td>15194</td>
+      <td>1014</td>
+      <td>1121</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast</td>
+      <td>magicblast</td>
+      <td>Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://ncbi.github.io/magicblast/</td>
+      <td>Next Gen Mappers</td>
+      <td>magicblast</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast</td>
+      <td>1.7.0</td>
+      <td>magicblast</td>
+      <td>1.7.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>738</td>
+      <td>738</td>
+      <td>151</td>
+      <td>151</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>740</td>
+      <td>740</td>
+      <td>152</td>
+      <td>152</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast2go</td>
+      <td>blast2go</td>
+      <td>Maps BLAST results to GO annotation terms</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go</td>
+      <td>Ontology Manipulation, Sequence Analysis</td>
+      <td>blast2go</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go</td>
+      <td>0.0.11</td>
+      <td>b2g4pipe</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1063</td>
+      <td>1237</td>
+      <td>257</td>
+      <td>300</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1063</td>
+      <td>1237</td>
+      <td>257</td>
+      <td>300</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast_parser</td>
+      <td>blast_parser</td>
+      <td>Convert 12- or 24-column BLAST output into 3-column hcluster_sg input</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/</td>
+      <td>Phylogenetics</td>
+      <td>blast_parser</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser</td>
+      <td>0.1.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>417</td>
+      <td>438</td>
+      <td>99</td>
+      <td>104</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>417</td>
+      <td>438</td>
+      <td>99</td>
+      <td>104</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast_plus_remote_blastp</td>
+      <td>blast_plus_remote_blastp</td>
+      <td>NCBI BLAST+ with -remote option</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://blast.ncbi.nlm.nih.gov/</td>
+      <td>Sequence Analysis</td>
+      <td>blast_plus_remote_blastp</td>
+      <td>galaxyp</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp</td>
+      <td>2.6.0</td>
+      <td>blast</td>
+      <td>2.16.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast_rbh</td>
+      <td>blast_reciprocal_best_hits</td>
+      <td>BLAST Reciprocal Best Hits (RBH) from two FASTA files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh</td>
+      <td>Fasta Manipulation, Sequence Analysis</td>
+      <td>blast_rbh</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh</td>
+      <td>0.3.0</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>24916</td>
+      <td>27120</td>
+      <td>283</td>
+      <td>347</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24916</td>
+      <td>27120</td>
+      <td>283</td>
+      <td>347</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast_to_scaffold</td>
+      <td>blast2scaffold</td>
+      <td>Generate DNA scaffold from blastn or tblastx alignments of Contigs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Sequence Analysis, Assembly</td>
+      <td>blast_to_scaffold</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold</td>
+      <td>1.1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast_unmatched</td>
+      <td>blast_unmatched</td>
+      <td>Extract unmatched query sequences from blast</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Fasta Manipulation</td>
+      <td>blast_unmatched</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched</td>
+      <td>1.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blastparser_and_hits</td>
+      <td>BlastParser_and_hits</td>
+      <td>Parse blast outputs and compile hits</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Assembly, RNA</td>
+      <td>blastparser_and_hits</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits</td>
+      <td>2.7.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blastx_to_scaffold</td>
+      <td>blastx2scaffold</td>
+      <td>Generate DNA scaffold from blastx alignment of Contigs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Sequence Analysis, Assembly</td>
+      <td>blastx_to_scaffold</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold</td>
+      <td>1.1.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blastxml_to_gapped_gff3</td>
+      <td>blastxml_to_gapped_gff3</td>
+      <td>BlastXML to gapped GFF3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3</td>
+      <td>Convert Formats, Sequence Analysis</td>
+      <td>blastxml_to_gapped_gff3</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3</td>
+      <td>1.1</td>
+      <td>bcbiogff</td>
+      <td>0.6.6</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>585</td>
+      <td>585</td>
+      <td>102</td>
+      <td>102</td>
+      <td>172</td>
+      <td>172</td>
+      <td>63</td>
+      <td>63</td>
+      <td>135</td>
+      <td>135</td>
+      <td>16</td>
+      <td>16</td>
+      <td>892</td>
+      <td>892</td>
+      <td>181</td>
+      <td>181</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blastxml_to_top_descr</td>
+      <td>blastxml_to_top_descr</td>
+      <td>Make table of top BLAST match descriptions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr</td>
+      <td>Convert Formats, Sequence Analysis, Text Manipulation</td>
+      <td>blastxml_to_top_descr</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr</td>
+      <td>0.1.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>264392</td>
+      <td>265217</td>
+      <td>483</td>
+      <td>552</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>264392</td>
+      <td>265217</td>
+      <td>483</td>
+      <td>552</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blat_coverage_report</td>
+      <td>generate_coverage_report</td>
+      <td>Polymorphism of the Reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Next Gen Mappers, Sequence Analysis</td>
+      <td>blat_coverage_report</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blat_mapping</td>
+      <td>blat2wig</td>
+      <td>Coverage of the Reads in wiggle format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Next Gen Mappers, Sequence Analysis</td>
+      <td>blat_mapping</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blobtoolkit</td>
+      <td>blobtoolkit</td>
+      <td>Identification and isolation non-target data in draft and publicly available genome assemblies.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://blobtoolkit.genomehubs.org/</td>
+      <td>Sequence Analysis, Assembly</td>
+      <td>blobtoolkit</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit</td>
+      <td>4.0.7</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1527</td>
+      <td>1527</td>
+      <td>79</td>
+      <td>79</td>
+      <td>6</td>
+      <td>6</td>
+      <td>1</td>
+      <td>1</td>
+      <td>317</td>
+      <td>317</td>
+      <td>26</td>
+      <td>26</td>
+      <td>1850</td>
+      <td>1850</td>
+      <td>106</td>
+      <td>106</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blockbuster</td>
+      <td>blockbuster</td>
+      <td>Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>blockbuster</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster</td>
+      <td>0.1.2</td>
+      <td>blockbuster</td>
+      <td>0.0.1.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>768</td>
+      <td>3043</td>
+      <td>97</td>
+      <td>119</td>
+      <td>14</td>
+      <td>14</td>
+      <td>11</td>
+      <td>11</td>
+      <td>276</td>
+      <td>276</td>
+      <td>9</td>
+      <td>9</td>
+      <td>1058</td>
+      <td>3333</td>
+      <td>117</td>
+      <td>139</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blockclust</td>
+      <td>blockclust</td>
+      <td>BlockClust detects transcripts with similar processing patterns.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust</td>
+      <td>RNA</td>
+      <td>blockclust</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust</td>
+      <td>1.1.1</td>
+      <td>blockclust</td>
+      <td>1.1.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>811</td>
+      <td>1501</td>
+      <td>54</td>
+      <td>79</td>
+      <td>64</td>
+      <td>64</td>
+      <td>29</td>
+      <td>29</td>
+      <td>561</td>
+      <td>561</td>
+      <td>15</td>
+      <td>15</td>
+      <td>1436</td>
+      <td>2126</td>
+      <td>98</td>
+      <td>123</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bowtie2</td>
+      <td>bowtie2</td>
+      <td>Bowtie2: Fast and sensitive read alignment</td>
+      <td>bowtie2</td>
+      <td>bowtie2</td>
+      <td></td>
+      <td>Bowtie 2</td>
+      <td>Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.</td>
+      <td>Read mapping</td>
+      <td>Mapping, Genomics, Mapping</td>
+      <td>To update</td>
+      <td>http://bowtie-bio.sourceforge.net/bowtie2</td>
+      <td>Next Gen Mappers</td>
+      <td>bowtie2</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2</td>
+      <td>2.5.3</td>
+      <td>bowtie2</td>
+      <td>2.5.4</td>
+      <td>Read mapping</td>
+      <td>Mapping, Genomics, Mapping</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>397893</td>
+      <td>427447</td>
+      <td>12133</td>
+      <td>13176</td>
+      <td>577209</td>
+      <td>903193</td>
+      <td>33086</td>
+      <td>52020</td>
+      <td>60105</td>
+      <td>67495</td>
+      <td>3779</td>
+      <td>4271</td>
+      <td>1035207</td>
+      <td>1398135</td>
+      <td>48998</td>
+      <td>69467</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bowtie_wrappers</td>
+      <td>bowtie_wrapper</td>
+      <td>Galaxy wrappers for the Bowtie short read mapping tools.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://bowtie-bio.sourceforge.net/</td>
+      <td>Next Gen Mappers</td>
+      <td>bowtie_wrappers</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers</td>
+      <td>1.2.0</td>
+      <td>bowtie</td>
+      <td>1.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>24164</td>
+      <td>25149</td>
+      <td>1320</td>
+      <td>1480</td>
+      <td>17537</td>
+      <td>203397</td>
+      <td>1330</td>
+      <td>17491</td>
+      <td>15654</td>
+      <td>15992</td>
+      <td>291</td>
+      <td>351</td>
+      <td>57355</td>
+      <td>244538</td>
+      <td>2941</td>
+      <td>19322</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bracken</td>
+      <td>est_abundance</td>
+      <td>Bayesian Reestimation of Abundance with KrakEN</td>
+      <td>bracken</td>
+      <td>bracken</td>
+      <td></td>
+      <td>Bracken</td>
+      <td>Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.</td>
+      <td>Statistical calculation</td>
+      <td>Metagenomics, Microbial ecology</td>
+      <td>Up-to-date</td>
+      <td>https://ccb.jhu.edu/software/bracken/</td>
+      <td>Sequence Analysis, Metagenomics</td>
+      <td>bracken</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken</td>
+      <td>3.0</td>
+      <td>bracken</td>
+      <td>3.0</td>
+      <td>Statistical calculation</td>
+      <td>Metagenomics, Microbial ecology</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>51378</td>
+      <td>51378</td>
+      <td>775</td>
+      <td>775</td>
+      <td>3298</td>
+      <td>3298</td>
+      <td>160</td>
+      <td>160</td>
+      <td>1660</td>
+      <td>1660</td>
+      <td>63</td>
+      <td>63</td>
+      <td>56336</td>
+      <td>56336</td>
+      <td>998</td>
+      <td>998</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>braker</td>
+      <td>braker</td>
+      <td>BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/Gaius-Augustus/BRAKER</td>
+      <td>Genome annotation</td>
+      <td>braker</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/braker</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/braker</td>
+      <td>2.1.6</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>165</td>
+      <td>165</td>
+      <td>48</td>
+      <td>48</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>165</td>
+      <td>165</td>
+      <td>48</td>
+      <td>48</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>braker3</td>
+      <td>braker3</td>
+      <td>BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .</td>
+      <td>braker3</td>
+      <td>braker3</td>
+      <td></td>
+      <td>BRAKER3</td>
+      <td>BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes</td>
+      <td>Genome annotation, Gene prediction</td>
+      <td>RNA-Seq, Genomics, Structure prediction, Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/Gaius-Augustus/BRAKER</td>
+      <td>Genome annotation</td>
+      <td>braker3</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/braker</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/braker3</td>
+      <td>3.0.8</td>
+      <td></td>
+      <td></td>
+      <td>Genome annotation, Gene prediction</td>
+      <td>RNA-Seq, Genomics, Structure prediction, Sequence analysis</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1938</td>
+      <td>1938</td>
+      <td>294</td>
+      <td>294</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>412</td>
+      <td>412</td>
+      <td>71</td>
+      <td>71</td>
+      <td>2350</td>
+      <td>2350</td>
+      <td>365</td>
+      <td>365</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>breseq</td>
+      <td>breseq</td>
+      <td>Predicts mutations in microbial genomes</td>
+      <td>breseq</td>
+      <td>breseq</td>
+      <td></td>
+      <td>breseq</td>
+      <td>Runs Breseq software on a set of fastq files.</td>
+      <td>Polymorphism detection</td>
+      <td>Sequencing, Sequence analysis, DNA mutation</td>
+      <td>To update</td>
+      <td>https://github.com/barricklab/breseq</td>
+      <td>Variant Analysis</td>
+      <td>breseq</td>
+      <td>iuc</td>
+      <td></td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq</td>
+      <td>0.35.5</td>
+      <td>breseq</td>
+      <td>0.39.0</td>
+      <td>Polymorphism detection</td>
+      <td>Sequencing, Sequence analysis, DNA mutation</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2976</td>
+      <td>2976</td>
+      <td>98</td>
+      <td>98</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>884</td>
+      <td>884</td>
+      <td>70</td>
+      <td>70</td>
+      <td>3860</td>
+      <td>3860</td>
+      <td>168</td>
+      <td>168</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>brew3r_r</td>
+      <td>brew3r_r</td>
+      <td>Extend 3' end of a GTF using another GTF as a template</td>
+      <td>brew3r.r</td>
+      <td>brew3r.r</td>
+      <td></td>
+      <td>BREW3R.r</td>
+      <td>This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.</td>
+      <td>Genome annotation</td>
+      <td>Transcriptomics, Genomics</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html</td>
+      <td>Transcriptomics, RNA</td>
+      <td>brew3r_r</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r</td>
+      <td>1.0.2</td>
+      <td></td>
+      <td></td>
+      <td>Genome annotation</td>
+      <td>Transcriptomics</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>6</td>
+      <td>6</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bumbershoot</td>
+      <td>idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://proteowizard.sourceforge.net/</td>
+      <td>Proteomics</td>
+      <td></td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot</td>
+      <td>3.0.21142</td>
+      <td>bumbershoot</td>
+      <td>3_0_21142_0e4f4a4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>1186</td>
+      <td>1356</td>
+      <td>21</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1186</td>
+      <td>1356</td>
+      <td>21</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bundle_collections</td>
+      <td>bundle_collection</td>
+      <td>Tool to bundle up list collection into a single zip to be download</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>bundle_collections</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections</td>
+      <td>1.3.0</td>
+      <td>perl-getopt-long</td>
+      <td>2.58</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1518</td>
+      <td>1526</td>
+      <td>73</td>
+      <td>76</td>
+      <td>1520</td>
+      <td>1528</td>
+      <td>74</td>
+      <td>77</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>busco</td>
+      <td>busco</td>
+      <td>BUSCO assess genome and annotation completeness</td>
+      <td>busco</td>
+      <td>busco</td>
+      <td></td>
+      <td>BUSCO</td>
+      <td>Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.</td>
+      <td>Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly</td>
+      <td>Sequence assembly, Genomics, Transcriptomics, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://gitlab.com/ezlab/busco/-/releases</td>
+      <td>Sequence Analysis</td>
+      <td>busco</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco</td>
+      <td>5.7.1</td>
+      <td>busco</td>
+      <td>5.7.1</td>
+      <td>Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly</td>
+      <td>Sequence assembly, Transcriptomics, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>102717</td>
+      <td>103051</td>
+      <td>3877</td>
+      <td>3926</td>
+      <td>34251</td>
+      <td>34251</td>
+      <td>3506</td>
+      <td>3506</td>
+      <td>33192</td>
+      <td>34369</td>
+      <td>2439</td>
+      <td>2525</td>
+      <td>170160</td>
+      <td>171671</td>
+      <td>9822</td>
+      <td>9957</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bwa</td>
+      <td>bwa_mem, bwa</td>
+      <td>Wrapper for bwa mem, aln, sampe, and samse</td>
+      <td>bwa</td>
+      <td>bwa</td>
+      <td></td>
+      <td>BWA</td>
+      <td>Fast, accurate, memory-efficient aligner for short and long sequencing reads</td>
+      <td>Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment</td>
+      <td>Mapping</td>
+      <td>Up-to-date</td>
+      <td>http://bio-bwa.sourceforge.net/</td>
+      <td>Next Gen Mappers</td>
+      <td>bwa</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa</td>
+      <td>0.7.18</td>
+      <td>bwa</td>
+      <td>0.7.18</td>
+      <td>Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment</td>
+      <td>Mapping</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>976935</td>
+      <td>1017671</td>
+      <td>13526</td>
+      <td>14401</td>
+      <td>474702</td>
+      <td>681286</td>
+      <td>32627</td>
+      <td>47624</td>
+      <td>79802</td>
+      <td>87191</td>
+      <td>4219</td>
+      <td>4954</td>
+      <td>1531439</td>
+      <td>1786148</td>
+      <td>50372</td>
+      <td>66979</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bwa_mem2</td>
+      <td>bwa_mem2</td>
+      <td>Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.</td>
+      <td>bwa-mem2</td>
+      <td>bwa-mem2</td>
+      <td></td>
+      <td>Bwa-mem2</td>
+      <td>Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,  dataset and the running machine.</td>
+      <td>Sequence alignment</td>
+      <td>Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bwa-mem2/bwa-mem2</td>
+      <td>Next Gen Mappers</td>
+      <td>bwa_mem2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2</td>
+      <td>2.2.1</td>
+      <td>bwa-mem2</td>
+      <td>2.2.1</td>
+      <td>Sequence alignment</td>
+      <td>Mapping</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>56619</td>
+      <td>56619</td>
+      <td>2324</td>
+      <td>2324</td>
+      <td>36631</td>
+      <td>36631</td>
+      <td>2808</td>
+      <td>2808</td>
+      <td>18121</td>
+      <td>18121</td>
+      <td>713</td>
+      <td>713</td>
+      <td>111371</td>
+      <td>111371</td>
+      <td>5845</td>
+      <td>5845</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bwameth</td>
+      <td>bwameth</td>
+      <td>Fast and accurate alignment of BS-seq reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/brentp/bwa-meth</td>
+      <td>Sequence Analysis, Next Gen Mappers</td>
+      <td>bwameth</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth</td>
+      <td>0.2.7</td>
+      <td>bwameth</td>
+      <td>0.2.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7970</td>
+      <td>11724</td>
+      <td>643</td>
+      <td>826</td>
+      <td>5524</td>
+      <td>5524</td>
+      <td>611</td>
+      <td>611</td>
+      <td>1242</td>
+      <td>1242</td>
+      <td>114</td>
+      <td>114</td>
+      <td>14736</td>
+      <td>18490</td>
+      <td>1368</td>
+      <td>1551</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>c3s</td>
+      <td>c3s</td>
+      <td>Copernicus Climate Change Service (C3S)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset</td>
+      <td>Climate Analysis</td>
+      <td>c3s</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s</td>
+      <td>0.3.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>234</td>
+      <td>234</td>
+      <td>11</td>
+      <td>11</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>92</td>
+      <td>92</td>
+      <td>3</td>
+      <td>3</td>
+      <td>330</td>
+      <td>330</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cactus</td>
+      <td>cactus_cactus, cactus_export</td>
+      <td>Cactus is a reference-free whole-genome multiple alignment program</td>
+      <td>cactus</td>
+      <td>cactus</td>
+      <td></td>
+      <td>Cactus</td>
+      <td>Cactus is a reference-free whole-genome multiple alignment program.</td>
+      <td>Multiple sequence alignment, Genome alignment</td>
+      <td>Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics</td>
+      <td>To update</td>
+      <td>https://github.com/ComparativeGenomicsToolkit/cactus</td>
+      <td>Sequence Analysis</td>
+      <td>cactus</td>
+      <td>galaxy-australia</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus</td>
+      <td>2.7.1</td>
+      <td></td>
+      <td></td>
+      <td>Multiple sequence alignment, Genome alignment</td>
+      <td>Genomics, Sequence assembly, Mapping, Phylogenetics</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>299</td>
+      <td>299</td>
+      <td>61</td>
+      <td>61</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1339</td>
+      <td>1339</td>
+      <td>95</td>
+      <td>95</td>
+      <td>1638</td>
+      <td>1638</td>
+      <td>156</td>
+      <td>156</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cads</td>
+      <td>cads</td>
+      <td>Copernicus Atmosphere Data Store (ADS)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://ads.atmosphere.copernicus.eu/#!/home</td>
+      <td>Climate Analysis</td>
+      <td>cads</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads</td>
+      <td>0.1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>52</td>
+      <td>52</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>52</td>
+      <td>52</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>calculate_contrast_threshold</td>
+      <td>calculate_contrast_threshold</td>
+      <td>Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold</td>
+      <td>Visualization, Genomic Interval Operations, SAM</td>
+      <td>calculate_contrast_threshold</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold</td>
+      <td>1.0.0</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>calculate_numeric_param</td>
+      <td>calculate_numeric_param</td>
+      <td>Calculate a numeric parameter value using integer and float values.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>calculate_numeric_param</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1393</td>
+      <td>1393</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1393</td>
+      <td>1393</td>
+      <td>10</td>
+      <td>10</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>calisp</td>
+      <td>calisp</td>
+      <td>Calgary approach to isotopes in proteomics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/kinestetika/Calisp/</td>
+      <td>Proteomics</td>
+      <td>calisp</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp</td>
+      <td>3.0.13</td>
+      <td>calisp</td>
+      <td>3.0.13</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>camera</td>
+      <td>abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Metabolomics</td>
+      <td>camera</td>
+      <td>workflow4metabolomics</td>
+      <td></td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera</td>
+      <td>1.48.0</td>
+      <td>r-snow</td>
+      <td>0.4_1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>677</td>
+      <td>787</td>
+      <td>114</td>
+      <td>120</td>
+      <td>60</td>
+      <td>60</td>
+      <td>30</td>
+      <td>30</td>
+      <td>734</td>
+      <td>746</td>
+      <td>26</td>
+      <td>26</td>
+      <td>1471</td>
+      <td>1593</td>
+      <td>170</td>
+      <td>176</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cami_amber</td>
+      <td>biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert</td>
+      <td>Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/CAMI-challenge/AMBER</td>
+      <td>Metagenomics</td>
+      <td>cami_amber</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber</td>
+      <td>2.0.7</td>
+      <td>cami-amber</td>
+      <td>2.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>195</td>
+      <td>195</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>195</td>
+      <td>195</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>canonical_correlation_analysis</td>
+      <td>cca1</td>
+      <td>Canonical Correlation Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>canonical_correlation_analysis</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis</td>
+      <td>1.0.0</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>66</td>
+      <td>75</td>
+      <td>16</td>
+      <td>18</td>
+      <td>141</td>
+      <td>505</td>
+      <td>31</td>
+      <td>147</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>207</td>
+      <td>580</td>
+      <td>47</td>
+      <td>165</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>canu</td>
+      <td>canu</td>
+      <td>Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).</td>
+      <td>canu</td>
+      <td>canu</td>
+      <td></td>
+      <td>CANU</td>
+      <td>De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.</td>
+      <td>De-novo assembly</td>
+      <td>Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/marbl/canu</td>
+      <td></td>
+      <td>canu</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/canu</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/canu</td>
+      <td>2.2</td>
+      <td>canu</td>
+      <td>2.2</td>
+      <td>De-novo assembly</td>
+      <td>Genomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>13360</td>
+      <td>14618</td>
+      <td>1383</td>
+      <td>1444</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3542</td>
+      <td>3542</td>
+      <td>385</td>
+      <td>385</td>
+      <td>16902</td>
+      <td>18160</td>
+      <td>1768</td>
+      <td>1829</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cap3</td>
+      <td>cap3</td>
+      <td>cap3 wrapper</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Assembly</td>
+      <td>cap3</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3</td>
+      <td>2.0.1</td>
+      <td>cap3</td>
+      <td>10.2011</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9869</td>
+      <td>9869</td>
+      <td>158</td>
+      <td>158</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6886</td>
+      <td>6886</td>
+      <td>146</td>
+      <td>146</td>
+      <td>16755</td>
+      <td>16755</td>
+      <td>304</td>
+      <td>304</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cardinal</td>
+      <td>cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots</td>
+      <td>Statistical and computational tools for analyzing mass spectrometry imaging datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cardinalmsi.org</td>
+      <td>Proteomics, Metabolomics</td>
+      <td></td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal</td>
+      <td>3.4.3</td>
+      <td>bioconductor-cardinal</td>
+      <td>3.4.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>9</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>11</td>
+      <td>9</td>
+      <td>0</td>
+      <td>41875</td>
+      <td>50702</td>
+      <td>663</td>
+      <td>713</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1</td>
+      <td>1</td>
+      <td>7512</td>
+      <td>7512</td>
+      <td>231</td>
+      <td>231</td>
+      <td>49399</td>
+      <td>58226</td>
+      <td>895</td>
+      <td>945</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cat</td>
+      <td>cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise</td>
+      <td>Contig Annotation Tool (CAT)</td>
+      <td>cat_bins</td>
+      <td>cat_bins</td>
+      <td></td>
+      <td>CAT and BAT</td>
+      <td>Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.</td>
+      <td>Taxonomic classification, Sequence assembly, Coding region prediction</td>
+      <td>Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly</td>
+      <td>To update</td>
+      <td>https://github.com/dutilh/CAT</td>
+      <td>Metagenomics</td>
+      <td>contig_annotation_tool</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat</td>
+      <td>5.2.3</td>
+      <td>cat</td>
+      <td>5.3</td>
+      <td>Taxonomic classification, Sequence assembly, Coding region prediction</td>
+      <td>Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly</td>
+      <td>5</td>
+      <td>2</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>2</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>3835</td>
+      <td>3835</td>
+      <td>597</td>
+      <td>597</td>
+      <td>1359</td>
+      <td>1359</td>
+      <td>467</td>
+      <td>467</td>
+      <td>646</td>
+      <td>646</td>
+      <td>98</td>
+      <td>98</td>
+      <td>5840</td>
+      <td>5840</td>
+      <td>1162</td>
+      <td>1162</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>categorize_elements_satisfying_criteria</td>
+      <td>categorize_elements_satisfying_criteria</td>
+      <td>Categorize Elements satisfying criteria.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>categorize_elements_satisfying_criteria</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>37</td>
+      <td>41</td>
+      <td>4</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>168</td>
+      <td>186</td>
+      <td>12</td>
+      <td>14</td>
+      <td>205</td>
+      <td>227</td>
+      <td>16</td>
+      <td>19</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ccat</td>
+      <td>peakcalling_ccat</td>
+      <td>Control-based ChIP-seq Analysis Tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>ChIP-seq</td>
+      <td>ccat</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat</td>
+      <td>0.0.2</td>
+      <td>ccat</td>
+      <td>3.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>88</td>
+      <td>175</td>
+      <td>28</td>
+      <td>39</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>88</td>
+      <td>175</td>
+      <td>28</td>
+      <td>39</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cd_hit_dup</td>
+      <td>cd_hit_dup</td>
+      <td>simple tool for removing duplicates from sequencing reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Metagenomics, Sequence Analysis</td>
+      <td>cd_hit_dup</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup</td>
+      <td>0.0.1</td>
+      <td>cd-hit-auxtools</td>
+      <td>4.8.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5946</td>
+      <td>7379</td>
+      <td>407</td>
+      <td>628</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5946</td>
+      <td>7379</td>
+      <td>407</td>
+      <td>628</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cdhit</td>
+      <td>cd_hit</td>
+      <td>Cluster or compare biological sequence datasets</td>
+      <td>cd-hit</td>
+      <td>cd-hit</td>
+      <td></td>
+      <td>cd-hit</td>
+      <td>Cluster a nucleotide dataset into representative sequences.</td>
+      <td>Sequence clustering</td>
+      <td>Sequencing</td>
+      <td>Up-to-date</td>
+      <td>http://weizhongli-lab.org/cd-hit/</td>
+      <td>Sequence Analysis, Fasta Manipulation</td>
+      <td>cd_hit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit</td>
+      <td>4.8.1</td>
+      <td>cd-hit</td>
+      <td>4.8.1</td>
+      <td>Sequence clustering</td>
+      <td>Sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>10414</td>
+      <td>10414</td>
+      <td>510</td>
+      <td>510</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>10418</td>
+      <td>10418</td>
+      <td>512</td>
+      <td>512</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cdo</td>
+      <td>cdo_info, cdo_operations</td>
+      <td>CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://code.mpimet.mpg.de/projects/cdo/</td>
+      <td>Climate Analysis</td>
+      <td></td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo</td>
+      <td>2.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cell-types-analysis</td>
+      <td>ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals</td>
+      <td>Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>suite_cell_types_analysis</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis</td>
+      <td>1.1.1</td>
+      <td>cell-types-analysis</td>
+      <td>0.1.11</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cellpose</td>
+      <td>cellpose</td>
+      <td>Cellpose is an anatomical segmentation algorithm</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/MouseLand/cellpose</td>
+      <td>Imaging</td>
+      <td>cellpose</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cellpose</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cellpose</td>
+      <td>3.0.10</td>
+      <td>cellpose</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cellprofiler</td>
+      <td>cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects</td>
+      <td>cellProfiler wrapper</td>
+      <td>CellProfiler</td>
+      <td>CellProfiler</td>
+      <td>cellprofiler</td>
+      <td>CellProfiler</td>
+      <td>Tool for quantifying data from biological images, particularly in high-throughput experiments.</td>
+      <td>Quantification, Image analysis, Parsing</td>
+      <td>Imaging, Microarray experiment, Genotype and phenotype</td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>cellprofiler</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Quantification, Image analysis, Parsing</td>
+      <td>Imaging, Microarray experiment, Genotype and phenotype</td>
+      <td>0</td>
+      <td>23</td>
+      <td>23</td>
+      <td>0</td>
+      <td>0</td>
+      <td>23</td>
+      <td>23</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>23</td>
+      <td>19</td>
+      <td>0</td>
+      <td>4773</td>
+      <td>4773</td>
+      <td>749</td>
+      <td>749</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5688</td>
+      <td>5688</td>
+      <td>94</td>
+      <td>94</td>
+      <td>10461</td>
+      <td>10461</td>
+      <td>843</td>
+      <td>843</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cellprofiler_v4</td>
+      <td>cp_cellprofiler4</td>
+      <td>cellProfiler4 wrapper</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/CellProfiler/CellProfiler</td>
+      <td>Imaging</td>
+      <td>cellprofiler4</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4</td>
+      <td>4.2.7</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>55</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>55</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cemitool</td>
+      <td>cemitool</td>
+      <td>Gene co-expression network analysis tool</td>
+      <td>cemitool</td>
+      <td>cemitool</td>
+      <td></td>
+      <td>CEMiTool</td>
+      <td>It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.</td>
+      <td>Enrichment analysis, Pathway or network analysis</td>
+      <td>Gene expression, Transcriptomics, Microarray experiment</td>
+      <td>Up-to-date</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>cemitool</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool</td>
+      <td>1.26.0</td>
+      <td>bioconductor-cemitool</td>
+      <td>1.26.0</td>
+      <td>Enrichment analysis, Pathway or network analysis</td>
+      <td>Transcriptomics, Microarray experiment</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>225</td>
+      <td>225</td>
+      <td>32</td>
+      <td>32</td>
+      <td>271</td>
+      <td>271</td>
+      <td>61</td>
+      <td>61</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>496</td>
+      <td>496</td>
+      <td>93</td>
+      <td>93</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cesm</td>
+      <td>cesm</td>
+      <td>Community Earth System Model (CESM)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://www.cesm.ucar.edu/</td>
+      <td>Climate Analysis</td>
+      <td>cesm</td>
+      <td>climate</td>
+      <td>https://github.com/ESCOMP/CESM</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm</td>
+      <td>2.1.3</td>
+      <td>cesm</td>
+      <td>2.1.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cfm</td>
+      <td>cfmid</td>
+      <td>Competitive Fragmentation Modeling (CFM)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://sourceforge.net/p/cfm-id/</td>
+      <td>Metabolomics</td>
+      <td>cfmid</td>
+      <td>computational-metabolomics</td>
+      <td>https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm</td>
+      <td>https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm</td>
+      <td>33</td>
+      <td>cfm</td>
+      <td>33</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chado</td>
+      <td>analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree</td>
+      <td>Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxy-genome-annotation/python-chado</td>
+      <td>Web Services</td>
+      <td></td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado</td>
+      <td></td>
+      <td>python-chado</td>
+      <td>2.3.9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>champ_blocs</td>
+      <td>cb_dissim, cb_ivr, cb_div</td>
+      <td>Compute indicators for turnover boulders fields</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/Marie59/champ_blocs</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs</td>
+      <td>0.0.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>183</td>
+      <td>183</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>183</td>
+      <td>183</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>change_case</td>
+      <td>ChangeCase</td>
+      <td>Convert column case.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>change_case</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case</td>
+      <td>1.0.1</td>
+      <td>perl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>10606</td>
+      <td>12531</td>
+      <td>2204</td>
+      <td>2547</td>
+      <td>9044</td>
+      <td>17167</td>
+      <td>1748</td>
+      <td>2394</td>
+      <td>923</td>
+      <td>938</td>
+      <td>240</td>
+      <td>245</td>
+      <td>20573</td>
+      <td>30636</td>
+      <td>4192</td>
+      <td>5186</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>charts</td>
+      <td>charts</td>
+      <td>Enables advanced visualization options in Galaxy Charts</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/</td>
+      <td>Visualization</td>
+      <td>charts</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts</td>
+      <td>1.0.1</td>
+      <td>r-getopt</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3383</td>
+      <td>4001</td>
+      <td>1576</td>
+      <td>1822</td>
+      <td>7870</td>
+      <td>13727</td>
+      <td>3823</td>
+      <td>6880</td>
+      <td>249</td>
+      <td>350</td>
+      <td>108</td>
+      <td>145</td>
+      <td>11502</td>
+      <td>18078</td>
+      <td>5507</td>
+      <td>8847</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chatgpt</td>
+      <td>chatgpt_openai_api</td>
+      <td>Using the OpenAI GPT models to generate text based on user input.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt</td>
+      <td>Machine Learning</td>
+      <td>chatgpt_openai_api</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt</td>
+      <td>2024</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>62</td>
+      <td>62</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>62</td>
+      <td>62</td>
+      <td>12</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>checkm</td>
+      <td>checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa</td>
+      <td>Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes</td>
+      <td>checkm</td>
+      <td>checkm</td>
+      <td></td>
+      <td>CheckM</td>
+      <td>CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.</td>
+      <td>Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation</td>
+      <td>Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Ecogenomics/CheckM</td>
+      <td>Metagenomics</td>
+      <td>checkm</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm</td>
+      <td>1.2.3</td>
+      <td>checkm-genome</td>
+      <td>1.2.3</td>
+      <td>Sequence assembly validation, Sequence composition calculation, Statistical calculation</td>
+      <td>Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7500</td>
+      <td>7500</td>
+      <td>930</td>
+      <td>930</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7500</td>
+      <td>7500</td>
+      <td>930</td>
+      <td>930</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>checkv</td>
+      <td>checkv_end_to_end</td>
+      <td>Assess quality of single-contig viral genomes</td>
+      <td>checkv</td>
+      <td>checkv</td>
+      <td></td>
+      <td>CheckV</td>
+      <td>CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.</td>
+      <td>Sequence assembly, Validation, Read mapping</td>
+      <td>Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://bitbucket.org/berkeleylab/checkv/</td>
+      <td>Metagenomics</td>
+      <td>checkv</td>
+      <td>ufz</td>
+      <td>https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv</td>
+      <td>1.0.3</td>
+      <td>checkv</td>
+      <td>1.0.3</td>
+      <td>Sequence assembly, Validation, Read mapping</td>
+      <td>Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cherri</td>
+      <td>cherri_eval, cherri_train</td>
+      <td>Computational Help Evaluating RNA-RNA interactions</td>
+      <td>cherri</td>
+      <td>cherri</td>
+      <td></td>
+      <td>cherri</td>
+      <td>CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.</td>
+      <td></td>
+      <td>Molecular interactions, pathways and networks, Structure analysis, Machine learning</td>
+      <td>To update</td>
+      <td>https://github.com/BackofenLab/Cherri</td>
+      <td>Transcriptomics, RNA</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri</td>
+      <td>0.7</td>
+      <td>cherri</td>
+      <td>0.8</td>
+      <td></td>
+      <td>Molecular interactions, pathways and networks, Structure analysis, Machine learning</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>207</td>
+      <td>207</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>207</td>
+      <td>207</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cherry_pick_fasta</td>
+      <td>cherry_pick_fasta</td>
+      <td>Pick fasta sequence with specific header content</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Fasta Manipulation</td>
+      <td>cherry_pick_fasta</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta</td>
+      <td>4.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chewbbaca</td>
+      <td>chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema</td>
+      <td>BSR-Based Allele Calling Algorithm</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/B-UMMI/chewBBACA/tree/master</td>
+      <td>Variant Analysis</td>
+      <td>chewbbaca</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca</td>
+      <td></td>
+      <td>chewbbaca</td>
+      <td>3.3.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>727</td>
+      <td>727</td>
+      <td>76</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>727</td>
+      <td>727</td>
+      <td>76</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chipseeker</td>
+      <td>chipseeker</td>
+      <td>A tool for ChIP peak annotation and visualization</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html</td>
+      <td>ChIP-seq, Genome annotation</td>
+      <td>chipseeker</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker</td>
+      <td>1.32.0</td>
+      <td>bioconductor-chipseeker</td>
+      <td>1.38.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>16468</td>
+      <td>18344</td>
+      <td>956</td>
+      <td>991</td>
+      <td>33692</td>
+      <td>34453</td>
+      <td>2559</td>
+      <td>2625</td>
+      <td>2948</td>
+      <td>2948</td>
+      <td>104</td>
+      <td>104</td>
+      <td>53108</td>
+      <td>55745</td>
+      <td>3619</td>
+      <td>3720</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chira</td>
+      <td>chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify</td>
+      <td>Chimeric Read Annotator for RNA-RNA interactome data</td>
+      <td>chira</td>
+      <td>chira</td>
+      <td></td>
+      <td>ChiRA</td>
+      <td>ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.</td>
+      <td></td>
+      <td>RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pavanvidem/chira</td>
+      <td>RNA, Transcriptomics, Sequence Analysis</td>
+      <td>chira</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira</td>
+      <td>1.4.3</td>
+      <td>chira</td>
+      <td>1.4.3</td>
+      <td></td>
+      <td>Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>16542</td>
+      <td>16542</td>
+      <td>287</td>
+      <td>287</td>
+      <td>1061</td>
+      <td>1061</td>
+      <td>102</td>
+      <td>102</td>
+      <td>27</td>
+      <td>27</td>
+      <td>5</td>
+      <td>5</td>
+      <td>17630</td>
+      <td>17630</td>
+      <td>394</td>
+      <td>394</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chopin2</td>
+      <td>chopin2</td>
+      <td>Domain-Agnostic Supervised Learning with Hyperdimensional Computing</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/cumbof/chopin2</td>
+      <td>Machine Learning</td>
+      <td>chopin2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2</td>
+      <td>1.0.9.post1</td>
+      <td>chopin2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chromeister</td>
+      <td>chromeister</td>
+      <td>ultra-fast pairwise genome comparisons</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/estebanpw/chromeister</td>
+      <td>Sequence Analysis</td>
+      <td>chromeister</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister</td>
+      <td>1.5.a</td>
+      <td>chromeister</td>
+      <td>1.5.a</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2696</td>
+      <td>2696</td>
+      <td>398</td>
+      <td>398</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1235</td>
+      <td>1235</td>
+      <td>186</td>
+      <td>186</td>
+      <td>3931</td>
+      <td>3931</td>
+      <td>584</td>
+      <td>584</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chromosome_diagram</td>
+      <td>chromosome_diagram</td>
+      <td>Chromosome Diagrams using Biopython</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Sequence Analysis, Visualization</td>
+      <td>chromosome_diagram</td>
+      <td>peterjc</td>
+      <td></td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram</td>
+      <td>0.0.3</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>circexplorer</td>
+      <td>circexplorer</td>
+      <td>A combined strategy to identify circular RNAs (circRNAs and ciRNAs)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/YangLab/CIRCexplorer</td>
+      <td>Sequence Analysis, RNA</td>
+      <td>circexplorer</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer</td>
+      <td>1.1.9.0</td>
+      <td>circexplorer</td>
+      <td>1.1.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>211</td>
+      <td>263</td>
+      <td>32</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>209</td>
+      <td>209</td>
+      <td>6</td>
+      <td>6</td>
+      <td>420</td>
+      <td>472</td>
+      <td>38</td>
+      <td>46</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>circexplorer2</td>
+      <td>circexplorer2</td>
+      <td>Comprehensive and integrative circular RNA analysis toolset.</td>
+      <td>circexplorer2</td>
+      <td>circexplorer2</td>
+      <td></td>
+      <td>CIRCexplorer2</td>
+      <td>Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.</td>
+      <td></td>
+      <td>RNA splicing, Gene transcripts, Literature and language</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/YangLab/CIRCexplorer2</td>
+      <td>RNA, Assembly</td>
+      <td>circexplorer2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2</td>
+      <td>2.3.8</td>
+      <td>circexplorer2</td>
+      <td>2.3.8</td>
+      <td></td>
+      <td>RNA splicing, Gene transcripts, Literature and language</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>524</td>
+      <td>524</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>524</td>
+      <td>524</td>
+      <td>32</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>circos</td>
+      <td>circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile</td>
+      <td>Build Circos Plots in Galaxy</td>
+      <td>galactic_circos</td>
+      <td>galactic_circos</td>
+      <td></td>
+      <td>Galactic Circos</td>
+      <td>Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.</td>
+      <td>Sequence visualisation</td>
+      <td></td>
+      <td>To update</td>
+      <td>http://circos.ca/</td>
+      <td>Graphics</td>
+      <td>circos</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos</td>
+      <td>0.69.8</td>
+      <td>circos</td>
+      <td>0.69.9</td>
+      <td>Sequence visualisation</td>
+      <td></td>
+      <td>11</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>26265</td>
+      <td>26265</td>
+      <td>2483</td>
+      <td>2483</td>
+      <td>31332</td>
+      <td>31332</td>
+      <td>3535</td>
+      <td>3535</td>
+      <td>26359</td>
+      <td>26359</td>
+      <td>999</td>
+      <td>999</td>
+      <td>83956</td>
+      <td>83956</td>
+      <td>7017</td>
+      <td>7017</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cite_seq_count</td>
+      <td>cite_seq_count</td>
+      <td>Count CMO/HTO</td>
+      <td>CITE-seq-Count</td>
+      <td>CITE-seq-Count</td>
+      <td></td>
+      <td>CITE-seq-Count</td>
+      <td>Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.</td>
+      <td>RNA-Seq quantification</td>
+      <td>Transcriptomics, Immunoproteins and antigens</td>
+      <td>To update</td>
+      <td>https://github.com/Hoohm/CITE-seq-Count</td>
+      <td>Single Cell, Transcriptomics, Proteomics</td>
+      <td>cite_seq_count</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count</td>
+      <td>1.4.4</td>
+      <td>cite-seq-count</td>
+      <td>1.4.5</td>
+      <td>RNA-Seq quantification</td>
+      <td>Transcriptomics, Immunoproteins and antigens</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21</td>
+      <td>21</td>
+      <td>4</td>
+      <td>4</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td>48</td>
+      <td>48</td>
+      <td>10</td>
+      <td>10</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>clair3</td>
+      <td>clair3</td>
+      <td>Symphonizing pileup and full-alignment for high-performance long-read variant calling</td>
+      <td>clair3</td>
+      <td>clair3</td>
+      <td></td>
+      <td>Clair3</td>
+      <td>Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.</td>
+      <td>Variant calling</td>
+      <td>Molecular genetics</td>
+      <td>To update</td>
+      <td>https://github.com/HKU-BAL/Clair3</td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>clair3</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3</td>
+      <td>1.0.8</td>
+      <td>clair3</td>
+      <td>1.0.10</td>
+      <td>Variant calling</td>
+      <td>Molecular genetics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3388</td>
+      <td>3388</td>
+      <td>187</td>
+      <td>187</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>3390</td>
+      <td>3390</td>
+      <td>189</td>
+      <td>189</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>clc_assembly_cell</td>
+      <td>clc_assembler, clc_mapper</td>
+      <td>Galaxy wrapper for the CLC Assembly Cell suite from CLCBio</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell</td>
+      <td>Assembly, Next Gen Mappers, SAM</td>
+      <td>clc_assembly_cell</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell</td>
+      <td>0.0.7</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>climate-stripes</td>
+      <td>climate_stripes</td>
+      <td>Create climate stripes from a tabular input file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.climate-lab-book.ac.uk/2018/warming-stripes/</td>
+      <td>Climate Analysis, Visualization</td>
+      <td>climate_stripes</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes</td>
+      <td>1.0.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>239</td>
+      <td>239</td>
+      <td>35</td>
+      <td>35</td>
+      <td>16</td>
+      <td>16</td>
+      <td>2</td>
+      <td>2</td>
+      <td>182</td>
+      <td>182</td>
+      <td>3</td>
+      <td>3</td>
+      <td>437</td>
+      <td>437</td>
+      <td>40</td>
+      <td>40</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>clinod</td>
+      <td>clinod</td>
+      <td>NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins</td>
+      <td>clinod</td>
+      <td>clinod</td>
+      <td></td>
+      <td>clinod</td>
+      <td>The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.compbio.dundee.ac.uk/www-nod/</td>
+      <td>Sequence Analysis</td>
+      <td>clinod</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod</td>
+      <td>0.1.0</td>
+      <td>clinod</td>
+      <td>1.3</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>548</td>
+      <td>548</td>
+      <td>18</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>548</td>
+      <td>548</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>clustalw</td>
+      <td>clustalw</td>
+      <td>ClustalW multiple sequence alignment program for DNA or proteins</td>
+      <td>clustal2</td>
+      <td>clustal2</td>
+      <td></td>
+      <td>Clustal 2 (Clustal W, Clustal X)</td>
+      <td>Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.</td>
+      <td>Multiple sequence alignment</td>
+      <td>Phylogeny, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://www.clustal.org/clustal2/</td>
+      <td>Phylogenetics, Sequence Analysis</td>
+      <td>clustalw</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw</td>
+      <td>2.1</td>
+      <td>clustalw</td>
+      <td>2.1</td>
+      <td>Multiple sequence alignment</td>
+      <td>Phylogeny, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>79867</td>
+      <td>80817</td>
+      <td>1675</td>
+      <td>1785</td>
+      <td>49493</td>
+      <td>87884</td>
+      <td>3703</td>
+      <td>7380</td>
+      <td>8797</td>
+      <td>9713</td>
+      <td>670</td>
+      <td>728</td>
+      <td>138157</td>
+      <td>178414</td>
+      <td>6048</td>
+      <td>9893</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cluster</td>
+      <td>gops_cluster_1</td>
+      <td>Cluster the intervals of a dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>cluster</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>513</td>
+      <td>813</td>
+      <td>18</td>
+      <td>35</td>
+      <td>2406</td>
+      <td>30579</td>
+      <td>156</td>
+      <td>1547</td>
+      <td>1353</td>
+      <td>1393</td>
+      <td>17</td>
+      <td>20</td>
+      <td>4272</td>
+      <td>32785</td>
+      <td>191</td>
+      <td>1602</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>clustering_from_distmat</td>
+      <td>clustering_from_distmat</td>
+      <td>Distance matrix-based hierarchical clustering using SciPy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/</td>
+      <td>Statistics</td>
+      <td>clustering_from_distmat</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat</td>
+      <td>1.1.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cmsearch_deoverlap</td>
+      <td>cmsearch_deoverlap</td>
+      <td>removes lower scoring overlaps from cmsearch results.</td>
+      <td>cmsearch-deoverlap</td>
+      <td>cmsearch-deoverlap</td>
+      <td></td>
+      <td>cmsearch-deoverlap</td>
+      <td>Removes lower scoring overlaps from cmsearch results.</td>
+      <td>Comparison, Alignment</td>
+      <td>Biology, Medicine</td>
+      <td>To update</td>
+      <td>https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl</td>
+      <td>RNA</td>
+      <td>cmsearch_deoverlap</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap</td>
+      <td>0.08+galaxy2</td>
+      <td>perl</td>
+      <td></td>
+      <td>Comparison, Alignment</td>
+      <td>Biology, Medicine</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2609</td>
+      <td>2609</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2609</td>
+      <td>2609</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cmv</td>
+      <td>cmcv, cmv, hmmcv, hmmv</td>
+      <td>cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/eggzilla/cmv</td>
+      <td>RNA</td>
+      <td>cmv</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv</td>
+      <td>1.0.8</td>
+      <td>cmv</td>
+      <td>1.0.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>90</td>
+      <td>112</td>
+      <td>11</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>90</td>
+      <td>112</td>
+      <td>11</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cnv-phenopacket</td>
+      <td>cnv_phenopacket</td>
+      <td>cnv-phenopacket Converts TSV metadata file to JSON.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pypi.org/project/cnv-phenopacket/</td>
+      <td>Variant Analysis</td>
+      <td>cnv_phenopacket</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket</td>
+      <td>1.0.2</td>
+      <td>cnv-phenopacket</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cnv-vcf2json</td>
+      <td>cnv_vcf2json</td>
+      <td>cnv-vcf2json Converts structural variants VCF file to JSON.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pypi.org/project/cnv-phenopacket/</td>
+      <td>Variant Analysis</td>
+      <td>cnv-vcf2json</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json</td>
+      <td>1.1.0</td>
+      <td>cnv-vcf2json</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cnvkit</td>
+      <td>cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target</td>
+      <td>detecting copy number variants and alterations genome-wide from high-throughput sequencing</td>
+      <td>cnvkit</td>
+      <td>cnvkit</td>
+      <td></td>
+      <td>CNVkit</td>
+      <td>CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.</td>
+      <td>Variant calling</td>
+      <td>DNA structural variation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/etal/cnvkit</td>
+      <td>Variant Analysis</td>
+      <td>cnvkit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit</td>
+      <td>0.9.11</td>
+      <td>cnvkit</td>
+      <td>0.9.11</td>
+      <td>Variant calling</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>618</td>
+      <td>618</td>
+      <td>177</td>
+      <td>177</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>618</td>
+      <td>618</td>
+      <td>177</td>
+      <td>177</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>codeml</td>
+      <td>codeml</td>
+      <td>Detects positive selection</td>
+      <td>paml</td>
+      <td>paml</td>
+      <td></td>
+      <td>PAML</td>
+      <td>Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.</td>
+      <td>Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis</td>
+      <td>Phylogenetics, Sequence analysis</td>
+      <td>To update</td>
+      <td>http://abacus.gene.ucl.ac.uk/software/paml.html</td>
+      <td>Phylogenetics</td>
+      <td>codeml</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml</td>
+      <td>4.9</td>
+      <td>paml</td>
+      <td>4.10.7</td>
+      <td>Probabilistic sequence generation</td>
+      <td>Phylogenetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>61197</td>
+      <td>61220</td>
+      <td>64</td>
+      <td>65</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>61197</td>
+      <td>61220</td>
+      <td>64</td>
+      <td>65</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cofold</td>
+      <td>cofold</td>
+      <td>Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.e-rna.org/cofold/</td>
+      <td>RNA</td>
+      <td>cofold</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold</td>
+      <td>2.0.4.0</td>
+      <td>cofold</td>
+      <td>2.0.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>316</td>
+      <td>355</td>
+      <td>25</td>
+      <td>29</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>316</td>
+      <td>355</td>
+      <td>25</td>
+      <td>29</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cojac</td>
+      <td>cooc_mutbamscan, cooc_pubmut, cooc_tabmut</td>
+      <td>co-occurrence of mutations on amplicons</td>
+      <td>cojac</td>
+      <td>cojac</td>
+      <td></td>
+      <td>COJAC</td>
+      <td>CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.</td>
+      <td></td>
+      <td>Genetic variation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cbg-ethz/cojac</td>
+      <td>Metagenomics, Sequence Analysis</td>
+      <td>cojac</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac</td>
+      <td>0.9.2</td>
+      <td>cojac</td>
+      <td>0.9.2</td>
+      <td></td>
+      <td>Genetic variation</td>
+      <td>2</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2758</td>
+      <td>2758</td>
+      <td>22</td>
+      <td>22</td>
+      <td>20</td>
+      <td>20</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2778</td>
+      <td>2778</td>
+      <td>32</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>colabfold</td>
+      <td>colabfold_alphafold, colabfold_msa</td>
+      <td>Protein prediction based on AlphaFold2</td>
+      <td>Colabfold</td>
+      <td>Colabfold</td>
+      <td></td>
+      <td>ColabFold</td>
+      <td>ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.</td>
+      <td>Database search, Protein structure prediction, Fold recognition</td>
+      <td>Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics</td>
+      <td>To update</td>
+      <td>https://github.com/sokrypton/ColabFold</td>
+      <td>Proteomics, Graphics</td>
+      <td>colabfold</td>
+      <td>iuc</td>
+      <td>https://github.com/sokrypton/ColabFold</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold</td>
+      <td>1.5.5</td>
+      <td></td>
+      <td></td>
+      <td>Database search, Protein structure prediction, Fold recognition</td>
+      <td>Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6771</td>
+      <td>6771</td>
+      <td>50</td>
+      <td>50</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6771</td>
+      <td>6771</td>
+      <td>50</td>
+      <td>50</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>colibread</td>
+      <td>commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak</td>
+      <td>Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://colibread.inria.fr/</td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>colibread</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread</td>
+      <td>24.7.14</td>
+      <td>commet</td>
+      <td>24.7.14</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>273</td>
+      <td>273</td>
+      <td>40</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>273</td>
+      <td>273</td>
+      <td>40</td>
+      <td>40</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>collapse_collection</td>
+      <td>collapse_dataset</td>
+      <td>Collection tool that collapses a list of files into a single datasset in order of appears in collection</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>collapse_collections</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection</td>
+      <td>5.1.0</td>
+      <td>gawk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>39518</td>
+      <td>40471</td>
+      <td>3555</td>
+      <td>3629</td>
+      <td>22007</td>
+      <td>24841</td>
+      <td>3536</td>
+      <td>4045</td>
+      <td>3969</td>
+      <td>4101</td>
+      <td>814</td>
+      <td>835</td>
+      <td>65494</td>
+      <td>69413</td>
+      <td>7905</td>
+      <td>8509</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>collection_column_join</td>
+      <td>collection_column_join</td>
+      <td>Column Join on Collections</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join</td>
+      <td>Text Manipulation</td>
+      <td>collection_column_join</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join</td>
+      <td>0.0.3</td>
+      <td>coreutils</td>
+      <td>8.25</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>23979</td>
+      <td>25337</td>
+      <td>3827</td>
+      <td>4011</td>
+      <td>21671</td>
+      <td>25163</td>
+      <td>4645</td>
+      <td>5045</td>
+      <td>2939</td>
+      <td>3036</td>
+      <td>688</td>
+      <td>701</td>
+      <td>48589</td>
+      <td>53536</td>
+      <td>9160</td>
+      <td>9757</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>collection_element_identifiers</td>
+      <td>collection_element_identifiers</td>
+      <td>Extract element identifiers of a collection</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers</td>
+      <td>Text Manipulation</td>
+      <td>collection_element_identifiers</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers</td>
+      <td>0.0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6905</td>
+      <td>7102</td>
+      <td>1620</td>
+      <td>1630</td>
+      <td>7761</td>
+      <td>7761</td>
+      <td>1897</td>
+      <td>1897</td>
+      <td>1157</td>
+      <td>1157</td>
+      <td>243</td>
+      <td>243</td>
+      <td>15823</td>
+      <td>16020</td>
+      <td>3760</td>
+      <td>3770</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>color_deconvolution</td>
+      <td>ip_color_deconvolution</td>
+      <td>Color-deconvolution methods</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>color_deconvolution</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution</td>
+      <td>0.8-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15</td>
+      <td>16</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>16</td>
+      <td>2</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>colorize_labels</td>
+      <td>colorize_labels</td>
+      <td>Colorize label map</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>colorize_labels</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels</td>
+      <td>3.2.1</td>
+      <td>networkx</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>column_arrange_by_header</td>
+      <td>bg_column_arrange_by_header</td>
+      <td>Column arrange by header name</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>column_arrange_by_header</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header</td>
+      <td>0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5356</td>
+      <td>5636</td>
+      <td>446</td>
+      <td>484</td>
+      <td>2026</td>
+      <td>2026</td>
+      <td>375</td>
+      <td>375</td>
+      <td>1400</td>
+      <td>1531</td>
+      <td>117</td>
+      <td>138</td>
+      <td>8782</td>
+      <td>9193</td>
+      <td>938</td>
+      <td>997</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>column_maker</td>
+      <td>Add_a_column1</td>
+      <td>Compute an expression on every row</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker</td>
+      <td>Text Manipulation</td>
+      <td>column_maker</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker</td>
+      <td>2.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2940752</td>
+      <td>3907183</td>
+      <td>5422</td>
+      <td>6121</td>
+      <td>263254</td>
+      <td>737503</td>
+      <td>6095</td>
+      <td>13728</td>
+      <td>96478</td>
+      <td>97667</td>
+      <td>884</td>
+      <td>974</td>
+      <td>3300484</td>
+      <td>4742353</td>
+      <td>12401</td>
+      <td>20823</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>column_order_header_sort</td>
+      <td>column_order_header_sort</td>
+      <td>Sort Column Order by heading</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort</td>
+      <td>Text Manipulation</td>
+      <td>column_order_header_sort</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort</td>
+      <td>0.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3735</td>
+      <td>3891</td>
+      <td>268</td>
+      <td>297</td>
+      <td>1923</td>
+      <td>1923</td>
+      <td>381</td>
+      <td>381</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5658</td>
+      <td>5814</td>
+      <td>649</td>
+      <td>678</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>column_remove_by_header</td>
+      <td>column_remove_by_header</td>
+      <td>Remove columns by header</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header</td>
+      <td>Text Manipulation</td>
+      <td>column_remove_by_header</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header</td>
+      <td>1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>8331</td>
+      <td>8917</td>
+      <td>613</td>
+      <td>662</td>
+      <td>5206</td>
+      <td>5206</td>
+      <td>716</td>
+      <td>716</td>
+      <td>1976</td>
+      <td>1976</td>
+      <td>27</td>
+      <td>27</td>
+      <td>15513</td>
+      <td>16099</td>
+      <td>1356</td>
+      <td>1405</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>combineJSON</td>
+      <td>combine_json</td>
+      <td>JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>combine_json</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>combine_assembly_stats</td>
+      <td>combine_stats</td>
+      <td>Combine multiple Assemblystats datasets into a single tabular report</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Assembly</td>
+      <td>combine_assemblystats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats</td>
+      <td>1.0</td>
+      <td>perl-getopt-long</td>
+      <td>2.58</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>combine_metaphlan_humann</td>
+      <td>combine_metaphlan_humann</td>
+      <td>Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances</td>
+      <td>combine_metaphlan_and_humann</td>
+      <td>combine_metaphlan_and_humann</td>
+      <td></td>
+      <td>Combine Metaphlan and HUMAnN</td>
+      <td>This tool combine MetaPhlAn outputs and HUMANnN outputs</td>
+      <td>Aggregation</td>
+      <td>Metagenomics, Molecular interactions, pathways and networks</td>
+      <td>To update</td>
+      <td></td>
+      <td>Metagenomics</td>
+      <td>combine_metaphlan2_humann2</td>
+      <td>bebatut</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann</td>
+      <td>0.3.0</td>
+      <td>python</td>
+      <td></td>
+      <td>Aggregation</td>
+      <td>Metagenomics, Molecular interactions, pathways and networks</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>530</td>
+      <td>530</td>
+      <td>65</td>
+      <td>65</td>
+      <td>8</td>
+      <td>8</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>538</td>
+      <td>538</td>
+      <td>71</td>
+      <td>71</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>combine_tabular_collection</td>
+      <td>combine</td>
+      <td>Combine Tabular Collection into a single file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>combine_tabular_collection</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compalignp</td>
+      <td>compalignp</td>
+      <td>Compute fractional identity between trusted alignment and test alignment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td></td>
+      <td>RNA, Sequence Analysis</td>
+      <td>compalignp</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp</td>
+      <td>1.0</td>
+      <td>compalignp</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>39</td>
+      <td>221</td>
+      <td>5</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>221</td>
+      <td>5</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compare_humann2_output</td>
+      <td>compare_humann2_output</td>
+      <td>Compare outputs of HUMAnN2 for several samples and extract similar and specific information</td>
+      <td>compare_humann2_outputs</td>
+      <td>compare_humann2_outputs</td>
+      <td></td>
+      <td>Compare HUMAnN2 outputs</td>
+      <td>This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples</td>
+      <td>Comparison</td>
+      <td>Metagenomics, Gene and protein families</td>
+      <td>To update</td>
+      <td></td>
+      <td>Metagenomics</td>
+      <td>compare_humann2_output</td>
+      <td>bebatut</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td>Comparison</td>
+      <td>Metagenomics, Gene and protein families</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>306</td>
+      <td>332</td>
+      <td>28</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>306</td>
+      <td>332</td>
+      <td>28</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compleasm</td>
+      <td>compleasm</td>
+      <td>Compleasm: a faster and more accurate reimplementation of BUSCO</td>
+      <td>compleasm</td>
+      <td>compleasm</td>
+      <td></td>
+      <td>compleasm</td>
+      <td>"Compleasm: a faster and more accurate reimplementation of BUSCO"</td>
+      <td>Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly</td>
+      <td>Sequence assembly, Genomics, Transcriptomics, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/huangnengCSU/compleasm</td>
+      <td>Sequence Analysis</td>
+      <td>compleasm</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm</td>
+      <td>0.2.6</td>
+      <td>compleasm</td>
+      <td>0.2.6</td>
+      <td>Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly</td>
+      <td>Sequence assembly, Transcriptomics, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>266</td>
+      <td>266</td>
+      <td>39</td>
+      <td>39</td>
+      <td>28</td>
+      <td>28</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>294</td>
+      <td>294</td>
+      <td>54</td>
+      <td>54</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>complement</td>
+      <td>gops_complement_1</td>
+      <td>Complement intervals of a dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>complement</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>187</td>
+      <td>233</td>
+      <td>15</td>
+      <td>20</td>
+      <td>495</td>
+      <td>4810</td>
+      <td>165</td>
+      <td>836</td>
+      <td>405</td>
+      <td>451</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1087</td>
+      <td>5494</td>
+      <td>187</td>
+      <td>863</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compose_text_param</td>
+      <td>compose_text_param</td>
+      <td>Compose a text parameter value using text, integer and float values</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>compose_text_param</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param</td>
+      <td>0.1.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45827</td>
+      <td>45831</td>
+      <td>689</td>
+      <td>691</td>
+      <td>7721</td>
+      <td>7721</td>
+      <td>303</td>
+      <td>303</td>
+      <td>1481</td>
+      <td>1481</td>
+      <td>121</td>
+      <td>121</td>
+      <td>55029</td>
+      <td>55033</td>
+      <td>1113</td>
+      <td>1115</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compress_file</td>
+      <td>compress_file</td>
+      <td>Compress files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file</td>
+      <td>Text Manipulation</td>
+      <td>compress_file</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file</td>
+      <td>0.1.0</td>
+      <td>gzip</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6343</td>
+      <td>6343</td>
+      <td>290</td>
+      <td>290</td>
+      <td>3674</td>
+      <td>3674</td>
+      <td>286</td>
+      <td>286</td>
+      <td>11832</td>
+      <td>11832</td>
+      <td>59</td>
+      <td>59</td>
+      <td>21849</td>
+      <td>21849</td>
+      <td>635</td>
+      <td>635</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compute_motif_frequencies_for_all_motifs</td>
+      <td>compute_motif_frequencies_for_all_motifs</td>
+      <td>Compute Motif Frequencies For All Motifs, motif by motif.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Statistics</td>
+      <td>compute_motif_frequencies_for_all_motifs</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>85</td>
+      <td>96</td>
+      <td>9</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>316</td>
+      <td>334</td>
+      <td>8</td>
+      <td>8</td>
+      <td>401</td>
+      <td>430</td>
+      <td>17</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compute_motifs_frequency</td>
+      <td>compute_motifs_frequency</td>
+      <td>Compute Motif Frequencies in indel flanking regions.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Statistics</td>
+      <td>compute_motifs_frequency</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>55</td>
+      <td>65</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>317</td>
+      <td>335</td>
+      <td>5</td>
+      <td>5</td>
+      <td>372</td>
+      <td>400</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compute_q_values</td>
+      <td>compute_q_values</td>
+      <td>Compute q-values based on multiple simultaneous tests p-values</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>compute_q_values</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values</td>
+      <td>1.0.1</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>35</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>35</td>
+      <td>0</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>concat</td>
+      <td>gops_concat_1</td>
+      <td>Concatenate two bed files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>concat</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat</td>
+      <td>1.0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>575128</td>
+      <td>575441</td>
+      <td>694</td>
+      <td>783</td>
+      <td>43420</td>
+      <td>85345</td>
+      <td>629</td>
+      <td>3508</td>
+      <td>19330</td>
+      <td>19418</td>
+      <td>104</td>
+      <td>117</td>
+      <td>637878</td>
+      <td>680204</td>
+      <td>1427</td>
+      <td>4408</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>concat_channels</td>
+      <td>ip_concat_channels</td>
+      <td>Concatenate images</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>concat_channels</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels</td>
+      <td>0.3-1</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>76</td>
+      <td>82</td>
+      <td>11</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>76</td>
+      <td>82</td>
+      <td>11</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>concat_multi_datasets</td>
+      <td>cat_multi_datasets</td>
+      <td>Concatenate multiple datasets tail-to-head, including collection datasets.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Text Manipulation</td>
+      <td>concatenate_multiple_datasets</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets</td>
+      <td>1.4.3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4822</td>
+      <td>4824</td>
+      <td>613</td>
+      <td>614</td>
+      <td>1317</td>
+      <td>1317</td>
+      <td>204</td>
+      <td>204</td>
+      <td>3088</td>
+      <td>3795</td>
+      <td>252</td>
+      <td>289</td>
+      <td>9227</td>
+      <td>9936</td>
+      <td>1069</td>
+      <td>1107</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>concat_paired</td>
+      <td>concat_fastqs</td>
+      <td>Concatenate paired datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/concat</td>
+      <td>Text Manipulation</td>
+      <td>concat_paired</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/concat</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired</td>
+      <td>0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>concoct</td>
+      <td>concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering</td>
+      <td>CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.</td>
+      <td>concoct</td>
+      <td>concoct</td>
+      <td></td>
+      <td>CONCOCT</td>
+      <td>A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.</td>
+      <td>Sequence clustering, Read binning</td>
+      <td>Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BinPro/CONCOCT</td>
+      <td>Metagenomics</td>
+      <td>concoct</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct</td>
+      <td>1.1.0</td>
+      <td>concoct</td>
+      <td>1.1.0</td>
+      <td>Sequence clustering, Read binning</td>
+      <td>Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2105</td>
+      <td>2105</td>
+      <td>155</td>
+      <td>155</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2105</td>
+      <td>2105</td>
+      <td>155</td>
+      <td>155</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>condense_characters</td>
+      <td>Condense characters1</td>
+      <td>Condense consecutive characters.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>condense_characters</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>47</td>
+      <td>2173</td>
+      <td>28</td>
+      <td>368</td>
+      <td>195</td>
+      <td>205</td>
+      <td>8</td>
+      <td>8</td>
+      <td>242</td>
+      <td>2378</td>
+      <td>36</td>
+      <td>376</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>consensus_from_alignments</td>
+      <td>aligned_to_consensus</td>
+      <td>Tool to compute a consensus sequence from several aligned fasta sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>consalign</td>
+      <td>ecology</td>
+      <td>https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments</td>
+      <td>1.0.0</td>
+      <td>r-bioseq</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1184</td>
+      <td>1184</td>
+      <td>154</td>
+      <td>154</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1184</td>
+      <td>1184</td>
+      <td>154</td>
+      <td>154</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>consolidate_vcfs</td>
+      <td>consolidate_vcfs</td>
+      <td>Combines freebayes and mpileup files for use by vcf2snvalignment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>consolidate_vcfs</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>convert_characters</td>
+      <td>Convert characters1</td>
+      <td>Convert delimiters to tab.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>convert_characters</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters</td>
+      <td>1.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>23589</td>
+      <td>28986</td>
+      <td>1061</td>
+      <td>1200</td>
+      <td>23507</td>
+      <td>160693</td>
+      <td>2302</td>
+      <td>8699</td>
+      <td>5413</td>
+      <td>6446</td>
+      <td>251</td>
+      <td>329</td>
+      <td>52509</td>
+      <td>196125</td>
+      <td>3614</td>
+      <td>10228</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>convert_solid_color2nuc</td>
+      <td>color2nuc</td>
+      <td>Convert Color Space to Nucleotides</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation</td>
+      <td>convert_solid_color2nuc</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cooler</td>
+      <td>cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify</td>
+      <td>cooler different tools to process Hi-C from mirnylab</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/open2c/cooler</td>
+      <td>Epigenetics</td>
+      <td>cooler</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler</td>
+      <td>0.9.3</td>
+      <td>htslib</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>170</td>
+      <td>170</td>
+      <td>26</td>
+      <td>26</td>
+      <td>195</td>
+      <td>195</td>
+      <td>39</td>
+      <td>39</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>365</td>
+      <td>365</td>
+      <td>65</td>
+      <td>65</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>coordinates_of_roi</td>
+      <td>ip_coordinates_of_roi</td>
+      <td>Coordinates of ROI</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>coordinates_of_roi</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi</td>
+      <td>0.0.4-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>16077</td>
+      <td>16547</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16077</td>
+      <td>16547</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>coprarna</td>
+      <td>coprarna</td>
+      <td>Target prediction for prokaryotic trans-acting small RNAs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/PatrickRWright/CopraRNA</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>coprarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/PatrickRWright/CopraRNA</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna</td>
+      <td>2.1.1</td>
+      <td>coprarna</td>
+      <td>2.1.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>correlation</td>
+      <td>cor2</td>
+      <td>Correlation for numeric columns</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>correlation</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation</td>
+      <td>1.0.0</td>
+      <td>rpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>398</td>
+      <td>876</td>
+      <td>106</td>
+      <td>134</td>
+      <td>412</td>
+      <td>5568</td>
+      <td>105</td>
+      <td>755</td>
+      <td>192</td>
+      <td>239</td>
+      <td>21</td>
+      <td>27</td>
+      <td>1002</td>
+      <td>6683</td>
+      <td>232</td>
+      <td>916</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>correlation_analysis</td>
+      <td>correlation_analysis</td>
+      <td>[Metabolomics][W4M] Metabolites Correlation Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>correlation_analysis</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis</td>
+      <td>1.0.1+galaxy0</td>
+      <td>r-batch</td>
+      <td>1.1_4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cosg</td>
+      <td>cosg</td>
+      <td>Marker gene identification for single-cell sequencing data using COSG.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/genecell/COSG</td>
+      <td>Transcriptomics, Sequence Analysis, Single Cell</td>
+      <td>cosg</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg</td>
+      <td>1.0.1</td>
+      <td>cosg</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>count_gff_features</td>
+      <td>count_gff_features</td>
+      <td>Count GFF Features</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>count_gff_features</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features</td>
+      <td>0.2</td>
+      <td>galaxy-ops</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>280</td>
+      <td>307</td>
+      <td>110</td>
+      <td>124</td>
+      <td>712</td>
+      <td>1277</td>
+      <td>332</td>
+      <td>628</td>
+      <td>476</td>
+      <td>541</td>
+      <td>55</td>
+      <td>79</td>
+      <td>1468</td>
+      <td>2125</td>
+      <td>497</td>
+      <td>831</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>count_objects</td>
+      <td>ip_count_objects</td>
+      <td>Count Objects</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>count_objects</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects</td>
+      <td>0.0.5-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>314</td>
+      <td>326</td>
+      <td>73</td>
+      <td>75</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>129</td>
+      <td>129</td>
+      <td>6</td>
+      <td>6</td>
+      <td>443</td>
+      <td>455</td>
+      <td>79</td>
+      <td>81</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>count_roi_variants</td>
+      <td>count_roi_variants</td>
+      <td>Count sequence variants in region of interest in BAM file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants</td>
+      <td>Assembly, SAM</td>
+      <td>count_roi_variants</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants</td>
+      <td>0.0.6</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>coverage</td>
+      <td>gops_coverage_1</td>
+      <td>Coverage of a set of intervals on second set of intervals</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>coverage</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1560</td>
+      <td>1725</td>
+      <td>43</td>
+      <td>58</td>
+      <td>4328</td>
+      <td>44209</td>
+      <td>193</td>
+      <td>2113</td>
+      <td>283</td>
+      <td>316</td>
+      <td>16</td>
+      <td>18</td>
+      <td>6171</td>
+      <td>46250</td>
+      <td>252</td>
+      <td>2189</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>coverage_report</td>
+      <td>CoverageReport2</td>
+      <td>Generate Detailed Coverage Report from BAM file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc</td>
+      <td>Sequence Analysis</td>
+      <td>coverage_report</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report</td>
+      <td>0.0.4</td>
+      <td>perl-number-format</td>
+      <td>1.76</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>coverage_stats</td>
+      <td>coverage_stats</td>
+      <td>BAM coverage statistics using samtools idxstats and depth</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats</td>
+      <td>Assembly, SAM</td>
+      <td>coverage_stats</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats</td>
+      <td>0.1.0</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>coverm</td>
+      <td>coverm_contig, coverm_genome</td>
+      <td>CoverM genome and contig wrappers</td>
+      <td>coverm</td>
+      <td>coverm</td>
+      <td></td>
+      <td>CoverM</td>
+      <td>Read coverage calculator for metagenomics</td>
+      <td>Local alignment</td>
+      <td>Bioinformatics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/wwood/CoverM</td>
+      <td>Sequence Analysis</td>
+      <td>coverm</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tools/coverm</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm</td>
+      <td>0.7.0</td>
+      <td>coverm</td>
+      <td>0.7.0</td>
+      <td>Local alignment</td>
+      <td>Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1081</td>
+      <td>1081</td>
+      <td>151</td>
+      <td>151</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1081</td>
+      <td>1081</td>
+      <td>151</td>
+      <td>151</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cpat</td>
+      <td>cpat</td>
+      <td>Coding-potential assessment tool using an alignment-free logistic regression model.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/liguowang/cpat</td>
+      <td>Transcriptomics</td>
+      <td>cpat</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cpat</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cpat</td>
+      <td>3.0.5</td>
+      <td>cpat</td>
+      <td>3.0.5</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>204</td>
+      <td>204</td>
+      <td>47</td>
+      <td>47</td>
+      <td>165</td>
+      <td>165</td>
+      <td>40</td>
+      <td>40</td>
+      <td>125</td>
+      <td>125</td>
+      <td>7</td>
+      <td>7</td>
+      <td>494</td>
+      <td>494</td>
+      <td>94</td>
+      <td>94</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cpm_tpm_rpk</td>
+      <td>cpm_tpm_rpk</td>
+      <td>Generate CPM,TPM or RPK from raw counts</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>cpm_tpm_rpk</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk</td>
+      <td>0.6.0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>crispr_studio</td>
+      <td>crispr_studio</td>
+      <td>CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.</td>
+      <td>crisprstudio</td>
+      <td>crisprstudio</td>
+      <td></td>
+      <td>CRISPRStudio</td>
+      <td>CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.</td>
+      <td>Visualisation</td>
+      <td>Sequence analysis, Genomics, Data visualisation</td>
+      <td>To update</td>
+      <td>https://github.com/moineaulab/CRISPRStudio</td>
+      <td>Sequence Analysis</td>
+      <td>crispr_studio</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio</td>
+      <td>1+galaxy0</td>
+      <td>crispr_studio</td>
+      <td>1</td>
+      <td>Visualisation</td>
+      <td>Sequence analysis, Genomics, Data visualisation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1052</td>
+      <td>1053</td>
+      <td>75</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1052</td>
+      <td>1053</td>
+      <td>75</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>crosscontamination_barcode_filter</td>
+      <td>crosscontamination_barcode_filter</td>
+      <td>Barcode contamination discovery tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, Visualization</td>
+      <td>crosscontamination_barcode_filter</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter</td>
+      <td>0.3</td>
+      <td>r-ggplot2</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>276</td>
+      <td>390</td>
+      <td>61</td>
+      <td>76</td>
+      <td>131</td>
+      <td>131</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>407</td>
+      <td>521</td>
+      <td>103</td>
+      <td>118</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>crossmap</td>
+      <td>crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig</td>
+      <td>CrossMap converts genome coordinates or annotation files between genome assemblies</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://crossmap.sourceforge.net/</td>
+      <td>Convert Formats, Genomic Interval Operations</td>
+      <td>crossmap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap</td>
+      <td>0.7.0</td>
+      <td>crossmap</td>
+      <td>0.7.0</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>6</td>
+      <td>5</td>
+      <td>0</td>
+      <td>2182</td>
+      <td>2182</td>
+      <td>331</td>
+      <td>331</td>
+      <td>5251</td>
+      <td>5251</td>
+      <td>903</td>
+      <td>903</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7433</td>
+      <td>7433</td>
+      <td>1234</td>
+      <td>1234</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>crt</td>
+      <td>crispr_recognition_tool</td>
+      <td>CRISPR Recognition Tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>crispr_recognition_tool</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/crt</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/crt</td>
+      <td>1.2.0</td>
+      <td>crisper_recognition_tool</td>
+      <td>1.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4066</td>
+      <td>4139</td>
+      <td>166</td>
+      <td>180</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4066</td>
+      <td>4139</td>
+      <td>166</td>
+      <td>180</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cryptogenotyper</td>
+      <td>CryptoGenotyper</td>
+      <td>CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/CryptoGenotyper</td>
+      <td>Sequence Analysis</td>
+      <td>cryptogenotyper</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/CryptoGenotyper</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper</td>
+      <td>1.0</td>
+      <td>cryptogenotyper</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9942</td>
+      <td>9942</td>
+      <td>26</td>
+      <td>26</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9942</td>
+      <td>9942</td>
+      <td>26</td>
+      <td>26</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>csvtk</td>
+      <td>csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq</td>
+      <td>Rapid data investigation and manipulation of csv/tsv files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bioinf.shenwei.me/csvtk/</td>
+      <td>Text Manipulation</td>
+      <td>csvtk</td>
+      <td>nml</td>
+      <td>https://github.com/shenwei356/csvtk</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk</td>
+      <td>0.20.0</td>
+      <td>csvtk</td>
+      <td>0.30.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cta</td>
+      <td>cta_astro_tool</td>
+      <td>Basic simulation of CTA telescope observations using gammapy package</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Astronomy</td>
+      <td>cta_astro_tool</td>
+      <td>astroteam</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta</td>
+      <td>0.0.1+galaxy0</td>
+      <td>unzip</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ctd_batch</td>
+      <td>ctdBatch_1</td>
+      <td>CTD analysis of chemicals, diseases, or genes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>ctd_batch</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>196</td>
+      <td>211</td>
+      <td>41</td>
+      <td>48</td>
+      <td>1</td>
+      <td>447</td>
+      <td>1</td>
+      <td>161</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>197</td>
+      <td>658</td>
+      <td>42</td>
+      <td>209</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cuffcompare</td>
+      <td>cuffcompare</td>
+      <td>Galaxy wrappers for the Cuffcompare tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
+      <td>Transcriptomics</td>
+      <td>cuffcompare</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare</td>
+      <td>2.2.1</td>
+      <td>cufflinks</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>768</td>
+      <td>1199</td>
+      <td>171</td>
+      <td>300</td>
+      <td>2205</td>
+      <td>24981</td>
+      <td>754</td>
+      <td>5750</td>
+      <td>251</td>
+      <td>493</td>
+      <td>46</td>
+      <td>98</td>
+      <td>3224</td>
+      <td>26673</td>
+      <td>971</td>
+      <td>6148</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cuffdiff</td>
+      <td>cuffdiff</td>
+      <td>Galaxy wrappers for the Cuffdiff tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
+      <td>Transcriptomics</td>
+      <td>cuffdiff</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff</td>
+      <td>2.2.1</td>
+      <td>cufflinks</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4176</td>
+      <td>6065</td>
+      <td>564</td>
+      <td>725</td>
+      <td>24284</td>
+      <td>117007</td>
+      <td>4952</td>
+      <td>20249</td>
+      <td>971</td>
+      <td>4231</td>
+      <td>193</td>
+      <td>616</td>
+      <td>29431</td>
+      <td>127303</td>
+      <td>5709</td>
+      <td>21590</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cufflinks</td>
+      <td>cufflinks</td>
+      <td>Galaxy wrappers for the Cufflinks tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
+      <td>Transcriptomics</td>
+      <td>cufflinks</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks</td>
+      <td>2.2.1</td>
+      <td>cufflinks</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>26122</td>
+      <td>33320</td>
+      <td>870</td>
+      <td>1213</td>
+      <td>70653</td>
+      <td>349091</td>
+      <td>6984</td>
+      <td>27076</td>
+      <td>3963</td>
+      <td>10315</td>
+      <td>440</td>
+      <td>836</td>
+      <td>100738</td>
+      <td>392726</td>
+      <td>8294</td>
+      <td>29125</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cuffmerge</td>
+      <td>cuffmerge</td>
+      <td>Galaxy wrappers for the Cuffmerge tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
+      <td>Transcriptomics</td>
+      <td>cuffmerge</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge</td>
+      <td>2.2.1</td>
+      <td>cufflinks</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2406</td>
+      <td>3448</td>
+      <td>351</td>
+      <td>637</td>
+      <td>20978</td>
+      <td>67769</td>
+      <td>3641</td>
+      <td>13764</td>
+      <td>1209</td>
+      <td>3057</td>
+      <td>227</td>
+      <td>573</td>
+      <td>24593</td>
+      <td>74274</td>
+      <td>4219</td>
+      <td>14974</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cuffnorm</td>
+      <td>cuffnorm</td>
+      <td>The Cuffnorm tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
+      <td>Transcriptomics</td>
+      <td>cuffnorm</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm</td>
+      <td>2.2.1</td>
+      <td>cufflinks</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>374</td>
+      <td>701</td>
+      <td>81</td>
+      <td>114</td>
+      <td>1032</td>
+      <td>13499</td>
+      <td>273</td>
+      <td>1166</td>
+      <td>262</td>
+      <td>322</td>
+      <td>53</td>
+      <td>70</td>
+      <td>1668</td>
+      <td>14522</td>
+      <td>407</td>
+      <td>1350</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cuffquant</td>
+      <td>cuffquant</td>
+      <td>The Cuffquant tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
+      <td>Transcriptomics</td>
+      <td>cuffquant</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant</td>
+      <td>2.2.1</td>
+      <td>cufflinks</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>408</td>
+      <td>732</td>
+      <td>54</td>
+      <td>71</td>
+      <td>1964</td>
+      <td>15883</td>
+      <td>267</td>
+      <td>1310</td>
+      <td>308</td>
+      <td>422</td>
+      <td>26</td>
+      <td>46</td>
+      <td>2680</td>
+      <td>17037</td>
+      <td>347</td>
+      <td>1427</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cummerbund</td>
+      <td>cummeRbund</td>
+      <td>Wrapper for the Bioconductor cummeRbund library</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/cummeRbund.html</td>
+      <td>RNA, Visualization</td>
+      <td>cummerbund</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund</td>
+      <td>2.16.0</td>
+      <td>fonts-conda-ecosystem</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1251</td>
+      <td>1803</td>
+      <td>98</td>
+      <td>166</td>
+      <td>3461</td>
+      <td>15159</td>
+      <td>486</td>
+      <td>2044</td>
+      <td>2425</td>
+      <td>3338</td>
+      <td>57</td>
+      <td>159</td>
+      <td>7137</td>
+      <td>20300</td>
+      <td>641</td>
+      <td>2369</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cummerbund_to_tabular</td>
+      <td>cummerbund_to_cuffdiff</td>
+      <td>Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats, Next Gen Mappers</td>
+      <td>cummerbund_to_tabular</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>888</td>
+      <td>1208</td>
+      <td>43</td>
+      <td>97</td>
+      <td>1334</td>
+      <td>2683</td>
+      <td>101</td>
+      <td>479</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2222</td>
+      <td>3891</td>
+      <td>144</td>
+      <td>576</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>curve_fitting</td>
+      <td>ip_curve_fitting</td>
+      <td>Polynomial curve fitting to data points</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis</td>
+      <td>Imaging</td>
+      <td>curve_fitting</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting</td>
+      <td>0.0.3-2</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>custom_pro_db</td>
+      <td>custom_pro_db</td>
+      <td>CustomProDB</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/customProDB.html</td>
+      <td>Proteomics</td>
+      <td>custom_pro_db</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db</td>
+      <td>1.22.0</td>
+      <td>bioconductor-rgalaxy</td>
+      <td>1.37.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1729</td>
+      <td>1744</td>
+      <td>144</td>
+      <td>146</td>
+      <td>450</td>
+      <td>450</td>
+      <td>72</td>
+      <td>72</td>
+      <td>361</td>
+      <td>361</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2540</td>
+      <td>2555</td>
+      <td>228</td>
+      <td>230</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>custom_pro_db_annotation_data_manager</td>
+      <td></td>
+      <td>CustomProDB Annotation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/customProDB.html</td>
+      <td>Proteomics</td>
+      <td>custom_pro_db_annotation_data_manager</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cut_columns</td>
+      <td>Cut1</td>
+      <td>Select columns from a dataset.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>cut_columns</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns</td>
+      <td>1.0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1973168</td>
+      <td>2034965</td>
+      <td>11939</td>
+      <td>12833</td>
+      <td>352364</td>
+      <td>803522</td>
+      <td>12967</td>
+      <td>30199</td>
+      <td>128777</td>
+      <td>133584</td>
+      <td>2341</td>
+      <td>2572</td>
+      <td>2454309</td>
+      <td>2972071</td>
+      <td>27247</td>
+      <td>45604</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cutadapt</td>
+      <td>cutadapt</td>
+      <td>Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).</td>
+      <td>cutadapt</td>
+      <td>cutadapt</td>
+      <td></td>
+      <td>Cutadapt</td>
+      <td>Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.</td>
+      <td>Sequence trimming, Primer removal, Read pre-processing</td>
+      <td>Genomics, Probes and primers, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://cutadapt.readthedocs.org/en/stable/</td>
+      <td>Fasta Manipulation, Fastq Manipulation, Sequence Analysis</td>
+      <td>cutadapt</td>
+      <td>lparsons</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt</td>
+      <td>4.9</td>
+      <td>cutadapt</td>
+      <td>4.9</td>
+      <td>Sequence trimming, Primer removal, Read pre-processing</td>
+      <td>Genomics, Probes and primers, Sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>259754</td>
+      <td>272370</td>
+      <td>11716</td>
+      <td>12601</td>
+      <td>334550</td>
+      <td>362356</td>
+      <td>18618</td>
+      <td>20162</td>
+      <td>64377</td>
+      <td>65986</td>
+      <td>3507</td>
+      <td>3627</td>
+      <td>658681</td>
+      <td>700712</td>
+      <td>33841</td>
+      <td>36390</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cutesv</td>
+      <td>cutesv</td>
+      <td>Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.</td>
+      <td>cuteSV</td>
+      <td>cuteSV</td>
+      <td></td>
+      <td>cuteSV</td>
+      <td>Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis</td>
+      <td>Split read mapping, Genotyping, Structural variation detection</td>
+      <td>DNA structural variation, Sequencing, Computer science</td>
+      <td>To update</td>
+      <td>https://github.com/tjiangHIT/cuteSV</td>
+      <td>Variant Analysis</td>
+      <td>cutesv</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv</td>
+      <td>1.0.8</td>
+      <td>cutesv</td>
+      <td>2.1.1</td>
+      <td>Split read mapping, Genotyping, Structural variation detection</td>
+      <td>Sequencing, Computer science</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>260</td>
+      <td>260</td>
+      <td>43</td>
+      <td>43</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>119</td>
+      <td>8</td>
+      <td>8</td>
+      <td>379</td>
+      <td>379</td>
+      <td>51</td>
+      <td>51</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cwpair2</td>
+      <td>cwpair2</td>
+      <td>Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>ChIP-seq</td>
+      <td>cwpair2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2</td>
+      <td>1.1.1</td>
+      <td>matplotlib</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>173</td>
+      <td>280</td>
+      <td>41</td>
+      <td>83</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>173</td>
+      <td>280</td>
+      <td>41</td>
+      <td>83</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dada2</td>
+      <td>dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts</td>
+      <td>DADA2 wrappers</td>
+      <td>dada2</td>
+      <td>dada2</td>
+      <td></td>
+      <td>dada2</td>
+      <td>This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.</td>
+      <td>Variant calling, DNA barcoding</td>
+      <td>Sequencing, Genetic variation, Microbial ecology, Metagenomics</td>
+      <td>To update</td>
+      <td>https://benjjneb.github.io/dada2/index.html</td>
+      <td>Metagenomics</td>
+      <td>dada2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2</td>
+      <td></td>
+      <td>bioconductor-dada2</td>
+      <td>1.30.0</td>
+      <td>Variant calling, DNA barcoding</td>
+      <td>Sequencing, Genetic variation, Microbial ecology, Metagenomics</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>92240</td>
+      <td>92240</td>
+      <td>2716</td>
+      <td>2716</td>
+      <td>179176</td>
+      <td>179176</td>
+      <td>5317</td>
+      <td>5317</td>
+      <td>12478</td>
+      <td>12478</td>
+      <td>394</td>
+      <td>394</td>
+      <td>283894</td>
+      <td>283894</td>
+      <td>8427</td>
+      <td>8427</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>das_tool</td>
+      <td>Fasta_to_Contig2Bin, das_tool</td>
+      <td>DAS Tool for genome resolved metagenomics</td>
+      <td>dastool</td>
+      <td>dastool</td>
+      <td></td>
+      <td>dastool</td>
+      <td>DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.</td>
+      <td>Read binning</td>
+      <td>Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cmks/DAS_Tool</td>
+      <td>Metagenomics</td>
+      <td>das_tool</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool</td>
+      <td>1.1.7</td>
+      <td>das_tool</td>
+      <td>1.1.7</td>
+      <td>Read binning</td>
+      <td>Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1323</td>
+      <td>1323</td>
+      <td>47</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1323</td>
+      <td>1323</td>
+      <td>47</td>
+      <td>47</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>data-hca</td>
+      <td>hca_matrix_downloader</td>
+      <td>Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, Sequence Analysis</td>
+      <td>suite_human_cell_atlas_tools</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca</td>
+      <td>v0.0.4+galaxy0</td>
+      <td>hca-matrix-downloader</td>
+      <td>0.0.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>441</td>
+      <td>451</td>
+      <td>83</td>
+      <td>87</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>444</td>
+      <td>454</td>
+      <td>85</td>
+      <td>89</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>data-scxa</td>
+      <td>retrieve_scxa</td>
+      <td>Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, Sequence Analysis</td>
+      <td>suite_ebi_expression_atlas</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa</td>
+      <td>v0.0.2+galaxy2</td>
+      <td>wget</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>867</td>
+      <td>877</td>
+      <td>213</td>
+      <td>216</td>
+      <td>339</td>
+      <td>339</td>
+      <td>94</td>
+      <td>94</td>
+      <td>64</td>
+      <td>64</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1270</td>
+      <td>1280</td>
+      <td>312</td>
+      <td>315</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>data_exploration</td>
+      <td>tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs</td>
+      <td>Explore data through multiple statistical tools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/Marie59/Data_explo_tools</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration</td>
+      <td>0.0.0</td>
+      <td>r-tangles</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>967</td>
+      <td>967</td>
+      <td>308</td>
+      <td>308</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>967</td>
+      <td>967</td>
+      <td>308</td>
+      <td>308</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>data_manager_eggnog_mapper</td>
+      <td></td>
+      <td>downloads eggnog data for eggnog-mapper</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>data_manager_eggnog_mapper</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>data_manager_eggnog_mapper_abspath</td>
+      <td></td>
+      <td>download eggnog data for eggnog-mapper</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>data_manager_eggnog_mapper_abspath</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>data_source_iris_tcga</td>
+      <td>data_source_iris_tcga</td>
+      <td>IRIS-TCGA Data source tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Data Source</td>
+      <td>data_source_iris_tcga</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga</td>
+      <td>1.0.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>datamash</td>
+      <td>datamash_ops, datamash_reverse, datamash_transpose</td>
+      <td>GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.gnu.org/software/datamash/</td>
+      <td>Text Manipulation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash</td>
+      <td>1.8</td>
+      <td>datamash</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>748586</td>
+      <td>760943</td>
+      <td>7066</td>
+      <td>7307</td>
+      <td>98089</td>
+      <td>112831</td>
+      <td>5306</td>
+      <td>6131</td>
+      <td>16235</td>
+      <td>16317</td>
+      <td>2161</td>
+      <td>2171</td>
+      <td>862910</td>
+      <td>890091</td>
+      <td>14533</td>
+      <td>15609</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dbbuilder</td>
+      <td>dbbuilder</td>
+      <td>Protein Database Downloader</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder</td>
+      <td>Proteomics</td>
+      <td>dbbuilder</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder</td>
+      <td>0.3.4</td>
+      <td>wget</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4813</td>
+      <td>5555</td>
+      <td>687</td>
+      <td>805</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>961</td>
+      <td>961</td>
+      <td>87</td>
+      <td>87</td>
+      <td>5774</td>
+      <td>6516</td>
+      <td>774</td>
+      <td>892</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>decontaminator</td>
+      <td>decontaminator</td>
+      <td>Deep Learning method for novel virus detection in sequencing data</td>
+      <td>decontaminator</td>
+      <td>decontaminator</td>
+      <td></td>
+      <td>decontaminator</td>
+      <td>Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.</td>
+      <td>Filtering</td>
+      <td>Metagenomics</td>
+      <td>To update</td>
+      <td>https://github.com/cbib/decontaminator</td>
+      <td>Machine Learning</td>
+      <td>decontaminator</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator</td>
+      <td>1.0.0</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Filtering</td>
+      <td>Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>decoupler</td>
+      <td>score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk</td>
+      <td>decoupler - Ensemble of methods to infer biological activities</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://decoupler-py.readthedocs.io/en/latest/</td>
+      <td>Transcriptomics</td>
+      <td>suite_decoupler</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler</td>
+      <td>1.4.0+galaxy3</td>
+      <td>decoupler</td>
+      <td>1.5.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>decoyfasta</td>
+      <td></td>
+      <td>Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>decoyfasta</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>deepmicro</td>
+      <td>deepmicro</td>
+      <td>Representation learning and classification framework</td>
+      <td>DeepMicro</td>
+      <td>DeepMicro</td>
+      <td></td>
+      <td>DeepMicro</td>
+      <td>Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.</td>
+      <td>Essential dynamics, Splitting, Community profiling</td>
+      <td>Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/paulzierep/DeepMicro</td>
+      <td>Machine Learning</td>
+      <td>deepmicro</td>
+      <td>iuc</td>
+      <td>https://github.com/paulzierep/DeepMicro</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro</td>
+      <td>1.4</td>
+      <td>deepmicro</td>
+      <td>1.4</td>
+      <td>Essential dynamics, Splitting</td>
+      <td>Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>558</td>
+      <td>558</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>558</td>
+      <td>558</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>deepsig</td>
+      <td>deepsig</td>
+      <td>Predictor of signal peptides in proteins based on deep learning</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BolognaBiocomp/deepsig</td>
+      <td>Genome annotation</td>
+      <td>deepsig</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig</td>
+      <td>1.2.5</td>
+      <td>deepsig</td>
+      <td>1.2.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>37</td>
+      <td>37</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>deepvariant</td>
+      <td>deepvariant</td>
+      <td>DeepVariant is a deep learning-based variant caller</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/google/deepvariant</td>
+      <td>Variant Analysis</td>
+      <td>deepvariant</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant</td>
+      <td>1.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2561</td>
+      <td>2561</td>
+      <td>325</td>
+      <td>325</td>
+      <td>2916</td>
+      <td>2916</td>
+      <td>460</td>
+      <td>460</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5477</td>
+      <td>5477</td>
+      <td>785</td>
+      <td>785</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>deg_annotate</td>
+      <td>deg_annotate</td>
+      <td>Annotate DESeq2/DEXSeq output tables</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate</td>
+      <td>Transcriptomics</td>
+      <td>deg_annotate</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate</td>
+      <td>1.1.0</td>
+      <td>bedtools</td>
+      <td>2.31.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>22774</td>
+      <td>23146</td>
+      <td>4084</td>
+      <td>4155</td>
+      <td>33972</td>
+      <td>33972</td>
+      <td>5372</td>
+      <td>5372</td>
+      <td>4236</td>
+      <td>4236</td>
+      <td>846</td>
+      <td>846</td>
+      <td>60982</td>
+      <td>61354</td>
+      <td>10302</td>
+      <td>10373</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>delete_overlapping_indels</td>
+      <td>delete_overlapping_indels</td>
+      <td>Delete Overlapping Indels from a chromosome indels file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>delete_overlapping_indels</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>33</td>
+      <td>40</td>
+      <td>6</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>33</td>
+      <td>40</td>
+      <td>6</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>delly</td>
+      <td>delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge</td>
+      <td>Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.</td>
+      <td>delly2</td>
+      <td>delly2</td>
+      <td></td>
+      <td>Delly2</td>
+      <td>Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.</td>
+      <td>Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis</td>
+      <td>DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases</td>
+      <td>To update</td>
+      <td>https://github.com/dellytools/delly</td>
+      <td>Variant Analysis</td>
+      <td>delly</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly</td>
+      <td>0.9.1</td>
+      <td>delly</td>
+      <td>1.2.9</td>
+      <td>Indel detection, Structural variation detection, Genotyping</td>
+      <td>Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1451</td>
+      <td>1451</td>
+      <td>288</td>
+      <td>288</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1451</td>
+      <td>1451</td>
+      <td>288</td>
+      <td>288</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>deseq2</td>
+      <td>deseq2</td>
+      <td>Differential gene expression analysis based on the negative binomial distribution</td>
+      <td>DESeq2</td>
+      <td>DESeq2</td>
+      <td></td>
+      <td>DESeq2</td>
+      <td>R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.</td>
+      <td>Differential gene expression analysis, RNA-Seq analysis</td>
+      <td>RNA-Seq</td>
+      <td>To update</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>deseq2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2</td>
+      <td>2.11.40.8</td>
+      <td>bioconductor-deseq2</td>
+      <td>1.42.0</td>
+      <td>Differential gene expression analysis, RNA-Seq analysis</td>
+      <td>RNA-Seq</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>97434</td>
+      <td>109474</td>
+      <td>11355</td>
+      <td>12514</td>
+      <td>183905</td>
+      <td>246475</td>
+      <td>24951</td>
+      <td>31957</td>
+      <td>18551</td>
+      <td>20166</td>
+      <td>2647</td>
+      <td>2905</td>
+      <td>299890</td>
+      <td>376115</td>
+      <td>38953</td>
+      <td>47376</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>deseq2_normalization</td>
+      <td>deseq2_normalization</td>
+      <td>Normalizes gene hitlists</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Transcriptomics, Sequence Analysis, Statistics</td>
+      <td>deseq2_normalization</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization</td>
+      <td>1.40.2+galaxy0</td>
+      <td>bioconductor-deseq2</td>
+      <td>1.42.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>detection_viz</td>
+      <td>ip_detection_viz</td>
+      <td>Detection Visualization</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>detection_viz</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz</td>
+      <td>0.3-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>43</td>
+      <td>48</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>48</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dewseq</td>
+      <td>dewseq</td>
+      <td>DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers</td>
+      <td>Sequence Analysis, RNA, CLIP-seq</td>
+      <td>dewseq</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq</td>
+      <td>0.1.0+galaxy0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>89</td>
+      <td>89</td>
+      <td>18</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>89</td>
+      <td>89</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dexseq</td>
+      <td>dexseq, dexseq_count, plotdexseq</td>
+      <td>Inference of differential exon usage in RNA-Seq</td>
+      <td>dexseq</td>
+      <td>dexseq</td>
+      <td></td>
+      <td>DEXSeq</td>
+      <td>The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.</td>
+      <td>Enrichment analysis, Exonic splicing enhancer prediction</td>
+      <td>RNA-Seq</td>
+      <td>Up-to-date</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>dexseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq</td>
+      <td>1.48.0</td>
+      <td>bioconductor-dexseq</td>
+      <td>1.48.0</td>
+      <td>Enrichment analysis, Exonic splicing enhancer prediction</td>
+      <td>RNA-Seq</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>14874</td>
+      <td>16927</td>
+      <td>533</td>
+      <td>837</td>
+      <td>18475</td>
+      <td>28854</td>
+      <td>1403</td>
+      <td>2568</td>
+      <td>3854</td>
+      <td>4271</td>
+      <td>141</td>
+      <td>163</td>
+      <td>37203</td>
+      <td>50052</td>
+      <td>2077</td>
+      <td>3568</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dgidb_annotator</td>
+      <td>dgidb_annotate</td>
+      <td>Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Systems Biology, Variant Analysis</td>
+      <td>dgidb_annotator</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>59</td>
+      <td>69</td>
+      <td>26</td>
+      <td>30</td>
+      <td>0</td>
+      <td>304</td>
+      <td>0</td>
+      <td>133</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59</td>
+      <td>373</td>
+      <td>26</td>
+      <td>163</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dia_umpire</td>
+      <td>dia_umpire_se</td>
+      <td>DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://diaumpire.sourceforge.net/</td>
+      <td>Proteomics</td>
+      <td>dia_umpire</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire</td>
+      <td>2.1.3</td>
+      <td>dia_umpire</td>
+      <td>2.1.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>28</td>
+      <td>33</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>134</td>
+      <td>134</td>
+      <td>4</td>
+      <td>4</td>
+      <td>162</td>
+      <td>167</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dialignr</td>
+      <td>dialignr</td>
+      <td>DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/shubham1637/DIAlignR</td>
+      <td>Proteomics</td>
+      <td>dialignr</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr</td>
+      <td>1.2.0</td>
+      <td>bioconductor-dialignr</td>
+      <td>2.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diamond</td>
+      <td>bg_diamond, bg_diamond_makedb, bg_diamond_view</td>
+      <td>DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.</td>
+      <td>diamond</td>
+      <td>diamond</td>
+      <td></td>
+      <td>Diamond</td>
+      <td>Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.</td>
+      <td>Sequence alignment analysis</td>
+      <td>Sequence analysis, Proteins</td>
+      <td>To update</td>
+      <td>https://github.com/bbuchfink/diamond</td>
+      <td>Sequence Analysis</td>
+      <td>diamond</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond</td>
+      <td>2.0.15</td>
+      <td>diamond</td>
+      <td>2.1.9</td>
+      <td>Sequence alignment analysis</td>
+      <td>Sequence analysis, Proteins</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>61376</td>
+      <td>61746</td>
+      <td>1847</td>
+      <td>1895</td>
+      <td>23164</td>
+      <td>28729</td>
+      <td>1140</td>
+      <td>1556</td>
+      <td>63034</td>
+      <td>63034</td>
+      <td>522</td>
+      <td>522</td>
+      <td>147574</td>
+      <td>153509</td>
+      <td>3509</td>
+      <td>3973</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diann</td>
+      <td>diann</td>
+      <td>DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/vdemichev/DiaNN</td>
+      <td>Proteomics</td>
+      <td>diann</td>
+      <td>galaxyp</td>
+      <td>https://github.com/vdemichev/DiaNN</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann</td>
+      <td>1.8.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>72</td>
+      <td>72</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>171</td>
+      <td>171</td>
+      <td>14</td>
+      <td>14</td>
+      <td>243</td>
+      <td>243</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diapysef</td>
+      <td>diapysef</td>
+      <td>diapysef is a convenience package for working with DIA-PASEF data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pypi.org/project/diapysef/</td>
+      <td>Proteomics</td>
+      <td>diapysef</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef</td>
+      <td>0.3.5.0</td>
+      <td>diapysef</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>262</td>
+      <td>262</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>256</td>
+      <td>256</td>
+      <td>6</td>
+      <td>6</td>
+      <td>518</td>
+      <td>518</td>
+      <td>44</td>
+      <td>44</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diff</td>
+      <td>diff</td>
+      <td>GNU diff tool that calculates the differences between two files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.gnu.org/software/diffutils/</td>
+      <td>Text Manipulation</td>
+      <td>diff</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/diff</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/diff</td>
+      <td>3.7</td>
+      <td>diffutils</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>362</td>
+      <td>362</td>
+      <td>99</td>
+      <td>99</td>
+      <td>23</td>
+      <td>23</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>385</td>
+      <td>385</td>
+      <td>116</td>
+      <td>116</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diffacto</td>
+      <td>diffacto</td>
+      <td>Diffacto comparative protein abundance estimation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/statisticalbiotechnology/diffacto</td>
+      <td>Proteomics</td>
+      <td>diffacto</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto</td>
+      <td>1.0.6</td>
+      <td>diffacto</td>
+      <td>1.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diffbind</td>
+      <td>diffbind</td>
+      <td>Diffbind provides functions for  processing  ChIP-Seq  data.</td>
+      <td>diffbind</td>
+      <td>diffbind</td>
+      <td></td>
+      <td>DiffBind</td>
+      <td>Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.</td>
+      <td>Differential binding analysis</td>
+      <td>ChIP-seq</td>
+      <td>Up-to-date</td>
+      <td>http://bioconductor.org/packages/release/bioc/html/DiffBind.html</td>
+      <td>ChIP-seq</td>
+      <td>diffbind</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind</td>
+      <td>3.12.0</td>
+      <td>bioconductor-diffbind</td>
+      <td>3.12.0</td>
+      <td>Differential binding analysis</td>
+      <td>ChIP-seq</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7092</td>
+      <td>7663</td>
+      <td>606</td>
+      <td>652</td>
+      <td>14367</td>
+      <td>18624</td>
+      <td>1360</td>
+      <td>1916</td>
+      <td>1477</td>
+      <td>1640</td>
+      <td>69</td>
+      <td>84</td>
+      <td>22936</td>
+      <td>27927</td>
+      <td>2035</td>
+      <td>2652</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diffbind</td>
+      <td></td>
+      <td>Diffbind provides functions for  processing  ChIP-Seq  data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://bioconductor.org/packages/release/bioc/html/DiffBind.html</td>
+      <td>ChIP-seq</td>
+      <td>diffbind</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/diffbind</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/diffbind</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>digestdb</td>
+      <td>digestdb</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>digestdb</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb</td>
+      <td>0.1.0</td>
+      <td>trans_proteomic_pipeline</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dimet</td>
+      <td>dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@</td>
+      <td>DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cbib/DIMet</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet</td>
+      <td>0.2.4</td>
+      <td>dimet</td>
+      <td>0.2.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>directag_and_tagrecon</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>directag_and_tagrecon</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>disco</td>
+      <td>disco</td>
+      <td>DISCO is a overlap-layout-consensus (OLC) metagenome assembler</td>
+      <td>disco</td>
+      <td>disco</td>
+      <td></td>
+      <td>DISCO</td>
+      <td>DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.</td>
+      <td>Protein sequence analysis</td>
+      <td>Structure determination</td>
+      <td>To update</td>
+      <td>http://disco.omicsbio.org/</td>
+      <td>Metagenomics, Assembly</td>
+      <td>disco</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco</td>
+      <td></td>
+      <td>disco</td>
+      <td>1.2</td>
+      <td>Protein sequence analysis</td>
+      <td>Structure determination</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>358</td>
+      <td>406</td>
+      <td>124</td>
+      <td>139</td>
+      <td>1361</td>
+      <td>1361</td>
+      <td>384</td>
+      <td>384</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1719</td>
+      <td>1767</td>
+      <td>508</td>
+      <td>523</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>divide_pg_snp</td>
+      <td>dividePgSnp</td>
+      <td>Separate pgSnp alleles into columns</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>divide_pg_snp</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>26</td>
+      <td>32</td>
+      <td>8</td>
+      <td>9</td>
+      <td>86</td>
+      <td>172</td>
+      <td>20</td>
+      <td>53</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>112</td>
+      <td>204</td>
+      <td>28</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dnabot</td>
+      <td>dnabot</td>
+      <td>DNA assembly using BASIC on OpenTrons</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT</td>
+      <td>Synthetic Biology</td>
+      <td>dnabot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot</td>
+      <td>3.1.0</td>
+      <td>dnabot</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dnaweaver</td>
+      <td>dnaweaver</td>
+      <td>Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Edinburgh-Genome-Foundry/DnaWeaver</td>
+      <td>Synthetic Biology</td>
+      <td>dnaweaver</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver</td>
+      <td>1.0.2</td>
+      <td>dnaweaver_synbiocad</td>
+      <td>1.0.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dorina</td>
+      <td>dorina_search</td>
+      <td>data source for RNA interactions in post-transcriptional regulation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA, Data Source</td>
+      <td>dorina</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>921</td>
+      <td>1626</td>
+      <td>4</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>921</td>
+      <td>1626</td>
+      <td>4</td>
+      <td>31</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dose_responses</td>
+      <td>dr_curve</td>
+      <td>A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools</td>
+      <td>Ecology</td>
+      <td>dose_response_analysis_tool</td>
+      <td>ufz</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses</td>
+      <td>3.0_1</td>
+      <td>r-drc</td>
+      <td>3.0_1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dot2ct</td>
+      <td>rnastructure_dot2ct</td>
+      <td>Dot-Bracket to Connect Table (CT)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, RNA</td>
+      <td>dot2ct</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct</td>
+      <td>5.7.a</td>
+      <td>rnastructure</td>
+      <td>6.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dotknot</td>
+      <td>dotknot</td>
+      <td>DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://dotknot.csse.uwa.edu.au/</td>
+      <td>RNA, Proteomics</td>
+      <td>dotknot</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot</td>
+      <td>1.3.1</td>
+      <td>vienna_rna</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>74</td>
+      <td>88</td>
+      <td>12</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>74</td>
+      <td>88</td>
+      <td>12</td>
+      <td>15</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dram</td>
+      <td>dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer</td>
+      <td>DRAM for distilling microbial metabolism to automate the curation of microbiome function</td>
+      <td>dram</td>
+      <td>dram</td>
+      <td></td>
+      <td>DRAM</td>
+      <td>Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes</td>
+      <td>Gene functional annotation</td>
+      <td>Metagenomics, Biological databases, Molecular genetics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/WrightonLabCSU/DRAM</td>
+      <td>Metagenomics</td>
+      <td>dram</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram</td>
+      <td>1.5.0</td>
+      <td>dram</td>
+      <td>1.5.0</td>
+      <td>Gene functional annotation</td>
+      <td>Metagenomics, Biological databases, Molecular genetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7358</td>
+      <td>7358</td>
+      <td>88</td>
+      <td>88</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7358</td>
+      <td>7358</td>
+      <td>88</td>
+      <td>88</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>draw_stacked_barplots</td>
+      <td>draw_stacked_barplots</td>
+      <td>Draw Stacked Bar Plots for different categories and different criteria</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Statistics</td>
+      <td>draw_stacked_barplots</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots</td>
+      <td>1.0.0</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>189</td>
+      <td>216</td>
+      <td>47</td>
+      <td>52</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>183</td>
+      <td>213</td>
+      <td>22</td>
+      <td>31</td>
+      <td>372</td>
+      <td>429</td>
+      <td>69</td>
+      <td>83</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>drep</td>
+      <td>drep_compare, drep_dereplicate</td>
+      <td>dRep compares and dereplicates genome sets</td>
+      <td>drep</td>
+      <td>drep</td>
+      <td></td>
+      <td>dRep</td>
+      <td>Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.</td>
+      <td>Genome comparison</td>
+      <td>Metagenomics, Genomics, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/MrOlm/drep</td>
+      <td>Metagenomics</td>
+      <td>drep</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep</td>
+      <td>3.5.0</td>
+      <td>drep</td>
+      <td>3.5.0</td>
+      <td>Genome comparison</td>
+      <td>Metagenomics, Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>916</td>
+      <td>916</td>
+      <td>113</td>
+      <td>113</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>916</td>
+      <td>916</td>
+      <td>113</td>
+      <td>113</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>droplet-barcode-plot</td>
+      <td>_dropletBarcodePlot</td>
+      <td>Make a cell barcode plot for droplet single-cell RNA-seq QC</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary</td>
+      <td>Sequence Analysis</td>
+      <td>droplet_barcode_plot</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot</td>
+      <td>1.6.1+galaxy2</td>
+      <td>scxa-plots</td>
+      <td>0.0.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1151</td>
+      <td>1151</td>
+      <td>184</td>
+      <td>184</td>
+      <td>356</td>
+      <td>356</td>
+      <td>77</td>
+      <td>77</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1510</td>
+      <td>1510</td>
+      <td>262</td>
+      <td>262</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dropletutils</td>
+      <td>dropletutils_empty_drops, dropletutils_read_10x</td>
+      <td>De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_dropletutils</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils</td>
+      <td>1.0.4</td>
+      <td>dropletutils-scripts</td>
+      <td>0.0.5</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1900</td>
+      <td>1901</td>
+      <td>412</td>
+      <td>413</td>
+      <td>609</td>
+      <td>609</td>
+      <td>131</td>
+      <td>131</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2509</td>
+      <td>2510</td>
+      <td>543</td>
+      <td>544</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dropletutils</td>
+      <td>dropletutils</td>
+      <td>DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data</td>
+      <td>dropletutils</td>
+      <td>dropletutils</td>
+      <td></td>
+      <td>DropletUtils</td>
+      <td>Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.</td>
+      <td>Loading, Community profiling</td>
+      <td>Gene expression, RNA-seq, Sequencing, Transcriptomics</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html</td>
+      <td>Single Cell, Sequence Analysis</td>
+      <td>dropletutils</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils</td>
+      <td>1.10.0</td>
+      <td>bioconductor-dropletutils</td>
+      <td>1.22.0</td>
+      <td></td>
+      <td>Sequencing, Transcriptomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4413</td>
+      <td>4442</td>
+      <td>430</td>
+      <td>431</td>
+      <td>4403</td>
+      <td>4403</td>
+      <td>255</td>
+      <td>255</td>
+      <td>1816</td>
+      <td>1816</td>
+      <td>33</td>
+      <td>33</td>
+      <td>10632</td>
+      <td>10661</td>
+      <td>718</td>
+      <td>719</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dwt_cor_ava_perclass</td>
+      <td>compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom</td>
+      <td>Compute P-values and Correlation Coefficients for Feature Occurrences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>dwt_cor_ava_perclass</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass</td>
+      <td>1.0.1</td>
+      <td>r-waveslim</td>
+      <td>1.7.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>136</td>
+      <td>141</td>
+      <td>8</td>
+      <td>11</td>
+      <td>136</td>
+      <td>141</td>
+      <td>8</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dwt_cor_avb_all</td>
+      <td>compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom</td>
+      <td>Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>dwt_cor_avb_all</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all</td>
+      <td>1.0.1</td>
+      <td>r-waveslim</td>
+      <td>1.7.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>124</td>
+      <td>124</td>
+      <td>7</td>
+      <td>7</td>
+      <td>124</td>
+      <td>124</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dwt_ivc_all</td>
+      <td>compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom</td>
+      <td>Compute P-values and Second Moments for Feature Occurrences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>dwt_ivc_all</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all</td>
+      <td>1.0.1</td>
+      <td>r-waveslim</td>
+      <td>1.7.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>123</td>
+      <td>5</td>
+      <td>7</td>
+      <td>121</td>
+      <td>123</td>
+      <td>5</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dwt_var_perclass</td>
+      <td>compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom</td>
+      <td>Compute P-values and Max Variances for Feature Occurrences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>dwt_var_perclass</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass</td>
+      <td>1.0.1</td>
+      <td>r-waveslim</td>
+      <td>1.7.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>131</td>
+      <td>132</td>
+      <td>7</td>
+      <td>8</td>
+      <td>131</td>
+      <td>132</td>
+      <td>7</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dwt_var_perfeature</td>
+      <td>dwt_var1</td>
+      <td>Wavelet variance using Discrete Wavelet Transfoms</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>dwt_var_perfeature</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature</td>
+      <td>1.0.2</td>
+      <td>r-bitops</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>30</td>
+      <td>36</td>
+      <td>2</td>
+      <td>4</td>
+      <td>11</td>
+      <td>11</td>
+      <td>4</td>
+      <td>4</td>
+      <td>206</td>
+      <td>220</td>
+      <td>6</td>
+      <td>7</td>
+      <td>247</td>
+      <td>267</td>
+      <td>12</td>
+      <td>15</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ear</td>
+      <td>make_ear</td>
+      <td>A tool to compile assembly reports and stastics from assembly pipeline</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ERGA-consortium/EARs/tree/main</td>
+      <td>Sequence Analysis, Assembly</td>
+      <td>erga_ear</td>
+      <td>bgruening</td>
+      <td>https://github.com/ERGA-consortium/EARs/tree/main</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/ear</td>
+      <td>24.08.26</td>
+      <td>reportlab</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>28</td>
+      <td>28</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>28</td>
+      <td>28</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ebi_tools</td>
+      <td>ebi_search_rest_results</td>
+      <td>Tools to query and download data from several EMBL-EBI databases</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.ebi.ac.uk/services/all</td>
+      <td>Web Services, Data Source</td>
+      <td>ebi_tools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools</td>
+      <td>0.1.1</td>
+      <td>six</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>276</td>
+      <td>406</td>
+      <td>133</td>
+      <td>163</td>
+      <td>1421</td>
+      <td>1421</td>
+      <td>547</td>
+      <td>547</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1697</td>
+      <td>1827</td>
+      <td>680</td>
+      <td>710</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ectyper</td>
+      <td>ectyper</td>
+      <td>EC-Typer - in silico serotyping of Escherichia coli species</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/ecoli_serotyping</td>
+      <td>Sequence Analysis</td>
+      <td>ectyper</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/ecoli_serotyping</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper</td>
+      <td>1.0.0</td>
+      <td>ectyper</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12996</td>
+      <td>12996</td>
+      <td>137</td>
+      <td>137</td>
+      <td>10</td>
+      <td>10</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13006</td>
+      <td>13006</td>
+      <td>138</td>
+      <td>138</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>edger</td>
+      <td>edger</td>
+      <td>Perform RNA-Seq differential expression analysis using edgeR pipeline</td>
+      <td>edger</td>
+      <td>edger</td>
+      <td></td>
+      <td>edgeR</td>
+      <td>Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.</td>
+      <td>Differential gene expression analysis</td>
+      <td>Genetics, RNA-Seq, ChIP-seq</td>
+      <td>To update</td>
+      <td>http://bioconductor.org/packages/release/bioc/html/edgeR.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>edger</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger</td>
+      <td>3.36.0</td>
+      <td>bioconductor-edger</td>
+      <td>4.0.16</td>
+      <td>Differential gene expression analysis</td>
+      <td>Genetics, RNA-Seq, ChIP-seq</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>19294</td>
+      <td>20905</td>
+      <td>2423</td>
+      <td>2618</td>
+      <td>48876</td>
+      <td>58723</td>
+      <td>6341</td>
+      <td>7527</td>
+      <td>8010</td>
+      <td>8705</td>
+      <td>846</td>
+      <td>892</td>
+      <td>76180</td>
+      <td>88333</td>
+      <td>9610</td>
+      <td>11037</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>edta</td>
+      <td>edta</td>
+      <td>The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations.</td>
+      <td>edta</td>
+      <td>edta</td>
+      <td></td>
+      <td>The Extensive de novo TE Annotator (EDTA)</td>
+      <td>The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.</td>
+      <td>De-novo assembly, Deisotoping, Genome annotation</td>
+      <td>Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms</td>
+      <td>To update</td>
+      <td>https://github.com/oushujun/EDTA</td>
+      <td>Variant Analysis</td>
+      <td>edta</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/edta</td>
+      <td></td>
+      <td>edta</td>
+      <td>2.2.0</td>
+      <td>De-novo assembly, Deisotoping, Genome annotation</td>
+      <td>Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4495</td>
+      <td>4495</td>
+      <td>111</td>
+      <td>111</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4495</td>
+      <td>4495</td>
+      <td>111</td>
+      <td>111</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>effectiveT3</td>
+      <td>effectiveT3</td>
+      <td>Find bacterial type III effectors in protein sequences</td>
+      <td>effectivet3</td>
+      <td>effectivet3</td>
+      <td></td>
+      <td>EffectiveT3</td>
+      <td>Prediction of putative Type-III secreted proteins.</td>
+      <td>Sequence classification</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>http://effectors.org</td>
+      <td>Sequence Analysis</td>
+      <td>effectivet3</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3</td>
+      <td>0.0.21</td>
+      <td>effectiveT3</td>
+      <td>1.0.1</td>
+      <td>Sequence classification</td>
+      <td>Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>eggnog_mapper</td>
+      <td>eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search</td>
+      <td>eggnog-mapper fast functional annotation of novel sequences</td>
+      <td>eggnog-mapper-v2</td>
+      <td>eggnog-mapper-v2</td>
+      <td></td>
+      <td>eggNOG-mapper v2</td>
+      <td>EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.</td>
+      <td>Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval</td>
+      <td>Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis</td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>eggnog_mapper</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper</td>
+      <td>2.1.8</td>
+      <td>eggnog-mapper</td>
+      <td>2.1.12</td>
+      <td>Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval</td>
+      <td>Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1</td>
+      <td>3</td>
+      <td>1</td>
+      <td>0</td>
+      <td>34432</td>
+      <td>34437</td>
+      <td>1149</td>
+      <td>1152</td>
+      <td>42</td>
+      <td>42</td>
+      <td>2</td>
+      <td>2</td>
+      <td>21027</td>
+      <td>21027</td>
+      <td>413</td>
+      <td>413</td>
+      <td>55501</td>
+      <td>55506</td>
+      <td>1564</td>
+      <td>1567</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>egsea</td>
+      <td>egsea</td>
+      <td>This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing</td>
+      <td>egsea</td>
+      <td>egsea</td>
+      <td></td>
+      <td>EGSEA</td>
+      <td>This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.</td>
+      <td>Gene set testing</td>
+      <td>Systems biology</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/EGSEA.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>egsea</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea</td>
+      <td>1.20.0</td>
+      <td>bioconductor-egsea</td>
+      <td>1.28.0</td>
+      <td>Gene set testing</td>
+      <td>Systems biology</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2809</td>
+      <td>3060</td>
+      <td>371</td>
+      <td>402</td>
+      <td>5179</td>
+      <td>5179</td>
+      <td>759</td>
+      <td>759</td>
+      <td>1931</td>
+      <td>1931</td>
+      <td>226</td>
+      <td>226</td>
+      <td>9919</td>
+      <td>10170</td>
+      <td>1356</td>
+      <td>1387</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>embl2fa</td>
+      <td>embl2fa</td>
+      <td>Converts EMBL flat format to fasta format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Text Manipulation</td>
+      <td>embl2fa</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa</td>
+      <td>0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>emboss_5</td>
+      <td>EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110</td>
+      <td>Galaxy wrappers for EMBOSS version 5.0.0 tools</td>
+      <td>emboss</td>
+      <td>emboss</td>
+      <td></td>
+      <td>EMBOSS</td>
+      <td>Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.</td>
+      <td>Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment</td>
+      <td>Molecular biology, Sequence analysis, Biology</td>
+      <td>To update</td>
+      <td>http://emboss.open-bio.org/</td>
+      <td>Sequence Analysis, Fasta Manipulation</td>
+      <td>emboss_5</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5</td>
+      <td>5.0.0</td>
+      <td>emboss</td>
+      <td>6.6.0</td>
+      <td>Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment</td>
+      <td>Molecular biology, Sequence analysis</td>
+      <td>107</td>
+      <td>107</td>
+      <td>107</td>
+      <td>0</td>
+      <td>107</td>
+      <td>107</td>
+      <td>107</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>107</td>
+      <td>0</td>
+      <td>0</td>
+      <td>107</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>107</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>107</td>
+      <td>107</td>
+      <td>107</td>
+      <td>0</td>
+      <td>143762</td>
+      <td>148864</td>
+      <td>4481</td>
+      <td>5039</td>
+      <td>151989</td>
+      <td>296028</td>
+      <td>13224</td>
+      <td>31140</td>
+      <td>24955</td>
+      <td>27001</td>
+      <td>2397</td>
+      <td>2705</td>
+      <td>320706</td>
+      <td>471893</td>
+      <td>20102</td>
+      <td>38884</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ena_upload</td>
+      <td>ena_upload</td>
+      <td>Submits experimental data and respective metadata to the European Nucleotide Archive (ENA).</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/usegalaxy-eu/ena-upload-cli</td>
+      <td>Data Export</td>
+      <td>ena_upload</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload</td>
+      <td>0.7.3</td>
+      <td>ena-upload-cli</td>
+      <td>0.7.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>366</td>
+      <td>366</td>
+      <td>41</td>
+      <td>41</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1302</td>
+      <td>1302</td>
+      <td>14</td>
+      <td>14</td>
+      <td>1668</td>
+      <td>1668</td>
+      <td>55</td>
+      <td>55</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>enasearch</td>
+      <td>enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data</td>
+      <td>A Python library for interacting with ENA's API</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bebatut/enasearch</td>
+      <td>Data Source</td>
+      <td>enasearch</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch</td>
+      <td></td>
+      <td>enasearch</td>
+      <td>0.2.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>1989</td>
+      <td>2302</td>
+      <td>367</td>
+      <td>453</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1989</td>
+      <td>2302</td>
+      <td>367</td>
+      <td>453</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>encyclopedia</td>
+      <td>encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut</td>
+      <td>Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/searleb/encyclopedia/wiki/Home</td>
+      <td>Proteomics</td>
+      <td>encyclopedia</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia</td>
+      <td>1.12.34</td>
+      <td>encyclopedia</td>
+      <td>2.12.30</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>4</td>
+      <td>7</td>
+      <td>0</td>
+      <td>2</td>
+      <td>4</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>738</td>
+      <td>738</td>
+      <td>98</td>
+      <td>98</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>42</td>
+      <td>42</td>
+      <td>4</td>
+      <td>4</td>
+      <td>781</td>
+      <td>781</td>
+      <td>103</td>
+      <td>103</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ensembl_vep</td>
+      <td>ensembl_vep</td>
+      <td>Ensembl VEP: Annotate VCFs with variant effect predictions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Ensembl/ensembl-vep</td>
+      <td>Variant Analysis</td>
+      <td>ensembl_vep</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep</td>
+      <td>112.0</td>
+      <td>ensembl-vep</td>
+      <td>112.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>171</td>
+      <td>171</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>171</td>
+      <td>171</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>eodie</td>
+      <td>eodie</td>
+      <td>Earth Observation Data Information Extractor</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://eodie.readthedocs.io/</td>
+      <td>Climate Analysis</td>
+      <td>eodie</td>
+      <td>climate</td>
+      <td>https://gitlab.com/eetun-tiimi/EODIE</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie</td>
+      <td>1.0.2</td>
+      <td>eodie</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45</td>
+      <td>45</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45</td>
+      <td>45</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>epicseg</td>
+      <td>epicseg_segment</td>
+      <td>EpiCSeg is a tool for conducting chromatin segmentation.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/lamortenera/epicseg</td>
+      <td>Epigenetics</td>
+      <td>epicseg</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/epicseg</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/epicseg</td>
+      <td>@VERSION_STRING@</td>
+      <td>epicseg</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>160</td>
+      <td>252</td>
+      <td>17</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>160</td>
+      <td>252</td>
+      <td>17</td>
+      <td>21</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>episcanpy</td>
+      <td>episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess</td>
+      <td>EpiScanpy – Epigenomics single cell analysis in python</td>
+      <td>episcanpy</td>
+      <td>episcanpy</td>
+      <td></td>
+      <td>epiScanpy</td>
+      <td>Epigenomics Single Cell Analysis in Python.</td>
+      <td>Enrichment analysis, Imputation</td>
+      <td>Epigenomics, Cell biology, DNA</td>
+      <td>To update</td>
+      <td>https://github.com/colomemaria/epiScanpy</td>
+      <td>Single Cell, Epigenetics</td>
+      <td>episcanpy</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy</td>
+      <td>0.3.2</td>
+      <td>episcanpy</td>
+      <td>0.4.0</td>
+      <td>Enrichment analysis, Imputation</td>
+      <td>Epigenomics, Cell biology, DNA</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>880</td>
+      <td>880</td>
+      <td>80</td>
+      <td>80</td>
+      <td>221</td>
+      <td>221</td>
+      <td>37</td>
+      <td>37</td>
+      <td>49</td>
+      <td>49</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1150</td>
+      <td>1150</td>
+      <td>120</td>
+      <td>120</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>essential_climate_variables</td>
+      <td>cds_essential_variability</td>
+      <td>Get Copernicus Essential Climate Variables for assessing climate variability</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview</td>
+      <td>Climate Analysis, Data Source</td>
+      <td>cds_essential_variability</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables</td>
+      <td>0.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>232</td>
+      <td>336</td>
+      <td>39</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>232</td>
+      <td>336</td>
+      <td>39</td>
+      <td>40</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ete</td>
+      <td>ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator</td>
+      <td>Analyse phylogenetic trees using the ETE Toolkit</td>
+      <td>ete</td>
+      <td>ete</td>
+      <td></td>
+      <td>ete</td>
+      <td>The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org</td>
+      <td>Phylogenetic analysis, Phylogenetic tree editing</td>
+      <td>Phylogenetics</td>
+      <td>To update</td>
+      <td>http://etetoolkit.org/</td>
+      <td>Phylogenetics</td>
+      <td>ete</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete</td>
+      <td>3.1.2</td>
+      <td>ete3</td>
+      <td>3.1.1</td>
+      <td>Phylogenetic tree editing</td>
+      <td>Phylogenetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>820</td>
+      <td>966</td>
+      <td>89</td>
+      <td>106</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>820</td>
+      <td>966</td>
+      <td>89</td>
+      <td>106</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>evidencemodeler</td>
+      <td>evidencemodeler</td>
+      <td>EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.</td>
+      <td>EvidenceModeler</td>
+      <td>EvidenceModeler</td>
+      <td></td>
+      <td>EvidenceModeler</td>
+      <td>The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.</td>
+      <td>Gene prediction</td>
+      <td>Gene expression, Gene structure</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file</td>
+      <td>Genome annotation</td>
+      <td>evidencemodeler</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler</td>
+      <td>2.1.0</td>
+      <td>evidencemodeler</td>
+      <td>2.1.0</td>
+      <td>Gene prediction</td>
+      <td>Gene expression, Gene structure</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>exomedepth</td>
+      <td>exomedepth</td>
+      <td>ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data</td>
+      <td>exomedepth</td>
+      <td>exomedepth</td>
+      <td></td>
+      <td>ExomeDepth</td>
+      <td>Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.</td>
+      <td>Sequence analysis, Variant calling, Genotyping, Copy number estimation</td>
+      <td>Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases</td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/package=ExomeDepth</td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>exomedepth</td>
+      <td>crs4</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth</td>
+      <td>1.1.0</td>
+      <td>r-exomedepth</td>
+      <td>1.1.16</td>
+      <td>Sequence analysis, Variant calling, Genotyping, Copy number estimation</td>
+      <td>Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>517</td>
+      <td>517</td>
+      <td>61</td>
+      <td>61</td>
+      <td>2995</td>
+      <td>2995</td>
+      <td>184</td>
+      <td>184</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3512</td>
+      <td>3512</td>
+      <td>245</td>
+      <td>245</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>exonerate</td>
+      <td>exonerate</td>
+      <td>Exonerate is a generic tool for pairwise sequence comparison.</td>
+      <td>exonerate</td>
+      <td>exonerate</td>
+      <td></td>
+      <td>Exonerate</td>
+      <td>A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.</td>
+      <td>Pairwise sequence alignment, Protein threading, Genome alignment</td>
+      <td>Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks</td>
+      <td>Up-to-date</td>
+      <td>https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate</td>
+      <td>Sequence Analysis</td>
+      <td>exonerate</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate</td>
+      <td>2.4.0</td>
+      <td>exonerate</td>
+      <td>2.4.0</td>
+      <td>Pairwise sequence alignment, Protein threading, Genome alignment</td>
+      <td>Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1030</td>
+      <td>1072</td>
+      <td>185</td>
+      <td>188</td>
+      <td>1058</td>
+      <td>1058</td>
+      <td>189</td>
+      <td>189</td>
+      <td>922</td>
+      <td>922</td>
+      <td>35</td>
+      <td>35</td>
+      <td>3010</td>
+      <td>3052</td>
+      <td>409</td>
+      <td>412</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>exparna</td>
+      <td>exparna</td>
+      <td>ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp</td>
+      <td>RNA</td>
+      <td>exparna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna</td>
+      <td>1.0.1</td>
+      <td>exparna</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>export2graphlan</td>
+      <td>export2graphlan</td>
+      <td>export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn</td>
+      <td>export2graphlan</td>
+      <td>export2graphlan</td>
+      <td></td>
+      <td>export2graphlan</td>
+      <td>export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.</td>
+      <td>Conversion</td>
+      <td>Taxonomy, Metabolomics, Biomarkers</td>
+      <td>To update</td>
+      <td>https://bitbucket.org/CibioCM/export2graphlan/overview</td>
+      <td>Metagenomics</td>
+      <td>export2graphlan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan</td>
+      <td>0.20</td>
+      <td>export2graphlan</td>
+      <td>0.22</td>
+      <td>Conversion</td>
+      <td>Taxonomy, Metabolomics, Biomarkers</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5396</td>
+      <td>5938</td>
+      <td>580</td>
+      <td>607</td>
+      <td>628</td>
+      <td>628</td>
+      <td>168</td>
+      <td>168</td>
+      <td>519</td>
+      <td>519</td>
+      <td>107</td>
+      <td>107</td>
+      <td>6543</td>
+      <td>7085</td>
+      <td>855</td>
+      <td>882</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>export_to_cluster</td>
+      <td>export_to_cluster</td>
+      <td>Export datasets to cluster</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/</td>
+      <td>Data Export</td>
+      <td>export_to_cluster</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster</td>
+      <td>0.0.2</td>
+      <td>EXPORT_DIR_PREFIX</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>express</td>
+      <td>express</td>
+      <td>Quantify the abundances of a set of target sequences from sampled subsequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>express</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/express</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/express</td>
+      <td>1.1.1</td>
+      <td>eXpress</td>
+      <td>1.5.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>278</td>
+      <td>337</td>
+      <td>34</td>
+      <td>45</td>
+      <td>0</td>
+      <td>1184</td>
+      <td>0</td>
+      <td>117</td>
+      <td>2402</td>
+      <td>2844</td>
+      <td>23</td>
+      <td>60</td>
+      <td>2680</td>
+      <td>4365</td>
+      <td>57</td>
+      <td>222</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>extract_genomic_dna</td>
+      <td>Extract genomic DNA 1</td>
+      <td>Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Genomic Interval Operations</td>
+      <td>extract_genomic_dna</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna</td>
+      <td>3.0.3+galaxy2</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9409</td>
+      <td>12735</td>
+      <td>813</td>
+      <td>923</td>
+      <td>20180</td>
+      <td>259099</td>
+      <td>2072</td>
+      <td>11791</td>
+      <td>168</td>
+      <td>611</td>
+      <td>20</td>
+      <td>63</td>
+      <td>29757</td>
+      <td>272445</td>
+      <td>2905</td>
+      <td>12777</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ez_histograms</td>
+      <td>ez_histograms</td>
+      <td>ggplot2 histograms and density plots</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/tidyverse/ggplot2</td>
+      <td>Visualization, Statistics</td>
+      <td>ez_histograms</td>
+      <td>artbio</td>
+      <td>https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms</td>
+      <td>3.4.4</td>
+      <td>r-ggplot2</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>falco</td>
+      <td>falco</td>
+      <td>A high throughput sequence QC analysis tool</td>
+      <td>falco</td>
+      <td>falco</td>
+      <td></td>
+      <td>Falco</td>
+      <td>A high-speed FastQC emulation for quality control of sequencing data.</td>
+      <td>Sequencing quality control, Visualisation, Read mapping</td>
+      <td>Workflows, Mapping, Imaging</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/smithlabcode/falco/</td>
+      <td>Sequence Analysis</td>
+      <td>falco</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco</td>
+      <td>1.2.4</td>
+      <td>falco</td>
+      <td>1.2.4</td>
+      <td>Sequencing quality control, Visualisation, Read mapping</td>
+      <td>Workflows, Mapping, Imaging</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4298</td>
+      <td>4298</td>
+      <td>34</td>
+      <td>34</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4298</td>
+      <td>4298</td>
+      <td>34</td>
+      <td>34</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fargene</td>
+      <td>fargene</td>
+      <td>fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )</td>
+      <td>fargene</td>
+      <td>fargene</td>
+      <td></td>
+      <td>fARGene</td>
+      <td>fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Metagenomics, Microbiology, Public health and epidemiology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/fannyhb/fargene</td>
+      <td>Sequence Analysis</td>
+      <td>fargene</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene</td>
+      <td>0.1</td>
+      <td>fargene</td>
+      <td>0.1</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Metagenomics, Microbiology, Public health and epidemiology</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>601</td>
+      <td>601</td>
+      <td>128</td>
+      <td>128</td>
+      <td>1165</td>
+      <td>1165</td>
+      <td>232</td>
+      <td>232</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1766</td>
+      <td>1766</td>
+      <td>360</td>
+      <td>360</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasplit</td>
+      <td>fasplit</td>
+      <td>faSplit is a tool to split a single FASTA file into several files</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Fasta Manipulation</td>
+      <td>ucsc_fasplit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit</td>
+      <td>469</td>
+      <td>ucsc-fasplit</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3278</td>
+      <td>3361</td>
+      <td>460</td>
+      <td>478</td>
+      <td>6144</td>
+      <td>6144</td>
+      <td>595</td>
+      <td>595</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>183</td>
+      <td>183</td>
+      <td>10561</td>
+      <td>10644</td>
+      <td>1238</td>
+      <td>1256</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta2bed</td>
+      <td>fasta2bed</td>
+      <td>Convert multiple fasta file into tabular bed file format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Sequence Analysis</td>
+      <td>fasta2bed</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed</td>
+      <td>1.0.0</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_clipping_histogram</td>
+      <td>cshl_fasta_clipping_histogram</td>
+      <td>Length Distribution chart</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Graphics, Statistics</td>
+      <td>fasta_clipping_histogram</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5191</td>
+      <td>5367</td>
+      <td>104</td>
+      <td>130</td>
+      <td>5191</td>
+      <td>5367</td>
+      <td>104</td>
+      <td>130</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_compute_length</td>
+      <td>fasta_compute_length</td>
+      <td>Compute sequence length</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length</td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_compute_length</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length</td>
+      <td>1.0.4</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>8547</td>
+      <td>9136</td>
+      <td>978</td>
+      <td>1129</td>
+      <td>17748</td>
+      <td>51150</td>
+      <td>1404</td>
+      <td>5670</td>
+      <td>4239</td>
+      <td>4404</td>
+      <td>162</td>
+      <td>190</td>
+      <td>30534</td>
+      <td>64690</td>
+      <td>2544</td>
+      <td>6989</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_concatenate_by_species</td>
+      <td>fasta_concatenate0</td>
+      <td>Concatenate FASTA alignment by species</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_concatenate_by_species</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species</td>
+      <td>0.0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>39695</td>
+      <td>39742</td>
+      <td>242</td>
+      <td>255</td>
+      <td>13660</td>
+      <td>19007</td>
+      <td>600</td>
+      <td>1398</td>
+      <td>1521</td>
+      <td>1603</td>
+      <td>92</td>
+      <td>112</td>
+      <td>54876</td>
+      <td>60352</td>
+      <td>934</td>
+      <td>1765</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_extract</td>
+      <td>fa-extract-sequence</td>
+      <td>extract single fasta from multiple fasta file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract</td>
+      <td>Sequence Analysis</td>
+      <td>fasta_extract</td>
+      <td>nml</td>
+      <td>https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract</td>
+      <td>1.1.0</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1286</td>
+      <td>1827</td>
+      <td>144</td>
+      <td>181</td>
+      <td>1296</td>
+      <td>1837</td>
+      <td>145</td>
+      <td>182</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_filter_by_id</td>
+      <td>fasta_filter_by_id</td>
+      <td>Filter FASTA sequences by ID (DEPRECATED)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id</td>
+      <td>Fasta Manipulation, Sequence Analysis, Text Manipulation</td>
+      <td>fasta_filter_by_id</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id</td>
+      <td>0.0.7</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_filter_by_length</td>
+      <td>fasta_filter_by_length</td>
+      <td>Filter sequences by length</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_filter_by_length</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length</td>
+      <td>1.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>47494</td>
+      <td>51924</td>
+      <td>889</td>
+      <td>997</td>
+      <td>50663</td>
+      <td>101663</td>
+      <td>1488</td>
+      <td>3742</td>
+      <td>3919</td>
+      <td>5601</td>
+      <td>241</td>
+      <td>276</td>
+      <td>102076</td>
+      <td>159188</td>
+      <td>2618</td>
+      <td>5015</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_formatter</td>
+      <td>cshl_fasta_formatter</td>
+      <td>FASTA Width formatter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_formatter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>5235</td>
+      <td>5486</td>
+      <td>237</td>
+      <td>288</td>
+      <td>4060</td>
+      <td>25609</td>
+      <td>480</td>
+      <td>2039</td>
+      <td>816</td>
+      <td>1093</td>
+      <td>73</td>
+      <td>89</td>
+      <td>10111</td>
+      <td>32188</td>
+      <td>790</td>
+      <td>2416</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_merge_files_and_filter_unique_sequences</td>
+      <td>fasta_merge_files_and_filter_unique_sequences</td>
+      <td>Concatenate FASTA database files together</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/</td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_merge_files_and_filter_unique_sequences</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences</td>
+      <td>1.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>30917</td>
+      <td>32191</td>
+      <td>1142</td>
+      <td>1257</td>
+      <td>36869</td>
+      <td>36869</td>
+      <td>1346</td>
+      <td>1346</td>
+      <td>5236</td>
+      <td>5236</td>
+      <td>230</td>
+      <td>230</td>
+      <td>73022</td>
+      <td>74296</td>
+      <td>2718</td>
+      <td>2833</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_nucleotide_changer</td>
+      <td>cshl_fasta_nucleotides_changer</td>
+      <td>RNA/DNA converter.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_nucleotide_changer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>497</td>
+      <td>808</td>
+      <td>71</td>
+      <td>108</td>
+      <td>2249</td>
+      <td>5479</td>
+      <td>216</td>
+      <td>703</td>
+      <td>415</td>
+      <td>437</td>
+      <td>18</td>
+      <td>20</td>
+      <td>3161</td>
+      <td>6724</td>
+      <td>305</td>
+      <td>831</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_nucleotide_color_plot</td>
+      <td>fasta_nucleotide_color_plot</td>
+      <td>Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot</td>
+      <td>Visualization</td>
+      <td>fasta_nucleotide_color_plot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot</td>
+      <td>1.0.1</td>
+      <td>openjdk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>164</td>
+      <td>179</td>
+      <td>42</td>
+      <td>47</td>
+      <td>758</td>
+      <td>905</td>
+      <td>128</td>
+      <td>170</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>922</td>
+      <td>1084</td>
+      <td>170</td>
+      <td>217</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_stats</td>
+      <td>fasta-stats</td>
+      <td>Display summary statistics for a fasta file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/</td>
+      <td>Sequence Analysis</td>
+      <td>fasta_stats</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats</td>
+      <td>2.0</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>43726</td>
+      <td>44512</td>
+      <td>3104</td>
+      <td>3259</td>
+      <td>19941</td>
+      <td>19941</td>
+      <td>3693</td>
+      <td>3693</td>
+      <td>16788</td>
+      <td>18589</td>
+      <td>2467</td>
+      <td>2650</td>
+      <td>80455</td>
+      <td>83042</td>
+      <td>9264</td>
+      <td>9602</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_to_tabular</td>
+      <td>fasta2tab</td>
+      <td>FASTA-to-Tabular converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_to_tabular</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular</td>
+      <td>1.1.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>108876</td>
+      <td>113638</td>
+      <td>1572</td>
+      <td>1793</td>
+      <td>82527</td>
+      <td>192112</td>
+      <td>2209</td>
+      <td>8565</td>
+      <td>5711</td>
+      <td>7649</td>
+      <td>275</td>
+      <td>334</td>
+      <td>197114</td>
+      <td>313399</td>
+      <td>4056</td>
+      <td>10692</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastani</td>
+      <td>fastani</td>
+      <td>Fast alignment-free computation of whole-genome Average Nucleotide Identity</td>
+      <td>fastani</td>
+      <td>fastani</td>
+      <td></td>
+      <td>FastANI</td>
+      <td>FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.</td>
+      <td>Genome alignment, Sequence similarity search</td>
+      <td>Microbiology, Genetic variation</td>
+      <td>To update</td>
+      <td>https://github.com/ParBLiSS/FastANI</td>
+      <td>Sequence Analysis</td>
+      <td>fastani</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani</td>
+      <td>1.3</td>
+      <td>fastani</td>
+      <td>1.34</td>
+      <td>Genome alignment, Sequence similarity search</td>
+      <td>Microbiology, Genetic variation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6685</td>
+      <td>6685</td>
+      <td>603</td>
+      <td>603</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6685</td>
+      <td>6685</td>
+      <td>603</td>
+      <td>603</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastg2protlib</td>
+      <td>fastg2protlib-peptides, fastg2protlib-validate</td>
+      <td>Generate FASTA from FASTG</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/fastg2protlib.git</td>
+      <td>Proteomics</td>
+      <td>fastg2protlib</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib</td>
+      <td>1.0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastk</td>
+      <td>fastk_fastk</td>
+      <td>FastK: A K-mer counter (for HQ assembly data sets)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/thegenemyers/FASTK</td>
+      <td>Assembly</td>
+      <td>fastk</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk</td>
+      <td>1.0.0</td>
+      <td>fastk</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>136</td>
+      <td>136</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>136</td>
+      <td>136</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastp</td>
+      <td>fastp</td>
+      <td>Fast all-in-one preprocessing for FASTQ files</td>
+      <td>fastp</td>
+      <td>fastp</td>
+      <td></td>
+      <td>fastp</td>
+      <td>A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.</td>
+      <td>Sequencing quality control, Sequence contamination filtering</td>
+      <td>Sequence analysis, Probes and primers</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/OpenGene/fastp</td>
+      <td>Sequence Analysis</td>
+      <td>fastp</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp</td>
+      <td>0.23.4</td>
+      <td>fastp</td>
+      <td>0.23.4</td>
+      <td>Sequence contamination filtering</td>
+      <td>Probes and primers</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1126086</td>
+      <td>1127111</td>
+      <td>6847</td>
+      <td>6909</td>
+      <td>422259</td>
+      <td>422259</td>
+      <td>10722</td>
+      <td>10722</td>
+      <td>76462</td>
+      <td>76462</td>
+      <td>2242</td>
+      <td>2242</td>
+      <td>1624807</td>
+      <td>1625832</td>
+      <td>19811</td>
+      <td>19873</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_combiner</td>
+      <td>fastq_combiner</td>
+      <td>Combine FASTA and QUAL into FASTQ</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation, Fasta Manipulation</td>
+      <td>fastq_combiner</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>8604</td>
+      <td>8799</td>
+      <td>215</td>
+      <td>240</td>
+      <td>54200</td>
+      <td>75329</td>
+      <td>919</td>
+      <td>2957</td>
+      <td>1562</td>
+      <td>1680</td>
+      <td>76</td>
+      <td>85</td>
+      <td>64366</td>
+      <td>85808</td>
+      <td>1210</td>
+      <td>3282</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_filter</td>
+      <td>fastq_filter</td>
+      <td>Filter FASTQ reads by quality score and length</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15582</td>
+      <td>18350</td>
+      <td>690</td>
+      <td>771</td>
+      <td>40489</td>
+      <td>121585</td>
+      <td>2715</td>
+      <td>9239</td>
+      <td>4657</td>
+      <td>5793</td>
+      <td>214</td>
+      <td>287</td>
+      <td>60728</td>
+      <td>145728</td>
+      <td>3619</td>
+      <td>10297</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_filter_by_id</td>
+      <td>fastq_filter_by_id</td>
+      <td>Filter FASTQ sequences by ID (DEPRECATED)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id</td>
+      <td>Fastq Manipulation, Sequence Analysis, Text Manipulation</td>
+      <td>fastq_filter_by_id</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id</td>
+      <td>0.0.7</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_groomer</td>
+      <td>fastq_groomer</td>
+      <td>Convert between various FASTQ quality formats.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_groomer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>92594</td>
+      <td>102535</td>
+      <td>2576</td>
+      <td>2995</td>
+      <td>179461</td>
+      <td>897457</td>
+      <td>9437</td>
+      <td>44701</td>
+      <td>15434</td>
+      <td>25533</td>
+      <td>664</td>
+      <td>1073</td>
+      <td>287489</td>
+      <td>1025525</td>
+      <td>12677</td>
+      <td>48769</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_info</td>
+      <td>fastq_info</td>
+      <td>FASTQ info allows to validate single or paired fastq files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/nunofonseca/fastq_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_info</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info</td>
+      <td>0.25.1</td>
+      <td>fastq_utils</td>
+      <td>0.25.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7560</td>
+      <td>7560</td>
+      <td>1266</td>
+      <td>1266</td>
+      <td>6539</td>
+      <td>6539</td>
+      <td>1581</td>
+      <td>1581</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14099</td>
+      <td>14099</td>
+      <td>2847</td>
+      <td>2847</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_manipulation</td>
+      <td>fastq_manipulation</td>
+      <td>Manipulate FASTQ reads on various attributes.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_manipulation</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2488</td>
+      <td>3132</td>
+      <td>215</td>
+      <td>267</td>
+      <td>6241</td>
+      <td>14508</td>
+      <td>834</td>
+      <td>2121</td>
+      <td>4121</td>
+      <td>4592</td>
+      <td>131</td>
+      <td>158</td>
+      <td>12850</td>
+      <td>22232</td>
+      <td>1180</td>
+      <td>2546</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_masker_by_quality</td>
+      <td>fastq_masker_by_quality</td>
+      <td>FASTQ Masker by quality score</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_masker_by_quality</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>234</td>
+      <td>249</td>
+      <td>43</td>
+      <td>44</td>
+      <td>2648</td>
+      <td>8092</td>
+      <td>288</td>
+      <td>983</td>
+      <td>442</td>
+      <td>466</td>
+      <td>12</td>
+      <td>17</td>
+      <td>3324</td>
+      <td>8807</td>
+      <td>343</td>
+      <td>1044</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_pair</td>
+      <td>fastq_pair</td>
+      <td>Paired-end fastq pairer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/linsalrob/fastq-pair</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_pair</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair</td>
+      <td>1.0+galaxy0</td>
+      <td>fastq-pair</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_pair_names</td>
+      <td>fastq_pair_names</td>
+      <td>Extract FASTQ paired read names</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names</td>
+      <td>Sequence Analysis</td>
+      <td>fastq_pair_names</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names</td>
+      <td>0.0.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_paired_end_deinterlacer</td>
+      <td>fastq_paired_end_deinterlacer</td>
+      <td>FASTQ de-interlacer on paired end reads.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_paired_end_deinterlacer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5873</td>
+      <td>8936</td>
+      <td>532</td>
+      <td>657</td>
+      <td>14738</td>
+      <td>20229</td>
+      <td>1889</td>
+      <td>2366</td>
+      <td>2316</td>
+      <td>2711</td>
+      <td>225</td>
+      <td>261</td>
+      <td>22927</td>
+      <td>31876</td>
+      <td>2646</td>
+      <td>3284</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_paired_end_interlacer</td>
+      <td>fastq_paired_end_interlacer</td>
+      <td>FASTQ interlacer on paired end reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_paired_end_interlacer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>18216</td>
+      <td>19573</td>
+      <td>2348</td>
+      <td>2492</td>
+      <td>23484</td>
+      <td>25936</td>
+      <td>3482</td>
+      <td>3851</td>
+      <td>6207</td>
+      <td>6551</td>
+      <td>1402</td>
+      <td>1442</td>
+      <td>47907</td>
+      <td>52060</td>
+      <td>7232</td>
+      <td>7785</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_paired_end_joiner</td>
+      <td>fastq_paired_end_joiner</td>
+      <td>FASTQ joiner on paired end reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_paired_end_joiner</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15628</td>
+      <td>17130</td>
+      <td>536</td>
+      <td>679</td>
+      <td>24157</td>
+      <td>58368</td>
+      <td>1954</td>
+      <td>5716</td>
+      <td>1941</td>
+      <td>2266</td>
+      <td>172</td>
+      <td>214</td>
+      <td>41726</td>
+      <td>77764</td>
+      <td>2662</td>
+      <td>6609</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_paired_end_splitter</td>
+      <td>fastq_paired_end_splitter</td>
+      <td>FASTQ splitter on joined paired end reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_paired_end_splitter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3169</td>
+      <td>3521</td>
+      <td>459</td>
+      <td>535</td>
+      <td>19309</td>
+      <td>30747</td>
+      <td>1410</td>
+      <td>3441</td>
+      <td>807</td>
+      <td>1023</td>
+      <td>219</td>
+      <td>247</td>
+      <td>23285</td>
+      <td>35291</td>
+      <td>2088</td>
+      <td>4223</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_paired_unpaired</td>
+      <td>fastq_paired_unpaired</td>
+      <td>Divide FASTQ file into paired and unpaired reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired</td>
+      <td>Sequence Analysis, Text Manipulation</td>
+      <td>fastq_paired_unpaired</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired</td>
+      <td>0.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_provider</td>
+      <td>fastq_provider</td>
+      <td>Retrieval and download of FASTQ files from ENA and other repositories such as HCA.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ebi-gene-expression-group/atlas-fastq-provider</td>
+      <td>Data Source, RNA, Transcriptomics</td>
+      <td>atlas_fastq_provider</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider</td>
+      <td>0.4.4</td>
+      <td>atlas-fastq-provider</td>
+      <td>0.4.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_quality_boxplot</td>
+      <td>cshl_fastq_quality_boxplot</td>
+      <td>Draw quality score boxplot</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fastq Manipulation, Graphics, Statistics</td>
+      <td>fastq_quality_boxplot</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1271</td>
+      <td>1393</td>
+      <td>131</td>
+      <td>176</td>
+      <td>12763</td>
+      <td>58819</td>
+      <td>2073</td>
+      <td>8850</td>
+      <td>430</td>
+      <td>479</td>
+      <td>32</td>
+      <td>51</td>
+      <td>14464</td>
+      <td>60691</td>
+      <td>2236</td>
+      <td>9077</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_quality_converter</td>
+      <td>cshl_fastq_quality_converter</td>
+      <td>Quality format converter (ASCII-Numeric)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_quality_converter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>335</td>
+      <td>352</td>
+      <td>44</td>
+      <td>47</td>
+      <td>1583</td>
+      <td>9696</td>
+      <td>269</td>
+      <td>2229</td>
+      <td>1131</td>
+      <td>1254</td>
+      <td>15</td>
+      <td>27</td>
+      <td>3049</td>
+      <td>11302</td>
+      <td>328</td>
+      <td>2303</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_quality_filter</td>
+      <td>cshl_fastq_quality_filter</td>
+      <td>Filter by quality</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_quality_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>17279</td>
+      <td>18386</td>
+      <td>3826</td>
+      <td>4062</td>
+      <td>55268</td>
+      <td>136888</td>
+      <td>6055</td>
+      <td>12590</td>
+      <td>7685</td>
+      <td>9356</td>
+      <td>1854</td>
+      <td>2043</td>
+      <td>80232</td>
+      <td>164630</td>
+      <td>11735</td>
+      <td>18695</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_quality_trimmer</td>
+      <td>cshl_fastq_quality_trimmer</td>
+      <td>FASTQ trimmer based on quality</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/agordon/fastx_toolkit</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_quality_trimmer</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer</td>
+      <td>0.0.14+galaxy0</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_stats</td>
+      <td>fastq_stats</td>
+      <td>FASTQ Summary Statistics by column</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_stats</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3858</td>
+      <td>4595</td>
+      <td>680</td>
+      <td>815</td>
+      <td>15213</td>
+      <td>81513</td>
+      <td>3159</td>
+      <td>14109</td>
+      <td>3855</td>
+      <td>4163</td>
+      <td>184</td>
+      <td>256</td>
+      <td>22926</td>
+      <td>90271</td>
+      <td>4023</td>
+      <td>15180</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_to_fasta</td>
+      <td>cshl_fastq_to_fasta</td>
+      <td>FASTQ to FASTA converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Convert Formats</td>
+      <td>fastq_to_fasta</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>36069</td>
+      <td>37805</td>
+      <td>1151</td>
+      <td>1234</td>
+      <td>45213</td>
+      <td>99852</td>
+      <td>2691</td>
+      <td>6370</td>
+      <td>8457</td>
+      <td>13335</td>
+      <td>408</td>
+      <td>609</td>
+      <td>89739</td>
+      <td>150992</td>
+      <td>4250</td>
+      <td>8213</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_to_tabular</td>
+      <td>fastq_to_tabular</td>
+      <td>FASTQ to Tabular converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_to_tabular</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>12895</td>
+      <td>14110</td>
+      <td>269</td>
+      <td>297</td>
+      <td>13315</td>
+      <td>30673</td>
+      <td>612</td>
+      <td>1810</td>
+      <td>5125</td>
+      <td>5373</td>
+      <td>64</td>
+      <td>87</td>
+      <td>31335</td>
+      <td>50156</td>
+      <td>945</td>
+      <td>2194</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_trimmer</td>
+      <td>fastq_trimmer</td>
+      <td>FASTQ Trimmer by quality</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_trimmer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>10114</td>
+      <td>11383</td>
+      <td>582</td>
+      <td>665</td>
+      <td>23906</td>
+      <td>92351</td>
+      <td>1986</td>
+      <td>8818</td>
+      <td>1588</td>
+      <td>2607</td>
+      <td>108</td>
+      <td>212</td>
+      <td>35608</td>
+      <td>106341</td>
+      <td>2676</td>
+      <td>9695</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_trimmer_by_quality</td>
+      <td>fastq_quality_trimmer</td>
+      <td>FASTQ Quality Trimmer by sliding window</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_trimmer_by_quality</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4881</td>
+      <td>6165</td>
+      <td>859</td>
+      <td>967</td>
+      <td>29458</td>
+      <td>99179</td>
+      <td>3455</td>
+      <td>11369</td>
+      <td>2171</td>
+      <td>2678</td>
+      <td>259</td>
+      <td>338</td>
+      <td>36510</td>
+      <td>108022</td>
+      <td>4573</td>
+      <td>12674</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_utils</td>
+      <td>fastq_filter_n, fastq_trim_poly_at</td>
+      <td>Set of tools for handling fastq files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/nunofonseca/fastq_utils</td>
+      <td>Transcriptomics, RNA</td>
+      <td>fastq_utils</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils</td>
+      <td>0.25.1+galaxy0</td>
+      <td>fastq_utils</td>
+      <td>0.25.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastqc</td>
+      <td>fastqc</td>
+      <td>Read QC reports using FastQC</td>
+      <td>fastqc</td>
+      <td>fastqc</td>
+      <td></td>
+      <td>FastQC</td>
+      <td>This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.</td>
+      <td>Sequence composition calculation, Sequencing quality control, Statistical calculation</td>
+      <td>Sequencing, Data quality management, Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.bioinformatics.babraham.ac.uk/projects/fastqc/</td>
+      <td>Fastq Manipulation</td>
+      <td>fastqc</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc</td>
+      <td>0.74+galaxy1</td>
+      <td>fastqc</td>
+      <td>0.12.1</td>
+      <td>Sequence composition calculation, Sequencing quality control, Statistical calculation</td>
+      <td>Sequencing, Data quality management, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1784056</td>
+      <td>1913280</td>
+      <td>41344</td>
+      <td>43940</td>
+      <td>2269843</td>
+      <td>3195869</td>
+      <td>90828</td>
+      <td>140008</td>
+      <td>410004</td>
+      <td>445555</td>
+      <td>14195</td>
+      <td>16026</td>
+      <td>4463903</td>
+      <td>5554704</td>
+      <td>146367</td>
+      <td>199974</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastqc_stats</td>
+      <td>FastQC_Summary</td>
+      <td>Summary multiple FastQC into a single tabular line report</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Sequence Analysis</td>
+      <td>fastqc_stats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats</td>
+      <td>1.2</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastqe</td>
+      <td>fastqe</td>
+      <td>FASTQE</td>
+      <td>fastqe</td>
+      <td>fastqe</td>
+      <td></td>
+      <td>FASTQE</td>
+      <td>Compute quality stats for FASTQ files and print those stats as emoji... for some reason.</td>
+      <td>Sequencing quality control</td>
+      <td>Sequence analysis, Sequencing</td>
+      <td>To update</td>
+      <td>https://fastqe.com/</td>
+      <td>Sequence Analysis</td>
+      <td>fastqe</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe</td>
+      <td>0.3.1+galaxy0</td>
+      <td>fastqe</td>
+      <td>0.3.1</td>
+      <td>Sequencing quality control</td>
+      <td>Sequence analysis, Sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5162</td>
+      <td>5162</td>
+      <td>2350</td>
+      <td>2350</td>
+      <td>10176</td>
+      <td>10176</td>
+      <td>4714</td>
+      <td>4714</td>
+      <td>2610</td>
+      <td>2610</td>
+      <td>991</td>
+      <td>991</td>
+      <td>17948</td>
+      <td>17948</td>
+      <td>8055</td>
+      <td>8055</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastqsolexa_to_fasta_qual</td>
+      <td>fastqsolexa_to_fasta_qual</td>
+      <td>FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats, Fastq Manipulation</td>
+      <td>fastqsolexa_to_fasta_qual</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastqtofasta</td>
+      <td>fastq_to_fasta_python</td>
+      <td>FASTQ to FASTA converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastqtofasta</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>208349</td>
+      <td>217568</td>
+      <td>3421</td>
+      <td>3732</td>
+      <td>131388</td>
+      <td>245005</td>
+      <td>5108</td>
+      <td>13227</td>
+      <td>18655</td>
+      <td>18655</td>
+      <td>679</td>
+      <td>679</td>
+      <td>358392</td>
+      <td>481228</td>
+      <td>9208</td>
+      <td>17638</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasttree</td>
+      <td>fasttree</td>
+      <td>FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL</td>
+      <td>fasttree</td>
+      <td>fasttree</td>
+      <td></td>
+      <td>FastTree</td>
+      <td>Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.</td>
+      <td>Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)</td>
+      <td>Phylogenetics, Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.microbesonline.org/fasttree/</td>
+      <td>Phylogenetics</td>
+      <td>fasttree</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree</td>
+      <td>2.1.10</td>
+      <td>fasttree</td>
+      <td>2.1.11</td>
+      <td></td>
+      <td>Phylogenetics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>65542</td>
+      <td>65631</td>
+      <td>1049</td>
+      <td>1071</td>
+      <td>25992</td>
+      <td>25992</td>
+      <td>2147</td>
+      <td>2147</td>
+      <td>6733</td>
+      <td>7339</td>
+      <td>649</td>
+      <td>745</td>
+      <td>98267</td>
+      <td>98962</td>
+      <td>3845</td>
+      <td>3963</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_artifacts_filter</td>
+      <td>cshl_fastx_artifacts_filter</td>
+      <td>Remove sequencing artifacts</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td>fastx_artifacts_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1769</td>
+      <td>2020</td>
+      <td>88</td>
+      <td>101</td>
+      <td>6948</td>
+      <td>24960</td>
+      <td>358</td>
+      <td>2424</td>
+      <td>623</td>
+      <td>998</td>
+      <td>32</td>
+      <td>50</td>
+      <td>9340</td>
+      <td>27978</td>
+      <td>478</td>
+      <td>2575</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_barcode_splitter</td>
+      <td>cshl_fastx_barcode_splitter</td>
+      <td>Barcode Splitter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td>fastx_barcode_splitter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>16957</td>
+      <td>18124</td>
+      <td>225</td>
+      <td>260</td>
+      <td>37001</td>
+      <td>89126</td>
+      <td>919</td>
+      <td>2720</td>
+      <td>863</td>
+      <td>989</td>
+      <td>56</td>
+      <td>68</td>
+      <td>54821</td>
+      <td>108239</td>
+      <td>1200</td>
+      <td>3048</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_clipper</td>
+      <td>cshl_fastx_clipper</td>
+      <td>Clip adapter sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td>fastx_clipper</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3140</td>
+      <td>3520</td>
+      <td>178</td>
+      <td>212</td>
+      <td>13975</td>
+      <td>117900</td>
+      <td>1198</td>
+      <td>6006</td>
+      <td>409</td>
+      <td>712</td>
+      <td>36</td>
+      <td>55</td>
+      <td>17524</td>
+      <td>122132</td>
+      <td>1412</td>
+      <td>6273</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_collapser</td>
+      <td>cshl_fastx_collapser</td>
+      <td>Collapse sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation</td>
+      <td>fastx_collapser</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>64187</td>
+      <td>67981</td>
+      <td>326</td>
+      <td>349</td>
+      <td>87477</td>
+      <td>185555</td>
+      <td>781</td>
+      <td>3067</td>
+      <td>16563</td>
+      <td>17125</td>
+      <td>58</td>
+      <td>78</td>
+      <td>168227</td>
+      <td>270661</td>
+      <td>1165</td>
+      <td>3494</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_nucleotides_distribution</td>
+      <td>cshl_fastx_nucleotides_distribution</td>
+      <td>Draw nucleotides distribution chart</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fastq Manipulation, Graphics</td>
+      <td>fastx_nucleotides_distribution</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>174</td>
+      <td>272</td>
+      <td>61</td>
+      <td>92</td>
+      <td>4295</td>
+      <td>25068</td>
+      <td>1056</td>
+      <td>4180</td>
+      <td>1127</td>
+      <td>1171</td>
+      <td>70</td>
+      <td>89</td>
+      <td>5596</td>
+      <td>26511</td>
+      <td>1187</td>
+      <td>4361</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_quality_statistics</td>
+      <td>cshl_fastx_quality_statistics</td>
+      <td>Compute quality statistics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fastq Manipulation, Statistics</td>
+      <td>fastx_quality_statistics</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2218</td>
+      <td>2344</td>
+      <td>168</td>
+      <td>206</td>
+      <td>20551</td>
+      <td>60032</td>
+      <td>3784</td>
+      <td>9866</td>
+      <td>2347</td>
+      <td>2460</td>
+      <td>234</td>
+      <td>256</td>
+      <td>25116</td>
+      <td>64836</td>
+      <td>4186</td>
+      <td>10328</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_renamer</td>
+      <td>cshl_fastx_renamer</td>
+      <td>Rename sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td>fastx_renamer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2364</td>
+      <td>2526</td>
+      <td>180</td>
+      <td>214</td>
+      <td>6572</td>
+      <td>11745</td>
+      <td>303</td>
+      <td>1024</td>
+      <td>462</td>
+      <td>696</td>
+      <td>49</td>
+      <td>64</td>
+      <td>9398</td>
+      <td>14967</td>
+      <td>532</td>
+      <td>1302</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_reverse_complement</td>
+      <td>cshl_fastx_reverse_complement</td>
+      <td>Reverse-Complement</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fastq Manipulation, Fasta Manipulation</td>
+      <td>fastx_reverse_complement</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>10707</td>
+      <td>12597</td>
+      <td>356</td>
+      <td>415</td>
+      <td>21568</td>
+      <td>67304</td>
+      <td>574</td>
+      <td>1527</td>
+      <td>719</td>
+      <td>861</td>
+      <td>61</td>
+      <td>78</td>
+      <td>32994</td>
+      <td>80762</td>
+      <td>991</td>
+      <td>2020</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_trimmer</td>
+      <td>cshl_fastx_trimmer</td>
+      <td>Trim sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td>fastx_trimmer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>13584</td>
+      <td>14557</td>
+      <td>550</td>
+      <td>641</td>
+      <td>123676</td>
+      <td>206733</td>
+      <td>2034</td>
+      <td>8390</td>
+      <td>2819</td>
+      <td>4757</td>
+      <td>229</td>
+      <td>267</td>
+      <td>140079</td>
+      <td>226047</td>
+      <td>2813</td>
+      <td>9298</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fates-emerald</td>
+      <td>ctsm_fates</td>
+      <td>EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api</td>
+      <td>Climate Analysis</td>
+      <td>ctsm_fates</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald</td>
+      <td>2.0</td>
+      <td>fates-emerald</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>264</td>
+      <td>264</td>
+      <td>69</td>
+      <td>69</td>
+      <td>34</td>
+      <td>34</td>
+      <td>11</td>
+      <td>11</td>
+      <td>103</td>
+      <td>103</td>
+      <td>1</td>
+      <td>1</td>
+      <td>401</td>
+      <td>401</td>
+      <td>81</td>
+      <td>81</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fatovcf</td>
+      <td>fatovcf</td>
+      <td>Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Convert Formats</td>
+      <td>ucsc_fatovcf</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf</td>
+      <td>448</td>
+      <td>ucsc-fatovcf</td>
+      <td>448</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>385</td>
+      <td>385</td>
+      <td>46</td>
+      <td>46</td>
+      <td>587</td>
+      <td>587</td>
+      <td>107</td>
+      <td>107</td>
+      <td>58</td>
+      <td>58</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1030</td>
+      <td>1030</td>
+      <td>158</td>
+      <td>158</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>feature_alignment</td>
+      <td>feature_alignment</td>
+      <td>TRIC integrates information from all available runs via a graph-based alignment strategy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>feature_alignment</td>
+      <td>galaxyp</td>
+      <td>https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment</td>
+      <td>0.11.0</td>
+      <td>msproteomicstools</td>
+      <td>0.11.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>featurecounter</td>
+      <td>featureCoverage1</td>
+      <td>Feature coverage</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>featurecounter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter</td>
+      <td>2.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>22308</td>
+      <td>22388</td>
+      <td>16</td>
+      <td>19</td>
+      <td>350</td>
+      <td>13711</td>
+      <td>54</td>
+      <td>349</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22658</td>
+      <td>36099</td>
+      <td>70</td>
+      <td>368</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>featurecounts</td>
+      <td>featurecounts</td>
+      <td>featureCounts counts the number of reads aligned to defined masked regions in a reference genome</td>
+      <td>featurecounts</td>
+      <td>featurecounts</td>
+      <td></td>
+      <td>FeatureCounts</td>
+      <td>featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.</td>
+      <td>Read summarisation, RNA-Seq quantification</td>
+      <td>RNA-Seq</td>
+      <td>To update</td>
+      <td>http://bioinf.wehi.edu.au/featureCounts</td>
+      <td>RNA, Transcriptomics, Sequence Analysis</td>
+      <td>featurecounts</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts</td>
+      <td>2.0.3</td>
+      <td>subread</td>
+      <td>2.0.6</td>
+      <td>Read summarisation, RNA-Seq quantification</td>
+      <td>RNA-Seq</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>740719</td>
+      <td>770524</td>
+      <td>11699</td>
+      <td>12547</td>
+      <td>643892</td>
+      <td>784396</td>
+      <td>23272</td>
+      <td>27598</td>
+      <td>66108</td>
+      <td>68867</td>
+      <td>2348</td>
+      <td>2463</td>
+      <td>1450719</td>
+      <td>1623787</td>
+      <td>37319</td>
+      <td>42608</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>feelnc</td>
+      <td>feelnc</td>
+      <td>Galaxy wrapper for FEELnc</td>
+      <td>feelnc</td>
+      <td>feelnc</td>
+      <td></td>
+      <td>FEELnc</td>
+      <td>A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.</td>
+      <td>Annotation, Classification</td>
+      <td>RNA-seq, Functional, regulatory and non-coding RNA</td>
+      <td>To update</td>
+      <td>https://github.com/tderrien/FEELnc</td>
+      <td>Sequence Analysis</td>
+      <td>feelnc</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc</td>
+      <td>0.2.1</td>
+      <td>feelnc</td>
+      <td>0.2</td>
+      <td>Annotation, Classification</td>
+      <td>Functional, regulatory and non-coding RNA</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1375</td>
+      <td>1500</td>
+      <td>95</td>
+      <td>99</td>
+      <td>797</td>
+      <td>797</td>
+      <td>116</td>
+      <td>116</td>
+      <td>59</td>
+      <td>59</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2231</td>
+      <td>2356</td>
+      <td>214</td>
+      <td>218</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>feelnc2asko</td>
+      <td>feelnc2asko</td>
+      <td>Convert FeelNC GTF to GFF3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/tderrien/FEELnc</td>
+      <td>Convert Formats</td>
+      <td>feelnc2asko</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko</td>
+      <td>0.1</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>feht</td>
+      <td>feht</td>
+      <td>Automatically identify makers predictive of groups.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Sequence Analysis</td>
+      <td>feht</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht</td>
+      <td>0.1.0</td>
+      <td>feht</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fermikit</td>
+      <td>fermi2, fermikit_variants</td>
+      <td>FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lh3/fermikit</td>
+      <td>Assembly, Variant Analysis</td>
+      <td>fermikit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit</td>
+      <td>r193</td>
+      <td>fermi2</td>
+      <td>r193</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fetch_fasta_from_ncbi</td>
+      <td>retrieve_fasta_from_NCBI</td>
+      <td>Fetch fasta sequences from NCBI using eutils wrappers</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Fasta Manipulation, Data Source</td>
+      <td>fetch_fasta_from_ncbi</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi</td>
+      <td>3.1.0</td>
+      <td>urllib3</td>
+      <td>1.12</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fgsea</td>
+      <td>fgsea</td>
+      <td>Perform gene set testing using fgsea</td>
+      <td>fgsea</td>
+      <td>fgsea</td>
+      <td></td>
+      <td>fgsea</td>
+      <td>The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.</td>
+      <td>Gene-set enrichment analysis</td>
+      <td>Genetics</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/fgsea.html</td>
+      <td>Visualization, Transcriptomics, Statistics</td>
+      <td>fgsea</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea</td>
+      <td>1.8.0+galaxy1</td>
+      <td>bioconductor-fgsea</td>
+      <td>1.28.0</td>
+      <td>Gene-set enrichment analysis</td>
+      <td>Genetics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5618</td>
+      <td>5820</td>
+      <td>582</td>
+      <td>607</td>
+      <td>21673</td>
+      <td>21673</td>
+      <td>938</td>
+      <td>938</td>
+      <td>869</td>
+      <td>869</td>
+      <td>110</td>
+      <td>110</td>
+      <td>28160</td>
+      <td>28362</td>
+      <td>1630</td>
+      <td>1655</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>file_manipulation</td>
+      <td>bg_uniq</td>
+      <td>This tool returns all unique lines from a tab-separated file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation</td>
+      <td>Text Manipulation</td>
+      <td>unique</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation</td>
+      <td>0.4</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6690</td>
+      <td>8818</td>
+      <td>554</td>
+      <td>612</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6690</td>
+      <td>8818</td>
+      <td>554</td>
+      <td>612</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_by_fasta_ids</td>
+      <td>filter_by_fasta_ids</td>
+      <td>Filter FASTA on the headers and/or the sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation, Proteomics</td>
+      <td>filter_by_fasta_ids</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids</td>
+      <td>2.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>26717</td>
+      <td>29932</td>
+      <td>1026</td>
+      <td>1072</td>
+      <td>42990</td>
+      <td>42990</td>
+      <td>1176</td>
+      <td>1176</td>
+      <td>9619</td>
+      <td>9619</td>
+      <td>230</td>
+      <td>230</td>
+      <td>79326</td>
+      <td>82541</td>
+      <td>2432</td>
+      <td>2478</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_compounds</td>
+      <td>filter_orgmet_anorg</td>
+      <td>Tool for filtering organometallics/anorganic compounds from a list of compounds.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools/</td>
+      <td>Metabolomics</td>
+      <td>filter_compounds</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds</td>
+      <td>3.1.1</td>
+      <td>openbabel</td>
+      <td>2.3.90dev7d621d9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_density</td>
+      <td>filterdensity</td>
+      <td>Filter out position based on distance between SNVs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>filter_density</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_spades_repeats</td>
+      <td>filter_spades_repeat</td>
+      <td>Remove short and repeat contigs/scaffolds</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools/</td>
+      <td>Assembly</td>
+      <td>filter_spades_repeats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools/</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats</td>
+      <td>1.0.1</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_stats</td>
+      <td>filterstat</td>
+      <td>SNVPhyl filter_stats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>filter_stats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_transcripts_via_tracking</td>
+      <td>filter_combined_via_tracking</td>
+      <td>Filter Combined Transcripts</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>filter_transcripts_via_tracking</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>23</td>
+      <td>24</td>
+      <td>9</td>
+      <td>10</td>
+      <td>62</td>
+      <td>635</td>
+      <td>26</td>
+      <td>241</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>87</td>
+      <td>661</td>
+      <td>37</td>
+      <td>253</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_vcf</td>
+      <td>filtervcf</td>
+      <td>SNVPhyl filter_vcf</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>filter_vcf</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filtlong</td>
+      <td>filtlong</td>
+      <td>Filtlong - Filtering long reads by quality</td>
+      <td>filtlong</td>
+      <td>filtlong</td>
+      <td></td>
+      <td>Filtlong</td>
+      <td>Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.</td>
+      <td>Filtering, Sequencing quality control</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/rrwick/Filtlong</td>
+      <td>Fastq Manipulation, Sequence Analysis</td>
+      <td>filtlong</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong</td>
+      <td>0.2.1</td>
+      <td>filtlong</td>
+      <td>0.2.1</td>
+      <td>Filtering, Sequencing quality control</td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>53310</td>
+      <td>53944</td>
+      <td>1499</td>
+      <td>1575</td>
+      <td>25043</td>
+      <td>25043</td>
+      <td>726</td>
+      <td>726</td>
+      <td>10824</td>
+      <td>10824</td>
+      <td>593</td>
+      <td>593</td>
+      <td>89177</td>
+      <td>89811</td>
+      <td>2818</td>
+      <td>2894</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>find_diag_hits</td>
+      <td>find_diag_hits</td>
+      <td>Find diagnostic hits</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Metagenomics</td>
+      <td>find_diag_hits</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits</td>
+      <td>1.0.0</td>
+      <td>taxonomy</td>
+      <td>0.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>62</td>
+      <td>70</td>
+      <td>10</td>
+      <td>12</td>
+      <td>3</td>
+      <td>1787</td>
+      <td>1</td>
+      <td>204</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>1857</td>
+      <td>11</td>
+      <td>216</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>find_repeats</td>
+      <td>findrepeat</td>
+      <td>Find repetitive regions on a reference genome using MUMMer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>find_repeats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>find_subsequences</td>
+      <td>bg_find_subsequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>find_subsequences</td>
+      <td>bgruening</td>
+      <td></td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences</td>
+      <td>0.3</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>554</td>
+      <td>784</td>
+      <td>69</td>
+      <td>79</td>
+      <td>2820</td>
+      <td>3047</td>
+      <td>323</td>
+      <td>361</td>
+      <td>20</td>
+      <td>20</td>
+      <td>1</td>
+      <td>1</td>
+      <td>3394</td>
+      <td>3851</td>
+      <td>393</td>
+      <td>441</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fisher_test</td>
+      <td>fishertest</td>
+      <td>Fisher's exact test on two-column hit lists.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Statistics</td>
+      <td>fishertest</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test</td>
+      <td>2.32.0+galaxy0</td>
+      <td>bioconductor-qvalue</td>
+      <td>2.34.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>flair</td>
+      <td>flair_collapse, flair_correct</td>
+      <td>FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/BrooksLabUCSC/flair</td>
+      <td>Nanopore</td>
+      <td>flair</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair</td>
+      <td>1.5</td>
+      <td>flair</td>
+      <td>2.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1985</td>
+      <td>1985</td>
+      <td>41</td>
+      <td>41</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1985</td>
+      <td>1985</td>
+      <td>41</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>flanking_features</td>
+      <td>flanking_features_1</td>
+      <td>Fetch closest non-overlapping feature for every interval</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>flanking_features</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features</td>
+      <td>4.0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>589</td>
+      <td>731</td>
+      <td>51</td>
+      <td>63</td>
+      <td>2445</td>
+      <td>32847</td>
+      <td>304</td>
+      <td>2549</td>
+      <td>1214</td>
+      <td>1294</td>
+      <td>15</td>
+      <td>22</td>
+      <td>4248</td>
+      <td>34872</td>
+      <td>370</td>
+      <td>2634</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>flash</td>
+      <td>flash</td>
+      <td>Fast Length Adjustment of SHort reads</td>
+      <td>flash</td>
+      <td>flash</td>
+      <td></td>
+      <td>FLASH</td>
+      <td>Identifies paired-end reads which overlap in the middle, converting them to single long reads</td>
+      <td>Read pre-processing, Sequence merging, Sequence assembly</td>
+      <td>Sequencing, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://ccb.jhu.edu/software/FLASH/</td>
+      <td>Assembly, Fastq Manipulation</td>
+      <td>flash</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash</td>
+      <td>1.2.11</td>
+      <td>flash</td>
+      <td>1.2.11</td>
+      <td>Read pre-processing, Sequence merging, Sequence assembly</td>
+      <td>Sequencing, Sequence assembly</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>22017</td>
+      <td>22304</td>
+      <td>239</td>
+      <td>255</td>
+      <td>9399</td>
+      <td>14886</td>
+      <td>462</td>
+      <td>709</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>31420</td>
+      <td>37194</td>
+      <td>702</td>
+      <td>965</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>flashlfq</td>
+      <td>flashlfq</td>
+      <td>FlashLFQ mass-spectrometry proteomics label-free quantification</td>
+      <td>flashlfq</td>
+      <td>flashlfq</td>
+      <td></td>
+      <td>FlashLFQ</td>
+      <td>FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.</td>
+      <td>Label-free quantification</td>
+      <td>Proteomics experiment, Proteomics</td>
+      <td>To update</td>
+      <td>https://github.com/smith-chem-wisc/FlashLFQ</td>
+      <td>Proteomics</td>
+      <td>flashlfq</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq</td>
+      <td>1.0.3.1</td>
+      <td>flashlfq</td>
+      <td>1.2.6</td>
+      <td>Label-free quantification</td>
+      <td>Proteomics experiment, Proteomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>661</td>
+      <td>715</td>
+      <td>52</td>
+      <td>54</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>167</td>
+      <td>167</td>
+      <td>15</td>
+      <td>15</td>
+      <td>828</td>
+      <td>882</td>
+      <td>67</td>
+      <td>69</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>flexynesis</td>
+      <td>flexynesis</td>
+      <td>This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BIMSBbioinfo/flexynesis/tree/main</td>
+      <td>Machine Learning, Statistics, Systems Biology</td>
+      <td>flexynesis</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis</td>
+      <td>0.2.10</td>
+      <td>flexynesis</td>
+      <td>0.2.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>flye</td>
+      <td>flye</td>
+      <td>Assembly of long and error-prone reads.</td>
+      <td>Flye</td>
+      <td>Flye</td>
+      <td></td>
+      <td>Flye</td>
+      <td>Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.</td>
+      <td>Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly</td>
+      <td>Sequence assembly, Metagenomics, Whole genome sequencing, Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/fenderglass/Flye/</td>
+      <td>Assembly</td>
+      <td>flye</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/flye</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/flye</td>
+      <td>2.9.5</td>
+      <td>flye</td>
+      <td>2.9.5</td>
+      <td>Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly</td>
+      <td>Sequence assembly, Metagenomics, Whole genome sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>32514</td>
+      <td>32675</td>
+      <td>3379</td>
+      <td>3422</td>
+      <td>19434</td>
+      <td>19434</td>
+      <td>2537</td>
+      <td>2537</td>
+      <td>9843</td>
+      <td>9843</td>
+      <td>1624</td>
+      <td>1624</td>
+      <td>61791</td>
+      <td>61952</td>
+      <td>7540</td>
+      <td>7583</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>footprint</td>
+      <td>footprint</td>
+      <td>Find transcription factor footprints</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/</td>
+      <td>Epigenetics</td>
+      <td>footprint</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/footprint</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/footprint</td>
+      <td>1.0.0</td>
+      <td>footprint</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>format_cd_hit_output</td>
+      <td>format_cd_hit_output</td>
+      <td>Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation</td>
+      <td>format_cd_hit_output</td>
+      <td>bebatut</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output</td>
+      <td>1.0.0+galaxy1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>189</td>
+      <td>203</td>
+      <td>57</td>
+      <td>60</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>189</td>
+      <td>203</td>
+      <td>57</td>
+      <td>60</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>format_metaphlan2_output</td>
+      <td>format_metaphlan2_output</td>
+      <td>Format MetaPhlAn2 output to extract abundance at different taxonomic levels</td>
+      <td>format_metaphlan2_output</td>
+      <td>format_metaphlan2_output</td>
+      <td></td>
+      <td>Format metaphlan2 output</td>
+      <td>This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).</td>
+      <td>Formatting</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>To update</td>
+      <td></td>
+      <td>Metagenomics</td>
+      <td>format_metaphlan2_output</td>
+      <td>bebatut</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td>Formatting</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5940</td>
+      <td>6474</td>
+      <td>558</td>
+      <td>608</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5940</td>
+      <td>6474</td>
+      <td>558</td>
+      <td>608</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fraggenescan</td>
+      <td>fraggenescan</td>
+      <td>Tool for finding (fragmented) genes in short read</td>
+      <td>fraggenescan</td>
+      <td>fraggenescan</td>
+      <td></td>
+      <td>FragGeneScan</td>
+      <td>Application for finding (fragmented) genes in short reads</td>
+      <td>Gene prediction</td>
+      <td>Genetics, Sequence analysis</td>
+      <td>To update</td>
+      <td>https://sourceforge.net/projects/fraggenescan/</td>
+      <td>Sequence Analysis</td>
+      <td>fraggenescan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan</td>
+      <td></td>
+      <td>fraggenescan</td>
+      <td>1.31</td>
+      <td>Gene prediction</td>
+      <td>Genetics, Sequence analysis</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1257</td>
+      <td>1450</td>
+      <td>150</td>
+      <td>162</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1052</td>
+      <td>1052</td>
+      <td>45</td>
+      <td>45</td>
+      <td>2309</td>
+      <td>2502</td>
+      <td>195</td>
+      <td>207</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fragpipe</td>
+      <td>fragpipe</td>
+      <td>Data analysis for mass spectrometry-based proteomics.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://fragpipe.nesvilab.org/</td>
+      <td>Proteomics</td>
+      <td>fragpipe</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe</td>
+      <td>20.0</td>
+      <td>fragpipe</td>
+      <td>20.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>64</td>
+      <td>64</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>64</td>
+      <td>64</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>free_energy</td>
+      <td></td>
+      <td>Free energy tools of BRIDGE.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>freeenergy</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>freebayes</td>
+      <td>freebayes, bamleftalign</td>
+      <td>Galaxy Freebayes Bayesian genetic variant detector tool</td>
+      <td>freebayes</td>
+      <td>freebayes</td>
+      <td></td>
+      <td>FreeBayes</td>
+      <td>Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.</td>
+      <td>Variant calling, Statistical calculation</td>
+      <td>Genomics, Genetic variation, Rare diseases</td>
+      <td>To update</td>
+      <td>https://github.com/ekg/freebayes</td>
+      <td>Variant Analysis</td>
+      <td>freebayes</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes</td>
+      <td>1.3.6</td>
+      <td>freebayes</td>
+      <td>1.3.8</td>
+      <td>Variant calling, Statistical calculation</td>
+      <td>Genomics, Genetic variation, Rare diseases</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>149715</td>
+      <td>171093</td>
+      <td>8158</td>
+      <td>8794</td>
+      <td>144708</td>
+      <td>256315</td>
+      <td>15996</td>
+      <td>25107</td>
+      <td>19156</td>
+      <td>21936</td>
+      <td>2251</td>
+      <td>2571</td>
+      <td>313579</td>
+      <td>449344</td>
+      <td>26405</td>
+      <td>36472</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>freec</td>
+      <td>control_freec</td>
+      <td>Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.</td>
+      <td>freec</td>
+      <td>freec</td>
+      <td></td>
+      <td>FREEC</td>
+      <td>A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.</td>
+      <td>Copy number estimation, Variant calling, Genome alignment</td>
+      <td>DNA structural variation, Oncology, Human genetics, Data mining</td>
+      <td>To update</td>
+      <td>http://boevalab.inf.ethz.ch/FREEC/</td>
+      <td>Variant Analysis</td>
+      <td>control_freec</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec</td>
+      <td>11.6</td>
+      <td>gawk</td>
+      <td></td>
+      <td>Copy number estimation, Variant calling, Genome alignment</td>
+      <td>Oncology, Human genetics, Data mining</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>748</td>
+      <td>748</td>
+      <td>91</td>
+      <td>91</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1</td>
+      <td>1</td>
+      <td>760</td>
+      <td>760</td>
+      <td>92</td>
+      <td>92</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>freyja</td>
+      <td>freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants</td>
+      <td>lineage abundances estimation</td>
+      <td>freyja</td>
+      <td>freyja</td>
+      <td></td>
+      <td>Freyja</td>
+      <td>Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset</td>
+      <td>RNA-Seq quantification</td>
+      <td>Metagenomics</td>
+      <td>To update</td>
+      <td>https://github.com/andersen-lab/Freyja</td>
+      <td>Metagenomics, Sequence Analysis</td>
+      <td>freyja</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja</td>
+      <td>1.4.4</td>
+      <td>freyja</td>
+      <td>1.5.1</td>
+      <td>RNA-Seq quantification</td>
+      <td>Metagenomics</td>
+      <td>2</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21757</td>
+      <td>21757</td>
+      <td>101</td>
+      <td>101</td>
+      <td>217</td>
+      <td>217</td>
+      <td>21</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21974</td>
+      <td>21974</td>
+      <td>122</td>
+      <td>122</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>frogs</td>
+      <td>FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom</td>
+      <td>Suite for metabarcoding analysis</td>
+      <td>frogs</td>
+      <td>frogs</td>
+      <td></td>
+      <td>FROGS</td>
+      <td>The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing</td>
+      <td>To update</td>
+      <td>http://frogs.toulouse.inrae.fr/</td>
+      <td>Metagenomics</td>
+      <td>frogs</td>
+      <td>frogs</td>
+      <td>https://github.com/geraldinepascal/FROGS-wrappers/</td>
+      <td>https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs</td>
+      <td>4.1.0</td>
+      <td>frogs</td>
+      <td>5.0.0</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fromHicupToJuicebox</td>
+      <td>fromHicupToJuicebox</td>
+      <td>Convert the output of hicup (as sam or bam) to the input of juicebox.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Epigenetics</td>
+      <td>from_hicup_to_juicebox</td>
+      <td>lldelisle</td>
+      <td></td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox</td>
+      <td>0.0.2</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fromgtfTobed12</td>
+      <td>fromgtfTobed12</td>
+      <td>Convert GTF files to BED12 format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pythonhosted.org/gffutils/contents.html</td>
+      <td>Convert Formats</td>
+      <td>fromgtftobed12</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12</td>
+      <td>0.11.1+galaxy1</td>
+      <td>gffutils</td>
+      <td>0.13</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fsd</td>
+      <td>fsd, fsd_beforevsafter, fsd_regions, td</td>
+      <td>Tool that plots a histogram of sizes of read families</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics</td>
+      <td>duplex_family_size_distribution</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd</td>
+      <td>1.0.2</td>
+      <td>matplotlib</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>578</td>
+      <td>578</td>
+      <td>34</td>
+      <td>34</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>578</td>
+      <td>578</td>
+      <td>34</td>
+      <td>34</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>funannotate</td>
+      <td>funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort</td>
+      <td>Funannotate is a genome prediction, annotation, and comparison software package.</td>
+      <td>funannotate</td>
+      <td>funannotate</td>
+      <td></td>
+      <td>funannotate</td>
+      <td>funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).</td>
+      <td>Genome annotation</td>
+      <td>Genomics</td>
+      <td>To update</td>
+      <td>https://funannotate.readthedocs.io</td>
+      <td>Genome annotation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate</td>
+      <td>1.8.15</td>
+      <td></td>
+      <td></td>
+      <td>Genome annotation</td>
+      <td>Genomics</td>
+      <td>3</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>3</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8648</td>
+      <td>8648</td>
+      <td>1408</td>
+      <td>1408</td>
+      <td>32</td>
+      <td>32</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6406</td>
+      <td>6406</td>
+      <td>597</td>
+      <td>597</td>
+      <td>15086</td>
+      <td>15086</td>
+      <td>2011</td>
+      <td>2011</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>garnett</td>
+      <td>garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file</td>
+      <td>De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_garnett</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett</td>
+      <td>0.2.8</td>
+      <td>garnett-cli</td>
+      <td>0.0.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gatk4</td>
+      <td>filtermutectcalls, mergemutectstats, mutect2</td>
+      <td>Find somatic variations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>gatk4</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4</td>
+      <td>4.1.7.0</td>
+      <td>gatk4</td>
+      <td>4.5.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gatk4</td>
+      <td>gatk4_mutect2</td>
+      <td>A Galaxy wrapper for Mutect2 from GATK</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://software.broadinstitute.org/gatk/gatk4</td>
+      <td>Variant Analysis</td>
+      <td>gatk4_mutect2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4</td>
+      <td>4.1.7.0</td>
+      <td>gatk4</td>
+      <td>4.5.0.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3463</td>
+      <td>3463</td>
+      <td>452</td>
+      <td>452</td>
+      <td>9040</td>
+      <td>9040</td>
+      <td>1639</td>
+      <td>1639</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12503</td>
+      <td>12503</td>
+      <td>2091</td>
+      <td>2091</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gblocks</td>
+      <td>gblocks</td>
+      <td>Gblocks</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://molevol.cmima.csic.es/castresana/Gblocks.html</td>
+      <td>Sequence Analysis</td>
+      <td>gblocks</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks</td>
+      <td>0.91b</td>
+      <td>gblocks</td>
+      <td>0.91b</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>466</td>
+      <td>466</td>
+      <td>62</td>
+      <td>62</td>
+      <td>466</td>
+      <td>466</td>
+      <td>62</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gc_derivatization</td>
+      <td>gc_derivatization</td>
+      <td>In silico derivatization for GC.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/gc-meox-tms</td>
+      <td>Metabolomics</td>
+      <td>gc_derivatization</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization</td>
+      <td>1.0.1</td>
+      <td>gc-meox-tms</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gcms2isocor</td>
+      <td>gcms2isocor</td>
+      <td>Conversion from GCMS PostRun Analysis to Isocor</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Metabolomics</td>
+      <td>gcms2isocor</td>
+      <td>genouest</td>
+      <td></td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor</td>
+      <td>0.1.0</td>
+      <td>openjdk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gcms2isocor</td>
+      <td>gcms2isocor</td>
+      <td>Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/p2m2/p2m2tools</td>
+      <td>Metabolomics</td>
+      <td>gcms2isocor</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor</td>
+      <td>0.2.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gdal</td>
+      <td>gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo</td>
+      <td>Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.gdal.org</td>
+      <td>Ecology</td>
+      <td>gdal</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal</td>
+      <td>3.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>1409</td>
+      <td>1498</td>
+      <td>39</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1409</td>
+      <td>1498</td>
+      <td>39</td>
+      <td>42</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gdcwebapp</td>
+      <td>data_source_gdcwebapp</td>
+      <td>GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://bioinf.iasi.cnr.it/gdcwebapp/</td>
+      <td>Data Source, Convert Formats</td>
+      <td>gdcwebapp</td>
+      <td>iuc</td>
+      <td>https://github.com/fabio-cumbo/GDCWebApp4Galaxy</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp</td>
+      <td>1.0.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gecko</td>
+      <td>gecko</td>
+      <td>Ungapped genome comparison</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/otorreno/gecko</td>
+      <td>Sequence Analysis</td>
+      <td>gecko</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko</td>
+      <td>1.2</td>
+      <td>gecko</td>
+      <td>1.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>723</td>
+      <td>723</td>
+      <td>235</td>
+      <td>235</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>786</td>
+      <td>786</td>
+      <td>95</td>
+      <td>95</td>
+      <td>1509</td>
+      <td>1509</td>
+      <td>330</td>
+      <td>330</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gemini</td>
+      <td>gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@</td>
+      <td>GEMINI: a flexible framework for exploring genome variation</td>
+      <td>gemini</td>
+      <td>gemini</td>
+      <td></td>
+      <td>GEMINI</td>
+      <td>GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.</td>
+      <td>Sequence analysis, Genetic variation analysis</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/arq5x/gemini</td>
+      <td>Sequence Analysis, Next Gen Mappers</td>
+      <td>gemini</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini</td>
+      <td>0.20.1</td>
+      <td>gemini</td>
+      <td>0.30.2</td>
+      <td>Sequence analysis, Genetic variation analysis</td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>4967</td>
+      <td>5475</td>
+      <td>1863</td>
+      <td>1992</td>
+      <td>992</td>
+      <td>1118</td>
+      <td>279</td>
+      <td>370</td>
+      <td>3756</td>
+      <td>3811</td>
+      <td>423</td>
+      <td>425</td>
+      <td>9715</td>
+      <td>10404</td>
+      <td>2565</td>
+      <td>2787</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genebed_maf_to_fasta</td>
+      <td>GeneBed_Maf_Fasta2</td>
+      <td>Stitch gene blocks given a set of coding exon intervals</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/</td>
+      <td>Genomic Interval Operations</td>
+      <td>genebed_maf_to_fasta</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta</td>
+      <td>1.0.1+galaxy0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>2</td>
+      <td>2</td>
+      <td>221</td>
+      <td>2905</td>
+      <td>23</td>
+      <td>279</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>225</td>
+      <td>2909</td>
+      <td>25</td>
+      <td>281</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genehunter_modscore</td>
+      <td>genehunter_modscore</td>
+      <td>Maximised LOD score pedigree analysis utility</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1</td>
+      <td>Variant Analysis</td>
+      <td>genehunter_modscore</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore</td>
+      <td>3.0.0</td>
+      <td>ghm</td>
+      <td>3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>geneiobio</td>
+      <td>gene_iobio_display_generation_iframe</td>
+      <td>Gene.iobio is an interactive tool for variant and trio analysis.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/iobio/gene.iobio</td>
+      <td>Sequence Analysis</td>
+      <td>geneiobio</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio</td>
+      <td>4.7.1+galaxy1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>101</td>
+      <td>101</td>
+      <td>25</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59</td>
+      <td>59</td>
+      <td>6</td>
+      <td>6</td>
+      <td>160</td>
+      <td>160</td>
+      <td>31</td>
+      <td>31</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genenotebook</td>
+      <td>genenotebook_build</td>
+      <td>Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://genenotebook.github.io</td>
+      <td>Web Services</td>
+      <td></td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook</td>
+      <td>0.4.16</td>
+      <td>genoboo</td>
+      <td>0.4.16</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>generate_pc_lda_matrix</td>
+      <td>generate_matrix_for_pca_and_lda1</td>
+      <td>Generate a Matrix for using PC and LDA</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>generate_pc_lda_matrix</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>115</td>
+      <td>124</td>
+      <td>29</td>
+      <td>30</td>
+      <td>518</td>
+      <td>1029</td>
+      <td>102</td>
+      <td>261</td>
+      <td>184</td>
+      <td>198</td>
+      <td>14</td>
+      <td>17</td>
+      <td>817</td>
+      <td>1351</td>
+      <td>145</td>
+      <td>308</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genetrack</td>
+      <td>genetrack</td>
+      <td>Contains a tool that separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>ChIP-seq</td>
+      <td>genetrack</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack</td>
+      <td></td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>445</td>
+      <td>660</td>
+      <td>104</td>
+      <td>197</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>445</td>
+      <td>660</td>
+      <td>104</td>
+      <td>197</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genform</td>
+      <td>genform</td>
+      <td>genform: generation of molecular formulas by high-resolution MS and MS/MS data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://sourceforge.net/projects/genform/</td>
+      <td>Metabolomics</td>
+      <td>genform</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform</td>
+      <td></td>
+      <td>genform</td>
+      <td>r8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>68</td>
+      <td>68</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>68</td>
+      <td>68</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genomad</td>
+      <td>genomad_end_to_end</td>
+      <td>Identify virus and plasmid genomes from nucleotide sequences</td>
+      <td>genomad</td>
+      <td>genomad</td>
+      <td></td>
+      <td>geNomad</td>
+      <td>geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.</td>
+      <td>Sequence annotation, Taxonomic classification</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/apcamargo/genomad/</td>
+      <td>Metagenomics</td>
+      <td>genomad</td>
+      <td>ufz</td>
+      <td>https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad</td>
+      <td>1.8.0</td>
+      <td>genomad</td>
+      <td>1.8.1</td>
+      <td>Sequence annotation, Taxonomic classification</td>
+      <td>Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genomescope</td>
+      <td>genomescope</td>
+      <td>Analyze unassembled short reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tbenavi1/genomescope2.0</td>
+      <td>Statistics</td>
+      <td>genomescope</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope</td>
+      <td>2.0.1</td>
+      <td>genomescope2</td>
+      <td>2.0.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3181</td>
+      <td>3181</td>
+      <td>665</td>
+      <td>665</td>
+      <td>2112</td>
+      <td>2112</td>
+      <td>435</td>
+      <td>435</td>
+      <td>1622</td>
+      <td>1622</td>
+      <td>148</td>
+      <td>148</td>
+      <td>6915</td>
+      <td>6915</td>
+      <td>1248</td>
+      <td>1248</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genomic_super_signature</td>
+      <td>genomic_super_signature</td>
+      <td>Interpretation of RNAseq experiments through robust, efficient comparison to public databases</td>
+      <td>genomicsupersignature</td>
+      <td>genomicsupersignature</td>
+      <td></td>
+      <td>GenomicSuperSignature</td>
+      <td>GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.</td>
+      <td>Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction</td>
+      <td>RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment</td>
+      <td>To update</td>
+      <td>https://github.com/shbrief/GenomicSuperSignature</td>
+      <td>Sequence Analysis, RNA, Transcriptomics</td>
+      <td>genomic_super_signature</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature</td>
+      <td>1.2.0</td>
+      <td>bioconductor-genomicsupersignature</td>
+      <td>1.10.0</td>
+      <td>Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction</td>
+      <td>RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>47</td>
+      <td>47</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>47</td>
+      <td>47</td>
+      <td>13</td>
+      <td>13</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genrich</td>
+      <td>genrich</td>
+      <td>Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/jsh58/Genrich</td>
+      <td>ChIP-seq</td>
+      <td>genrich</td>
+      <td>iuc</td>
+      <td>https://github.com/jsh58/Genrich</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich</td>
+      <td>0.5+galaxy2</td>
+      <td>genrich</td>
+      <td>0.6.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3534</td>
+      <td>3577</td>
+      <td>402</td>
+      <td>405</td>
+      <td>2840</td>
+      <td>2840</td>
+      <td>419</td>
+      <td>419</td>
+      <td>571</td>
+      <td>571</td>
+      <td>31</td>
+      <td>31</td>
+      <td>6945</td>
+      <td>6988</td>
+      <td>852</td>
+      <td>855</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>getTn5ExtendedCoverage</td>
+      <td>getTn5ExtendedCoverage</td>
+      <td>Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Epigenetics</td>
+      <td>gettn5extendedcoverage</td>
+      <td>lldelisle</td>
+      <td></td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage</td>
+      <td>0.0.2</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>get_flanks</td>
+      <td>get_flanks1</td>
+      <td>Get flanks returns flanking region/s for every gene</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>get_flanks</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3768</td>
+      <td>325011</td>
+      <td>1462</td>
+      <td>2044</td>
+      <td>9350</td>
+      <td>242043</td>
+      <td>2201</td>
+      <td>6583</td>
+      <td>787</td>
+      <td>1070</td>
+      <td>119</td>
+      <td>146</td>
+      <td>13905</td>
+      <td>568124</td>
+      <td>3782</td>
+      <td>8773</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>get_hrun</td>
+      <td>get_hrun</td>
+      <td>Annotate indel variants with homopolymer context</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun</td>
+      <td>Variant Analysis</td>
+      <td>get_hrun</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun</td>
+      <td>0.5.9.2</td>
+      <td>pyfaidx</td>
+      <td>0.8.1.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>get_orfs_or_cdss</td>
+      <td>get_orfs_or_cdss</td>
+      <td>Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss</td>
+      <td>Sequence Analysis</td>
+      <td>get_orfs_or_cdss</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss</td>
+      <td>0.2.3</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>746</td>
+      <td>746</td>
+      <td>136</td>
+      <td>136</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1504</td>
+      <td>1504</td>
+      <td>244</td>
+      <td>244</td>
+      <td>2250</td>
+      <td>2250</td>
+      <td>380</td>
+      <td>380</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>get_pairs</td>
+      <td>get_pairs</td>
+      <td>Separate paired and unpaired reads from two fastq files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fastq Manipulation</td>
+      <td>get_pairs</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs</td>
+      <td>0.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>get_reference_fasta</td>
+      <td>get_fasta_reference</td>
+      <td>Obtain reference genome sequence.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Data Source, Fasta Manipulation</td>
+      <td>get_reference_fasta</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta</td>
+      <td>0.3.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>getindelrates_3way</td>
+      <td>indelRates_3way</td>
+      <td>Estimate Indel Rates for 3-way alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>getindelrates_3way</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>290</td>
+      <td>20</td>
+      <td>86</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>290</td>
+      <td>20</td>
+      <td>86</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>getindels_2way</td>
+      <td>getIndels_2way</td>
+      <td>Fetch Indels from pairwise alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>getindels_2way</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way</td>
+      <td>1.0.0</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>74</td>
+      <td>237</td>
+      <td>24</td>
+      <td>61</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>74</td>
+      <td>237</td>
+      <td>24</td>
+      <td>61</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>getmlst</td>
+      <td>getmlst</td>
+      <td>Download MLST datasets by species from pubmlst.org</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>getmlst</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst</td>
+      <td>0.1.4.1</td>
+      <td>srst2</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>getorganelle</td>
+      <td>get_annotated_regions_from_gb, get_organelle_from_reads</td>
+      <td>GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.</td>
+      <td>getorganelle</td>
+      <td>getorganelle</td>
+      <td></td>
+      <td>GetOrganelle</td>
+      <td>A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.</td>
+      <td>De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming</td>
+      <td>Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Kinggerm/GetOrganelle</td>
+      <td>Assembly</td>
+      <td>getorganelle</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle</td>
+      <td>1.7.7.1</td>
+      <td>getorganelle</td>
+      <td>1.7.7.1</td>
+      <td>De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming</td>
+      <td>Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1542</td>
+      <td>1542</td>
+      <td>159</td>
+      <td>159</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>587</td>
+      <td>587</td>
+      <td>64</td>
+      <td>64</td>
+      <td>2129</td>
+      <td>2129</td>
+      <td>223</td>
+      <td>223</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gfa_to_fa</td>
+      <td>gfa_to_fa</td>
+      <td>gfa_to_fa - Converting GFA format to Fasta format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://gfa-spec.github.io/GFA-spec/</td>
+      <td>Convert Formats</td>
+      <td>gfa_to_fa</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa</td>
+      <td>0.1.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9664</td>
+      <td>9775</td>
+      <td>763</td>
+      <td>765</td>
+      <td>5623</td>
+      <td>5623</td>
+      <td>493</td>
+      <td>493</td>
+      <td>1000</td>
+      <td>1000</td>
+      <td>135</td>
+      <td>135</td>
+      <td>16287</td>
+      <td>16398</td>
+      <td>1391</td>
+      <td>1393</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gfastats</td>
+      <td>gfastats</td>
+      <td>Tool for generating sequence statistics and simultaneous genome assembly file manipulation.</td>
+      <td>gfastats</td>
+      <td>gfastats</td>
+      <td></td>
+      <td>gfastats</td>
+      <td>gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.</td>
+      <td>Data handling</td>
+      <td>Computational biology</td>
+      <td>To update</td>
+      <td>https://github.com/vgl-hub/gfastats</td>
+      <td>Sequence Analysis</td>
+      <td>gfastats</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/gfastats</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/gfastats</td>
+      <td>1.3.6</td>
+      <td>gfastats</td>
+      <td>1.3.7</td>
+      <td>Data handling</td>
+      <td>Computational biology</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11748</td>
+      <td>11748</td>
+      <td>767</td>
+      <td>767</td>
+      <td>6560</td>
+      <td>6560</td>
+      <td>397</td>
+      <td>397</td>
+      <td>2556</td>
+      <td>2556</td>
+      <td>106</td>
+      <td>106</td>
+      <td>20864</td>
+      <td>20864</td>
+      <td>1270</td>
+      <td>1270</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gff3_rebase</td>
+      <td>gff3.rebase</td>
+      <td>Rebase a GFF against a parent GFF (e.g. an original genome)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase</td>
+      <td>Sequence Analysis</td>
+      <td>gff3_rebase</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase</td>
+      <td>1.2</td>
+      <td>bcbiogff</td>
+      <td>0.6.6</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>806</td>
+      <td>812</td>
+      <td>68</td>
+      <td>68</td>
+      <td>197</td>
+      <td>197</td>
+      <td>37</td>
+      <td>37</td>
+      <td>132</td>
+      <td>132</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1135</td>
+      <td>1141</td>
+      <td>117</td>
+      <td>117</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gffcompare</td>
+      <td>gffcompare</td>
+      <td>Galaxy wrappers for Geo Pertea's GffCompare package.</td>
+      <td>gffcompare</td>
+      <td>gffcompare</td>
+      <td></td>
+      <td>gffcompare</td>
+      <td>Program for comparing, annotating, merging and tracking transcripts in GFF files.</td>
+      <td>Sequence annotation</td>
+      <td>Nucleic acids, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/gpertea/gffcompare/</td>
+      <td>Transcriptomics</td>
+      <td>gffcompare</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare</td>
+      <td>0.12.6</td>
+      <td>gffcompare</td>
+      <td>0.12.6</td>
+      <td>Sequence annotation</td>
+      <td>Nucleic acids, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3560</td>
+      <td>3980</td>
+      <td>916</td>
+      <td>999</td>
+      <td>5281</td>
+      <td>8000</td>
+      <td>1713</td>
+      <td>2521</td>
+      <td>1468</td>
+      <td>1642</td>
+      <td>208</td>
+      <td>225</td>
+      <td>10309</td>
+      <td>13622</td>
+      <td>2837</td>
+      <td>3745</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gffcompare_to_bed</td>
+      <td>gffcompare_to_bed</td>
+      <td>Filter and convert a gffCompare GTF to BED</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/gpertea/gffcompare/</td>
+      <td>Convert Formats</td>
+      <td>gffcompare_to_bed</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed</td>
+      <td>0.2.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1375</td>
+      <td>2230</td>
+      <td>329</td>
+      <td>347</td>
+      <td>1071</td>
+      <td>1071</td>
+      <td>362</td>
+      <td>362</td>
+      <td>492</td>
+      <td>492</td>
+      <td>64</td>
+      <td>64</td>
+      <td>2938</td>
+      <td>3793</td>
+      <td>755</td>
+      <td>773</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gffread</td>
+      <td>gffread</td>
+      <td>gffread filters and/or converts GFF3/GTF2 records</td>
+      <td>gffread</td>
+      <td>gffread</td>
+      <td></td>
+      <td>gffread</td>
+      <td>program for filtering, converting and manipulating GFF files</td>
+      <td>Sequence annotation</td>
+      <td>Nucleic acids, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/</td>
+      <td>Sequence Analysis</td>
+      <td>gffread</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread</td>
+      <td>0.12.7</td>
+      <td>gffread</td>
+      <td>0.12.7</td>
+      <td>Sequence annotation</td>
+      <td>Nucleic acids, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>12828</td>
+      <td>13716</td>
+      <td>1740</td>
+      <td>1829</td>
+      <td>15217</td>
+      <td>23818</td>
+      <td>2588</td>
+      <td>3486</td>
+      <td>4423</td>
+      <td>4423</td>
+      <td>732</td>
+      <td>732</td>
+      <td>32468</td>
+      <td>41957</td>
+      <td>5060</td>
+      <td>6047</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ggplot2</td>
+      <td>ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin</td>
+      <td>ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.</td>
+      <td>ggplot2</td>
+      <td>ggplot2</td>
+      <td></td>
+      <td>ggplot2</td>
+      <td>Plotting system for R, based on the grammar of graphics.</td>
+      <td>Visualisation</td>
+      <td>Data visualisation</td>
+      <td>To update</td>
+      <td>https://github.com/tidyverse/ggplot2</td>
+      <td>Visualization</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2</td>
+      <td>3.4.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td>Visualisation</td>
+      <td>Data visualisation</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>24606</td>
+      <td>25662</td>
+      <td>3463</td>
+      <td>3630</td>
+      <td>26805</td>
+      <td>26808</td>
+      <td>5143</td>
+      <td>5144</td>
+      <td>8174</td>
+      <td>8237</td>
+      <td>1259</td>
+      <td>1279</td>
+      <td>59585</td>
+      <td>60707</td>
+      <td>9865</td>
+      <td>10053</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ggupset</td>
+      <td>emc-ggupset</td>
+      <td>Create Upset Plots with ggupset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/const-ae/ggupset</td>
+      <td>Graphics</td>
+      <td>ggupset</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset</td>
+      <td>1.0</td>
+      <td>r-ggupset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gi2taxonomy</td>
+      <td>Fetch Taxonomic Ranks</td>
+      <td>Fetch taxonomic representation</td>
+      <td>gi2taxonomy</td>
+      <td>gi2taxonomy</td>
+      <td></td>
+      <td>gi2taxonomy</td>
+      <td>The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).</td>
+      <td>Database search, ID mapping</td>
+      <td>Taxonomy</td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Metagenomics</td>
+      <td>gi2taxonomy</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy</td>
+      <td>1.1.1</td>
+      <td>taxonomy</td>
+      <td>0.10.0</td>
+      <td>Database search, ID mapping</td>
+      <td>Taxonomy</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>490</td>
+      <td>682</td>
+      <td>74</td>
+      <td>109</td>
+      <td>127</td>
+      <td>14058</td>
+      <td>20</td>
+      <td>1798</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>617</td>
+      <td>14740</td>
+      <td>94</td>
+      <td>1907</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>glimmer</td>
+      <td>glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based</td>
+      <td>Glimmer makes gene predictions.</td>
+      <td>gemini</td>
+      <td>gemini</td>
+      <td></td>
+      <td>GEMINI</td>
+      <td>GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.</td>
+      <td>Sequence analysis, Genetic variation analysis</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://ccb.jhu.edu/software/glimmer/</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer</td>
+      <td></td>
+      <td>glimmer</td>
+      <td>3.02</td>
+      <td>Sequence analysis, Genetic variation analysis</td>
+      <td>Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4343</td>
+      <td>4343</td>
+      <td>407</td>
+      <td>407</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4343</td>
+      <td>4343</td>
+      <td>407</td>
+      <td>407</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>glimmer_hmm</td>
+      <td></td>
+      <td>GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://ccb.jhu.edu/software/glimmerhmm/</td>
+      <td>Sequence Analysis</td>
+      <td>glimmer_hmm</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gmaj</td>
+      <td>gmaj_1</td>
+      <td>GMAJ Multiple Alignment Viewer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Visualization</td>
+      <td>gmaj</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj</td>
+      <td>2.0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>6</td>
+      <td>6</td>
+      <td>85</td>
+      <td>984</td>
+      <td>29</td>
+      <td>230</td>
+      <td>10</td>
+      <td>11</td>
+      <td>7</td>
+      <td>8</td>
+      <td>106</td>
+      <td>1006</td>
+      <td>42</td>
+      <td>244</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gnali</td>
+      <td>gnali</td>
+      <td>A tool to find nonessential, loss-of-function gene variants</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/gnali/</td>
+      <td>Variant Analysis</td>
+      <td>gnali</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/gnali/</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali</td>
+      <td>1.1.0</td>
+      <td>gnali</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>goenrichment</td>
+      <td>goenrichment, goslimmer</td>
+      <td>Performs GO Enrichment analysis.</td>
+      <td>goenrichment</td>
+      <td>goenrichment</td>
+      <td></td>
+      <td>GOEnrichment</td>
+      <td>GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.</td>
+      <td>Gene-set enrichment analysis</td>
+      <td>Transcriptomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/DanFaria/GOEnrichment</td>
+      <td>Genome annotation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment</td>
+      <td>2.0.1</td>
+      <td>goenrichment</td>
+      <td>2.0.1</td>
+      <td>Gene-set enrichment analysis</td>
+      <td>Transcriptomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>5800</td>
+      <td>6212</td>
+      <td>826</td>
+      <td>871</td>
+      <td>7756</td>
+      <td>7756</td>
+      <td>1048</td>
+      <td>1048</td>
+      <td>1149</td>
+      <td>1149</td>
+      <td>215</td>
+      <td>215</td>
+      <td>14705</td>
+      <td>15117</td>
+      <td>2089</td>
+      <td>2134</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>goseq</td>
+      <td>goseq</td>
+      <td>goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data</td>
+      <td>goseq</td>
+      <td>goseq</td>
+      <td></td>
+      <td>GOseq</td>
+      <td>Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.</td>
+      <td>Gene functional annotation</td>
+      <td>RNA-Seq</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/goseq.html</td>
+      <td>Statistics, RNA, Micro-array Analysis</td>
+      <td>goseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq</td>
+      <td>1.50.0</td>
+      <td>bioconductor-goseq</td>
+      <td>1.54.0</td>
+      <td>Gene functional annotation</td>
+      <td>RNA-Seq</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20207</td>
+      <td>21960</td>
+      <td>2807</td>
+      <td>3139</td>
+      <td>24488</td>
+      <td>26198</td>
+      <td>3066</td>
+      <td>3321</td>
+      <td>4155</td>
+      <td>4155</td>
+      <td>545</td>
+      <td>545</td>
+      <td>48850</td>
+      <td>52313</td>
+      <td>6418</td>
+      <td>7005</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gotohscan</td>
+      <td>rbc_gotohscan</td>
+      <td>Find subsequences in db</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>gotohscan</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan</td>
+      <td>1.3.0</td>
+      <td>gotohscan</td>
+      <td>1.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>34</td>
+      <td>72</td>
+      <td>5</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>72</td>
+      <td>5</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gprofiler</td>
+      <td>gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense</td>
+      <td>functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://biit.cs.ut.ee/gprofiler</td>
+      <td>Statistics, Web Services</td>
+      <td>gprofiler</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler</td>
+      <td>@TOOL_VERSION@+galaxy11</td>
+      <td>r-gprofiler2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>4001</td>
+      <td>4001</td>
+      <td>614</td>
+      <td>614</td>
+      <td>7882</td>
+      <td>7882</td>
+      <td>1238</td>
+      <td>1238</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11883</td>
+      <td>11883</td>
+      <td>1852</td>
+      <td>1852</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graph_converter</td>
+      <td>graph_converter</td>
+      <td>Convert between different graph formats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats</td>
+      <td>graph_converter</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graphclust</td>
+      <td>graphclust</td>
+      <td>GraphClust can be used for structural clustering of RNA sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.bioinf.uni-freiburg.de/Software/GraphClust/</td>
+      <td>RNA</td>
+      <td>graphclust</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/graphclust</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/graphclust</td>
+      <td>0.1</td>
+      <td>GraphClust</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graphembed</td>
+      <td>graphembed</td>
+      <td>Compute a 2D embedding of a data matrix given supervised class information</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/fabriziocosta/GraphEmbed</td>
+      <td>Statistics, Graphics</td>
+      <td>graphembed</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed</td>
+      <td>2.4</td>
+      <td>graph_embed</td>
+      <td>2.4</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>78</td>
+      <td>78</td>
+      <td>6</td>
+      <td>6</td>
+      <td>120</td>
+      <td>120</td>
+      <td>43</td>
+      <td>43</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>198</td>
+      <td>198</td>
+      <td>49</td>
+      <td>49</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graphicsmagick</td>
+      <td>graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage</td>
+      <td>Contains tools based on GraphicsMagick</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.graphicsmagick.org</td>
+      <td>Imaging</td>
+      <td>graphicsmagick</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick</td>
+      <td>1.3.45</td>
+      <td>graphicsmagick</td>
+      <td>1.3.26</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1725</td>
+      <td>2708</td>
+      <td>97</td>
+      <td>99</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1727</td>
+      <td>2710</td>
+      <td>99</td>
+      <td>101</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graphlan</td>
+      <td>graphlan, graphlan_annotate</td>
+      <td>GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees</td>
+      <td>graphlan</td>
+      <td>graphlan</td>
+      <td></td>
+      <td>GraPhlAn</td>
+      <td>GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.</td>
+      <td>Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification</td>
+      <td>Metagenomics, Phylogenetics, Phylogenomics, Cladistics</td>
+      <td>To update</td>
+      <td>https://github.com/biobakery/graphlan</td>
+      <td>Metagenomics, Graphics, Phylogenetics</td>
+      <td>graphlan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan</td>
+      <td></td>
+      <td>graphlan</td>
+      <td>1.1.3</td>
+      <td>Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification</td>
+      <td>Metagenomics, Phylogenetics, Phylogenomics, Cladistics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>9816</td>
+      <td>10927</td>
+      <td>1285</td>
+      <td>1350</td>
+      <td>1273</td>
+      <td>1273</td>
+      <td>368</td>
+      <td>368</td>
+      <td>1104</td>
+      <td>1104</td>
+      <td>242</td>
+      <td>242</td>
+      <td>12193</td>
+      <td>13304</td>
+      <td>1895</td>
+      <td>1960</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graphmap</td>
+      <td>graphmap_align, graphmap_overlap</td>
+      <td>Mapper for long, error-prone reads.</td>
+      <td>graphmap</td>
+      <td>graphmap</td>
+      <td></td>
+      <td>graphmap</td>
+      <td>Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1</td>
+      <td>Sequence trimming, EST assembly, Read mapping</td>
+      <td>Gene transcripts, RNA-Seq, RNA splicing</td>
+      <td>To update</td>
+      <td>https://github.com/isovic/graphmap/</td>
+      <td>Assembly</td>
+      <td>graphmap</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/graphmap</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/graphmap</td>
+      <td>0.5.2</td>
+      <td>graphmap</td>
+      <td>0.6.4</td>
+      <td>Sequence trimming, EST assembly, Read mapping</td>
+      <td>Gene transcripts, RNA-Seq, RNA splicing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>7012</td>
+      <td>7344</td>
+      <td>323</td>
+      <td>338</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7012</td>
+      <td>7344</td>
+      <td>323</td>
+      <td>338</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graphprot</td>
+      <td>graphprot_predict_profile</td>
+      <td>GraphProt models binding preferences of RNA-binding proteins.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/dmaticzka/GraphProt</td>
+      <td>Sequence Analysis, RNA, CLIP-seq</td>
+      <td>graphprot</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot</td>
+      <td>1.1.7+galaxy2</td>
+      <td>graphprot</td>
+      <td>1.1.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>463</td>
+      <td>484</td>
+      <td>18</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>463</td>
+      <td>484</td>
+      <td>18</td>
+      <td>19</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gromacs</td>
+      <td>gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj</td>
+      <td>GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/gromacs</td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>gromacs</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs</td>
+      <td>2022</td>
+      <td>gromacs</td>
+      <td>2021.3</td>
+      <td></td>
+      <td></td>
+      <td>14</td>
+      <td>8</td>
+      <td>15</td>
+      <td>0</td>
+      <td>14</td>
+      <td>8</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>15</td>
+      <td>9</td>
+      <td>0</td>
+      <td>184067</td>
+      <td>184203</td>
+      <td>3441</td>
+      <td>3451</td>
+      <td>9382</td>
+      <td>9382</td>
+      <td>1438</td>
+      <td>1438</td>
+      <td>10325</td>
+      <td>10325</td>
+      <td>648</td>
+      <td>648</td>
+      <td>203774</td>
+      <td>203910</td>
+      <td>5527</td>
+      <td>5537</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_center_scale</td>
+      <td>center_scale</td>
+      <td>Center or scale (standardize) data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Statistics</td>
+      <td>gsc_center_scale</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale</td>
+      <td>4.3.1+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_filter_cells</td>
+      <td>filter_cells</td>
+      <td>Filter single cell RNAseq data on libray depth and number of detected genes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>gsc_filter_cells</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells</td>
+      <td>4.3.1+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_filter_genes</td>
+      <td>filter_genes</td>
+      <td>Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>gsc_filter_genes</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes</td>
+      <td>4.3.1+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_gene_expression_correlations</td>
+      <td>single_cell_gene_expression_correlations</td>
+      <td>Compute single-cell paire-wise gene expressions correlations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>gsc_gene_expression_correlations</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations</td>
+      <td>4.3.1+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_high_dimensions_visualisation</td>
+      <td>high_dimensions_visualisation</td>
+      <td>Generates PCA, t-SNE and HCPC visualisation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics, Visualization</td>
+      <td>gsc_high_dimensions_visualisation</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation</td>
+      <td>4.3+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_mannwhitney_de</td>
+      <td>mannwhitney_de</td>
+      <td>Perform a mann-whitney differential testing between two sets of gene expression data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>gsc_mannwhitney_de</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de</td>
+      <td>4.1.3+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_scran_normalize</td>
+      <td>scran_normalize</td>
+      <td>Normalize raw counts using scran</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>gsc_scran_normalize</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize</td>
+      <td>1.28.1+galaxy0</td>
+      <td>bioconductor-scran</td>
+      <td>1.30.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>89</td>
+      <td>89</td>
+      <td>24</td>
+      <td>24</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>10</td>
+      <td>10</td>
+      <td>2</td>
+      <td>2</td>
+      <td>102</td>
+      <td>102</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_signature_score</td>
+      <td>signature_score</td>
+      <td>Compute signature scores from single cell RNAseq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>gsc_signature_score</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score</td>
+      <td>2.3.9+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gstf_preparation</td>
+      <td>gstf_preparation</td>
+      <td>GeneSeqToFamily preparation converts data for the workflow</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/</td>
+      <td>Convert Formats</td>
+      <td>gstf_preparation</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation</td>
+      <td>0.4.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>377</td>
+      <td>400</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>377</td>
+      <td>400</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gtdb_to_taxdump</td>
+      <td>gtdb_to_taxdump</td>
+      <td>Convert GTDB taxonomy to NCBI taxdump format</td>
+      <td>gtdb_to_taxdump</td>
+      <td>gtdb_to_taxdump</td>
+      <td></td>
+      <td>gtdb_to_taxdump</td>
+      <td>Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.</td>
+      <td>Data handling, Mapping, Generation</td>
+      <td>Computational biology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/nick-youngblut/gtdb_to_taxdump</td>
+      <td>Metagenomics</td>
+      <td>gtdb_to_taxdump</td>
+      <td>iuc</td>
+      <td>https://github.com/nick-youngblut/gtdb_to_taxdump</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump</td>
+      <td>0.1.9</td>
+      <td>gtdb_to_taxdump</td>
+      <td>0.1.9</td>
+      <td>Data handling, Mapping, Generation</td>
+      <td>Computational biology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gtdbtk</td>
+      <td>gtdbtk_classify_wf</td>
+      <td>GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes.</td>
+      <td>GTDB-Tk</td>
+      <td>GTDB-Tk</td>
+      <td></td>
+      <td>GTDB-Tk</td>
+      <td>a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).</td>
+      <td>Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval</td>
+      <td>Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Ecogenomics/GTDBTk</td>
+      <td>Metagenomics</td>
+      <td>gtdbtk</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk</td>
+      <td>2.4.0</td>
+      <td>gtdbtk</td>
+      <td>2.4.0</td>
+      <td>Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval</td>
+      <td>Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>476</td>
+      <td>476</td>
+      <td>87</td>
+      <td>87</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>588</td>
+      <td>588</td>
+      <td>74</td>
+      <td>74</td>
+      <td>1064</td>
+      <td>1064</td>
+      <td>161</td>
+      <td>161</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gtf-2-gene-list</td>
+      <td>_ensembl_gtf2gene_list</td>
+      <td>Utility to extract annotations from Ensembl GTF files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary</td>
+      <td>Sequence Analysis</td>
+      <td>gtf2gene_list</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list</td>
+      <td>1.52.0+galaxy0</td>
+      <td>atlas-gene-annotation-manipulation</td>
+      <td>1.1.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1982</td>
+      <td>1983</td>
+      <td>323</td>
+      <td>324</td>
+      <td>1040</td>
+      <td>1040</td>
+      <td>343</td>
+      <td>343</td>
+      <td>205</td>
+      <td>205</td>
+      <td>38</td>
+      <td>38</td>
+      <td>3227</td>
+      <td>3228</td>
+      <td>704</td>
+      <td>705</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gtfToBed12</td>
+      <td>gtftobed12</td>
+      <td>Convert GTF files to BED12 format</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README</td>
+      <td>Convert Formats</td>
+      <td>gtftobed12</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12</td>
+      <td>357</td>
+      <td>ucsc-gtftogenepred</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>8329</td>
+      <td>9363</td>
+      <td>3336</td>
+      <td>3828</td>
+      <td>8009</td>
+      <td>8009</td>
+      <td>3130</td>
+      <td>3130</td>
+      <td>1577</td>
+      <td>1577</td>
+      <td>344</td>
+      <td>344</td>
+      <td>17915</td>
+      <td>18949</td>
+      <td>6810</td>
+      <td>7302</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gubbins</td>
+      <td>gubbins</td>
+      <td>Gubbins - bacterial recombination detection</td>
+      <td>gubbins</td>
+      <td>gubbins</td>
+      <td></td>
+      <td>Gubbins</td>
+      <td>Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.</td>
+      <td>Genotyping, Phylogenetic inference, Ancestral reconstruction</td>
+      <td>Phylogeny, Genotype and phenotype, Whole genome sequencing</td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>gubbins</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins</td>
+      <td>3.2.1</td>
+      <td>gubbins</td>
+      <td>3.3.5</td>
+      <td>Genotyping, Phylogenetic inference, Ancestral reconstruction</td>
+      <td>Phylogeny, Genotype and phenotype, Whole genome sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3690</td>
+      <td>3811</td>
+      <td>326</td>
+      <td>336</td>
+      <td>3323</td>
+      <td>3323</td>
+      <td>235</td>
+      <td>235</td>
+      <td>1895</td>
+      <td>2429</td>
+      <td>234</td>
+      <td>258</td>
+      <td>8908</td>
+      <td>9563</td>
+      <td>795</td>
+      <td>829</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>guppy</td>
+      <td>guppy-basecaller</td>
+      <td>A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Nanopore</td>
+      <td>guppy_basecaller</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy</td>
+      <td>6.5.7+galaxy0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1</td>
+      <td>1</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gvcftools</td>
+      <td>gvcftools_extract_variants</td>
+      <td>gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/sequencing/gvcftools</td>
+      <td>Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools</td>
+      <td>0.1</td>
+      <td>gvcftools</td>
+      <td>0.17.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gwastools</td>
+      <td>gwastools_manhattan_plot</td>
+      <td></td>
+      <td>gwastools</td>
+      <td>gwastools</td>
+      <td></td>
+      <td>GWASTools</td>
+      <td>Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.</td>
+      <td>Deposition, Analysis, Annotation</td>
+      <td>GWAS study</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/GWASTools.html</td>
+      <td>Visualization, Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td></td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools</td>
+      <td>0.1.0</td>
+      <td>bioconductor-gwastools</td>
+      <td>1.48.0</td>
+      <td>Deposition, Analysis, Annotation</td>
+      <td>GWAS study</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hamronization</td>
+      <td>hamronize_summarize, hamronize_tool</td>
+      <td>Convert AMR gene detection tool output to hAMRonization specification format.</td>
+      <td>hamronization</td>
+      <td>hamronization</td>
+      <td></td>
+      <td>hAMRonization</td>
+      <td>Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure</td>
+      <td>Data handling, Antimicrobial resistance prediction, Parsing</td>
+      <td>Public health and epidemiology, Microbiology, Bioinformatics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pha4ge/hAMRonization</td>
+      <td>Sequence Analysis</td>
+      <td>hamronization</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization</td>
+      <td>1.1.4</td>
+      <td>hamronization</td>
+      <td>1.1.4</td>
+      <td>Antimicrobial resistance prediction, Parsing</td>
+      <td>Public health and epidemiology, Microbiology, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7303</td>
+      <td>7303</td>
+      <td>222</td>
+      <td>222</td>
+      <td>20</td>
+      <td>20</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7323</td>
+      <td>7323</td>
+      <td>224</td>
+      <td>224</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hansel</td>
+      <td>bio_hansel</td>
+      <td>Heidelberg and Enteritidis SNP Elucidation</td>
+      <td>Biohansel</td>
+      <td>Biohansel</td>
+      <td></td>
+      <td>BioHansel</td>
+      <td>BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.</td>
+      <td>Genotyping, SNP detection, Genome assembly</td>
+      <td>Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/bio_hansel</td>
+      <td>Sequence Analysis</td>
+      <td>bio_hansel</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel</td>
+      <td>2.6.1</td>
+      <td>bio_hansel</td>
+      <td>2.6.1</td>
+      <td>Genotyping, SNP detection, Genome assembly</td>
+      <td>Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>349</td>
+      <td>359</td>
+      <td>32</td>
+      <td>33</td>
+      <td>364</td>
+      <td>364</td>
+      <td>53</td>
+      <td>53</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>713</td>
+      <td>723</td>
+      <td>85</td>
+      <td>86</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hapcut2</td>
+      <td>hapcut2</td>
+      <td>Robust and accurate haplotype assembly for diverse sequencing technologies</td>
+      <td>hapcut2</td>
+      <td>hapcut2</td>
+      <td></td>
+      <td>HapCUT2</td>
+      <td>HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md</td>
+      <td>Haplotype mapping, Variant classification</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/vibansal/HapCUT2</td>
+      <td>Assembly</td>
+      <td>hapcut2</td>
+      <td>galaxy-australia</td>
+      <td>https://github.com/galaxyproject/tools-iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2</td>
+      <td>1.3.4</td>
+      <td>hapcut2</td>
+      <td>1.3.4</td>
+      <td>Haplotype mapping, Variant classification</td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>103</td>
+      <td>103</td>
+      <td>4</td>
+      <td>4</td>
+      <td>103</td>
+      <td>103</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hapog</td>
+      <td>hapog</td>
+      <td>Hapo-G - Haplotype-Aware Polishing of Genomes</td>
+      <td>hapog</td>
+      <td>hapog</td>
+      <td></td>
+      <td>Hapo-G</td>
+      <td>Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.</td>
+      <td>Genome assembly, Optimisation and refinement</td>
+      <td>Sequence assembly, Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/institut-de-genomique/HAPO-G</td>
+      <td>Assembly</td>
+      <td>hapog</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog</td>
+      <td>1.3.8</td>
+      <td>hapog</td>
+      <td>1.3.8</td>
+      <td>Genome assembly, Optimisation and refinement</td>
+      <td>Sequence assembly, Genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>502</td>
+      <td>502</td>
+      <td>66</td>
+      <td>66</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>502</td>
+      <td>502</td>
+      <td>66</td>
+      <td>66</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>happy</td>
+      <td>som.py</td>
+      <td>A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.</td>
+      <td>hap.py</td>
+      <td>hap.py</td>
+      <td></td>
+      <td>hap.py</td>
+      <td>This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.</td>
+      <td>Variant calling, Sequence analysis, Genotyping</td>
+      <td>Genomics, DNA polymorphism</td>
+      <td>To update</td>
+      <td>https://github.com/Illumina/hap.py</td>
+      <td>Variant Analysis</td>
+      <td>happy</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy</td>
+      <td>0.3.14</td>
+      <td>hap.py</td>
+      <td>0.3.15</td>
+      <td>Variant calling, Sequence analysis, Genotyping</td>
+      <td>Genomics, DNA polymorphism</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hardklor</td>
+      <td>hardklor, kronik</td>
+      <td>Hardklör</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>hardklor</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor</td>
+      <td>2.30.1+galaxy1</td>
+      <td>hardklor</td>
+      <td>2.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>98</td>
+      <td>111</td>
+      <td>5</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>111</td>
+      <td>5</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hclust2</td>
+      <td>hclust2</td>
+      <td>Plots heatmaps</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/nsegata/hclust2/</td>
+      <td>Data Visualization</td>
+      <td>hclust2</td>
+      <td>rnateam</td>
+      <td>https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hclust2</td>
+      <td>0.99</td>
+      <td>hclust2</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hcluster_sg</td>
+      <td>hcluster_sg</td>
+      <td>Hierarchically clustering on a sparse graph</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/douglasgscofield/hcluster</td>
+      <td>Phylogenetics</td>
+      <td>hcluster_sg</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg</td>
+      <td>0.5.1.1</td>
+      <td>hcluster_sg</td>
+      <td>0.5.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>243</td>
+      <td>263</td>
+      <td>54</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>243</td>
+      <td>263</td>
+      <td>54</td>
+      <td>57</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hcluster_sg_parser</td>
+      <td>hcluster_sg_parser</td>
+      <td>Converts hcluster_sg 3-column output into lists of ids</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/</td>
+      <td>Phylogenetics</td>
+      <td>hcluster_sg_parser</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser</td>
+      <td>0.2.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>266</td>
+      <td>293</td>
+      <td>22</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>266</td>
+      <td>293</td>
+      <td>22</td>
+      <td>25</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>heatmap2</td>
+      <td>ggplot2_heatmap2</td>
+      <td>heatmap.2 function from the R gplots package</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/cran/gplots</td>
+      <td>Visualization</td>
+      <td>ggplot2_heatmap2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2</td>
+      <td>3.1.3.1</td>
+      <td>r-gplots</td>
+      <td>2.17.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>46700</td>
+      <td>50808</td>
+      <td>4645</td>
+      <td>5114</td>
+      <td>64214</td>
+      <td>70429</td>
+      <td>5799</td>
+      <td>6830</td>
+      <td>7783</td>
+      <td>7912</td>
+      <td>704</td>
+      <td>724</td>
+      <td>118697</td>
+      <td>129149</td>
+      <td>11148</td>
+      <td>12668</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>heinz</td>
+      <td>heinz_bum, heinz, heinz_scoring, heinz_visualization</td>
+      <td>An algorithm for identification of the optimal scoring subnetwork.</td>
+      <td>heinz</td>
+      <td>bionet, heinz</td>
+      <td></td>
+      <td>Heinz</td>
+      <td>Tool for single-species active module discovery.</td>
+      <td>Pathway or network analysis</td>
+      <td>Genetics, Gene expression, Molecular interactions, pathways and networks</td>
+      <td>To update</td>
+      <td>https://github.com/ls-cwi/heinz</td>
+      <td>Transcriptomics, Visualization, Statistics</td>
+      <td>heinz</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz</td>
+      <td>1.0</td>
+      <td>bioconductor-bionet</td>
+      <td>1.62.0</td>
+      <td>Pathway or network analysis</td>
+      <td>Genetics, Gene expression, Molecular interactions, pathways and networks</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>1281</td>
+      <td>1434</td>
+      <td>367</td>
+      <td>442</td>
+      <td>1559</td>
+      <td>1559</td>
+      <td>636</td>
+      <td>636</td>
+      <td>678</td>
+      <td>678</td>
+      <td>52</td>
+      <td>52</td>
+      <td>3518</td>
+      <td>3671</td>
+      <td>1055</td>
+      <td>1130</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>helixer</td>
+      <td>helixer</td>
+      <td>Gene calling with Deep Neural Networks</td>
+      <td>helixer</td>
+      <td>helixer</td>
+      <td></td>
+      <td>Helixer</td>
+      <td>Deep Learning to predict gene annotations</td>
+      <td>Gene prediction, Genome annotation</td>
+      <td>Sequence analysis, Gene transcripts</td>
+      <td>To update</td>
+      <td>https://github.com/weberlab-hhu/Helixer</td>
+      <td>Genome annotation</td>
+      <td>helixer</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/helixer</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/helixer</td>
+      <td>0.3.3</td>
+      <td></td>
+      <td></td>
+      <td>Gene prediction, Genome annotation</td>
+      <td>Sequence analysis, Gene transcripts</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>267</td>
+      <td>267</td>
+      <td>39</td>
+      <td>39</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>80</td>
+      <td>80</td>
+      <td>7</td>
+      <td>7</td>
+      <td>347</td>
+      <td>347</td>
+      <td>46</td>
+      <td>46</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hess</td>
+      <td>hess_astro_tool</td>
+      <td>Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Astronomy</td>
+      <td>hess_astro_tool</td>
+      <td>astroteam</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess</td>
+      <td>0.0.2+galaxy0</td>
+      <td>ipython</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hgv_fundo</td>
+      <td>hgv_funDo</td>
+      <td>FunDO human genes associated with disease terms</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>hgv_fundo</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>145</td>
+      <td>1794</td>
+      <td>33</td>
+      <td>397</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>145</td>
+      <td>1794</td>
+      <td>33</td>
+      <td>397</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hgv_hilbertvis</td>
+      <td>hgv_hilbertvis</td>
+      <td>HVIS visualization of genomic data with the Hilbert curve</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.ebi.ac.uk/huber-srv/hilbert/</td>
+      <td>Graphics, Visualization</td>
+      <td>hgv_hilbertvis</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis</td>
+      <td>1.0.0</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>265</td>
+      <td>16</td>
+      <td>60</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>265</td>
+      <td>16</td>
+      <td>60</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hgvsparser</td>
+      <td>hgvsparser</td>
+      <td>Parsing and building variant descriptor strings compliant with the HGVS standard</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/VariantEffect/hgvsParseR/tree/master</td>
+      <td>Variant Analysis</td>
+      <td>hgvsparser</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser</td>
+      <td>0.1.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6346</td>
+      <td>6346</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6346</td>
+      <td>6346</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hicexplorer</td>
+      <td>hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations</td>
+      <td>HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/deeptools/HiCExplorer</td>
+      <td>Sequence Analysis, Visualization</td>
+      <td>hicexplorer</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer</td>
+      <td>3.7.5</td>
+      <td>hicexplorer</td>
+      <td>3.7.5</td>
+      <td></td>
+      <td></td>
+      <td>38</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>38</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>33</td>
+      <td>36</td>
+      <td>33</td>
+      <td>0</td>
+      <td>44449</td>
+      <td>68602</td>
+      <td>3236</td>
+      <td>4177</td>
+      <td>46</td>
+      <td>46</td>
+      <td>21</td>
+      <td>21</td>
+      <td>1328</td>
+      <td>1328</td>
+      <td>67</td>
+      <td>67</td>
+      <td>45823</td>
+      <td>69976</td>
+      <td>3324</td>
+      <td>4265</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hicstuff</td>
+      <td>hicstuff_pipeline</td>
+      <td>A toolkit to generate and manipulate Hi-C matrices</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/koszullab/hicstuff</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff</td>
+      <td>3.1.5</td>
+      <td>hicstuff</td>
+      <td>3.2.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hictk</td>
+      <td>hictk</td>
+      <td>Convert cooler to juicebox_hic</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/paulsengroup/hictk</td>
+      <td>Convert Formats, Epigenetics</td>
+      <td>hictk</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hictk</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hictk</td>
+      <td>1.0.0</td>
+      <td>hictk</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hicup</td>
+      <td>hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater</td>
+      <td>The HiCUP-Pipeline from the Bioinformatics Babraham Institute.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html</td>
+      <td>Epigenetics</td>
+      <td>hicup</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hicup</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hicup</td>
+      <td>0.9.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>7</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>6</td>
+      <td>0</td>
+      <td>901</td>
+      <td>1020</td>
+      <td>160</td>
+      <td>184</td>
+      <td>440</td>
+      <td>440</td>
+      <td>111</td>
+      <td>111</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1341</td>
+      <td>1460</td>
+      <td>271</td>
+      <td>295</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hifiasm</td>
+      <td>hifiasm</td>
+      <td>A fast haplotype-resolved de novo assembler</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/chhylp123/hifiasm</td>
+      <td>Assembly</td>
+      <td>hifiasm</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm</td>
+      <td>0.19.9</td>
+      <td>hifiasm</td>
+      <td>0.19.9</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1819</td>
+      <td>1819</td>
+      <td>539</td>
+      <td>539</td>
+      <td>1334</td>
+      <td>1334</td>
+      <td>389</td>
+      <td>389</td>
+      <td>2472</td>
+      <td>2472</td>
+      <td>137</td>
+      <td>137</td>
+      <td>5625</td>
+      <td>5625</td>
+      <td>1065</td>
+      <td>1065</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hifiasm_meta</td>
+      <td>hifiasm_meta</td>
+      <td>A hifiasm fork for metagenome assembly using Hifi reads.</td>
+      <td>hifiasm-meta</td>
+      <td>hifiasm-meta</td>
+      <td></td>
+      <td>Hifiasm-meta</td>
+      <td>Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly, Metagenomics</td>
+      <td>To update</td>
+      <td>https://github.com/xfengnefx/hifiasm-meta</td>
+      <td>Metagenomics</td>
+      <td>hifiasm_meta</td>
+      <td>galaxy-australia</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta</td>
+      <td>0.3.1</td>
+      <td>hifiasm_meta</td>
+      <td>hamtv0.3.1</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly, Metagenomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>156</td>
+      <td>156</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>220</td>
+      <td>220</td>
+      <td>11</td>
+      <td>11</td>
+      <td>376</td>
+      <td>376</td>
+      <td>31</td>
+      <td>31</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>high_dim_heatmap</td>
+      <td>high_dim_heatmap</td>
+      <td>gplot heatmap.2 function adapted for plotting large heatmaps</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/cran/gplots</td>
+      <td>Visualization</td>
+      <td>high_dim_heatmap</td>
+      <td>artbio</td>
+      <td>https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap</td>
+      <td>3.1.3+galaxy0</td>
+      <td>r-gplots</td>
+      <td>2.17.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hirondelle_crim_ogc_api_processes</td>
+      <td>hirondelle_crim</td>
+      <td>This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AquaINFRA/galaxy</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes</td>
+      <td>0.2.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hisat</td>
+      <td>hisat</td>
+      <td>HISAT is a fast and sensitive spliced alignment program.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://ccb.jhu.edu/software/hisat/index.shtml</td>
+      <td>Assembly</td>
+      <td>hisat</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat</td>
+      <td>1.0.3</td>
+      <td>hisat</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>228</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>228</td>
+      <td>0</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hisat2</td>
+      <td>hisat2</td>
+      <td>HISAT2 is a fast and sensitive spliced alignment program.</td>
+      <td>hisat2</td>
+      <td>hisat2</td>
+      <td></td>
+      <td>HISAT2</td>
+      <td>Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).</td>
+      <td>Sequence alignment</td>
+      <td>RNA-seq</td>
+      <td>Up-to-date</td>
+      <td>http://ccb.jhu.edu/software/hisat2/</td>
+      <td>Assembly</td>
+      <td>hisat2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2</td>
+      <td>2.2.1</td>
+      <td>hisat2</td>
+      <td>2.2.1</td>
+      <td>Sequence alignment</td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>337151</td>
+      <td>353499</td>
+      <td>10046</td>
+      <td>10719</td>
+      <td>699868</td>
+      <td>896164</td>
+      <td>26656</td>
+      <td>34018</td>
+      <td>87016</td>
+      <td>94859</td>
+      <td>5302</td>
+      <td>5695</td>
+      <td>1124035</td>
+      <td>1344522</td>
+      <td>42004</td>
+      <td>50432</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>histogram</td>
+      <td>histogram_rpy</td>
+      <td>Histogram of a numeric column</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Statistics</td>
+      <td>histogram</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram</td>
+      <td>1.0.4</td>
+      <td>rpy2</td>
+      <td>2.7.8</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3748</td>
+      <td>4661</td>
+      <td>866</td>
+      <td>1002</td>
+      <td>5993</td>
+      <td>48272</td>
+      <td>1507</td>
+      <td>7101</td>
+      <td>549</td>
+      <td>746</td>
+      <td>152</td>
+      <td>253</td>
+      <td>10290</td>
+      <td>53679</td>
+      <td>2525</td>
+      <td>8356</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hivclustering</td>
+      <td>hivclustering</td>
+      <td>Infers transmission networks from pairwise distances inferred by tn93</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pypi.org/project/hivclustering/</td>
+      <td>Next Gen Mappers</td>
+      <td>hivclustering</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering</td>
+      <td>1.3.1</td>
+      <td>python-hivclustering</td>
+      <td>1.8.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hivtrace</td>
+      <td>hivtrace</td>
+      <td>An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>hivtrace</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace</td>
+      <td>1.0.1</td>
+      <td>hivtrace</td>
+      <td>1.5.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hmmer3</td>
+      <td>hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer</td>
+      <td>HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).</td>
+      <td>hmmer3</td>
+      <td>hmmer3</td>
+      <td></td>
+      <td>HMMER3</td>
+      <td>This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.</td>
+      <td>Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search</td>
+      <td>Sequence analysis, Sequence sites, features and motifs, Gene and protein families</td>
+      <td>Up-to-date</td>
+      <td>http://hmmer.org/</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3</td>
+      <td>3.4</td>
+      <td>hmmer</td>
+      <td>3.4</td>
+      <td>Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search</td>
+      <td>Sequence analysis, Sequence sites, features and motifs, Gene and protein families</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>35919</td>
+      <td>36952</td>
+      <td>1283</td>
+      <td>1321</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3023</td>
+      <td>3023</td>
+      <td>180</td>
+      <td>180</td>
+      <td>38942</td>
+      <td>39975</td>
+      <td>1463</td>
+      <td>1501</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>homer</td>
+      <td></td>
+      <td>Software for motif discovery and next generation sequencing analysis.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://homer.salk.edu/homer/</td>
+      <td>Sequence Analysis</td>
+      <td>homer</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/homer</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/homer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>homer</td>
+      <td>homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide</td>
+      <td>HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.</td>
+      <td>homer</td>
+      <td>homer</td>
+      <td></td>
+      <td>homer</td>
+      <td>HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.</td>
+      <td>Sequence motif discovery</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://homer.ucsd.edu/homer/index.html</td>
+      <td>Sequence Analysis</td>
+      <td>data_manager_homer_preparse</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer</td>
+      <td>4.11</td>
+      <td>homer</td>
+      <td>4.11</td>
+      <td>Sequence motif discovery</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8531</td>
+      <td>8531</td>
+      <td>633</td>
+      <td>633</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8531</td>
+      <td>8531</td>
+      <td>633</td>
+      <td>633</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>htseq-clip</td>
+      <td>htseq_clip</td>
+      <td>htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/EMBL-Hentze-group/htseq-clip</td>
+      <td>Sequence Analysis, RNA, CLIP-seq</td>
+      <td>htseq_clip</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip</td>
+      <td>0.1.0+galaxy0</td>
+      <td>htseq-clip</td>
+      <td>2.19.0b0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>98</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>98</td>
+      <td>19</td>
+      <td>19</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>htseq_count</td>
+      <td>htseq_count</td>
+      <td>Count aligned reads (SAM/BAM) that overlap genomic features (GFF)</td>
+      <td>htseq</td>
+      <td>htseq</td>
+      <td></td>
+      <td>HTSeq</td>
+      <td>Python framework to process and analyse high-throughput sequencing (HTS) data</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://readthedocs.org/projects/htseq/</td>
+      <td>Genomic Interval Operations, SAM, Sequence Analysis, RNA</td>
+      <td>htseq_count</td>
+      <td>lparsons</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count</td>
+      <td>2.0.5</td>
+      <td>htseq</td>
+      <td>2.0.5</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>144907</td>
+      <td>168824</td>
+      <td>3703</td>
+      <td>4366</td>
+      <td>213407</td>
+      <td>346792</td>
+      <td>10798</td>
+      <td>16485</td>
+      <td>27209</td>
+      <td>33124</td>
+      <td>2613</td>
+      <td>2854</td>
+      <td>385523</td>
+      <td>548740</td>
+      <td>17114</td>
+      <td>23705</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>humann</td>
+      <td>humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways</td>
+      <td>HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution</td>
+      <td>humann</td>
+      <td>humann</td>
+      <td></td>
+      <td>humann</td>
+      <td>HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”</td>
+      <td>Species frequency estimation, Taxonomic classification, Phylogenetic analysis</td>
+      <td>Metagenomics, Phylogenomics</td>
+      <td>Up-to-date</td>
+      <td>http://huttenhower.sph.harvard.edu/humann</td>
+      <td>Metagenomics</td>
+      <td>humann</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann</td>
+      <td>3.9</td>
+      <td>humann</td>
+      <td>3.9</td>
+      <td>Species frequency estimation, Taxonomic classification, Phylogenetic analysis</td>
+      <td>Metagenomics, Phylogenomics</td>
+      <td>6</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>6</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>26659</td>
+      <td>26659</td>
+      <td>2067</td>
+      <td>2067</td>
+      <td>865</td>
+      <td>865</td>
+      <td>174</td>
+      <td>174</td>
+      <td>3238</td>
+      <td>3238</td>
+      <td>351</td>
+      <td>351</td>
+      <td>30762</td>
+      <td>30762</td>
+      <td>2592</td>
+      <td>2592</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hybpiper</td>
+      <td>hybpiper</td>
+      <td>Analyse targeted sequence capture data</td>
+      <td>HybPiper</td>
+      <td>HybPiper</td>
+      <td></td>
+      <td>HybPiper</td>
+      <td>Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.</td>
+      <td>Sequence trimming, Sequence assembly, Read mapping</td>
+      <td>Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics</td>
+      <td>To update</td>
+      <td>https://github.com/mossmatters/HybPiper</td>
+      <td>Sequence Analysis, Phylogenetics</td>
+      <td>hybpiper</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper</td>
+      <td>2.1.6</td>
+      <td>hybpiper</td>
+      <td>2.3.0</td>
+      <td>Sequence trimming, Sequence assembly, Read mapping</td>
+      <td>Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1571</td>
+      <td>1571</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>144</td>
+      <td>144</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1715</td>
+      <td>1715</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hyperstack_to_bleach_corrected_movie</td>
+      <td>hyperstack_to_bleach_corrected_movie</td>
+      <td>Generate blach corrected movie from hyperstack</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>hyperstack_to_bleach_corrected_movie</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie</td>
+      <td>20230328</td>
+      <td>Fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hyphy</td>
+      <td>hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary</td>
+      <td>Hypothesis Testing using Phylogenies</td>
+      <td>HyPhy</td>
+      <td>HyPhy</td>
+      <td></td>
+      <td>HyPhy</td>
+      <td>Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.</td>
+      <td>Statistical calculation</td>
+      <td>Phylogeny, Small molecules, Molecular interactions, pathways and networks</td>
+      <td>To update</td>
+      <td>http://www.hyphy.org</td>
+      <td>Phylogenetics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy</td>
+      <td>2.5.47</td>
+      <td>hyphy</td>
+      <td>2.5.62</td>
+      <td>Statistical calculation</td>
+      <td>Phylogeny, Small molecules, Molecular interactions, pathways and networks</td>
+      <td>17</td>
+      <td>2</td>
+      <td>17</td>
+      <td>0</td>
+      <td>17</td>
+      <td>2</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>17</td>
+      <td>12</td>
+      <td>0</td>
+      <td>11429</td>
+      <td>11429</td>
+      <td>428</td>
+      <td>428</td>
+      <td>7751</td>
+      <td>7751</td>
+      <td>676</td>
+      <td>676</td>
+      <td>715</td>
+      <td>715</td>
+      <td>58</td>
+      <td>58</td>
+      <td>19895</td>
+      <td>19895</td>
+      <td>1162</td>
+      <td>1162</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hypo</td>
+      <td>hypo</td>
+      <td>Super Fast &amp; Accurate Polisher for Long Read Genome Assemblies</td>
+      <td>HyPo</td>
+      <td>HyPo</td>
+      <td></td>
+      <td>HyPo</td>
+      <td>HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.</td>
+      <td>Optimisation and refinement, Genome assembly</td>
+      <td>Sequence assembly, Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/kensung-lab/hypo</td>
+      <td>Assembly</td>
+      <td>hypo</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo</td>
+      <td>1.0.3</td>
+      <td>hypo</td>
+      <td>1.0.3</td>
+      <td>Optimisation and refinement, Genome assembly</td>
+      <td>Sequence assembly, Genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>473</td>
+      <td>93</td>
+      <td>93</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>473</td>
+      <td>93</td>
+      <td>93</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>icescreen</td>
+      <td>icescreen</td>
+      <td>ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.</td>
+      <td>icescreen</td>
+      <td>icescreen</td>
+      <td></td>
+      <td>ICEscreen</td>
+      <td>A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.</td>
+      <td>Database search, Protein feature detection</td>
+      <td>Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation</td>
+      <td>To update</td>
+      <td>https://icescreen.migale.inrae.fr/</td>
+      <td>Genome annotation</td>
+      <td>icescreen</td>
+      <td>iuc</td>
+      <td>https://forgemia.inra.fr/ices_imes_analysis/icescreen</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen</td>
+      <td>1.3.1</td>
+      <td>icescreen</td>
+      <td>1.3.2</td>
+      <td>Database search, Protein feature detection</td>
+      <td>Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>idba_ud</td>
+      <td>idba_hybrid, idba_tran, idba_ud</td>
+      <td>Wrappers for the idba assembler variants.</td>
+      <td>idba</td>
+      <td>idba</td>
+      <td></td>
+      <td>IDBA</td>
+      <td>A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly</td>
+      <td>To update</td>
+      <td>https://i.cs.hku.hk/~alse/hkubrg/projects/index.html</td>
+      <td>Assembly</td>
+      <td>idba</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud</td>
+      <td></td>
+      <td>idba</td>
+      <td>1.1.3</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1200</td>
+      <td>1220</td>
+      <td>187</td>
+      <td>195</td>
+      <td>1588</td>
+      <td>1588</td>
+      <td>267</td>
+      <td>267</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2788</td>
+      <td>2808</td>
+      <td>454</td>
+      <td>462</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>idconvert</td>
+      <td>idconvert</td>
+      <td>Convert mass spectrometry identification files on linux or MacOSX</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>idconvert</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert</td>
+      <td></td>
+      <td>proteowizard</td>
+      <td>3_0_9992</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>241</td>
+      <td>276</td>
+      <td>24</td>
+      <td>33</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>241</td>
+      <td>276</td>
+      <td>24</td>
+      <td>33</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>idr</td>
+      <td>idr</td>
+      <td>Galaxy wrappers for the IDR package from Nathan Boleu</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/nboley/idr</td>
+      <td>Sequence Analysis</td>
+      <td>idr</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr</td>
+      <td>2.0.3</td>
+      <td>idr</td>
+      <td>2.0.4.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2953</td>
+      <td>3027</td>
+      <td>109</td>
+      <td>114</td>
+      <td>1710</td>
+      <td>1710</td>
+      <td>199</td>
+      <td>199</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4663</td>
+      <td>4737</td>
+      <td>308</td>
+      <td>313</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>idr_download</td>
+      <td>idr_download_by_ids</td>
+      <td>Image Data Resource downloading tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://idr.openmicroscopy.org</td>
+      <td>Data Source</td>
+      <td>idr_download_by_ids</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download</td>
+      <td>0.45</td>
+      <td>omero-py</td>
+      <td>5.11.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>404</td>
+      <td>404</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>24</td>
+      <td>1</td>
+      <td>1</td>
+      <td>428</td>
+      <td>428</td>
+      <td>38</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>iedb_api</td>
+      <td>iedb_api</td>
+      <td>Get epitope binding predictions from IEDB-API</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://tools.immuneepitope.org/main/tools-api/</td>
+      <td>Data Source, Sequence Analysis</td>
+      <td>iedb_api</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api</td>
+      <td>2.15.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1539</td>
+      <td>1539</td>
+      <td>35</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1539</td>
+      <td>1539</td>
+      <td>35</td>
+      <td>35</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>illumina_methylation_analyser</td>
+      <td>illumina_methylation_analyser</td>
+      <td>Methylation analyzer for Illumina 450k DNA emthylation microarrays</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser</td>
+      <td>Sequence Analysis</td>
+      <td>illumina_methylation_analyser</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser</td>
+      <td>0.1</td>
+      <td>Rscript</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>image_info</td>
+      <td>ip_imageinfo</td>
+      <td>Extracts image metadata</td>
+      <td></td>
+      <td></td>
+      <td>python-bioformats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>image_info</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info</td>
+      <td>5.7.1</td>
+      <td>bftools</td>
+      <td>6.7.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>273</td>
+      <td>659</td>
+      <td>101</td>
+      <td>102</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>153</td>
+      <td>153</td>
+      <td>15</td>
+      <td>15</td>
+      <td>426</td>
+      <td>812</td>
+      <td>116</td>
+      <td>117</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>image_math</td>
+      <td>image_math</td>
+      <td>Process images using arithmetic expressions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>image_math</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math</td>
+      <td>1.26.4</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>image_registration_affine</td>
+      <td>ip_image_registration</td>
+      <td>Intensity-based Image Registration</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>image_registration_affine</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine</td>
+      <td>0.0.3-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>imagecoordinates_flipaxis</td>
+      <td>imagecoordinates_flipaxis</td>
+      <td>Flip coordinate axes</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>imagecoordinates_flipaxis</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis</td>
+      <td>0.1-2</td>
+      <td>pandas</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>21409</td>
+      <td>21849</td>
+      <td>10</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21409</td>
+      <td>21849</td>
+      <td>10</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>imagej2</td>
+      <td>imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary</td>
+      <td>ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.</td>
+      <td>imagej</td>
+      <td>imagej</td>
+      <td>imagej2</td>
+      <td>ImageJ2</td>
+      <td>It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.</td>
+      <td>Image analysis, Image annotation, Visualisation</td>
+      <td>Imaging</td>
+      <td>To update</td>
+      <td>http://fiji.sc</td>
+      <td>Imaging</td>
+      <td>imagej2</td>
+      <td>imgteam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>Image analysis, Image annotation, Visualisation</td>
+      <td>Imaging</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>0</td>
+      <td>1731</td>
+      <td>1731</td>
+      <td>109</td>
+      <td>109</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1731</td>
+      <td>1731</td>
+      <td>109</td>
+      <td>109</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>improviser</td>
+      <td>proteomics_improviser</td>
+      <td>Visualisation of PepXML files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.improviser.uni-freiburg.de/</td>
+      <td>Proteomics</td>
+      <td>proteomics_improviser</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser</td>
+      <td>1.1.0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>incucyte_stack_and_upload_omero</td>
+      <td>incucyte_stack_and_upload_omero</td>
+      <td>Combine images to stack and upload to the omero server</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>incucyte_stack_and_upload_omero</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero</td>
+      <td>20231221</td>
+      <td>Fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>indels_3way</td>
+      <td>indels_3way</td>
+      <td>Fetch Indels from 3-way alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>indels_3way</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way</td>
+      <td>1.0.3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>18</td>
+      <td>22</td>
+      <td>1</td>
+      <td>1</td>
+      <td>44</td>
+      <td>292</td>
+      <td>3</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>62</td>
+      <td>314</td>
+      <td>4</td>
+      <td>22</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>infercnv</td>
+      <td>infercnv</td>
+      <td>Infer Copy Number Variation from Single-Cell RNA-Seq Data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/broadinstitute/infercnv</td>
+      <td>Transcriptomics, Variant Analysis</td>
+      <td>infercnv</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv</td>
+      <td>1.20.0</td>
+      <td>bioconductor-infercnv</td>
+      <td>1.20.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>infernal</td>
+      <td>infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat</td>
+      <td>Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.</td>
+      <td>infernal</td>
+      <td>infernal</td>
+      <td></td>
+      <td>Infernal</td>
+      <td>Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.</td>
+      <td>Nucleic acid feature detection</td>
+      <td>Sequence sites, features and motifs, Structural genomics</td>
+      <td>To update</td>
+      <td>http://infernal.janelia.org/</td>
+      <td>RNA</td>
+      <td>infernal</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/infernal</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal</td>
+      <td>1.1.4</td>
+      <td>infernal</td>
+      <td>1.1.5</td>
+      <td>Nucleic acid feature detection</td>
+      <td>Sequence sites, features and motifs, Structural genomics</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>59700</td>
+      <td>112582</td>
+      <td>223</td>
+      <td>282</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1157</td>
+      <td>1221</td>
+      <td>34</td>
+      <td>35</td>
+      <td>60857</td>
+      <td>113803</td>
+      <td>257</td>
+      <td>317</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>influx_data_manager</td>
+      <td>influx_data_manager</td>
+      <td>Handling influx_si data inputs in Galaxy workflows</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/</td>
+      <td>Metabolomics</td>
+      <td>influx_si_data_manager</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager</td>
+      <td>1.0.2</td>
+      <td>influx-si-data-manager</td>
+      <td>1.0.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>influx_si</td>
+      <td>influx_si</td>
+      <td>metabolic flux estimation based on [in]stationary labeling</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/sgsokol/influx</td>
+      <td>Metabolomics</td>
+      <td>influx_si</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si</td>
+      <td>7.0.1</td>
+      <td>influx_si</td>
+      <td>7.0.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>inforna</td>
+      <td></td>
+      <td>INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp</td>
+      <td>RNA</td>
+      <td>inforna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>instagraal</td>
+      <td>instagraal</td>
+      <td>Large genome reassembly based on Hi-C data</td>
+      <td>instagraal</td>
+      <td>instagraal</td>
+      <td></td>
+      <td>instaGRAAL</td>
+      <td>Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)</td>
+      <td>Genome assembly, Mapping assembly, Genetic mapping, Scaffolding</td>
+      <td>Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites</td>
+      <td>To update</td>
+      <td>https://github.com/koszullab/instaGRAAL</td>
+      <td>Assembly</td>
+      <td>instagraal</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/instagraal</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/instagraal</td>
+      <td>0.1.6</td>
+      <td></td>
+      <td></td>
+      <td>Genome assembly, Mapping assembly, Genetic mapping, Scaffolding</td>
+      <td>Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>157</td>
+      <td>157</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>157</td>
+      <td>157</td>
+      <td>14</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>instrain</td>
+      <td>instrain_compare, instrain_profile</td>
+      <td>InStrain is a tool for analysis of co-occurring genome populations from metagenomes</td>
+      <td>instrain</td>
+      <td>instrain</td>
+      <td></td>
+      <td>InStrain</td>
+      <td>InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification</td>
+      <td>SNP detection, Genome comparison</td>
+      <td>Mapping, Metagenomics</td>
+      <td>To update</td>
+      <td>https://instrain.readthedocs.io/en/latest/#</td>
+      <td>Metagenomics</td>
+      <td>instrain</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain</td>
+      <td>1.5.3</td>
+      <td>instrain</td>
+      <td>1.9.0</td>
+      <td>SNP detection, Genome comparison</td>
+      <td>Mapping, Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>102</td>
+      <td>102</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>102</td>
+      <td>102</td>
+      <td>16</td>
+      <td>16</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>intarna</td>
+      <td>intarna</td>
+      <td>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BackofenLab/IntaRNA</td>
+      <td>RNA</td>
+      <td>intarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna</td>
+      <td>3.4.1</td>
+      <td>intarna</td>
+      <td>3.4.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3071</td>
+      <td>7652</td>
+      <td>41</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3071</td>
+      <td>7652</td>
+      <td>41</td>
+      <td>47</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>integron_finder</td>
+      <td>integron_finder</td>
+      <td>"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"</td>
+      <td>integron_finder</td>
+      <td>integron_finder</td>
+      <td></td>
+      <td>Integron Finder</td>
+      <td>A tool to detect Integron in DNA sequences.</td>
+      <td>Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation</td>
+      <td>Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/gem-pasteur/Integron_Finder</td>
+      <td>Sequence Analysis</td>
+      <td>integronfinder</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder</td>
+      <td>2.0.5</td>
+      <td>integron_finder</td>
+      <td>2.0.5</td>
+      <td>Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation</td>
+      <td>Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55149</td>
+      <td>55149</td>
+      <td>161</td>
+      <td>161</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6085</td>
+      <td>6085</td>
+      <td>73</td>
+      <td>73</td>
+      <td>61234</td>
+      <td>61234</td>
+      <td>234</td>
+      <td>234</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>intermine_galaxy_exchange</td>
+      <td>galaxy_intermine_exchange</td>
+      <td>InterMine Exporter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/intermine</td>
+      <td>Convert Formats</td>
+      <td>intermine_galaxy_exchange</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange</td>
+      <td>0.0.1</td>
+      <td>coreutils</td>
+      <td>8.25</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>37</td>
+      <td>46</td>
+      <td>6</td>
+      <td>12</td>
+      <td>72</td>
+      <td>87</td>
+      <td>13</td>
+      <td>15</td>
+      <td>108</td>
+      <td>108</td>
+      <td>1</td>
+      <td>1</td>
+      <td>217</td>
+      <td>241</td>
+      <td>20</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>interpolation</td>
+      <td>interpolation_run_idw_interpolation</td>
+      <td>Run IDW interpolation based on a .csv and .geojson file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AquaINFRA/galaxy</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation</td>
+      <td>1.0</td>
+      <td>r-getopt</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>interproscan</td>
+      <td>interproscan</td>
+      <td>Interproscan queries the interpro database and provides annotations.</td>
+      <td>interproscan_ebi</td>
+      <td>interproscan_ebi</td>
+      <td></td>
+      <td>InterProScan (EBI)</td>
+      <td>Scan sequences against the InterPro protein signature databases.</td>
+      <td>Sequence motif recognition, Protein feature detection</td>
+      <td>Gene and protein families, Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.ebi.ac.uk/Tools/pfa/iprscan5/</td>
+      <td>Sequence Analysis</td>
+      <td>interproscan</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan</td>
+      <td>5.59-91.0</td>
+      <td>interproscan</td>
+      <td>5.59_91.0</td>
+      <td>Sequence motif recognition, Protein feature detection</td>
+      <td>Gene and protein families, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>34689</td>
+      <td>55189</td>
+      <td>1634</td>
+      <td>1713</td>
+      <td>65</td>
+      <td>65</td>
+      <td>15</td>
+      <td>15</td>
+      <td>10897</td>
+      <td>10897</td>
+      <td>607</td>
+      <td>607</td>
+      <td>45651</td>
+      <td>66151</td>
+      <td>2256</td>
+      <td>2335</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>intersect</td>
+      <td>gops_intersect_1</td>
+      <td>Intersect the intervals of two datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>intersect</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20472</td>
+      <td>349984</td>
+      <td>2351</td>
+      <td>3007</td>
+      <td>45587</td>
+      <td>778988</td>
+      <td>4359</td>
+      <td>14116</td>
+      <td>6087</td>
+      <td>7417</td>
+      <td>484</td>
+      <td>561</td>
+      <td>72146</td>
+      <td>1136389</td>
+      <td>7194</td>
+      <td>17684</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>interval2maf</td>
+      <td>Interval2Maf1</td>
+      <td>Extract MAF blocks given a set of intervals</td>
+      <td>bx-python</td>
+      <td>bx-python</td>
+      <td></td>
+      <td>bx-python</td>
+      <td>Tools for manipulating biological data, particularly multiple sequence alignments.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/</td>
+      <td>Genomic Interval Operations</td>
+      <td>interval2maf</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf</td>
+      <td>1.0.1+galaxy1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>32</td>
+      <td>107</td>
+      <td>7</td>
+      <td>10</td>
+      <td>758</td>
+      <td>19538</td>
+      <td>87</td>
+      <td>1246</td>
+      <td>16</td>
+      <td>24</td>
+      <td>2</td>
+      <td>2</td>
+      <td>806</td>
+      <td>19669</td>
+      <td>96</td>
+      <td>1258</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>intervene</td>
+      <td>intervene_pairwise, intervene_upset</td>
+      <td>Create pairwise and upset plots</td>
+      <td>intervene</td>
+      <td>intervene</td>
+      <td></td>
+      <td>Intervene</td>
+      <td>Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.</td>
+      <td>Sequence comparison, Sequence visualisation</td>
+      <td>Computational biology</td>
+      <td>Up-to-date</td>
+      <td>https://intervene.readthedocs.io</td>
+      <td>Statistics</td>
+      <td>intervene</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene</td>
+      <td>0.6.5</td>
+      <td>intervene</td>
+      <td>0.6.5</td>
+      <td>Sequence comparison, Sequence visualisation</td>
+      <td>Computational biology</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1557</td>
+      <td>1607</td>
+      <td>278</td>
+      <td>292</td>
+      <td>4458</td>
+      <td>4458</td>
+      <td>458</td>
+      <td>458</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6015</td>
+      <td>6065</td>
+      <td>736</td>
+      <td>750</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ipo</td>
+      <td>ipo4retgroup, ipo4xcmsSet</td>
+      <td>[W4M][LC-MS] IPO</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/rietho/IPO</td>
+      <td>Metabolomics</td>
+      <td>ipo</td>
+      <td>lecorguille</td>
+      <td>https://github.com/rietho/IPO</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo</td>
+      <td>1.10.0</td>
+      <td>bioconductor-ipo</td>
+      <td>1.28.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>iprscan5</td>
+      <td></td>
+      <td>Interproscan queries the interpro database and provides annotations.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.ebi.ac.uk/Tools/pfa/iprscan5/</td>
+      <td>Sequence Analysis</td>
+      <td>iprscan5</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>iqtree</td>
+      <td>iqtree</td>
+      <td>Efficient phylogenomic software by maximum likelihood</td>
+      <td>iqtree</td>
+      <td>iqtree</td>
+      <td></td>
+      <td>iqtree</td>
+      <td>A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time</td>
+      <td>Phylogenetic analysis, Sequence analysis</td>
+      <td>Phylogenetics</td>
+      <td>Up-to-date</td>
+      <td>http://www.iqtree.org/</td>
+      <td>Phylogenetics</td>
+      <td>iqtree</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree</td>
+      <td>2.3.6</td>
+      <td>iqtree</td>
+      <td>2.3.6</td>
+      <td>Phylogenetic analysis, Sequence analysis</td>
+      <td>Phylogenetics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>28279</td>
+      <td>28481</td>
+      <td>1623</td>
+      <td>1646</td>
+      <td>24662</td>
+      <td>24662</td>
+      <td>2093</td>
+      <td>2093</td>
+      <td>9780</td>
+      <td>10086</td>
+      <td>979</td>
+      <td>992</td>
+      <td>62721</td>
+      <td>63229</td>
+      <td>4695</td>
+      <td>4731</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>irissv</td>
+      <td>irissv</td>
+      <td>Refine insertion sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/mkirsche/Iris</td>
+      <td>Variant Analysis</td>
+      <td>irissv</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tools/irissv/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv</td>
+      <td>1.0.5</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>isescan</td>
+      <td>isescan</td>
+      <td>"ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."</td>
+      <td>ISEScan</td>
+      <td>ISEScan</td>
+      <td></td>
+      <td>ISEScan</td>
+      <td>Automated identification of insertion sequence elements in prokaryotic genomes.</td>
+      <td>Structural variation detection</td>
+      <td>Genomics, DNA structural variation, Sequence analysis, Genetic variation</td>
+      <td>To update</td>
+      <td>https://github.com/xiezhq/ISEScan</td>
+      <td>Sequence Analysis</td>
+      <td>ISEScan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan</td>
+      <td>1.7.2.3</td>
+      <td>isescan</td>
+      <td>1.7.2.1</td>
+      <td>Structural variation detection</td>
+      <td>Genomics, Sequence analysis, Genetic variation</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59386</td>
+      <td>59386</td>
+      <td>151</td>
+      <td>151</td>
+      <td>56</td>
+      <td>56</td>
+      <td>1</td>
+      <td>1</td>
+      <td>4741</td>
+      <td>4741</td>
+      <td>59</td>
+      <td>59</td>
+      <td>64183</td>
+      <td>64183</td>
+      <td>211</td>
+      <td>211</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>isoformswitchanalyzer</td>
+      <td>isoformswitchanalyzer</td>
+      <td>Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.</td>
+      <td>IsoformSwitchAnalyzeR</td>
+      <td>IsoformSwitchAnalyzeR</td>
+      <td></td>
+      <td>IsoformSwitchAnalyzeR</td>
+      <td>Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.</td>
+      <td>Sequence comparison, Sequence analysis</td>
+      <td>Computational biology, Gene transcripts</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>isoformswitchanalyzer</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer</td>
+      <td>1.20.0</td>
+      <td>bioconductor-isoformswitchanalyzer</td>
+      <td>2.2.0</td>
+      <td>Sequence comparison, Sequence analysis</td>
+      <td>Computational biology, Gene transcripts</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1301</td>
+      <td>1301</td>
+      <td>59</td>
+      <td>59</td>
+      <td>1331</td>
+      <td>1331</td>
+      <td>60</td>
+      <td>60</td>
+      <td>507</td>
+      <td>507</td>
+      <td>9</td>
+      <td>9</td>
+      <td>3139</td>
+      <td>3139</td>
+      <td>128</td>
+      <td>128</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>isolib</td>
+      <td>isolib</td>
+      <td>Create an isotopic pattern library for given compounds and adducts.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools/</td>
+      <td>Metabolomics</td>
+      <td>isolib</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/isolib</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/isolib</td>
+      <td>1.0.1+galaxy0</td>
+      <td>bioconductor-metabocoreutils</td>
+      <td>1.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>isoplot</td>
+      <td>isoplot</td>
+      <td>Isoplot is a software for the visualisation of MS data from C13 labelling experiments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Metabolomics, Visualization</td>
+      <td>isoplot</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/llegregam/Isoplot/tree/main</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot</td>
+      <td>1.3.0+galaxy1</td>
+      <td>isoplot</td>
+      <td>1.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>itsx</td>
+      <td>itsx</td>
+      <td>ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.</td>
+      <td>ITSx</td>
+      <td>ITSx</td>
+      <td></td>
+      <td>ITSx</td>
+      <td>TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.</td>
+      <td>Sequence feature detection</td>
+      <td>Functional, regulatory and non-coding RNA, Microbiology</td>
+      <td>Up-to-date</td>
+      <td>https://microbiology.se/software/itsx/</td>
+      <td>Metagenomics</td>
+      <td>itsx</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/itsx</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/itsx</td>
+      <td>1.1.3</td>
+      <td>itsx</td>
+      <td>1.1.3</td>
+      <td>Sequence feature detection</td>
+      <td>Functional, regulatory and non-coding RNA, Microbiology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1426</td>
+      <td>1426</td>
+      <td>71</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1426</td>
+      <td>1426</td>
+      <td>71</td>
+      <td>71</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ivar</td>
+      <td>ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants</td>
+      <td>iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/andersen-lab/ivar</td>
+      <td>Sequence Analysis</td>
+      <td>ivar</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar</td>
+      <td>1.4.3</td>
+      <td>ivar</td>
+      <td>1.4.3</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>1252220</td>
+      <td>1252220</td>
+      <td>2366</td>
+      <td>2366</td>
+      <td>126027</td>
+      <td>126027</td>
+      <td>2496</td>
+      <td>2496</td>
+      <td>41901</td>
+      <td>41901</td>
+      <td>993</td>
+      <td>993</td>
+      <td>1420148</td>
+      <td>1420148</td>
+      <td>5855</td>
+      <td>5855</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>iwtomics</td>
+      <td>iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot</td>
+      <td>Interval-Wise Testing for Omics Data</td>
+      <td>iwtomics</td>
+      <td>iwtomics</td>
+      <td></td>
+      <td>IWTomics</td>
+      <td>Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.</td>
+      <td>Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison</td>
+      <td>Statistics and probability</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/IWTomics.html</td>
+      <td>Statistics</td>
+      <td>iwtomics</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics</td>
+      <td>1.0.0</td>
+      <td>bioconductor-iwtomics</td>
+      <td>1.26.0</td>
+      <td>Differential gene expression analysis, Peak calling, Genome annotation, Comparison</td>
+      <td>Statistics and probability</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>675</td>
+      <td>690</td>
+      <td>27</td>
+      <td>28</td>
+      <td>159</td>
+      <td>251</td>
+      <td>29</td>
+      <td>49</td>
+      <td>383</td>
+      <td>383</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1217</td>
+      <td>1324</td>
+      <td>68</td>
+      <td>89</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jasminesv</td>
+      <td>jasminesv</td>
+      <td>Merge structural variants across samples</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/mkirsche/Jasmine/</td>
+      <td>Variant Analysis</td>
+      <td>jasminesv</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/jasminesv/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv</td>
+      <td>1.0.11</td>
+      <td>jasminesv</td>
+      <td>1.1.5</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>32</td>
+      <td>32</td>
+      <td>9</td>
+      <td>9</td>
+      <td>53</td>
+      <td>53</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>85</td>
+      <td>85</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jbrowse</td>
+      <td>jbrowse_to_standalone, jbrowse</td>
+      <td>JBrowse Genome Browser integrated as a Galaxy Tool</td>
+      <td>jbrowse</td>
+      <td>jbrowse</td>
+      <td></td>
+      <td>JBrowse</td>
+      <td>Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.</td>
+      <td>Genome visualisation</td>
+      <td>Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://jbrowse.org</td>
+      <td>Sequence Analysis</td>
+      <td>jbrowse</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse</td>
+      <td>1.16.11</td>
+      <td>jbrowse</td>
+      <td>1.16.11</td>
+      <td>Genome visualisation</td>
+      <td>Genomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>21153</td>
+      <td>22174</td>
+      <td>5514</td>
+      <td>5779</td>
+      <td>17428</td>
+      <td>17428</td>
+      <td>6458</td>
+      <td>6458</td>
+      <td>15673</td>
+      <td>17267</td>
+      <td>3248</td>
+      <td>3786</td>
+      <td>54254</td>
+      <td>56869</td>
+      <td>15220</td>
+      <td>16023</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jbrowse</td>
+      <td>jbrowse_to_container</td>
+      <td>A tool allowing to export a JBrowse dataset into a JBrowse docker container</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://jbrowse.org</td>
+      <td>Web Services</td>
+      <td>jbrowse_to_container</td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse</td>
+      <td></td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jbrowse2</td>
+      <td>jbrowse2</td>
+      <td>JBrowse2 Genome Browser integrated as a Galaxy Tool</td>
+      <td>jbrowse_2</td>
+      <td>jbrowse_2</td>
+      <td></td>
+      <td>JBrowse 2</td>
+      <td>Modular genome browser with views of synteny and structural variation.</td>
+      <td>Genome visualisation, Structure visualisation, Pathway visualisation</td>
+      <td>Mapping, Structural variation, Genomics, Gene structure, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://jbrowse.org</td>
+      <td>Sequence Analysis</td>
+      <td>jbrowse2</td>
+      <td>fubar</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2</td>
+      <td>2.15.4</td>
+      <td>jbrowse2</td>
+      <td>2.15.4</td>
+      <td>Genome visualisation, Structure visualisation, Pathway visualisation</td>
+      <td>Mapping, Structural variation, Genomics, Gene structure, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1312</td>
+      <td>1312</td>
+      <td>219</td>
+      <td>219</td>
+      <td>116</td>
+      <td>116</td>
+      <td>58</td>
+      <td>58</td>
+      <td>37</td>
+      <td>37</td>
+      <td>6</td>
+      <td>6</td>
+      <td>1465</td>
+      <td>1465</td>
+      <td>283</td>
+      <td>283</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jcvi_gff_stats</td>
+      <td>jcvi_gff_stats</td>
+      <td>Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/tanghaibao/jcvi</td>
+      <td>Sequence Analysis</td>
+      <td>jcvi_gff_stats</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats</td>
+      <td>0.8.4</td>
+      <td>jcvi</td>
+      <td>1.4.16</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2747</td>
+      <td>2926</td>
+      <td>596</td>
+      <td>637</td>
+      <td>2311</td>
+      <td>2311</td>
+      <td>741</td>
+      <td>741</td>
+      <td>1145</td>
+      <td>1145</td>
+      <td>469</td>
+      <td>469</td>
+      <td>6203</td>
+      <td>6382</td>
+      <td>1806</td>
+      <td>1847</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jellyfish</td>
+      <td>jellyfish</td>
+      <td>Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA</td>
+      <td>Jellyfish</td>
+      <td>Jellyfish</td>
+      <td></td>
+      <td>Jellyfish</td>
+      <td>A command-line algorithm for counting k-mers in DNA sequence.</td>
+      <td>k-mer counting</td>
+      <td>Sequence analysis, Genomics</td>
+      <td>To update</td>
+      <td>https://github.com/gmarcais/Jellyfish</td>
+      <td>Assembly</td>
+      <td>jellyfish</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish</td>
+      <td></td>
+      <td>kmer-jellyfish</td>
+      <td>2.3.1</td>
+      <td>k-mer counting</td>
+      <td>Sequence analysis, Genomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1825</td>
+      <td>1825</td>
+      <td>237</td>
+      <td>237</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>971</td>
+      <td>971</td>
+      <td>56</td>
+      <td>56</td>
+      <td>2796</td>
+      <td>2796</td>
+      <td>293</td>
+      <td>293</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>join</td>
+      <td>gops_join_1</td>
+      <td>Join the intervals of two datasets side-by-side</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>join</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15624</td>
+      <td>330820</td>
+      <td>1864</td>
+      <td>2438</td>
+      <td>52317</td>
+      <td>513688</td>
+      <td>10198</td>
+      <td>39421</td>
+      <td>1329</td>
+      <td>1645</td>
+      <td>213</td>
+      <td>289</td>
+      <td>69270</td>
+      <td>846153</td>
+      <td>12275</td>
+      <td>42148</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>join_files_by_id</td>
+      <td>join_files_by_id</td>
+      <td>This tool will join datasets according to a column with identifier</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id</td>
+      <td>Text Manipulation</td>
+      <td>join_files_by_id</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id</td>
+      <td>1.0</td>
+      <td>r-data.table</td>
+      <td>1.11.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>join_files_on_column_fuzzy</td>
+      <td>join_files_on_column_fuzzy</td>
+      <td>Join two files on a common column, allowing a certain difference.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>join_files_on_column_fuzzy</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy</td>
+      <td>1.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1980</td>
+      <td>2697</td>
+      <td>345</td>
+      <td>410</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1081</td>
+      <td>1081</td>
+      <td>44</td>
+      <td>44</td>
+      <td>3061</td>
+      <td>3778</td>
+      <td>389</td>
+      <td>454</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jq</td>
+      <td>jq</td>
+      <td>JQ is a lightweight and flexible command-line JSON processor</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://stedolan.github.io/jq/</td>
+      <td>Text Manipulation</td>
+      <td>jq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq</td>
+      <td>1.0</td>
+      <td>jq</td>
+      <td>1.5</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>660</td>
+      <td>2374</td>
+      <td>61</td>
+      <td>63</td>
+      <td>336</td>
+      <td>336</td>
+      <td>82</td>
+      <td>82</td>
+      <td>281</td>
+      <td>281</td>
+      <td>11</td>
+      <td>11</td>
+      <td>1277</td>
+      <td>2991</td>
+      <td>154</td>
+      <td>156</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jupyter_job</td>
+      <td>run_jupyter_job</td>
+      <td>Run jupyter notebook script in Galaxy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Machine Learning</td>
+      <td>run_jupyter_job</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job</td>
+      <td>0.0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>30</td>
+      <td>30</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>30</td>
+      <td>30</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>justdiff</td>
+      <td>justdiff</td>
+      <td>Unix diff</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Text Manipulation</td>
+      <td>justdiff</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff</td>
+      <td>3.10+galaxy0</td>
+      <td>diffutils</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>justgzip</td>
+      <td>justgzip</td>
+      <td>Compress fastq sequence files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Convert Formats</td>
+      <td>justgzip</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip</td>
+      <td>2.8+galaxy0</td>
+      <td>pigz</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jvarkit</td>
+      <td>jvarkit_wgscoverageplotter</td>
+      <td>Jvarkit : Java utilities for Bioinformatics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://lindenb.github.io/jvarkit/</td>
+      <td>SAM</td>
+      <td>jvarkit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit</td>
+      <td>20201223</td>
+      <td>jvarkit-wgscoverageplotter</td>
+      <td>20201223</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7179</td>
+      <td>7179</td>
+      <td>509</td>
+      <td>509</td>
+      <td>11138</td>
+      <td>11138</td>
+      <td>1145</td>
+      <td>1145</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18317</td>
+      <td>18317</td>
+      <td>1654</td>
+      <td>1654</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kallisto</td>
+      <td>kallisto_pseudo, kallisto_quant</td>
+      <td>kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.</td>
+      <td>kallisto</td>
+      <td>kallisto</td>
+      <td></td>
+      <td>kallisto</td>
+      <td>A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.</td>
+      <td>Gene expression profiling</td>
+      <td>Transcriptomics, RNA-seq, Gene expression</td>
+      <td>To update</td>
+      <td>https://pachterlab.github.io/kallisto/</td>
+      <td>Transcriptomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto</td>
+      <td>0.48.0</td>
+      <td>kallisto</td>
+      <td>0.51.1</td>
+      <td>Gene expression profiling</td>
+      <td>Transcriptomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>28398</td>
+      <td>29031</td>
+      <td>932</td>
+      <td>965</td>
+      <td>73705</td>
+      <td>80087</td>
+      <td>2603</td>
+      <td>3025</td>
+      <td>5333</td>
+      <td>5567</td>
+      <td>218</td>
+      <td>230</td>
+      <td>107436</td>
+      <td>114685</td>
+      <td>3753</td>
+      <td>4220</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kaptive</td>
+      <td>kaptive</td>
+      <td>Kaptive reports information about capsular (K) loci found in genome assemblies.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>kaptive</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive</td>
+      <td>0.3.0</td>
+      <td>kaptive</td>
+      <td>3.0.0b5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kat_filter</td>
+      <td>kat_@EXECUTABLE@</td>
+      <td>Filtering kmers or reads from a database of kmers hashes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>kat_filter</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter</td>
+      <td>2.3</td>
+      <td>kat</td>
+      <td>2.4.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kat_sect</td>
+      <td>kat_@EXECUTABLE@</td>
+      <td>SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>kat_sect</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect</td>
+      <td>2.3</td>
+      <td>kat</td>
+      <td>2.4.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kc-align</td>
+      <td>kc-align</td>
+      <td>Kc-Align custom tool</td>
+      <td>kc-align</td>
+      <td>kc-align</td>
+      <td></td>
+      <td>kc-align</td>
+      <td>A fast and accurate tool for performing codon-aware multiple sequence alignments</td>
+      <td>Multiple sequence alignment</td>
+      <td>Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/davebx/kc-align</td>
+      <td>Sequence Analysis</td>
+      <td>kc_align</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align</td>
+      <td>1.0.2</td>
+      <td>kcalign</td>
+      <td>1.0.2</td>
+      <td>Multiple sequence alignment</td>
+      <td>Mapping</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>379</td>
+      <td>379</td>
+      <td>53</td>
+      <td>53</td>
+      <td>8259</td>
+      <td>8259</td>
+      <td>271</td>
+      <td>271</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8638</td>
+      <td>8638</td>
+      <td>324</td>
+      <td>324</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kegalign</td>
+      <td>kegalign</td>
+      <td>A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/galaxyproject/KegAlign</td>
+      <td>Next Gen Mappers</td>
+      <td>kegalign</td>
+      <td>richard-burhans</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign</td>
+      <td>0.1.2.7</td>
+      <td>kegalign-full</td>
+      <td>0.1.2.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kernel_canonical_correlation_analysis</td>
+      <td>kcca1</td>
+      <td>Kernel Canonical Correlation Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>kernel_canonical_correlation_analysis</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis</td>
+      <td>1.0.0</td>
+      <td>rpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>62</td>
+      <td>70</td>
+      <td>4</td>
+      <td>4</td>
+      <td>207</td>
+      <td>334</td>
+      <td>27</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>269</td>
+      <td>404</td>
+      <td>31</td>
+      <td>75</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kernel_principal_component_analysis</td>
+      <td>kpca1</td>
+      <td>Kernel Principal Component Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>kernel_principal_component_analysis</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis</td>
+      <td>1.0.0</td>
+      <td>rpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>144</td>
+      <td>157</td>
+      <td>26</td>
+      <td>30</td>
+      <td>268</td>
+      <td>707</td>
+      <td>83</td>
+      <td>248</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>412</td>
+      <td>864</td>
+      <td>109</td>
+      <td>278</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>khmer</td>
+      <td>khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median</td>
+      <td>In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more</td>
+      <td>khmer</td>
+      <td>khmer</td>
+      <td></td>
+      <td>khmer</td>
+      <td>khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.</td>
+      <td>Standardisation and normalisation, De-novo assembly</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://khmer.readthedocs.org/</td>
+      <td>Assembly, Next Gen Mappers</td>
+      <td>khmer</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer</td>
+      <td>3.0.0a3</td>
+      <td>khmer</td>
+      <td>3.0.0a3</td>
+      <td>Standardisation and normalisation, De-novo assembly</td>
+      <td>Sequence assembly</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>1995</td>
+      <td>2091</td>
+      <td>174</td>
+      <td>193</td>
+      <td>1430</td>
+      <td>1430</td>
+      <td>389</td>
+      <td>389</td>
+      <td>1580</td>
+      <td>1580</td>
+      <td>56</td>
+      <td>56</td>
+      <td>5005</td>
+      <td>5101</td>
+      <td>619</td>
+      <td>638</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>king</td>
+      <td>king</td>
+      <td>Kinship-based INference for Gwas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://people.virginia.edu/~wc9c/KING/</td>
+      <td>Variant Analysis</td>
+      <td>king</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/king</td>
+      <td>2.2.7</td>
+      <td>king</td>
+      <td>2.2.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kinwalker</td>
+      <td></td>
+      <td>Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.bioinf.uni-leipzig.de/Software/Kinwalker/</td>
+      <td>RNA</td>
+      <td>kinwalker</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kleborate</td>
+      <td>kleborate</td>
+      <td>Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)</td>
+      <td>kleborate</td>
+      <td>kleborate</td>
+      <td></td>
+      <td>Kleborate</td>
+      <td>Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).</td>
+      <td>Multilocus sequence typing, Genome assembly, Virulence prediction</td>
+      <td>Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing</td>
+      <td>To update</td>
+      <td>https://github.com/katholt/Kleborate/wiki</td>
+      <td>Metagenomics</td>
+      <td>kleborate</td>
+      <td>iuc</td>
+      <td>https://github.com/katholt/Kleborate</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate</td>
+      <td>2.3.2</td>
+      <td>kleborate</td>
+      <td>3.1.0</td>
+      <td>Multilocus sequence typing, Genome assembly, Virulence prediction</td>
+      <td>Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>503</td>
+      <td>503</td>
+      <td>58</td>
+      <td>58</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>503</td>
+      <td>503</td>
+      <td>58</td>
+      <td>58</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kma</td>
+      <td>kma_map</td>
+      <td>Map with KMA</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/genomicepidemiology/kma</td>
+      <td>Next Gen Mappers</td>
+      <td>kma</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma</td>
+      <td>1.4.14</td>
+      <td>kma</td>
+      <td>1.4.15</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kmd_hmdb_data_plot</td>
+      <td>kmd_hmdb_data_plot</td>
+      <td>retrieves data from KMD HMDB API and produce plot and csv file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics</td>
+      <td>Metabolomics</td>
+      <td>kmd_hmdb_data_plot</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot</td>
+      <td>1.0.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kofamscan</td>
+      <td>kofamscan</td>
+      <td>Gene function annotation tool based on KEGG Orthology and hidden Markov model</td>
+      <td>kofamscan</td>
+      <td>kofamscan</td>
+      <td></td>
+      <td>kofamscan</td>
+      <td>KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.</td>
+      <td>Sequence analysis, Gene functional annotation</td>
+      <td>Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/takaram/kofam_scan</td>
+      <td>Sequence Analysis</td>
+      <td>kofamscan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan</td>
+      <td>1.3.0</td>
+      <td>kofamscan</td>
+      <td>1.3.0</td>
+      <td>Sequence analysis, Gene functional annotation</td>
+      <td>Genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1342</td>
+      <td>1342</td>
+      <td>63</td>
+      <td>63</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1342</td>
+      <td>1342</td>
+      <td>63</td>
+      <td>63</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kraken</td>
+      <td>kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken</td>
+      <td>Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.</td>
+      <td>kraken</td>
+      <td>kraken</td>
+      <td></td>
+      <td>Kraken</td>
+      <td>System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.</td>
+      <td>Taxonomic classification</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>To update</td>
+      <td>http://ccb.jhu.edu/software/kraken/</td>
+      <td>Metagenomics</td>
+      <td>kraken</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken</td>
+      <td></td>
+      <td>kraken</td>
+      <td>1.1.1</td>
+      <td>Taxonomic classification</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>48136</td>
+      <td>48164</td>
+      <td>2754</td>
+      <td>2760</td>
+      <td>59952</td>
+      <td>130398</td>
+      <td>5869</td>
+      <td>8654</td>
+      <td>29008</td>
+      <td>31148</td>
+      <td>1936</td>
+      <td>2200</td>
+      <td>137096</td>
+      <td>209710</td>
+      <td>10559</td>
+      <td>13614</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kraken2</td>
+      <td>kraken2</td>
+      <td>Kraken2 for taxonomic designation.</td>
+      <td>kraken2</td>
+      <td>kraken2</td>
+      <td></td>
+      <td>kraken2</td>
+      <td>Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.</td>
+      <td>Taxonomic classification</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>http://ccb.jhu.edu/software/kraken/</td>
+      <td>Metagenomics</td>
+      <td>kraken2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2</td>
+      <td>2.1.3</td>
+      <td>kraken2</td>
+      <td>2.1.3</td>
+      <td>Taxonomic classification</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>271367</td>
+      <td>271786</td>
+      <td>6384</td>
+      <td>6409</td>
+      <td>101752</td>
+      <td>101752</td>
+      <td>4662</td>
+      <td>4662</td>
+      <td>53562</td>
+      <td>53562</td>
+      <td>1663</td>
+      <td>1663</td>
+      <td>426681</td>
+      <td>427100</td>
+      <td>12709</td>
+      <td>12734</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kraken2tax</td>
+      <td>Kraken2Tax</td>
+      <td>Convert Kraken output to Galaxy taxonomy data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Metagenomics</td>
+      <td>kraken2tax</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax</td>
+      <td>1.2+galaxy0</td>
+      <td>gawk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>23008</td>
+      <td>23014</td>
+      <td>1060</td>
+      <td>1061</td>
+      <td>16194</td>
+      <td>24490</td>
+      <td>1719</td>
+      <td>2168</td>
+      <td>14898</td>
+      <td>14898</td>
+      <td>436</td>
+      <td>436</td>
+      <td>54100</td>
+      <td>62402</td>
+      <td>3215</td>
+      <td>3665</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kraken_biom</td>
+      <td>kraken_biom</td>
+      <td>Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/smdabdoub/kraken-biom</td>
+      <td>Metagenomics</td>
+      <td>kraken_biom</td>
+      <td>iuc</td>
+      <td>https://github.com/smdabdoub/kraken-biom</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom</td>
+      <td>1.2.0</td>
+      <td>kraken-biom</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3185</td>
+      <td>3185</td>
+      <td>495</td>
+      <td>495</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>385</td>
+      <td>385</td>
+      <td>48</td>
+      <td>48</td>
+      <td>3570</td>
+      <td>3570</td>
+      <td>543</td>
+      <td>543</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kraken_taxonomy_report</td>
+      <td>kraken_taxonomy_report</td>
+      <td>Kraken taxonomy report</td>
+      <td>Kraken-Taxonomy-Report</td>
+      <td>Kraken-Taxonomy-Report</td>
+      <td></td>
+      <td>Kraken-Taxonomy-Report</td>
+      <td>view report of classification for multiple samples</td>
+      <td>Visualisation, Classification</td>
+      <td>Metagenomics, Taxonomy</td>
+      <td>To update</td>
+      <td>https://github.com/blankenberg/Kraken-Taxonomy-Report</td>
+      <td>Metagenomics</td>
+      <td>kraken_taxonomy_report</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report</td>
+      <td>0.0.3</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td>Visualisation, Classification</td>
+      <td>Metagenomics, Taxonomy</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3981</td>
+      <td>3986</td>
+      <td>769</td>
+      <td>771</td>
+      <td>4087</td>
+      <td>5610</td>
+      <td>991</td>
+      <td>1284</td>
+      <td>88</td>
+      <td>88</td>
+      <td>41</td>
+      <td>41</td>
+      <td>8156</td>
+      <td>9684</td>
+      <td>1801</td>
+      <td>2096</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>krakentools</td>
+      <td>krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa</td>
+      <td>KrakenTools is a suite of scripts to be used alongside the Kraken</td>
+      <td>krakentools</td>
+      <td>krakentools</td>
+      <td></td>
+      <td>KrakenTools</td>
+      <td>KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files</td>
+      <td>Visualisation, Aggregation</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/jenniferlu717/KrakenTools</td>
+      <td>Metagenomics</td>
+      <td>krakentools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools</td>
+      <td>1.2</td>
+      <td>krakentools</td>
+      <td>1.2</td>
+      <td>Visualisation, Aggregation</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48516</td>
+      <td>48516</td>
+      <td>2373</td>
+      <td>2373</td>
+      <td>8787</td>
+      <td>8787</td>
+      <td>943</td>
+      <td>943</td>
+      <td>4369</td>
+      <td>4369</td>
+      <td>393</td>
+      <td>393</td>
+      <td>61672</td>
+      <td>61672</td>
+      <td>3709</td>
+      <td>3709</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>krocus</td>
+      <td>krocus</td>
+      <td>Predict MLST directly from uncorrected long reads</td>
+      <td>krocus</td>
+      <td>krocus</td>
+      <td></td>
+      <td>krocus</td>
+      <td>Predict MLST directly from uncorrected long reads</td>
+      <td>Multilocus sequence typing, k-mer counting</td>
+      <td>Public health and epidemiology</td>
+      <td>To update</td>
+      <td>https://github.com/quadram-institute-bioscience/krocus</td>
+      <td>Sequence Analysis</td>
+      <td>krocus</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus</td>
+      <td>1.0.1</td>
+      <td>krocus</td>
+      <td>1.0.3</td>
+      <td>Multilocus sequence typing, k-mer counting</td>
+      <td>Public health and epidemiology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>label_to_binary</td>
+      <td>label_to_binary</td>
+      <td>Convert label map to binary image</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>label_to_binary</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary</td>
+      <td>1.26.4</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>labelimage2points</td>
+      <td>ip_labelimage_to_points</td>
+      <td>Label Image to Points</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>labelimage2points</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points</td>
+      <td>0.2-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>34</td>
+      <td>38</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>38</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>labels</td>
+      <td>bg_labels</td>
+      <td>remaps and annotates alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/labels</td>
+      <td>Sequence Analysis</td>
+      <td>labels</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/labels</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/labels</td>
+      <td>1.0.5.0</td>
+      <td>labels</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>landmark_registration</td>
+      <td>ip_landmark_registration</td>
+      <td>Landmark Registration</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>landmark_registration</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration</td>
+      <td>0.1.0-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>887</td>
+      <td>927</td>
+      <td>13</td>
+      <td>15</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>891</td>
+      <td>931</td>
+      <td>16</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>last</td>
+      <td>last_al, last_db, last_split, last_train, last_maf_convert</td>
+      <td>LAST finds similar regions between sequences.</td>
+      <td>last</td>
+      <td>last</td>
+      <td></td>
+      <td>LAST</td>
+      <td>Short read alignment program incorporating quality scores</td>
+      <td>Sequence alignment</td>
+      <td>Genomics, Comparative genomics</td>
+      <td>To update</td>
+      <td>http://last.cbrc.jp/</td>
+      <td>Sequence Analysis</td>
+      <td>last</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/last</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/last</td>
+      <td>1205</td>
+      <td>last</td>
+      <td>1584</td>
+      <td>Sequence alignment</td>
+      <td>Comparative genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>329</td>
+      <td>329</td>
+      <td>94</td>
+      <td>94</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>329</td>
+      <td>329</td>
+      <td>94</td>
+      <td>94</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lastz</td>
+      <td>lastz_wrapper_2, lastz_d_wrapper</td>
+      <td>Galaxy wrappers for the Lastz and Lastz_d</td>
+      <td>lastz</td>
+      <td>lastz</td>
+      <td></td>
+      <td>LASTZ</td>
+      <td>A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.</td>
+      <td>Sequence alignment, Read mapping</td>
+      <td>Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lastz/lastz</td>
+      <td>Next Gen Mappers</td>
+      <td>lastz</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz</td>
+      <td>1.04.22</td>
+      <td>lastz</td>
+      <td>1.04.22</td>
+      <td>Sequence alignment, Read mapping</td>
+      <td>Genomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>77409</td>
+      <td>84356</td>
+      <td>447</td>
+      <td>475</td>
+      <td>156658</td>
+      <td>193590</td>
+      <td>870</td>
+      <td>3511</td>
+      <td>38579</td>
+      <td>38780</td>
+      <td>173</td>
+      <td>203</td>
+      <td>272646</td>
+      <td>316726</td>
+      <td>1490</td>
+      <td>4189</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lastz_paired_reads</td>
+      <td>lastz_paired_reads_wrapper</td>
+      <td>Galaxy wrapper for the Lastz alignment tool on paired reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Next Gen Mappers</td>
+      <td>lastz_paired_reads</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads</td>
+      <td>1.1.1</td>
+      <td>lastz</td>
+      <td>1.04.22</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7</td>
+      <td>9</td>
+      <td>3</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>10</td>
+      <td>5</td>
+      <td>5</td>
+      <td>15</td>
+      <td>19</td>
+      <td>8</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lca_wrapper</td>
+      <td>lca1</td>
+      <td>Find lowest diagnostic rank</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Metagenomics</td>
+      <td>lca_wrapper</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper</td>
+      <td>1.0.1</td>
+      <td>taxonomy</td>
+      <td>0.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>89</td>
+      <td>137</td>
+      <td>4</td>
+      <td>20</td>
+      <td>118</td>
+      <td>6136</td>
+      <td>15</td>
+      <td>1112</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>207</td>
+      <td>6273</td>
+      <td>19</td>
+      <td>1132</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lcrgenie</td>
+      <td>lcrgenie</td>
+      <td>Ligase Chain Reaction Genie</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/neilswainston/LCRGenie</td>
+      <td>Synthetic Biology</td>
+      <td>lcrgenie</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie</td>
+      <td>1.0.2</td>
+      <td>lcr_genie</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lda_analysis</td>
+      <td>lda_analy1</td>
+      <td>Perform Linear Discriminant Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Statistics</td>
+      <td>lda_analysis</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis</td>
+      <td>1.0.1</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>147</td>
+      <td>159</td>
+      <td>46</td>
+      <td>48</td>
+      <td>793</td>
+      <td>1538</td>
+      <td>101</td>
+      <td>314</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>3</td>
+      <td>940</td>
+      <td>1701</td>
+      <td>147</td>
+      <td>365</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>legsta</td>
+      <td>legsta</td>
+      <td>Performs in silico Legionella pneumophila sequence based typing.</td>
+      <td>legsta</td>
+      <td>legsta</td>
+      <td></td>
+      <td>legsta</td>
+      <td>Performs in silico Legionella pneumophila sequence based typing</td>
+      <td>Sequence analysis</td>
+      <td>Public health and epidemiology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tseemann/legsta</td>
+      <td>Sequence Analysis</td>
+      <td>legsta</td>
+      <td>iuc</td>
+      <td>https://github.com/tseemann/legsta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta</td>
+      <td>0.5.1</td>
+      <td>legsta</td>
+      <td>0.5.1</td>
+      <td>Sequence analysis</td>
+      <td>Public health and epidemiology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>92</td>
+      <td>92</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>92</td>
+      <td>92</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>length_and_gc_content</td>
+      <td>length_and_gc_content</td>
+      <td>Gets gene length and gc content from a fasta and a GTF file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content</td>
+      <td>Fasta Manipulation, Statistics, RNA, Micro-array Analysis</td>
+      <td>length_and_gc_content</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content</td>
+      <td>0.1.2</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4349</td>
+      <td>4466</td>
+      <td>666</td>
+      <td>698</td>
+      <td>2093</td>
+      <td>2286</td>
+      <td>928</td>
+      <td>998</td>
+      <td>201</td>
+      <td>201</td>
+      <td>77</td>
+      <td>77</td>
+      <td>6643</td>
+      <td>6953</td>
+      <td>1671</td>
+      <td>1773</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lfq_protein_quant</td>
+      <td>lfq_protein_quant</td>
+      <td>Enable protein summarisation and quantitation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/compomics/LFQ_galaxy_p</td>
+      <td>Proteomics</td>
+      <td>lfq_protein_quant</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant</td>
+      <td>1.0</td>
+      <td>bioconductor-msnbase</td>
+      <td>2.28.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>78</td>
+      <td>116</td>
+      <td>12</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>78</td>
+      <td>116</td>
+      <td>12</td>
+      <td>19</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lighter</td>
+      <td>lighter</td>
+      <td>Lighter is a kmer-based error correction method for whole genome sequencing data</td>
+      <td>lighter</td>
+      <td>lighter</td>
+      <td></td>
+      <td>Lighter</td>
+      <td>Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.</td>
+      <td>k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection</td>
+      <td>Sequencing, Whole genome sequencing, DNA, Genomics</td>
+      <td>To update</td>
+      <td>https://github.com/mourisl/Lighter</td>
+      <td>Sequence Analysis, Fasta Manipulation</td>
+      <td>lighter</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/lighter</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/lighter</td>
+      <td>1.0</td>
+      <td>lighter</td>
+      <td>1.1.3</td>
+      <td>k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection</td>
+      <td>Whole genome sequencing, DNA, Genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>149</td>
+      <td>171</td>
+      <td>27</td>
+      <td>30</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>149</td>
+      <td>171</td>
+      <td>27</td>
+      <td>30</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>limma_voom</td>
+      <td>limma_voom</td>
+      <td>Perform RNA-Seq differential expression analysis using limma voom pipeline</td>
+      <td>limma</td>
+      <td>limma</td>
+      <td></td>
+      <td>limma</td>
+      <td>Data analysis, linear models and differential expression for microarray data.</td>
+      <td>RNA-Seq analysis</td>
+      <td>Molecular biology, Genetics</td>
+      <td>Up-to-date</td>
+      <td>http://bioconductor.org/packages/release/bioc/html/limma.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>limma_voom</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom</td>
+      <td>3.58.1</td>
+      <td>bioconductor-limma</td>
+      <td>3.58.1</td>
+      <td>RNA-Seq analysis</td>
+      <td>Molecular biology, Genetics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>23442</td>
+      <td>24466</td>
+      <td>2379</td>
+      <td>2475</td>
+      <td>45734</td>
+      <td>49342</td>
+      <td>4565</td>
+      <td>5032</td>
+      <td>9327</td>
+      <td>9517</td>
+      <td>835</td>
+      <td>842</td>
+      <td>78503</td>
+      <td>83325</td>
+      <td>7779</td>
+      <td>8349</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lineagespot</td>
+      <td>lineagespot</td>
+      <td>Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)</td>
+      <td>lineagespot</td>
+      <td>lineagespot</td>
+      <td></td>
+      <td>lineagespot</td>
+      <td>Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).</td>
+      <td>Variant calling</td>
+      <td>Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation</td>
+      <td>To update</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html</td>
+      <td>Metagenomics, Sequence Analysis</td>
+      <td>lineagespot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot</td>
+      <td>1.6.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td>Variant calling</td>
+      <td>Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>39</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>39</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>linear_regression</td>
+      <td>LinearRegression1</td>
+      <td>Perform Linear Regression</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>linear_regression</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression</td>
+      <td>1.0.1</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>146</td>
+      <td>1103</td>
+      <td>31</td>
+      <td>271</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>146</td>
+      <td>1103</td>
+      <td>31</td>
+      <td>271</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>links</td>
+      <td>links</td>
+      <td>Scaffold genome assemblies with long reads.</td>
+      <td>links</td>
+      <td>links</td>
+      <td></td>
+      <td>LINKS</td>
+      <td>LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.</td>
+      <td>Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming</td>
+      <td>Sequence assembly, Mapping, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bcgsc/LINKS</td>
+      <td>Assembly</td>
+      <td>links</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/links</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/links</td>
+      <td>2.0.1</td>
+      <td>links</td>
+      <td>2.0.1</td>
+      <td>Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming</td>
+      <td>Sequence assembly, Mapping, Sequencing</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>512</td>
+      <td>512</td>
+      <td>126</td>
+      <td>126</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>480</td>
+      <td>480</td>
+      <td>65</td>
+      <td>65</td>
+      <td>992</td>
+      <td>992</td>
+      <td>191</td>
+      <td>191</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>locarna</td>
+      <td>locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile</td>
+      <td>LocARNA - A suite for multiple alignment and folding of RNAs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://www.bioinf.uni-freiburg.de/Software/LocARNA/</td>
+      <td>RNA</td>
+      <td>locarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna</td>
+      <td>2.0.1</td>
+      <td>locarna</td>
+      <td>2.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>314</td>
+      <td>350</td>
+      <td>36</td>
+      <td>46</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>314</td>
+      <td>350</td>
+      <td>36</td>
+      <td>46</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lofreq</td>
+      <td>lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi</td>
+      <td>LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://csb5.github.io/lofreq/</td>
+      <td>Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq</td>
+      <td>2.1.5</td>
+      <td>lofreq</td>
+      <td>2.1.5</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>4176367</td>
+      <td>4176367</td>
+      <td>4301</td>
+      <td>4301</td>
+      <td>509615</td>
+      <td>509615</td>
+      <td>8213</td>
+      <td>8213</td>
+      <td>106342</td>
+      <td>106342</td>
+      <td>1815</td>
+      <td>1815</td>
+      <td>4792324</td>
+      <td>4792324</td>
+      <td>14329</td>
+      <td>14329</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>logistic_regression_vif</td>
+      <td>LogisticRegression</td>
+      <td>Perform Logistic Regression with vif</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis, Statistics</td>
+      <td>logistic_regression_vif</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif</td>
+      <td>1.0.1</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>64</td>
+      <td>173</td>
+      <td>12</td>
+      <td>48</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>64</td>
+      <td>173</td>
+      <td>12</td>
+      <td>48</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>logol</td>
+      <td>logol_wrapper</td>
+      <td>Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://logol.genouest.org/web/app.php/logol</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/logol</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/logol</td>
+      <td>1.7.8</td>
+      <td>logol</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>longorf</td>
+      <td>longORF</td>
+      <td>obtain longest ORF in six-frame translations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>longorf</td>
+      <td>mbernt</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf</td>
+      <td>0.3.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lorikeet</td>
+      <td>lorikeet_spoligotype</td>
+      <td>Tools for M. tuberculosis DNA fingerprinting (spoligotyping)</td>
+      <td>lorikeet</td>
+      <td>lorikeet</td>
+      <td></td>
+      <td>lorikeet</td>
+      <td>Tools for M. tuberculosis DNA fingerprinting (spoligotyping)</td>
+      <td>Sequence analysis, Genotyping</td>
+      <td>Genotype and phenotype</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/AbeelLab/lorikeet</td>
+      <td>Sequence Analysis</td>
+      <td>lorikeet_spoligotype</td>
+      <td>iuc</td>
+      <td>https://github.com/AbeelLab/lorikeet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet</td>
+      <td>20</td>
+      <td>lorikeet</td>
+      <td>20</td>
+      <td>Sequence analysis, Genotyping</td>
+      <td>Genotype and phenotype</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>822</td>
+      <td>822</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>822</td>
+      <td>822</td>
+      <td>14</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lotus2</td>
+      <td>lotus2</td>
+      <td>LotuS2 OTU processing pipeline</td>
+      <td>lotus2</td>
+      <td>lotus2</td>
+      <td></td>
+      <td>lotus2</td>
+      <td>LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.</td>
+      <td>Sequence feature detection, DNA barcoding</td>
+      <td>Metagenomics, Taxonomy, Microbial ecology</td>
+      <td>To update</td>
+      <td>http://lotus2.earlham.ac.uk/</td>
+      <td>Metagenomics</td>
+      <td>lotus2</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2</td>
+      <td>2.32</td>
+      <td>lotus2</td>
+      <td>2.34.1</td>
+      <td>Sequence feature detection, DNA barcoding</td>
+      <td>Metagenomics, Taxonomy, Microbial ecology</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1219</td>
+      <td>1219</td>
+      <td>182</td>
+      <td>182</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>37</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1256</td>
+      <td>1256</td>
+      <td>186</td>
+      <td>186</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ltq_iquant_cli</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>ltq_iquant_cli</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lumpy_smoove</td>
+      <td>lumpy_smoove, vcf2hrdetect</td>
+      <td>Galaxy wrapper of the lumpy-using smoove workflow</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>lumpy_smoove</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove</td>
+      <td>0.2.8+galaxy1</td>
+      <td>svtyper</td>
+      <td>0.7.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lumpy_sv</td>
+      <td>lumpy_prep, lumpy_sv</td>
+      <td>LUMPY - a general probabilistic framework for structural variant discovery</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://layerlab.org/software/</td>
+      <td>Variant Analysis</td>
+      <td>lumpy_sv</td>
+      <td>iuc</td>
+      <td>https://github.com/arq5x/lumpy-sv</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv</td>
+      <td>0.3.1</td>
+      <td>lumpy-sv</td>
+      <td>0.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1534</td>
+      <td>1534</td>
+      <td>199</td>
+      <td>199</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1534</td>
+      <td>1534</td>
+      <td>199</td>
+      <td>199</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lumpy_sv</td>
+      <td>lumpy</td>
+      <td>Find structural variations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>lumpy_sv</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv</td>
+      <td>1.3</td>
+      <td>lumpy-sv</td>
+      <td>0.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>m6anet</td>
+      <td>m6anet</td>
+      <td>m6anet to detect m6A RNA modifications from nanopore data</td>
+      <td>m6Anet</td>
+      <td>m6Anet</td>
+      <td></td>
+      <td>m6Anet</td>
+      <td>Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.</td>
+      <td>Quantification, Imputation, Gene expression profiling</td>
+      <td>RNA-Seq, Transcriptomics, RNA, Machine learning</td>
+      <td>Up-to-date</td>
+      <td>https://m6anet.readthedocs.io/en/latest</td>
+      <td>Sequence Analysis</td>
+      <td>m6anet</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet</td>
+      <td>2.1.0</td>
+      <td>m6anet</td>
+      <td>2.1.0</td>
+      <td>Quantification, Imputation, Gene expression profiling</td>
+      <td>RNA-Seq, Transcriptomics, RNA, Machine learning</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>44</td>
+      <td>44</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>44</td>
+      <td>44</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maaslin2</td>
+      <td>maaslin2</td>
+      <td>MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.</td>
+      <td>maaslin2</td>
+      <td>maaslin2</td>
+      <td></td>
+      <td>MaAsLin2</td>
+      <td>MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.</td>
+      <td>Filtering, Statistical calculation, Standardisation and normalisation, Visualisation</td>
+      <td>Metagenomics, Statistics and probability</td>
+      <td>Up-to-date</td>
+      <td>http://huttenhower.sph.harvard.edu/maaslin</td>
+      <td>Metagenomics</td>
+      <td>maaslin2</td>
+      <td>iuc</td>
+      <td>https://github.com/biobakery/Maaslin2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2</td>
+      <td>1.18.0</td>
+      <td>bioconductor-maaslin2</td>
+      <td>1.18.0</td>
+      <td>Filtering, Standardisation and normalisation, Visualisation</td>
+      <td>Metagenomics, Statistics and probability</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2835</td>
+      <td>2835</td>
+      <td>59</td>
+      <td>59</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2835</td>
+      <td>2835</td>
+      <td>59</td>
+      <td>59</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>macs2</td>
+      <td>macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak</td>
+      <td>MACS - Model-based Analysis of ChIP-Seq</td>
+      <td>macs</td>
+      <td>macs</td>
+      <td></td>
+      <td>MACS</td>
+      <td>Model-based Analysis of ChIP-seq data.</td>
+      <td>Peak calling, Enrichment analysis, Gene regulatory network analysis</td>
+      <td>ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/taoliu/MACS</td>
+      <td>Sequence Analysis, Statistics</td>
+      <td>macs2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2</td>
+      <td>2.2.9.1</td>
+      <td>macs2</td>
+      <td>2.2.9.1</td>
+      <td>Peak calling, Enrichment analysis, Gene regulatory network analysis</td>
+      <td>ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites</td>
+      <td>9</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>87810</td>
+      <td>96069</td>
+      <td>4980</td>
+      <td>5629</td>
+      <td>153500</td>
+      <td>227569</td>
+      <td>12946</td>
+      <td>18825</td>
+      <td>10988</td>
+      <td>12301</td>
+      <td>692</td>
+      <td>807</td>
+      <td>252298</td>
+      <td>335939</td>
+      <td>18618</td>
+      <td>25261</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maf_cpg_filter</td>
+      <td>cpgFilter</td>
+      <td>Mask CpG/non-CpG sites from MAF file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>maf_cpg_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>85</td>
+      <td>356</td>
+      <td>6</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>85</td>
+      <td>356</td>
+      <td>6</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maf_stats</td>
+      <td>maf_stats1</td>
+      <td>MAF Coverage statistics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/</td>
+      <td>Genomic Interval Operations</td>
+      <td>maf_stats</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats</td>
+      <td>1.0.2+galaxy0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15</td>
+      <td>21</td>
+      <td>7</td>
+      <td>9</td>
+      <td>227</td>
+      <td>2470</td>
+      <td>52</td>
+      <td>464</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>243</td>
+      <td>2492</td>
+      <td>60</td>
+      <td>474</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mafft</td>
+      <td>rbc_mafft_add, rbc_mafft</td>
+      <td>Multiple alignment program for amino acid or nucleotide sequences</td>
+      <td>MAFFT</td>
+      <td>MAFFT</td>
+      <td></td>
+      <td>MAFFT</td>
+      <td>MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.</td>
+      <td>Multiple sequence alignment</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://mafft.cbrc.jp/alignment/software/</td>
+      <td>RNA</td>
+      <td>mafft</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mafft</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mafft</td>
+      <td>7.526</td>
+      <td>mafft</td>
+      <td>7.525</td>
+      <td>Multiple sequence alignment</td>
+      <td>Sequence analysis</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>172433</td>
+      <td>174456</td>
+      <td>1865</td>
+      <td>1951</td>
+      <td>108640</td>
+      <td>122790</td>
+      <td>4266</td>
+      <td>5521</td>
+      <td>20027</td>
+      <td>20027</td>
+      <td>1172</td>
+      <td>1172</td>
+      <td>301100</td>
+      <td>317273</td>
+      <td>7303</td>
+      <td>8644</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maftoaxt</td>
+      <td>maftoaxt</td>
+      <td>Convert dataset from MAF to axt format</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Convert Formats</td>
+      <td>ucsc_maftoaxt</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt</td>
+      <td>469</td>
+      <td>ucsc-maftoaxt</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mageck</td>
+      <td>mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test</td>
+      <td>Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.</td>
+      <td>mageck</td>
+      <td>mageck</td>
+      <td></td>
+      <td>MAGeCK</td>
+      <td>Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.</td>
+      <td>Genetic variation analysis</td>
+      <td>Genetics, Genetic variation, Genomics</td>
+      <td>To update</td>
+      <td>https://sourceforge.net/projects/mageck/</td>
+      <td>Genome editing</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck</td>
+      <td>0.5.9.2</td>
+      <td>mageck</td>
+      <td>0.5.9.5</td>
+      <td>Genetic variation analysis</td>
+      <td>Genetics, Genetic variation, Genomics</td>
+      <td>3</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>3</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>11761</td>
+      <td>12093</td>
+      <td>873</td>
+      <td>889</td>
+      <td>5762</td>
+      <td>5762</td>
+      <td>473</td>
+      <td>473</td>
+      <td>5610</td>
+      <td>5610</td>
+      <td>343</td>
+      <td>343</td>
+      <td>23133</td>
+      <td>23465</td>
+      <td>1689</td>
+      <td>1705</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mahotas_features</td>
+      <td>ip_mahotas_features</td>
+      <td>Compute image features using mahotas.</td>
+      <td></td>
+      <td></td>
+      <td>mahotas-feature-computation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/luispedro/mahotas</td>
+      <td>Imaging</td>
+      <td>mahotas_features</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features</td>
+      <td>0.7-2</td>
+      <td>mahotas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>39</td>
+      <td>44</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>44</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>make_nr</td>
+      <td>make_nr</td>
+      <td>Make a FASTA file non-redundant</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr</td>
+      <td>Fasta Manipulation, Sequence Analysis</td>
+      <td>make_nr</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr</td>
+      <td>0.0.3</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maker</td>
+      <td>maker, maker_map_ids</td>
+      <td>MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.</td>
+      <td>maker</td>
+      <td>maker</td>
+      <td></td>
+      <td>MAKER</td>
+      <td>Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.</td>
+      <td>Genome annotation</td>
+      <td>Genomics, DNA, Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.yandell-lab.org/software/maker.html</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker</td>
+      <td>2.31.11</td>
+      <td>maker</td>
+      <td>3.01.03</td>
+      <td>Genome annotation</td>
+      <td>Genomics, DNA, Sequence analysis</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>6417</td>
+      <td>6861</td>
+      <td>1315</td>
+      <td>1366</td>
+      <td>7235</td>
+      <td>7235</td>
+      <td>1858</td>
+      <td>1858</td>
+      <td>4112</td>
+      <td>4112</td>
+      <td>902</td>
+      <td>902</td>
+      <td>17764</td>
+      <td>18208</td>
+      <td>4075</td>
+      <td>4126</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maldiquant</td>
+      <td>maldi_quant_peak_detection, maldi_quant_preprocessing</td>
+      <td>MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://strimmerlab.org/software/maldiquant/</td>
+      <td>Proteomics</td>
+      <td>MALDIquant</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant</td>
+      <td>1.22.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1452</td>
+      <td>3822</td>
+      <td>61</td>
+      <td>68</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1065</td>
+      <td>1065</td>
+      <td>39</td>
+      <td>39</td>
+      <td>2517</td>
+      <td>4887</td>
+      <td>100</td>
+      <td>107</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>malt</td>
+      <td>malt_run</td>
+      <td>Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/husonlab/malt</td>
+      <td>Next Gen Mappers</td>
+      <td>malt_run</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt</td>
+      <td>0.5.3</td>
+      <td>malt</td>
+      <td>0.62</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>24</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>24</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>manta</td>
+      <td>manta</td>
+      <td>Structural variant and indel caller for mapped sequencing data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>manta</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/manta</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/manta</td>
+      <td>1.6</td>
+      <td>manta</td>
+      <td>1.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>34</td>
+      <td>34</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>34</td>
+      <td>34</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>map_param_value</td>
+      <td>map_param_value</td>
+      <td>Map a parameter value to another value</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>map_param_value</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3780</td>
+      <td>3780</td>
+      <td>67</td>
+      <td>67</td>
+      <td>1012</td>
+      <td>1012</td>
+      <td>57</td>
+      <td>57</td>
+      <td>105</td>
+      <td>105</td>
+      <td>3</td>
+      <td>3</td>
+      <td>4897</td>
+      <td>4897</td>
+      <td>127</td>
+      <td>127</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>map_peptides_to_bed</td>
+      <td>map_peptides_to_bed</td>
+      <td>Map peptides to a reference genome for display by a genome browser</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>map_peptides_to_bed</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed</td>
+      <td>0.2</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>38</td>
+      <td>44</td>
+      <td>6</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>38</td>
+      <td>44</td>
+      <td>6</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mapping_quality_stats</td>
+      <td>mapqstatistics</td>
+      <td>Collects and shows the distribution of MAPQ values in a BAM alignment file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Sequence Analysis, Statistics</td>
+      <td>mapping_quality_stats</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats</td>
+      <td>0.22.0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mapping_to_ucsc</td>
+      <td>mapToUCSC</td>
+      <td>Format mapping data as UCSC custom track</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Visualization, Convert Formats, Next Gen Mappers</td>
+      <td>mapping_to_ucsc</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mapseq</td>
+      <td>mapseq</td>
+      <td>fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.</td>
+      <td>mapseq</td>
+      <td>mapseq</td>
+      <td></td>
+      <td>MAPseq</td>
+      <td>Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .</td>
+      <td>k-mer counting</td>
+      <td>Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs</td>
+      <td>To update</td>
+      <td>https://github.com/jfmrod/MAPseq</td>
+      <td>Metagenomics</td>
+      <td>mapseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq</td>
+      <td>2.1.1</td>
+      <td>perl</td>
+      <td></td>
+      <td>k-mer counting</td>
+      <td>Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7871</td>
+      <td>7871</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7871</td>
+      <td>7871</td>
+      <td>32</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>marine_omics</td>
+      <td>sanntis_marine</td>
+      <td>The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic &amp; metagenomic data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Finn-Lab/SanntiS</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics</td>
+      <td>0.9.3.5</td>
+      <td>sanntis</td>
+      <td>0.9.3.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>51</td>
+      <td>51</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>51</td>
+      <td>51</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mash</td>
+      <td>mash_screen, mash_sketch</td>
+      <td>Fast genome and metagenome distance estimation using MinHash</td>
+      <td>mash</td>
+      <td>mash</td>
+      <td></td>
+      <td>Mash</td>
+      <td>Fast genome and metagenome distance estimation using MinHash.</td>
+      <td>Sequence distance matrix generation</td>
+      <td>Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/marbl/Mash</td>
+      <td>Metagenomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash</td>
+      <td>2.3</td>
+      <td>mash</td>
+      <td>2.3</td>
+      <td>Sequence distance matrix generation</td>
+      <td>Metagenomics, Statistics and probability, Sequence analysis, DNA mutation</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>10119</td>
+      <td>10119</td>
+      <td>61</td>
+      <td>61</td>
+      <td>19</td>
+      <td>19</td>
+      <td>9</td>
+      <td>9</td>
+      <td>647</td>
+      <td>647</td>
+      <td>7</td>
+      <td>7</td>
+      <td>10785</td>
+      <td>10785</td>
+      <td>77</td>
+      <td>77</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mashmap</td>
+      <td>mashmap</td>
+      <td>Fast local alignment boundaries</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap</td>
+      <td>Sequence Analysis</td>
+      <td>mashmap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap</td>
+      <td>3.1.3</td>
+      <td>mashmap</td>
+      <td>3.1.3</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>894</td>
+      <td>894</td>
+      <td>12</td>
+      <td>12</td>
+      <td>81</td>
+      <td>81</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>975</td>
+      <td>975</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>masigpro</td>
+      <td>masigpro</td>
+      <td>Identify significantly differential expression profiles in time-course microarray experiments</td>
+      <td>masigpro</td>
+      <td>masigpro</td>
+      <td></td>
+      <td>maSigPro</td>
+      <td>Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.</td>
+      <td>Regression analysis</td>
+      <td>Gene expression, Molecular genetics, Microarray experiment, RNA-Seq</td>
+      <td>To update</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>masigpro</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro</td>
+      <td>1.49.3</td>
+      <td>coreutils</td>
+      <td>8.25</td>
+      <td>Regression analysis</td>
+      <td>Gene expression, Microarray experiment, RNA-Seq</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>471</td>
+      <td>582</td>
+      <td>35</td>
+      <td>40</td>
+      <td>589</td>
+      <td>589</td>
+      <td>80</td>
+      <td>80</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1060</td>
+      <td>1171</td>
+      <td>115</td>
+      <td>120</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>matchms</td>
+      <td>matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting</td>
+      <td>Searching, filtering and converting mass spectral libraries.</td>
+      <td>matchms</td>
+      <td>matchms</td>
+      <td></td>
+      <td>Matchms</td>
+      <td>Tool to import, process, clean, and compare mass spectrometry data.</td>
+      <td>Spectral library search, Format validation, Filtering</td>
+      <td>Metabolomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/matchms/matchms</td>
+      <td>Metabolomics</td>
+      <td>matchms</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/matchms</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/matchms</td>
+      <td>0.27.0</td>
+      <td>matchms</td>
+      <td>0.27.0</td>
+      <td>Spectral library search, Format validation, Filtering</td>
+      <td>Metabolomics</td>
+      <td>2</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>2</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1620</td>
+      <td>1620</td>
+      <td>70</td>
+      <td>70</td>
+      <td>27</td>
+      <td>27</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1685</td>
+      <td>1685</td>
+      <td>12</td>
+      <td>12</td>
+      <td>3332</td>
+      <td>3332</td>
+      <td>90</td>
+      <td>90</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mauve_contig_mover</td>
+      <td>mauve_contig_mover</td>
+      <td>Order a draft genome relative to a related reference genome</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/mauve_contig_mover</td>
+      <td>Sequence Analysis</td>
+      <td>mauve_contig_mover</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/mauve_contig_mover</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover</td>
+      <td>1.0.10</td>
+      <td>mauve</td>
+      <td>2.4.0.r4736</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mavedb</td>
+      <td>mavedb_importer</td>
+      <td>data source for MaveDB</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Data Source</td>
+      <td>mavedb_importer</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb</td>
+      <td>0.9</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maxbin2</td>
+      <td>maxbin2</td>
+      <td>clusters metagenomic contigs into bins</td>
+      <td>maxbin</td>
+      <td>maxbin</td>
+      <td></td>
+      <td>MaxBin</td>
+      <td>Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.</td>
+      <td>Sequence assembly</td>
+      <td>Metagenomics, Sequence assembly, Microbiology</td>
+      <td>To update</td>
+      <td>https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html</td>
+      <td>Metagenomics</td>
+      <td>maxbin2</td>
+      <td>mbernt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2</td>
+      <td></td>
+      <td>maxbin2</td>
+      <td>2.2.7</td>
+      <td>Sequence assembly</td>
+      <td>Metagenomics, Sequence assembly, Microbiology</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2798</td>
+      <td>2798</td>
+      <td>314</td>
+      <td>314</td>
+      <td>2452</td>
+      <td>2452</td>
+      <td>508</td>
+      <td>508</td>
+      <td>914</td>
+      <td>914</td>
+      <td>89</td>
+      <td>89</td>
+      <td>6164</td>
+      <td>6164</td>
+      <td>911</td>
+      <td>911</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maxquant</td>
+      <td>maxquant, maxquant_mqpar</td>
+      <td>wrapper for MaxQuant</td>
+      <td>maxquant</td>
+      <td>maxquant</td>
+      <td></td>
+      <td>MaxQuant</td>
+      <td>Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.</td>
+      <td>Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting</td>
+      <td>Proteomics experiment, Proteomics, Statistics and probability</td>
+      <td>Up-to-date</td>
+      <td>https://www.maxquant.org/</td>
+      <td>Proteomics</td>
+      <td>maxquant</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant</td>
+      <td>2.0.3.0</td>
+      <td>maxquant</td>
+      <td>2.0.3.0</td>
+      <td>Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering</td>
+      <td>Proteomics experiment, Proteomics, Statistics and probability</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>6863</td>
+      <td>7021</td>
+      <td>1251</td>
+      <td>1264</td>
+      <td>2798</td>
+      <td>2798</td>
+      <td>543</td>
+      <td>543</td>
+      <td>3189</td>
+      <td>3189</td>
+      <td>352</td>
+      <td>352</td>
+      <td>12850</td>
+      <td>13008</td>
+      <td>2146</td>
+      <td>2159</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mcl</td>
+      <td>mcl</td>
+      <td>The Markov Cluster Algorithm, a cluster algorithm for graphs</td>
+      <td>mcl</td>
+      <td>mcl</td>
+      <td></td>
+      <td>MCL</td>
+      <td>MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.</td>
+      <td>Clustering, Network analysis, Gene regulatory network analysis</td>
+      <td>Molecular interactions, pathways and networks</td>
+      <td>Up-to-date</td>
+      <td>https://micans.org/mcl/man/mcl.html</td>
+      <td>Sequence Analysis</td>
+      <td>mcl</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/mcl</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl</td>
+      <td>22.282</td>
+      <td>mcl</td>
+      <td>22.282</td>
+      <td>Clustering, Gene regulatory network analysis</td>
+      <td>Molecular interactions, pathways and networks</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>35</td>
+      <td>35</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>35</td>
+      <td>35</td>
+      <td>13</td>
+      <td>13</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mdanalysis</td>
+      <td>mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf</td>
+      <td>MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/MDAnalysis/mdanalysis</td>
+      <td>Computational chemistry</td>
+      <td>mdanalysis</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis</td>
+      <td>1.0.0</td>
+      <td>mdanalysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>10</td>
+      <td>5</td>
+      <td>10</td>
+      <td>0</td>
+      <td>10</td>
+      <td>5</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>3209</td>
+      <td>3268</td>
+      <td>318</td>
+      <td>326</td>
+      <td>182</td>
+      <td>182</td>
+      <td>51</td>
+      <td>51</td>
+      <td>397</td>
+      <td>397</td>
+      <td>39</td>
+      <td>39</td>
+      <td>3788</td>
+      <td>3847</td>
+      <td>408</td>
+      <td>416</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mdfileconverter</td>
+      <td>md_converter</td>
+      <td>A tool for interconverting between different MD structure and trajectory file formats.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>md_converter</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter</td>
+      <td>1.9.7</td>
+      <td>mdtraj</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>26720</td>
+      <td>26762</td>
+      <td>251</td>
+      <td>253</td>
+      <td>784</td>
+      <td>784</td>
+      <td>54</td>
+      <td>54</td>
+      <td>977</td>
+      <td>977</td>
+      <td>53</td>
+      <td>53</td>
+      <td>28481</td>
+      <td>28523</td>
+      <td>358</td>
+      <td>360</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mdslicer</td>
+      <td>md_slicer</td>
+      <td>A tool for slicing trajectory files using MDTraj.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>md_converter</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer</td>
+      <td>1.9.9</td>
+      <td>mdtraj</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>174</td>
+      <td>174</td>
+      <td>19</td>
+      <td>19</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td>441</td>
+      <td>441</td>
+      <td>7</td>
+      <td>7</td>
+      <td>621</td>
+      <td>621</td>
+      <td>30</td>
+      <td>30</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mdtraj</td>
+      <td>traj_selections_and_merge</td>
+      <td>MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/mdtraj/mdtraj</td>
+      <td>Computational chemistry</td>
+      <td>mdtraj</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj</td>
+      <td>1.9.7</td>
+      <td>mdtraj</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>36</td>
+      <td>36</td>
+      <td>8</td>
+      <td>8</td>
+      <td>63</td>
+      <td>63</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>99</td>
+      <td>99</td>
+      <td>12</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mea</td>
+      <td>mea</td>
+      <td>Maximum expected accuracy prediction</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.bioinf.uni-leipzig.de/Software/mea</td>
+      <td>RNA</td>
+      <td>mea</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea</td>
+      <td>0.6.4.1</td>
+      <td>mea</td>
+      <td>0.6.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>73</td>
+      <td>86</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>73</td>
+      <td>86</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mean-per-zone</td>
+      <td>mean_per_zone</td>
+      <td>Creates a png image showing statistic over areas as defined in the vector file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/</td>
+      <td>Visualization, GIS, Climate Analysis</td>
+      <td>mean_per_zone</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone</td>
+      <td>0.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20</td>
+      <td>25</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>25</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>measure_gastruloids</td>
+      <td>measureGastruloids</td>
+      <td>Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>measure_gastruloids</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids</td>
+      <td>20221216</td>
+      <td>fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>medaka</td>
+      <td>medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant</td>
+      <td>Sequence correction provided by ONT Research</td>
+      <td>medaka</td>
+      <td>medaka</td>
+      <td></td>
+      <td>Medaka</td>
+      <td>medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.</td>
+      <td>Base-calling, Variant calling, Sequence assembly</td>
+      <td>Sequence assembly, Machine learning</td>
+      <td>To update</td>
+      <td>https://github.com/nanoporetech/medaka</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka</td>
+      <td>1.7.2</td>
+      <td>medaka</td>
+      <td>2.0.0</td>
+      <td>Base-calling, Variant calling, Sequence assembly</td>
+      <td>Sequence assembly, Machine learning</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>117975</td>
+      <td>117975</td>
+      <td>1693</td>
+      <td>1693</td>
+      <td>55063</td>
+      <td>55063</td>
+      <td>796</td>
+      <td>796</td>
+      <td>9325</td>
+      <td>9325</td>
+      <td>639</td>
+      <td>639</td>
+      <td>182363</td>
+      <td>182363</td>
+      <td>3128</td>
+      <td>3128</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>medenv</td>
+      <td>iabiodiv_smartbiodiv_med_environ</td>
+      <td>Retrieve environmental data from etopo, cmems and woa</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/jeremyfix/medenv</td>
+      <td>Ecology, Data Source</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/jeremyfix/medenv</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv</td>
+      <td>0.1.0</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>megablast_xml_parser</td>
+      <td>megablast_xml_parser</td>
+      <td>Parse blast XML output</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Next Gen Mappers, Convert Formats</td>
+      <td>megablast_xml_parser</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser</td>
+      <td>1.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>743</td>
+      <td>816</td>
+      <td>103</td>
+      <td>141</td>
+      <td>292</td>
+      <td>2868</td>
+      <td>82</td>
+      <td>459</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1035</td>
+      <td>3684</td>
+      <td>185</td>
+      <td>600</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>megahit</td>
+      <td>megahit</td>
+      <td>An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.</td>
+      <td>megahit</td>
+      <td>megahit</td>
+      <td></td>
+      <td>MEGAHIT</td>
+      <td>Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.</td>
+      <td>Genome assembly</td>
+      <td>Metagenomics, Sequencing, Ecology, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/voutcn/megahit</td>
+      <td>Sequence Analysis, Assembly, Metagenomics</td>
+      <td>megahit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit</td>
+      <td>1.2.9</td>
+      <td>megahit</td>
+      <td>1.2.9</td>
+      <td>Genome assembly</td>
+      <td>Metagenomics, Sequencing, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>12692</td>
+      <td>13292</td>
+      <td>1349</td>
+      <td>1400</td>
+      <td>16645</td>
+      <td>16645</td>
+      <td>2140</td>
+      <td>2140</td>
+      <td>6214</td>
+      <td>6214</td>
+      <td>431</td>
+      <td>431</td>
+      <td>35551</td>
+      <td>36151</td>
+      <td>3920</td>
+      <td>3971</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>megahit_contig2fastg</td>
+      <td>megahit_contig2fastg</td>
+      <td>A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)</td>
+      <td>megahit</td>
+      <td>megahit</td>
+      <td></td>
+      <td>MEGAHIT</td>
+      <td>Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.</td>
+      <td>Genome assembly</td>
+      <td>Metagenomics, Sequencing, Ecology, Sequence assembly</td>
+      <td>To update</td>
+      <td>https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp</td>
+      <td>Sequence Analysis, Assembly, Metagenomics</td>
+      <td>megahit_contig2fastg</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg</td>
+      <td>1.1.3</td>
+      <td>megahit</td>
+      <td>1.2.9</td>
+      <td>Genome assembly</td>
+      <td>Metagenomics, Sequencing, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>513</td>
+      <td>557</td>
+      <td>152</td>
+      <td>155</td>
+      <td>74</td>
+      <td>74</td>
+      <td>35</td>
+      <td>35</td>
+      <td>10</td>
+      <td>10</td>
+      <td>4</td>
+      <td>4</td>
+      <td>597</td>
+      <td>641</td>
+      <td>191</td>
+      <td>194</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>megan</td>
+      <td>megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma</td>
+      <td>MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).</td>
+      <td>megan</td>
+      <td>megan</td>
+      <td></td>
+      <td>MEGAN</td>
+      <td>Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.</td>
+      <td>Sequence analysis, Taxonomic classification</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/husonlab/megan-ce</td>
+      <td>Sequence Analysis</td>
+      <td>megan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan</td>
+      <td>6.21.7</td>
+      <td>megan</td>
+      <td>6.25.9</td>
+      <td>Sequence analysis, Taxonomic classification</td>
+      <td>Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4130</td>
+      <td>4130</td>
+      <td>447</td>
+      <td>447</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4130</td>
+      <td>4130</td>
+      <td>447</td>
+      <td>447</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>meme</td>
+      <td>meme_dreme, meme_fimo, meme_meme, meme_psp_gen</td>
+      <td>The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.</td>
+      <td>meme_meme</td>
+      <td>meme_fimo, meme_meme</td>
+      <td></td>
+      <td>meme_meme</td>
+      <td>An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.</td>
+      <td>Nucleic acid feature detection, Protein feature detection, Statistical calculation</td>
+      <td>Data mining, Sequence analysis, Genetic variation, Statistics and probability</td>
+      <td>To update</td>
+      <td>http://meme-suite.org/</td>
+      <td>ChIP-seq</td>
+      <td>meme</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme</td>
+      <td>5.5.6</td>
+      <td>meme</td>
+      <td>5.5.7</td>
+      <td>Nucleic acid feature detection, Protein feature detection, Statistical calculation</td>
+      <td>Data mining, Sequence analysis, Genetic variation, Statistics and probability</td>
+      <td>3</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>20990</td>
+      <td>22979</td>
+      <td>762</td>
+      <td>892</td>
+      <td>10975</td>
+      <td>25929</td>
+      <td>1551</td>
+      <td>3249</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31965</td>
+      <td>48908</td>
+      <td>2313</td>
+      <td>4141</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>meme_chip</td>
+      <td>meme_chip</td>
+      <td>Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://meme-suite.org/</td>
+      <td>ChIP-seq</td>
+      <td>meme_chip</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip</td>
+      <td>4.11.2</td>
+      <td>graphicsmagick</td>
+      <td>1.3.26</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6413</td>
+      <td>7000</td>
+      <td>705</td>
+      <td>743</td>
+      <td>7260</td>
+      <td>7260</td>
+      <td>1171</td>
+      <td>1171</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13673</td>
+      <td>14260</td>
+      <td>1876</td>
+      <td>1914</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>meneco</td>
+      <td>meneco</td>
+      <td>Meneco computes minimal completions to your draft network with reactions from a repair network</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://bioasp.github.io/meneco/</td>
+      <td>Systems Biology</td>
+      <td>meneco</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/meneco</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/meneco</td>
+      <td>1.5.2</td>
+      <td>meneco</td>
+      <td>1.5.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>meningotype</td>
+      <td>meningotype</td>
+      <td>Assign sequence type to N. meningitidis genome assemblies</td>
+      <td>meningotype</td>
+      <td>meningotype</td>
+      <td></td>
+      <td>meningotype</td>
+      <td>In silico typing of Neisseria meningitidis contigs.</td>
+      <td>Genotyping, Multilocus sequence typing</td>
+      <td>Microbiology, Genotype and phenotype</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/MDU-PHL/meningotype</td>
+      <td>Sequence Analysis</td>
+      <td>meningotype</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype</td>
+      <td>0.8.5</td>
+      <td>meningotype</td>
+      <td>0.8.5</td>
+      <td>Multilocus sequence typing</td>
+      <td>Microbiology, Genotype and phenotype</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>merge</td>
+      <td>gops_merge_1</td>
+      <td>Merge the overlapping intervals of a dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>merge</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>565922</td>
+      <td>566630</td>
+      <td>418</td>
+      <td>441</td>
+      <td>45844</td>
+      <td>107523</td>
+      <td>671</td>
+      <td>4353</td>
+      <td>19828</td>
+      <td>19994</td>
+      <td>100</td>
+      <td>137</td>
+      <td>631594</td>
+      <td>694147</td>
+      <td>1189</td>
+      <td>4931</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>merge_cols</td>
+      <td>mergeCols1</td>
+      <td>Merge columns together.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>merge_cols</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols</td>
+      <td>1.0.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>20905</td>
+      <td>31051</td>
+      <td>1906</td>
+      <td>2128</td>
+      <td>21780</td>
+      <td>132833</td>
+      <td>885</td>
+      <td>3172</td>
+      <td>1524</td>
+      <td>1925</td>
+      <td>122</td>
+      <td>152</td>
+      <td>44209</td>
+      <td>165809</td>
+      <td>2913</td>
+      <td>5452</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mergeneighboursinlabelimage</td>
+      <td>ip_merge_neighbours_in_label</td>
+      <td>Merge Neighbours in Label Image</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>mergeneighboursinlabelimage</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage</td>
+      <td>0.3-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>18</td>
+      <td>25</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>25</td>
+      <td>2</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>merlin</td>
+      <td>merlin</td>
+      <td>Pedigree Analysis package</td>
+      <td>merlin</td>
+      <td>merlin</td>
+      <td></td>
+      <td>Merlin</td>
+      <td>Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation</td>
+      <td>Haplotype mapping, Genetic mapping</td>
+      <td>GWAS study, Mapping</td>
+      <td>Up-to-date</td>
+      <td>http://csg.sph.umich.edu/abecasis/Merlin/</td>
+      <td>Variant Analysis</td>
+      <td>merlin</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin</td>
+      <td>1.1.2</td>
+      <td>merlin</td>
+      <td>1.1.2</td>
+      <td>Haplotype mapping</td>
+      <td>GWAS study, Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>merqury</td>
+      <td>merqury, merquryplot</td>
+      <td>Merqury is a tool for evaluating genomes assemblies based of k-mer operations.</td>
+      <td>merqury</td>
+      <td>merqury</td>
+      <td></td>
+      <td>Merqury</td>
+      <td>Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.</td>
+      <td>Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly</td>
+      <td>Sequence assembly, Whole genome sequencing, Plant biology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/marbl/merqury</td>
+      <td>Assembly</td>
+      <td>merqury</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury</td>
+      <td>1.3</td>
+      <td>merqury</td>
+      <td>1.3</td>
+      <td>Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly</td>
+      <td>Sequence assembly, Whole genome sequencing, Plant biology</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3150</td>
+      <td>3150</td>
+      <td>477</td>
+      <td>477</td>
+      <td>730</td>
+      <td>730</td>
+      <td>196</td>
+      <td>196</td>
+      <td>1183</td>
+      <td>1183</td>
+      <td>151</td>
+      <td>151</td>
+      <td>5063</td>
+      <td>5063</td>
+      <td>824</td>
+      <td>824</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>meryl</td>
+      <td>meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode</td>
+      <td>Meryl a k-mer counter.</td>
+      <td>meryl</td>
+      <td>meryl</td>
+      <td></td>
+      <td>Meryl</td>
+      <td>Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.</td>
+      <td>k-mer counting</td>
+      <td>Whole genome sequencing, Genomics, Sequence analysis, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/marbl/meryl</td>
+      <td>Assembly</td>
+      <td>meryl</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl</td>
+      <td>1.3</td>
+      <td>merqury</td>
+      <td>1.3</td>
+      <td>k-mer counting</td>
+      <td>Whole genome sequencing, Genomics, Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>meta_proteome_analyzer</td>
+      <td>meta_proteome_analyzer</td>
+      <td>MetaProteomeAnalyzer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/compomics/meta-proteome-analyzer/</td>
+      <td>Proteomics</td>
+      <td>meta_proteome_analyzer</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer</td>
+      <td>2.0.0</td>
+      <td>mpa-portable</td>
+      <td>2.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>126</td>
+      <td>126</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>126</td>
+      <td>126</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metabat2</td>
+      <td>metabat2_jgi_summarize_bam_contig_depths, metabat2</td>
+      <td>MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.</td>
+      <td>MetaBAT_2</td>
+      <td>MetaBAT_2</td>
+      <td></td>
+      <td>MetaBAT 2</td>
+      <td>an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning</td>
+      <td>Read binning, Sequence assembly, Genome annotation</td>
+      <td>Metagenomics, Sequence assembly, Metagenomic sequencing</td>
+      <td>To update</td>
+      <td>https://bitbucket.org/berkeleylab/metabat/src/master/</td>
+      <td>Metagenomics</td>
+      <td>metabat2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2</td>
+      <td>2.15</td>
+      <td>metabat2</td>
+      <td>2.17</td>
+      <td>Read binning, Sequence assembly, Genome annotation</td>
+      <td>Metagenomics, Sequence assembly, Metagenomic sequencing</td>
+      <td>2</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6135</td>
+      <td>6135</td>
+      <td>382</td>
+      <td>382</td>
+      <td>881</td>
+      <td>881</td>
+      <td>151</td>
+      <td>151</td>
+      <td>1094</td>
+      <td>1094</td>
+      <td>104</td>
+      <td>104</td>
+      <td>8110</td>
+      <td>8110</td>
+      <td>637</td>
+      <td>637</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metabuli</td>
+      <td>metabuli_classify</td>
+      <td>Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences</td>
+      <td>metabuli</td>
+      <td>metabuli</td>
+      <td></td>
+      <td>metabuli</td>
+      <td>Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid</td>
+      <td>Taxonomic classification</td>
+      <td>Taxonomy</td>
+      <td>To update</td>
+      <td>https://github.com/steineggerlab/Metabuli</td>
+      <td>Sequence Analysis, Metagenomics</td>
+      <td>metabuli</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli</td>
+      <td>1.0.5</td>
+      <td>metabuli</td>
+      <td>1.0.8</td>
+      <td>Taxonomic classification</td>
+      <td>Taxonomy</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metaeuk</td>
+      <td>metaeuk_easy_predict</td>
+      <td>MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand.</td>
+      <td>MetaEuk</td>
+      <td>MetaEuk</td>
+      <td></td>
+      <td>MetaEuk</td>
+      <td>MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics</td>
+      <td>Homology-based gene prediction</td>
+      <td>Metagenomics, Gene and protein families</td>
+      <td>To update</td>
+      <td>https://github.com/soedinglab/metaeuk</td>
+      <td>Sequence Analysis, Genome annotation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk</td>
+      <td>7.bba0d80</td>
+      <td>metaeuk</td>
+      <td>6.a5d39d9</td>
+      <td>Homology-based gene prediction</td>
+      <td>Metagenomics, Gene and protein families</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>312</td>
+      <td>312</td>
+      <td>40</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>312</td>
+      <td>312</td>
+      <td>40</td>
+      <td>40</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metagene_annotator</td>
+      <td>metagene_annotator</td>
+      <td>MetaGeneAnnotator gene-finding program for prokaryote and phage</td>
+      <td>metageneannotator</td>
+      <td>metageneannotator</td>
+      <td></td>
+      <td>MetaGeneAnnotator</td>
+      <td>Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.</td>
+      <td>Sequence annotation</td>
+      <td>Genomics, Model organisms, Data submission, annotation and curation</td>
+      <td>Up-to-date</td>
+      <td>http://metagene.nig.ac.jp/</td>
+      <td>Sequence Analysis</td>
+      <td>metagene_annotator</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator</td>
+      <td>1.0</td>
+      <td>metagene_annotator</td>
+      <td>1.0</td>
+      <td>Sequence annotation</td>
+      <td>Genomics, Model organisms, Data submission, annotation and curation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>980</td>
+      <td>980</td>
+      <td>323</td>
+      <td>323</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>980</td>
+      <td>980</td>
+      <td>323</td>
+      <td>323</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metagenomeseq</td>
+      <td>metagenomeseq_normalizaton</td>
+      <td>metagenomeSeq Normalization</td>
+      <td>metagenomeseq</td>
+      <td>metagenomeseq</td>
+      <td></td>
+      <td>metagenomeSeq</td>
+      <td>Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.</td>
+      <td>Sequence visualisation, Statistical calculation</td>
+      <td>Metagenomics, Sequencing</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html</td>
+      <td>Metagenomics</td>
+      <td>metagenomeseq_normalization</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq</td>
+      <td>1.16.0-0.0.1</td>
+      <td>bioconductor-metagenomeseq</td>
+      <td>1.43.0</td>
+      <td>Sequence visualisation, Statistical calculation</td>
+      <td>Metagenomics, Sequencing</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>556</td>
+      <td>756</td>
+      <td>17</td>
+      <td>21</td>
+      <td>310</td>
+      <td>514</td>
+      <td>35</td>
+      <td>55</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>866</td>
+      <td>1270</td>
+      <td>52</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metanovo</td>
+      <td>metanovo</td>
+      <td>Produce targeted databases for mass spectrometry analysis.</td>
+      <td>metanovo</td>
+      <td>metanovo</td>
+      <td></td>
+      <td>MetaNovo</td>
+      <td>An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.</td>
+      <td>Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis</td>
+      <td>Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/uct-cbio/proteomics-pipelines</td>
+      <td>Proteomics</td>
+      <td>metanovo</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo</td>
+      <td>1.9.4</td>
+      <td>metanovo</td>
+      <td>1.9.4</td>
+      <td>Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis</td>
+      <td>Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4471</td>
+      <td>4471</td>
+      <td>29</td>
+      <td>29</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4471</td>
+      <td>4471</td>
+      <td>29</td>
+      <td>29</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metaphlan</td>
+      <td>customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan</td>
+      <td>MetaPhlAn for Metagenomic Phylogenetic Analysis</td>
+      <td>metaphlan</td>
+      <td>metaphlan</td>
+      <td></td>
+      <td>MetaPhlAn</td>
+      <td>Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.</td>
+      <td>Nucleic acid sequence analysis, Phylogenetic tree analysis</td>
+      <td>Metagenomics, Phylogenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/biobakery/MetaPhlAn</td>
+      <td>Metagenomics</td>
+      <td>metaphlan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan</td>
+      <td>4.1.1</td>
+      <td>metaphlan</td>
+      <td>4.1.1</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Metagenomics, Phylogenomics</td>
+      <td>1</td>
+      <td>2</td>
+      <td>4</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>16629</td>
+      <td>16648</td>
+      <td>1183</td>
+      <td>1187</td>
+      <td>3983</td>
+      <td>3983</td>
+      <td>572</td>
+      <td>572</td>
+      <td>4747</td>
+      <td>4747</td>
+      <td>278</td>
+      <td>278</td>
+      <td>25359</td>
+      <td>25378</td>
+      <td>2033</td>
+      <td>2037</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metaquantome</td>
+      <td>metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz</td>
+      <td>quantitative analysis of microbiome taxonomy and function</td>
+      <td>metaQuantome</td>
+      <td>metaQuantome</td>
+      <td></td>
+      <td>metaQuantome</td>
+      <td>metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.</td>
+      <td>Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference</td>
+      <td>Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/galaxyproteomics/metaquantome/</td>
+      <td>Proteomics</td>
+      <td>metaquantome</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome</td>
+      <td>2.0.2</td>
+      <td>metaquantome</td>
+      <td>2.0.2</td>
+      <td>Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference</td>
+      <td>Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>2730</td>
+      <td>2831</td>
+      <td>260</td>
+      <td>262</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1540</td>
+      <td>1540</td>
+      <td>71</td>
+      <td>71</td>
+      <td>4270</td>
+      <td>4371</td>
+      <td>331</td>
+      <td>333</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metawrapmg</td>
+      <td>metawrapmg_binning</td>
+      <td>A flexible pipeline for genome-resolved metagenomic data analysis</td>
+      <td>metawrap</td>
+      <td>metawrap</td>
+      <td></td>
+      <td>MetaWRAP</td>
+      <td>MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.</td>
+      <td>Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing</td>
+      <td>Whole genome sequencing, Metagenomic sequencing, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bxlab/metaWRAP</td>
+      <td>Metagenomics</td>
+      <td>metawrapmg_binning</td>
+      <td>galaxy-australia</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg</td>
+      <td>1.3.0</td>
+      <td>metawrap-mg</td>
+      <td>1.3.0</td>
+      <td>Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing</td>
+      <td>Whole genome sequencing, Metagenomic sequencing, Metagenomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>142</td>
+      <td>142</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>379</td>
+      <td>379</td>
+      <td>47</td>
+      <td>47</td>
+      <td>521</td>
+      <td>521</td>
+      <td>79</td>
+      <td>79</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metfrag</td>
+      <td>metfrag</td>
+      <td>[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/computational-metabolomics/metfrag-galaxy</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>computational-metabolomics</td>
+      <td>https://github.com/computational-metabolomics/metfrag-galaxy</td>
+      <td>https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag</td>
+      <td>2.4.5+galaxy3</td>
+      <td>metfrag</td>
+      <td>2.4.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>192</td>
+      <td>192</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>192</td>
+      <td>192</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metfrag-vis</td>
+      <td>metfrag_vis</td>
+      <td>[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/computational-metabolomics/metfrag-galaxy</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>computational-metabolomics</td>
+      <td>https://github.com/computational-metabolomics/metfrag-galaxy</td>
+      <td>https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis</td>
+      <td>2.4.5+galaxy0</td>
+      <td>metfrag</td>
+      <td>2.4.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>50</td>
+      <td>50</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>50</td>
+      <td>50</td>
+      <td>14</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>methtools</td>
+      <td>methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling</td>
+      <td>tools for methylation analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methtools</td>
+      <td>Sequence Analysis</td>
+      <td>methtools</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methtools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methtools</td>
+      <td>0.1.1</td>
+      <td>methtools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>632</td>
+      <td>5461</td>
+      <td>155</td>
+      <td>453</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>632</td>
+      <td>5461</td>
+      <td>155</td>
+      <td>453</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>methyldackel</td>
+      <td>pileometh</td>
+      <td>A tool for processing bisulfite sequencing alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/dpryan79/MethylDackel</td>
+      <td>Sequence Analysis</td>
+      <td>pileometh</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel</td>
+      <td>0.5.2</td>
+      <td>methyldackel</td>
+      <td>0.6.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>14907</td>
+      <td>18971</td>
+      <td>638</td>
+      <td>894</td>
+      <td>2677</td>
+      <td>2677</td>
+      <td>230</td>
+      <td>230</td>
+      <td>2313</td>
+      <td>2313</td>
+      <td>83</td>
+      <td>83</td>
+      <td>19897</td>
+      <td>23961</td>
+      <td>951</td>
+      <td>1207</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>methylkit</td>
+      <td>methylkit</td>
+      <td>A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://bioconductor.org/packages/release/bioc/html/methylKit.html</td>
+      <td>Epigenetics</td>
+      <td>methylkit</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methylkit</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methylkit</td>
+      <td>0.99.2</td>
+      <td>bioconductor-methylkit</td>
+      <td>1.28.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metilene</td>
+      <td>metilene</td>
+      <td>Differential DNA methylation calling</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA, Statistics</td>
+      <td>metilene</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/metilene</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/metilene</td>
+      <td>0.2.6.1</td>
+      <td>metilene</td>
+      <td>0.2.8</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3209</td>
+      <td>4572</td>
+      <td>312</td>
+      <td>442</td>
+      <td>479</td>
+      <td>479</td>
+      <td>79</td>
+      <td>79</td>
+      <td>315</td>
+      <td>315</td>
+      <td>51</td>
+      <td>51</td>
+      <td>4003</td>
+      <td>5366</td>
+      <td>442</td>
+      <td>572</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mfassignr</td>
+      <td>mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot</td>
+      <td>The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements</td>
+      <td>mfassignr</td>
+      <td>mfassignr</td>
+      <td></td>
+      <td>MFAssignR</td>
+      <td>Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements.</td>
+      <td>Visualisation</td>
+      <td>Proteomics experiment, Molecular interactions, pathways and networks, Workflows</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/MFAssignR</td>
+      <td>Metabolomics</td>
+      <td>MFAssignR</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr</td>
+      <td>1.1.1</td>
+      <td>r-mfassignr</td>
+      <td>1.1.1</td>
+      <td>Visualisation</td>
+      <td>Proteomics experiment, Molecular interactions, pathways and networks, Workflows</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mg_toolkit</td>
+      <td>mg_toolkit_bulk_download, mg_toolkit_original_metadata</td>
+      <td>Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.</td>
+      <td>mg-toolkit</td>
+      <td>mg-toolkit</td>
+      <td></td>
+      <td>mg-toolkit</td>
+      <td>Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.</td>
+      <td>Data retrieval</td>
+      <td>Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/EBI-Metagenomics/emg-toolkit</td>
+      <td>Metagenomics</td>
+      <td>mg_toolkit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit</td>
+      <td>0.10.4</td>
+      <td>mg-toolkit</td>
+      <td>0.10.4</td>
+      <td>Data retrieval</td>
+      <td>Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mgf_formatter</td>
+      <td>mgf_formatter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td></td>
+      <td></td>
+      <td>mgf_formatter</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter</td>
+      <td>1.0.0</td>
+      <td>mgf-formatter</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mgnify_seqprep</td>
+      <td>mgnify_seqprep</td>
+      <td>A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.</td>
+      <td>seqprep</td>
+      <td>seqprep</td>
+      <td></td>
+      <td>SeqPrep</td>
+      <td>Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.</td>
+      <td>Nucleic acid design</td>
+      <td>Genomics, Sequence assembly, Sequencing, Probes and primers</td>
+      <td>To update</td>
+      <td>https://github.com/jstjohn/SeqPrep</td>
+      <td>Fastq Manipulation, Sequence Analysis</td>
+      <td>mgnify_seqprep</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep</td>
+      <td>1.2</td>
+      <td></td>
+      <td></td>
+      <td>Nucleic acid design</td>
+      <td>Genomics, Sequence assembly, Sequencing, Probes and primers</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>573</td>
+      <td>573</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>573</td>
+      <td>573</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>miclip</td>
+      <td>mi_clip</td>
+      <td>Identification of binding sites in CLIP-Seq data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/src/contrib/Archive/MiClip/</td>
+      <td>Sequence Analysis</td>
+      <td>miclip</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/miclip</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/miclip</td>
+      <td>1.2.0</td>
+      <td>Rscript</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>microsatbed</td>
+      <td>microsatbed</td>
+      <td>Select microsatellites for a bed file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/lmdu/pytrf</td>
+      <td>Sequence Analysis</td>
+      <td>microsatbed</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed</td>
+      <td>1.3.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>228</td>
+      <td>228</td>
+      <td>4</td>
+      <td>4</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>246</td>
+      <td>246</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>microsatellite_birthdeath</td>
+      <td>microsatellite_birthdeath</td>
+      <td>Identify microsatellite births and deaths</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>microsatellite_birthdeath</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>microsats_alignment_level</td>
+      <td>microsats_align1</td>
+      <td>Extract Orthologous Microsatellites from pair-wise alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>microsats_alignment_level</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level</td>
+      <td>1.0.0</td>
+      <td>sputnik</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>135</td>
+      <td>973</td>
+      <td>50</td>
+      <td>140</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>135</td>
+      <td>973</td>
+      <td>50</td>
+      <td>140</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>microsats_mutability</td>
+      <td>microsats_mutability1</td>
+      <td>Estimate microsatellite mutability by specified attributes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>microsats_mutability</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability</td>
+      <td>1.1.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>312</td>
+      <td>22</td>
+      <td>87</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>312</td>
+      <td>22</td>
+      <td>87</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>migmap</td>
+      <td>migmap</td>
+      <td>mapper for full-length T- and B-cell repertoire sequencing</td>
+      <td>MiGMAP</td>
+      <td>MiGMAP</td>
+      <td></td>
+      <td>MiGMAP</td>
+      <td>Mapper for full-length T- and B-cell repertoire sequencing.</td>
+      <td>Sequence analysis, Read mapping</td>
+      <td>Immunoproteins, genes and antigens, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/mikessh/migmap</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>migmap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap</td>
+      <td>1.0.3</td>
+      <td>migmap</td>
+      <td>1.0.3</td>
+      <td>Sequence analysis, Read mapping</td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1082</td>
+      <td>1229</td>
+      <td>25</td>
+      <td>33</td>
+      <td>1153</td>
+      <td>1376</td>
+      <td>70</td>
+      <td>89</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2235</td>
+      <td>2605</td>
+      <td>95</td>
+      <td>122</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>minced</td>
+      <td>minced</td>
+      <td>MinCED - Mining CRISPRs in Environmental Datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README</td>
+      <td>Sequence Analysis</td>
+      <td>minced</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/minced</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/minced</td>
+      <td>0.2.0</td>
+      <td>minced</td>
+      <td>0.4.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1213</td>
+      <td>1309</td>
+      <td>115</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1213</td>
+      <td>1309</td>
+      <td>115</td>
+      <td>124</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mine</td>
+      <td>maximal_information_based_nonparametric_exploration</td>
+      <td>Maximal Information-based Nonparametric Exploration</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>mine</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine</td>
+      <td>0.0.1</td>
+      <td>MINE</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9</td>
+      <td>11</td>
+      <td>8</td>
+      <td>8</td>
+      <td>17</td>
+      <td>63</td>
+      <td>6</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>74</td>
+      <td>14</td>
+      <td>27</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>minia</td>
+      <td>minia</td>
+      <td>Short-read assembler based on a de Bruijn graph</td>
+      <td>minia</td>
+      <td>minia</td>
+      <td></td>
+      <td>Minia</td>
+      <td>Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.</td>
+      <td>Genome assembly</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://gatb.inria.fr/software/minia/</td>
+      <td>Assembly</td>
+      <td>minia</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia</td>
+      <td>3.2.6</td>
+      <td>minia</td>
+      <td>3.2.6</td>
+      <td>Genome assembly</td>
+      <td>Sequence assembly</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7116</td>
+      <td>7116</td>
+      <td>256</td>
+      <td>256</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>278</td>
+      <td>278</td>
+      <td>60</td>
+      <td>60</td>
+      <td>7394</td>
+      <td>7394</td>
+      <td>316</td>
+      <td>316</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>miniasm</td>
+      <td>miniasm</td>
+      <td>Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)</td>
+      <td>miniasm</td>
+      <td>miniasm</td>
+      <td></td>
+      <td>miniasm</td>
+      <td>Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.</td>
+      <td>De-novo assembly</td>
+      <td>Genomics, Sequence assembly</td>
+      <td>To update</td>
+      <td>https://github.com/lh3/miniasm</td>
+      <td>Assembly</td>
+      <td>miniasm</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm</td>
+      <td>0.3_r179</td>
+      <td>miniasm</td>
+      <td>0.3</td>
+      <td>De-novo assembly</td>
+      <td>Genomics, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>13357</td>
+      <td>13479</td>
+      <td>554</td>
+      <td>562</td>
+      <td>8416</td>
+      <td>8416</td>
+      <td>448</td>
+      <td>448</td>
+      <td>898</td>
+      <td>898</td>
+      <td>85</td>
+      <td>85</td>
+      <td>22671</td>
+      <td>22793</td>
+      <td>1087</td>
+      <td>1095</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>minimap2</td>
+      <td>minimap2</td>
+      <td>A fast pairwise aligner for genomic and spliced nucleotide sequences</td>
+      <td>minimap2</td>
+      <td>minimap2</td>
+      <td></td>
+      <td>Minimap2</td>
+      <td>Pairwise aligner for genomic and spliced nucleotide sequences</td>
+      <td>Pairwise sequence alignment</td>
+      <td>Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lh3/minimap2</td>
+      <td>Next Gen Mappers</td>
+      <td>minimap2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2</td>
+      <td>2.28</td>
+      <td>minimap2</td>
+      <td>2.28</td>
+      <td>Pairwise sequence alignment</td>
+      <td>Mapping</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>346530</td>
+      <td>349075</td>
+      <td>4323</td>
+      <td>4419</td>
+      <td>108535</td>
+      <td>108535</td>
+      <td>4075</td>
+      <td>4075</td>
+      <td>22331</td>
+      <td>22331</td>
+      <td>1166</td>
+      <td>1166</td>
+      <td>477396</td>
+      <td>479941</td>
+      <td>9564</td>
+      <td>9660</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>minipolish</td>
+      <td>minipolish</td>
+      <td>Polishing miniasm assemblies</td>
+      <td>minipolish</td>
+      <td>minipolish</td>
+      <td></td>
+      <td>minipolish</td>
+      <td>A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.</td>
+      <td>Localised reassembly, Read depth analysis</td>
+      <td>Sequence assembly, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/rrwick/Minipolish</td>
+      <td>Sequence Analysis</td>
+      <td>minipolish</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/minipolish</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/minipolish</td>
+      <td>0.1.3</td>
+      <td>minipolish</td>
+      <td>0.1.3</td>
+      <td>Localised reassembly, Read depth analysis</td>
+      <td>Sequence assembly, Sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>229</td>
+      <td>229</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>229</td>
+      <td>229</td>
+      <td>32</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>miniprot</td>
+      <td>miniprot, miniprot_index</td>
+      <td>Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.</td>
+      <td>miniprot</td>
+      <td>miniprot</td>
+      <td></td>
+      <td>miniprot</td>
+      <td>Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.</td>
+      <td>Sequence alignment, Protein sequence analysis</td>
+      <td>Sequence sites, features and motifs, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lh3/miniprot</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot</td>
+      <td>0.13</td>
+      <td>miniprot</td>
+      <td>0.13</td>
+      <td>Sequence alignment, Protein sequence analysis</td>
+      <td>Sequence sites, features and motifs, Sequence analysis</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1244</td>
+      <td>1244</td>
+      <td>86</td>
+      <td>86</td>
+      <td>24</td>
+      <td>24</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1268</td>
+      <td>1268</td>
+      <td>101</td>
+      <td>101</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>miranda</td>
+      <td>miranda</td>
+      <td>Finds potential target sites for miRNAs in genomic sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.microrna.org/</td>
+      <td>RNA</td>
+      <td>miranda</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda</td>
+      <td>3.3a+galaxy1</td>
+      <td>miranda</td>
+      <td>3.3a</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6408</td>
+      <td>6514</td>
+      <td>94</td>
+      <td>99</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6408</td>
+      <td>6514</td>
+      <td>94</td>
+      <td>99</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>miranda2asko</td>
+      <td>miranda2asko</td>
+      <td>Converts miRanda output into AskOmics format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats</td>
+      <td>miranda2asko</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko</td>
+      <td>0.2</td>
+      <td>perl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mircounts</td>
+      <td>mircounts</td>
+      <td>Generates miRNA count lists from read alignments to mirBase.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Transcriptomics</td>
+      <td>mircounts</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts</td>
+      <td>1.6</td>
+      <td>tar</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1458</td>
+      <td>1458</td>
+      <td>36</td>
+      <td>36</td>
+      <td>1458</td>
+      <td>1458</td>
+      <td>36</td>
+      <td>36</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mirmachine</td>
+      <td>mirmachine</td>
+      <td>Tool to detect miRNA in genome sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/sinanugur/MirMachine</td>
+      <td>Sequence Analysis</td>
+      <td>mirmachine</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine</td>
+      <td>0.2.13</td>
+      <td>mirmachine</td>
+      <td>0.2.13</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mirnature</td>
+      <td>mirnature</td>
+      <td>Computational detection of canonical microRNAs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Bierinformatik/miRNAture</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>mirnature</td>
+      <td>iuc</td>
+      <td>https://github.com/Bierinformatik/miRNAture</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature</td>
+      <td>1.1</td>
+      <td>mirnature</td>
+      <td>1.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>misc</td>
+      <td>target_screen, use_theoretical_mz_annotations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/misc</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/misc</td>
+      <td>1.0.0</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mitobim</td>
+      <td>mitobim</td>
+      <td>assemble mitochondrial genomes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/chrishah/MITObim</td>
+      <td>Assembly</td>
+      <td>mitobim</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim</td>
+      <td>1.9.1</td>
+      <td>mitobim</td>
+      <td>1.9.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1117</td>
+      <td>1117</td>
+      <td>116</td>
+      <td>116</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>295</td>
+      <td>295</td>
+      <td>25</td>
+      <td>25</td>
+      <td>1412</td>
+      <td>1412</td>
+      <td>141</td>
+      <td>141</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mitohifi</td>
+      <td>mitohifi</td>
+      <td>Assembly mitogenomes from Pacbio HiFi read.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2</td>
+      <td>Assembly</td>
+      <td>mitohifi</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi</td>
+      <td>3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1020</td>
+      <td>1020</td>
+      <td>176</td>
+      <td>176</td>
+      <td>414</td>
+      <td>414</td>
+      <td>73</td>
+      <td>73</td>
+      <td>277</td>
+      <td>277</td>
+      <td>20</td>
+      <td>20</td>
+      <td>1711</td>
+      <td>1711</td>
+      <td>269</td>
+      <td>269</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mitos</td>
+      <td>mitos, mitos2</td>
+      <td>de-novo annotation of metazoan mitochondrial genomes</td>
+      <td>mitos</td>
+      <td>mitos</td>
+      <td></td>
+      <td>MITOS</td>
+      <td>De novo metazoan mitochondrial genome annotation.</td>
+      <td>Genome annotation</td>
+      <td>Zoology, Whole genome sequencing</td>
+      <td>To update</td>
+      <td>http://mitos.bioinf.uni-leipzig.de/</td>
+      <td>Sequence Analysis</td>
+      <td>mitos</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos</td>
+      <td>1.1.7</td>
+      <td>mitos</td>
+      <td>2.1.9</td>
+      <td>Genome annotation</td>
+      <td>Zoology, Whole genome sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>0</td>
+      <td>191295</td>
+      <td>191295</td>
+      <td>1111</td>
+      <td>1111</td>
+      <td>42265</td>
+      <td>42265</td>
+      <td>320</td>
+      <td>320</td>
+      <td>10904</td>
+      <td>10904</td>
+      <td>83</td>
+      <td>83</td>
+      <td>244464</td>
+      <td>244464</td>
+      <td>1514</td>
+      <td>1514</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mixmodel4repeated_measures</td>
+      <td>mixmodel4repeated_measures</td>
+      <td>[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>mixmodel4repeated_measures</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures</td>
+      <td>3.1.0</td>
+      <td>r-lme4</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mlst</td>
+      <td>mlst, mlst_list</td>
+      <td>Scan contig files against PubMLST typing schemes</td>
+      <td>mlst</td>
+      <td>mlst</td>
+      <td></td>
+      <td>MLST</td>
+      <td>Multi Locus Sequence Typing from an assembled genome or from a set of reads.</td>
+      <td>Multilocus sequence typing</td>
+      <td>Immunoproteins and antigens</td>
+      <td>To update</td>
+      <td>https://github.com/tseemann/mlst</td>
+      <td>Sequence Analysis</td>
+      <td>mlst</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst</td>
+      <td>2.22.0</td>
+      <td>mlst</td>
+      <td>2.23.0</td>
+      <td>Multilocus sequence typing</td>
+      <td>Immunoproteins and antigens</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>13300</td>
+      <td>13471</td>
+      <td>1480</td>
+      <td>1501</td>
+      <td>6532</td>
+      <td>6532</td>
+      <td>1167</td>
+      <td>1167</td>
+      <td>10334</td>
+      <td>11841</td>
+      <td>1083</td>
+      <td>1300</td>
+      <td>30166</td>
+      <td>31844</td>
+      <td>3730</td>
+      <td>3968</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>moFF</td>
+      <td>proteomics_moff</td>
+      <td>moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/compomics/moFF</td>
+      <td>Proteomics</td>
+      <td>proteomics_moff</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF</td>
+      <td>2.0.3</td>
+      <td>moff</td>
+      <td>2.0.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>331</td>
+      <td>762</td>
+      <td>20</td>
+      <td>34</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>137</td>
+      <td>137</td>
+      <td>4</td>
+      <td>4</td>
+      <td>468</td>
+      <td>899</td>
+      <td>24</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>moabs</td>
+      <td>moabs</td>
+      <td>MOABS for differential methylation analysis on Bisulfite sequencing data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/sunnyisgalaxy/moabs</td>
+      <td>Epigenetics</td>
+      <td>moabs</td>
+      <td>iuc</td>
+      <td>https://github.com/sunnyisgalaxy/moabs</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs</td>
+      <td>1.3.4.6</td>
+      <td>moabs</td>
+      <td>1.3.9.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>339</td>
+      <td>339</td>
+      <td>56</td>
+      <td>56</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>339</td>
+      <td>339</td>
+      <td>56</td>
+      <td>56</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mob_suite</td>
+      <td>mob_recon, mob_typer</td>
+      <td>MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/mob-suite</td>
+      <td>Sequence Analysis</td>
+      <td>mob_suite</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/mob-suite</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite</td>
+      <td>3.0.3</td>
+      <td>mob_suite</td>
+      <td>3.1.9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119024</td>
+      <td>119024</td>
+      <td>628</td>
+      <td>628</td>
+      <td>42</td>
+      <td>42</td>
+      <td>2</td>
+      <td>2</td>
+      <td>36310</td>
+      <td>36310</td>
+      <td>191</td>
+      <td>191</td>
+      <td>155376</td>
+      <td>155376</td>
+      <td>821</td>
+      <td>821</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>molecule2gspan</td>
+      <td>bg_mol2gspan</td>
+      <td>converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan</td>
+      <td>Convert Formats</td>
+      <td>molecule_to_gspan</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan</td>
+      <td>0.2</td>
+      <td>openbabel</td>
+      <td>2.3.90dev7d621d9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>monocle3</td>
+      <td>monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers</td>
+      <td>De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_monocle3</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3</td>
+      <td>0.1.4</td>
+      <td>monocle3-cli</td>
+      <td>0.0.9</td>
+      <td></td>
+      <td></td>
+      <td>9</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3610</td>
+      <td>3610</td>
+      <td>559</td>
+      <td>559</td>
+      <td>1728</td>
+      <td>1728</td>
+      <td>434</td>
+      <td>434</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5338</td>
+      <td>5338</td>
+      <td>993</td>
+      <td>993</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>morpheus</td>
+      <td>morpheus</td>
+      <td>Morpheus MS Search Application</td>
+      <td>morpheus</td>
+      <td>morpheus</td>
+      <td></td>
+      <td>Morpheus</td>
+      <td>A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.</td>
+      <td>Peptide database search</td>
+      <td>Proteomics</td>
+      <td>To update</td>
+      <td>https://cwenger.github.io/Morpheus</td>
+      <td>Proteomics</td>
+      <td>morpheus</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus</td>
+      <td>288</td>
+      <td>morpheus</td>
+      <td>290</td>
+      <td>Peptide database search</td>
+      <td>Proteomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>105</td>
+      <td>153</td>
+      <td>12</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>833</td>
+      <td>833</td>
+      <td>93</td>
+      <td>93</td>
+      <td>938</td>
+      <td>986</td>
+      <td>105</td>
+      <td>112</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>morphological_operations</td>
+      <td>morphological_operations</td>
+      <td>Apply morphological operations to images</td>
+      <td></td>
+      <td></td>
+      <td>scipy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>morphological_operations</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations</td>
+      <td>1.12.0</td>
+      <td>scipy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mosdepth</td>
+      <td>mosdepth</td>
+      <td>fast and flexible BAM/CRAM depth calculation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/brentp/mosdepth</td>
+      <td>SAM</td>
+      <td>mosdepth</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth</td>
+      <td>0.3.8</td>
+      <td>mosdepth</td>
+      <td>0.3.8</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1278</td>
+      <td>1278</td>
+      <td>87</td>
+      <td>87</td>
+      <td>168</td>
+      <td>168</td>
+      <td>24</td>
+      <td>24</td>
+      <td>102</td>
+      <td>102</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1548</td>
+      <td>1548</td>
+      <td>116</td>
+      <td>116</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mothur</td>
+      <td>mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn</td>
+      <td>Mothur wrappers</td>
+      <td>mothur</td>
+      <td>mothur</td>
+      <td></td>
+      <td>mothur</td>
+      <td>Open-source, platform-independent, community-supported software for describing and comparing microbial communities</td>
+      <td>DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis</td>
+      <td>Microbial ecology, Taxonomy, Sequence analysis, Phylogeny</td>
+      <td>To update</td>
+      <td>https://www.mothur.org</td>
+      <td>Metagenomics</td>
+      <td>mothur</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur</td>
+      <td>1.0</td>
+      <td>mothur</td>
+      <td>1.48.0</td>
+      <td>DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis</td>
+      <td>Microbial ecology, Taxonomy, Sequence analysis, Phylogeny</td>
+      <td>129</td>
+      <td>129</td>
+      <td>129</td>
+      <td>0</td>
+      <td>129</td>
+      <td>129</td>
+      <td>129</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>128</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>126</td>
+      <td>129</td>
+      <td>129</td>
+      <td>0</td>
+      <td>297546</td>
+      <td>326056</td>
+      <td>37506</td>
+      <td>41763</td>
+      <td>565218</td>
+      <td>682083</td>
+      <td>72163</td>
+      <td>89926</td>
+      <td>167400</td>
+      <td>182490</td>
+      <td>26963</td>
+      <td>28404</td>
+      <td>1030164</td>
+      <td>1190629</td>
+      <td>136632</td>
+      <td>160093</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>motus</td>
+      <td>mereg_mOTUs_tables, motus_profiler</td>
+      <td>Tool for profiling the abundance of microbial taxa.</td>
+      <td>mOTUs</td>
+      <td>mOTUs</td>
+      <td></td>
+      <td>Metagenomic operational taxonomic units (mOTUs)</td>
+      <td>Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/motu-tool/mOTUs</td>
+      <td>Metagenomics</td>
+      <td>motus</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/motus</td>
+      <td>3.1.0</td>
+      <td>motus</td>
+      <td>3.1.0</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mqc</td>
+      <td>mqc</td>
+      <td>Ribosome profiling mapping quality control tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/Biobix/mQC</td>
+      <td>Sequence Analysis</td>
+      <td>mqc</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc</td>
+      <td>1.9</td>
+      <td>mqc</td>
+      <td>1.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>71</td>
+      <td>76</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>71</td>
+      <td>76</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mqppep</td>
+      <td>mqppep_anova, mqppep_preproc</td>
+      <td>MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/</td>
+      <td>Proteomics</td>
+      <td>mqppep</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep</td>
+      <td>0.1.19</td>
+      <td>bioconductor-preprocesscore</td>
+      <td>1.64.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mrbayes</td>
+      <td>mrbayes</td>
+      <td>A program for the Bayesian estimation of phylogeny.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>mrbayes</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes</td>
+      <td>1.0.2</td>
+      <td>mrbayes</td>
+      <td>3.2.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ms2deepscore</td>
+      <td>ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training</td>
+      <td>Mass spectra similarity scoring using a trained ms2deepscore model.</td>
+      <td>ms2deepscore</td>
+      <td>ms2deepscore</td>
+      <td></td>
+      <td>MS2DeepScore</td>
+      <td>MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.</td>
+      <td>Spectrum calculation, Spectral library search, Network analysis</td>
+      <td>Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening</td>
+      <td>To update</td>
+      <td>https://github.com/matchms/ms2deepscore</td>
+      <td>Metabolomics</td>
+      <td>ms2deepscore</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore</td>
+      <td>2.0.0</td>
+      <td>ms2deepscore</td>
+      <td>2.1.0</td>
+      <td>Spectrum calculation, Spectral library search, Network analysis</td>
+      <td>Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ms2snoop</td>
+      <td>ms2snoop</td>
+      <td>[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>ms2snoop</td>
+      <td>workflow4metabolomics</td>
+      <td></td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop</td>
+      <td>2.2.1</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msPurity</td>
+      <td>mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching</td>
+      <td>[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/computational-metabolomics/mspurity-galaxy</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>computational-metabolomics</td>
+      <td>https://github.com/computational-metabolomics/mspurity-galaxy</td>
+      <td>https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity</td>
+      <td>1.28.0</td>
+      <td>bioconductor-mspurity</td>
+      <td>1.28.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>848</td>
+      <td>848</td>
+      <td>91</td>
+      <td>91</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>848</td>
+      <td>848</td>
+      <td>91</td>
+      <td>91</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msaboot</td>
+      <td>msaboot</td>
+      <td>A multiple sequences alignment bootstrapping tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/msaboot</td>
+      <td>Fasta Manipulation</td>
+      <td>msaboot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot</td>
+      <td>0.1.2</td>
+      <td>msaboot</td>
+      <td>0.1.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>864</td>
+      <td>929</td>
+      <td>91</td>
+      <td>101</td>
+      <td>1100</td>
+      <td>1100</td>
+      <td>175</td>
+      <td>175</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1964</td>
+      <td>2029</td>
+      <td>266</td>
+      <td>276</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msconvert</td>
+      <td>msconvert</td>
+      <td>msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container</td>
+      <td>msconvert</td>
+      <td>msconvert</td>
+      <td></td>
+      <td>msConvert</td>
+      <td>msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.</td>
+      <td>Filtering, Formatting</td>
+      <td>Proteomics, Proteomics experiment</td>
+      <td>To update</td>
+      <td>http://proteowizard.sourceforge.net/tools.shtml</td>
+      <td>Proteomics</td>
+      <td>msconvert</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert</td>
+      <td>3.0.20287</td>
+      <td></td>
+      <td></td>
+      <td>Filtering, Formatting</td>
+      <td>Proteomics, Proteomics experiment</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20749</td>
+      <td>22184</td>
+      <td>455</td>
+      <td>469</td>
+      <td>1239</td>
+      <td>1239</td>
+      <td>71</td>
+      <td>71</td>
+      <td>2666</td>
+      <td>2666</td>
+      <td>53</td>
+      <td>53</td>
+      <td>24654</td>
+      <td>26089</td>
+      <td>579</td>
+      <td>593</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msgfplus</td>
+      <td>msgfplus</td>
+      <td>MSGF+</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>msgfplus</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus</td>
+      <td>0.5</td>
+      <td>msgf_plus</td>
+      <td>2024.03.26</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>473</td>
+      <td>529</td>
+      <td>33</td>
+      <td>43</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>529</td>
+      <td>33</td>
+      <td>43</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msmetaenhancer</td>
+      <td>msmetaenhancer</td>
+      <td></td>
+      <td>msmetaenhancer</td>
+      <td>msmetaenhancer</td>
+      <td></td>
+      <td>MSMetaEnhancer</td>
+      <td>Tool for mass spectra metadata annotation.</td>
+      <td>Annotation, Standardisation and normalisation</td>
+      <td>Metabolomics, Compound libraries and screening, Data submission, annotation and curation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/MSMetaEnhancer</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer</td>
+      <td>0.4.0</td>
+      <td>msmetaenhancer</td>
+      <td>0.4.0</td>
+      <td>Annotation, Standardisation and normalisation</td>
+      <td>Metabolomics, Compound libraries and screening, Data submission, annotation and curation</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>203</td>
+      <td>203</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td>251</td>
+      <td>251</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msms_extractor</td>
+      <td>msms_extractor</td>
+      <td>Extract MS/MS scans from the mzML file(s) based on PSM report.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>msms_extractor</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor</td>
+      <td>1.0.0</td>
+      <td>proteowizard</td>
+      <td>3_0_9992</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>110</td>
+      <td>110</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>110</td>
+      <td>110</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msp_merge</td>
+      <td>msp_merge</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge</td>
+      <td>0.1.0</td>
+      <td>matchms</td>
+      <td>0.27.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msp_split</td>
+      <td>msp_split</td>
+      <td>[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/computational-metabolomics/mspurity-galaxy</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>tomnl</td>
+      <td>https://github.com/computational-metabolomics/mspurity-galaxy</td>
+      <td>https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split</td>
+      <td>0.0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msstats</td>
+      <td>msstats</td>
+      <td>MSstats tool for analyzing mass spectrometry proteomic datasets</td>
+      <td>msstatstmt</td>
+      <td>msstatstmt</td>
+      <td></td>
+      <td>MSstatsTMT</td>
+      <td>Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</td>
+      <td>Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling</td>
+      <td>Proteomics, Proteomics experiment, Protein expression</td>
+      <td>To update</td>
+      <td>https://github.com/MeenaChoi/MSstats</td>
+      <td>Proteomics</td>
+      <td></td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats</td>
+      <td>4.0.0</td>
+      <td>bioconductor-msstats</td>
+      <td>4.10.0</td>
+      <td>Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling</td>
+      <td>Proteomics, Proteomics experiment, Protein expression</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2353</td>
+      <td>2353</td>
+      <td>559</td>
+      <td>559</td>
+      <td>1122</td>
+      <td>1122</td>
+      <td>211</td>
+      <td>211</td>
+      <td>1091</td>
+      <td>1091</td>
+      <td>35</td>
+      <td>35</td>
+      <td>4566</td>
+      <td>4566</td>
+      <td>805</td>
+      <td>805</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msstatstmt</td>
+      <td>msstatstmt</td>
+      <td>MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://msstats.org/msstatstmt/</td>
+      <td>Proteomics</td>
+      <td>msstatstmt</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt</td>
+      <td>2.0.0</td>
+      <td>bioconductor-msstatstmt</td>
+      <td>2.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>795</td>
+      <td>795</td>
+      <td>104</td>
+      <td>104</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>461</td>
+      <td>461</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1256</td>
+      <td>1256</td>
+      <td>116</td>
+      <td>116</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mt2mq</td>
+      <td>mt2mq</td>
+      <td>Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>mt2mq</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq</td>
+      <td>1.1.0</td>
+      <td>r-tidyverse</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>275</td>
+      <td>275</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>275</td>
+      <td>275</td>
+      <td>38</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>multigps</td>
+      <td>multigps</td>
+      <td>Analyzes collections of multi-condition ChIP-seq data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://mahonylab.org/software/multigps/</td>
+      <td>ChIP-seq</td>
+      <td>multigps</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps</td>
+      <td>0.74.0</td>
+      <td>fonts-conda-ecosystem</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>485</td>
+      <td>871</td>
+      <td>159</td>
+      <td>298</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>485</td>
+      <td>871</td>
+      <td>159</td>
+      <td>298</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>multigsea</td>
+      <td>multigsea</td>
+      <td>GSEA-based pathway enrichment analysis for multi-omics data</td>
+      <td>multiGSEA</td>
+      <td>multiGSEA</td>
+      <td></td>
+      <td>multiGSEA</td>
+      <td>A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.</td>
+      <td>Gene-set enrichment analysis, Aggregation, Pathway analysis</td>
+      <td>Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules</td>
+      <td>Up-to-date</td>
+      <td>https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html</td>
+      <td>Transcriptomics, Proteomics, Statistics</td>
+      <td>multigsea</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea</td>
+      <td>1.12.0</td>
+      <td>bioconductor-multigsea</td>
+      <td>1.12.0</td>
+      <td>Gene-set enrichment analysis, Aggregation, Pathway analysis</td>
+      <td>Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>106</td>
+      <td>106</td>
+      <td>25</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>106</td>
+      <td>106</td>
+      <td>25</td>
+      <td>25</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>multiqc</td>
+      <td>multiqc</td>
+      <td>MultiQC aggregates results from bioinformatics analyses across many samples into a single report</td>
+      <td>multiqc</td>
+      <td>multiqc</td>
+      <td></td>
+      <td>MultiQC</td>
+      <td>MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.</td>
+      <td>Validation, Sequencing quality control</td>
+      <td>Sequencing, Bioinformatics, Sequence analysis, Genomics</td>
+      <td>To update</td>
+      <td>http://multiqc.info/</td>
+      <td>Fastq Manipulation, Statistics, Visualization</td>
+      <td>multiqc</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc</td>
+      <td>1.24.1</td>
+      <td>multiqc</td>
+      <td>1.25.1</td>
+      <td>Sequencing quality control</td>
+      <td>Sequencing, Bioinformatics, Sequence analysis, Genomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>182221</td>
+      <td>192389</td>
+      <td>19343</td>
+      <td>20494</td>
+      <td>163961</td>
+      <td>182413</td>
+      <td>26449</td>
+      <td>29758</td>
+      <td>40663</td>
+      <td>41855</td>
+      <td>5974</td>
+      <td>6157</td>
+      <td>386845</td>
+      <td>416657</td>
+      <td>51766</td>
+      <td>56409</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>multispecies_orthologous_microsats</td>
+      <td>multispecies_orthologous_microsats</td>
+      <td>Extract orthologous microsatellites</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>multispecies_orthologous_microsats</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats</td>
+      <td>1.0.0</td>
+      <td>bx-sputnik</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mummer</td>
+      <td>mummerplot_wrapper</td>
+      <td>Draw dotplots using mummer, mucmer, or promer with mummerplot</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://mummer.sourceforge.net/</td>
+      <td>Graphics, Sequence Analysis, Visualization</td>
+      <td>mummer</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer</td>
+      <td>0.0.8</td>
+      <td>ghostscript</td>
+      <td>9.18</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>883</td>
+      <td>921</td>
+      <td>199</td>
+      <td>211</td>
+      <td>730</td>
+      <td>730</td>
+      <td>199</td>
+      <td>199</td>
+      <td>136</td>
+      <td>202</td>
+      <td>34</td>
+      <td>49</td>
+      <td>1749</td>
+      <td>1853</td>
+      <td>432</td>
+      <td>459</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mummer4</td>
+      <td>mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords</td>
+      <td>Mummer4 Tools</td>
+      <td>mummer4</td>
+      <td>mummer4</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/mummer4/mummer</td>
+      <td>Sequence Analysis</td>
+      <td>mummer4</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4</td>
+      <td>4.0.0rc1</td>
+      <td>mummer4</td>
+      <td>4.0.0rc1</td>
+      <td></td>
+      <td></td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>21587</td>
+      <td>22119</td>
+      <td>1940</td>
+      <td>2033</td>
+      <td>29284</td>
+      <td>29284</td>
+      <td>3626</td>
+      <td>3626</td>
+      <td>8194</td>
+      <td>8194</td>
+      <td>545</td>
+      <td>545</td>
+      <td>59065</td>
+      <td>59597</td>
+      <td>6111</td>
+      <td>6204</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>music_deconvolution</td>
+      <td>music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution</td>
+      <td>Multi-subject Single Cell deconvolution (MuSiC)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/xuranw/MuSiC</td>
+      <td>Transcriptomics</td>
+      <td>music</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution</td>
+      <td>0.1.1</td>
+      <td>music-deconvolution</td>
+      <td>0.1.1</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>5</td>
+      <td>4</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2801</td>
+      <td>2801</td>
+      <td>289</td>
+      <td>289</td>
+      <td>364</td>
+      <td>364</td>
+      <td>80</td>
+      <td>80</td>
+      <td>1357</td>
+      <td>1357</td>
+      <td>21</td>
+      <td>21</td>
+      <td>4522</td>
+      <td>4522</td>
+      <td>390</td>
+      <td>390</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mutate_snp_codon</td>
+      <td>mutate_snp_codon_1</td>
+      <td>Mutate Codons with SNPs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>mutate_snp_codon</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>44</td>
+      <td>49</td>
+      <td>5</td>
+      <td>5</td>
+      <td>81</td>
+      <td>417</td>
+      <td>23</td>
+      <td>118</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>125</td>
+      <td>466</td>
+      <td>28</td>
+      <td>123</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mutational_patterns</td>
+      <td>mutational_patterns</td>
+      <td>Mutational patterns and signatures in base substitution catalogs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>mutational_patterns</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns</td>
+      <td>3.12.0</td>
+      <td>bioconductor-mutationalpatterns</td>
+      <td>3.12.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mykrobe</td>
+      <td>mykrobe_predict</td>
+      <td>Antibiotic resistance predictions</td>
+      <td>Mykrobe</td>
+      <td>Mykrobe</td>
+      <td></td>
+      <td>Mykrobe</td>
+      <td>Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed</td>
+      <td>Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming</td>
+      <td>Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics</td>
+      <td>To update</td>
+      <td>https://github.com/Mykrobe-tools/mykrobe</td>
+      <td>Sequence Analysis</td>
+      <td>mykrobe</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe</td>
+      <td>0.10.0</td>
+      <td>mykrobe</td>
+      <td>0.13.0</td>
+      <td>Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming</td>
+      <td>Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mykrobe_parser</td>
+      <td>mykrobe_parseR</td>
+      <td>RScript to parse the results of mykrobe predictor.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/mykrobe-parser</td>
+      <td>Sequence Analysis</td>
+      <td>mykrobe_parser</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/mykrobe-parser</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser</td>
+      <td>0.1.4.1</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mz_to_sqlite</td>
+      <td>mz_to_sqlite</td>
+      <td>Creates a SQLite database for proteomics data</td>
+      <td>mztosqlite</td>
+      <td>mztosqlite</td>
+      <td></td>
+      <td>mzToSQLite</td>
+      <td>Convert proteomics data files into a SQLite database</td>
+      <td>Conversion, Peptide database search</td>
+      <td>Proteomics, Biological databases</td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/mzToSQLite</td>
+      <td>Proteomics</td>
+      <td>mz_to_sqlite</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite</td>
+      <td>2.1.1+galaxy0</td>
+      <td>mztosqlite</td>
+      <td>2.1.1</td>
+      <td>Conversion, Peptide database search</td>
+      <td>Proteomics, Biological databases</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>854</td>
+      <td>860</td>
+      <td>110</td>
+      <td>111</td>
+      <td>79</td>
+      <td>79</td>
+      <td>15</td>
+      <td>15</td>
+      <td>274</td>
+      <td>274</td>
+      <td>13</td>
+      <td>13</td>
+      <td>1207</td>
+      <td>1213</td>
+      <td>138</td>
+      <td>139</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mzmine</td>
+      <td>mzmine_batch</td>
+      <td>mass-spectrometry data processing, with the main focus on LC-MS data</td>
+      <td>mzmine</td>
+      <td>mzmine</td>
+      <td></td>
+      <td>MZmine</td>
+      <td>Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.</td>
+      <td>Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation</td>
+      <td>Proteomics, Metabolomics, Proteomics experiment, Small molecules</td>
+      <td>Up-to-date</td>
+      <td>http://mzmine.github.io/</td>
+      <td>Metabolomics</td>
+      <td>mzmine_batch</td>
+      <td>iuc</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine</td>
+      <td>3.9.0</td>
+      <td>mzmine</td>
+      <td>3.9.0</td>
+      <td>Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation</td>
+      <td>Proteomics, Metabolomics, Proteomics experiment, Small molecules</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mzml_validator</td>
+      <td>mzml_validator</td>
+      <td>mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools</td>
+      <td>Metabolomics, Proteomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator</td>
+      <td>0.1.0+galaxy2</td>
+      <td>lxml</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mzxmlshaper</td>
+      <td>mzxmlshaper</td>
+      <td>Convert mzML, mzXML or netCDF files to mzML or mzXML</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://rdrr.io/bioc/mzR/</td>
+      <td>Metabolomics</td>
+      <td>mzxmlshaper</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper</td>
+      <td>1.0.0+galaxy0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>naltorfs</td>
+      <td>bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs</td>
+      <td>nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BlankenbergLab/nAltORFs</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs</td>
+      <td>0.1.2</td>
+      <td>naltorfs</td>
+      <td>0.1.2</td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>204</td>
+      <td>204</td>
+      <td>75</td>
+      <td>75</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>204</td>
+      <td>204</td>
+      <td>75</td>
+      <td>75</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nanocompore</td>
+      <td>nanocompore_db, nanocompore_sampcomp</td>
+      <td>Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.</td>
+      <td>Nanocompore</td>
+      <td>Nanocompore</td>
+      <td></td>
+      <td>Nanocompore</td>
+      <td>RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro</td>
+      <td>Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting</td>
+      <td>Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites</td>
+      <td>To update</td>
+      <td>https://nanocompore.rna.rocks/</td>
+      <td>Sequence Analysis</td>
+      <td>nanocompore</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore</td>
+      <td>1.0.0rc3.post2</td>
+      <td>nanocompore</td>
+      <td>1.0.4</td>
+      <td>PolyA signal detection, Genotyping, k-mer counting</td>
+      <td>Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>839</td>
+      <td>839</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>269</td>
+      <td>269</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1108</td>
+      <td>1108</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nanoplot</td>
+      <td>nanoplot</td>
+      <td>Plotting tool for long read sequencing data and alignments</td>
+      <td>nanoplot</td>
+      <td>nanoplot</td>
+      <td></td>
+      <td>NanoPlot</td>
+      <td>NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences</td>
+      <td>Scatter plot plotting, Box-Whisker plot plotting</td>
+      <td>Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/wdecoster/NanoPlot</td>
+      <td>Visualization</td>
+      <td>nanoplot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot</td>
+      <td>1.43.0</td>
+      <td>nanoplot</td>
+      <td>1.43.0</td>
+      <td>Scatter plot plotting, Box-Whisker plot plotting</td>
+      <td>Genomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>99052</td>
+      <td>100009</td>
+      <td>5671</td>
+      <td>5755</td>
+      <td>40386</td>
+      <td>40386</td>
+      <td>3371</td>
+      <td>3371</td>
+      <td>17919</td>
+      <td>17919</td>
+      <td>2188</td>
+      <td>2188</td>
+      <td>157357</td>
+      <td>158314</td>
+      <td>11230</td>
+      <td>11314</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nanopolish</td>
+      <td>nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants</td>
+      <td>Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/jts/nanopolish</td>
+      <td></td>
+      <td>nanopolish</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish</td>
+      <td>0.14.0</td>
+      <td>nanopolish</td>
+      <td>0.14.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>9284</td>
+      <td>9694</td>
+      <td>215</td>
+      <td>229</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2358</td>
+      <td>2358</td>
+      <td>49</td>
+      <td>49</td>
+      <td>11642</td>
+      <td>12052</td>
+      <td>264</td>
+      <td>278</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nanopolishcomp</td>
+      <td>nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate</td>
+      <td>NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.</td>
+      <td>nanopolishcomp</td>
+      <td>nanopolishcomp</td>
+      <td></td>
+      <td>NanopolishComp</td>
+      <td>NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.</td>
+      <td>Methylation analysis, Collapsing methods</td>
+      <td>Sequence analysis, Sequencing, Genetic variation</td>
+      <td>To update</td>
+      <td>https://a-slide.github.io/NanopolishComp</td>
+      <td>Sequence Analysis</td>
+      <td>nanopolishcomp</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp</td>
+      <td>0.6.11</td>
+      <td>nanopolishcomp</td>
+      <td>0.6.12</td>
+      <td>Methylation analysis, Collapsing methods</td>
+      <td>Sequence analysis, Sequencing, Genetic variation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1091</td>
+      <td>1091</td>
+      <td>44</td>
+      <td>44</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1091</td>
+      <td>1091</td>
+      <td>44</td>
+      <td>44</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nastiseq</td>
+      <td>nastiseq</td>
+      <td>A method to identify cis-NATs using ssRNA-seq</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/</td>
+      <td>RNA</td>
+      <td>nastiseq</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq</td>
+      <td>1.0</td>
+      <td>r-nastiseq</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>36</td>
+      <td>40</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>36</td>
+      <td>40</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_acc_download</td>
+      <td>ncbi_acc_download</td>
+      <td>Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/kblin/ncbi-acc-download</td>
+      <td>Data Source</td>
+      <td>ncbi_acc_download</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download</td>
+      <td>0.2.8</td>
+      <td>ncbi-acc-download</td>
+      <td>0.2.8</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6873</td>
+      <td>6873</td>
+      <td>1664</td>
+      <td>1664</td>
+      <td>17651</td>
+      <td>17651</td>
+      <td>4513</td>
+      <td>4513</td>
+      <td>6228</td>
+      <td>6228</td>
+      <td>972</td>
+      <td>972</td>
+      <td>30752</td>
+      <td>30752</td>
+      <td>7149</td>
+      <td>7149</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_blast_plus</td>
+      <td>blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper</td>
+      <td>NCBI BLAST+</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://blast.ncbi.nlm.nih.gov/</td>
+      <td>Sequence Analysis</td>
+      <td>ncbi_blast_plus</td>
+      <td>devteam</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus</td>
+      <td>2.14.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>16</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>15</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>15</td>
+      <td>16</td>
+      <td>16</td>
+      <td>15</td>
+      <td>0</td>
+      <td>391141</td>
+      <td>443752</td>
+      <td>9760</td>
+      <td>10546</td>
+      <td>306361</td>
+      <td>350178</td>
+      <td>11767</td>
+      <td>13684</td>
+      <td>227235</td>
+      <td>244814</td>
+      <td>3192</td>
+      <td>3617</td>
+      <td>924737</td>
+      <td>1038744</td>
+      <td>24719</td>
+      <td>27847</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_datasets</td>
+      <td>datasets_download_gene, datasets_download_genome</td>
+      <td>NCBI datasets downloads biological sequence data across all domains of life from NCBI.</td>
+      <td>ncbi_datasets</td>
+      <td>ncbi_datasets</td>
+      <td></td>
+      <td>NCBI Datasets</td>
+      <td>NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.</td>
+      <td>Data handling, Sequence database search, Data retrieval</td>
+      <td>Biological databases</td>
+      <td>To update</td>
+      <td>https://github.com/ncbi/datasets</td>
+      <td>Data Source</td>
+      <td>ncbi_datasets</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets</td>
+      <td>16.20.0</td>
+      <td>ncbi-datasets-cli</td>
+      <td></td>
+      <td>Data handling, Sequence database search, Data retrieval</td>
+      <td>Biological databases</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>4417</td>
+      <td>4417</td>
+      <td>1024</td>
+      <td>1024</td>
+      <td>6940</td>
+      <td>6940</td>
+      <td>2275</td>
+      <td>2275</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>11358</td>
+      <td>11358</td>
+      <td>3300</td>
+      <td>3300</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_egapx</td>
+      <td>ncbi_egapx</td>
+      <td>Eukaryotic Genome Annotation Pipeline - External (EGAPx)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ncbi/egapx</td>
+      <td>Genome annotation</td>
+      <td>ncbi_egapx</td>
+      <td>richard-burhans</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx</td>
+      <td>0.2-alpha</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_entrez_direct</td>
+      <td>ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch</td>
+      <td>NCBI Entrez Direct allow fetching data from NCBI Databases</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://www.ncbi.nlm.nih.gov/books/NBK179288/</td>
+      <td>Data Source</td>
+      <td>ncbi_entrez_direct</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct</td>
+      <td>22.4</td>
+      <td>entrez-direct</td>
+      <td>22.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_entrez_eutils</td>
+      <td>ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary</td>
+      <td>NCBI Entrez E-Utilties allow fetching data from NCBI Databases</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.ncbi.nlm.nih.gov/books/NBK25501/</td>
+      <td>Data Source</td>
+      <td>ncbi_entrez_eutils</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils</td>
+      <td>1.70</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>2794</td>
+      <td>3191</td>
+      <td>533</td>
+      <td>664</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2794</td>
+      <td>3191</td>
+      <td>533</td>
+      <td>664</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_fcs_adaptor</td>
+      <td>ncbi_fcs_adaptor</td>
+      <td>FCS-adaptor detects adaptor and vector contamination in genome sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ncbi/fcs</td>
+      <td>Sequence Analysis</td>
+      <td>ncbi_fcs_adaptor</td>
+      <td>richard-burhans</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor</td>
+      <td>0.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>842</td>
+      <td>842</td>
+      <td>93</td>
+      <td>93</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>842</td>
+      <td>842</td>
+      <td>93</td>
+      <td>93</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_fcs_gx</td>
+      <td>ncbi_fcs_gx</td>
+      <td>FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).</td>
+      <td>ncbi_fcs</td>
+      <td>ncbi_fcs</td>
+      <td></td>
+      <td>NCBI fcs</td>
+      <td>The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.</td>
+      <td>Sequence assembly validation, Sequence trimming, Sequence contamination filtering</td>
+      <td>Sequence analysis, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/ncbi/fcs-gx</td>
+      <td>Sequence Analysis</td>
+      <td>ncbi_fcs_gx</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx</td>
+      <td>0.5.4</td>
+      <td>ncbi-fcs-gx</td>
+      <td>0.5.4</td>
+      <td>Sequence assembly validation, Sequence trimming, Sequence contamination filtering</td>
+      <td>Sequence analysis, Sequence assembly</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>125</td>
+      <td>125</td>
+      <td>26</td>
+      <td>26</td>
+      <td>2489</td>
+      <td>2489</td>
+      <td>139</td>
+      <td>139</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2614</td>
+      <td>2614</td>
+      <td>165</td>
+      <td>165</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>necat</td>
+      <td>necat</td>
+      <td>Error correction and de-novo assembly for ONT Nanopore reads</td>
+      <td>necat</td>
+      <td>necat</td>
+      <td></td>
+      <td>NECAT</td>
+      <td>NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.</td>
+      <td>De-novo assembly</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/xiaochuanle/NECAT</td>
+      <td>Assembly</td>
+      <td>necat</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat</td>
+      <td>0.0.1_update20200803</td>
+      <td>necat</td>
+      <td>0.0.1_update20200803</td>
+      <td>De-novo assembly</td>
+      <td>Sequence assembly</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>790</td>
+      <td>790</td>
+      <td>160</td>
+      <td>160</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>790</td>
+      <td>790</td>
+      <td>160</td>
+      <td>160</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>netboxr</td>
+      <td>netboxr</td>
+      <td>netboxr enables automated discovery of biological process modules by network analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Systems Biology</td>
+      <td>netboxr</td>
+      <td>bgruening</td>
+      <td></td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/netboxr</td>
+      <td>1.6.0</td>
+      <td>bioconductor-netboxr</td>
+      <td>1.9.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>newick_utils</td>
+      <td>newick_display</td>
+      <td>Perform operations on Newick trees</td>
+      <td>newick_utilities</td>
+      <td>newick_utilities</td>
+      <td></td>
+      <td>Newick Utilities</td>
+      <td>The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.</td>
+      <td>Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction</td>
+      <td>Phylogeny, Genomics, Computer science</td>
+      <td>To update</td>
+      <td>http://cegg.unige.ch/newick_utils</td>
+      <td>Visualization, Metagenomics</td>
+      <td>newick_utils</td>
+      <td>iuc</td>
+      <td>https://github.com/tjunier/newick_utils</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils</td>
+      <td>1.6+galaxy1</td>
+      <td>newick_utils</td>
+      <td>1.6</td>
+      <td></td>
+      <td>Phylogeny, Genomics, Computer science</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>33637</td>
+      <td>34195</td>
+      <td>1113</td>
+      <td>1172</td>
+      <td>16257</td>
+      <td>16257</td>
+      <td>1816</td>
+      <td>1816</td>
+      <td>7582</td>
+      <td>7582</td>
+      <td>899</td>
+      <td>899</td>
+      <td>57476</td>
+      <td>58034</td>
+      <td>3828</td>
+      <td>3887</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nextclade</td>
+      <td>nextalign, nextclade</td>
+      <td>Identify differences between your sequences and a reference sequence used by Nextstrain</td>
+      <td>nextclade</td>
+      <td>nextclade</td>
+      <td></td>
+      <td>Nextclade</td>
+      <td>Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.</td>
+      <td>Methylation analysis, Variant calling</td>
+      <td>Genomics, Sequence analysis, Cladistics</td>
+      <td>To update</td>
+      <td>https://github.com/nextstrain/nextclade</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade</td>
+      <td>2.7.0</td>
+      <td>nextalign</td>
+      <td>2.14.0</td>
+      <td>Methylation analysis, Variant calling</td>
+      <td>Genomics, Cladistics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4411</td>
+      <td>4411</td>
+      <td>396</td>
+      <td>396</td>
+      <td>9708</td>
+      <td>9708</td>
+      <td>279</td>
+      <td>279</td>
+      <td>2099</td>
+      <td>2099</td>
+      <td>212</td>
+      <td>212</td>
+      <td>16218</td>
+      <td>16218</td>
+      <td>887</td>
+      <td>887</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nextdenovo</td>
+      <td>nextdenovo</td>
+      <td>String graph-based de novo assembler for long reads</td>
+      <td>nextdenovo</td>
+      <td>nextdenovo</td>
+      <td></td>
+      <td>NextDenovo</td>
+      <td>NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages.</td>
+      <td>De-novo assembly, Genome assembly</td>
+      <td>Sequencing, Sequence assembly</td>
+      <td>To update</td>
+      <td>https://github.com/Nextomics/NextDenovo</td>
+      <td>Assembly</td>
+      <td>nextdenovo</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo</td>
+      <td>2.5.0</td>
+      <td>nextdenovo</td>
+      <td>2.5.2</td>
+      <td>De-novo assembly, Genome assembly</td>
+      <td>Sequencing, Sequence assembly</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>391</td>
+      <td>391</td>
+      <td>158</td>
+      <td>158</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>391</td>
+      <td>391</td>
+      <td>158</td>
+      <td>158</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ngmlr</td>
+      <td>ngmlr</td>
+      <td>CoNvex Gap-cost alignMents for Long Reads</td>
+      <td>ngmlr</td>
+      <td>ngmlr</td>
+      <td></td>
+      <td>NGMLR</td>
+      <td>An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.</td>
+      <td>DNA mapping, Sequence alignment, Genetic variation analysis</td>
+      <td>Sequencing, Mapping, DNA structural variation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/philres/ngmlr</td>
+      <td>Next Gen Mappers</td>
+      <td>ngmlr</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr</td>
+      <td>0.2.7</td>
+      <td>ngmlr</td>
+      <td>0.2.7</td>
+      <td>DNA mapping, Sequence alignment, Genetic variation analysis</td>
+      <td>Sequencing, Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1403</td>
+      <td>1403</td>
+      <td>49</td>
+      <td>49</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1403</td>
+      <td>1403</td>
+      <td>49</td>
+      <td>49</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ngsutils</td>
+      <td>ngsutils_bam_filter</td>
+      <td>NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.</td>
+      <td>ngsutils</td>
+      <td>ngsutils</td>
+      <td></td>
+      <td>NGSUtils</td>
+      <td>NGSUtils is a suite of software tools for working with next-generation sequencing datasets</td>
+      <td>Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering</td>
+      <td>Genomics, Transcriptomics</td>
+      <td>To update</td>
+      <td>https://github.com/ngsutils/ngsutils</td>
+      <td>SAM</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils</td>
+      <td></td>
+      <td>ngsutils</td>
+      <td>0.5.9</td>
+      <td>Read pre-processing, Variant calling, Formatting, Sequence contamination filtering</td>
+      <td>Transcriptomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>24611</td>
+      <td>29662</td>
+      <td>633</td>
+      <td>716</td>
+      <td>15523</td>
+      <td>21395</td>
+      <td>740</td>
+      <td>1128</td>
+      <td>7751</td>
+      <td>8972</td>
+      <td>125</td>
+      <td>145</td>
+      <td>47885</td>
+      <td>60029</td>
+      <td>1498</td>
+      <td>1989</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nlstradamus</td>
+      <td>nlstradamus</td>
+      <td>Find nuclear localization signals (NLSs) in protein sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.moseslab.csb.utoronto.ca/NLStradamus</td>
+      <td>Fasta Manipulation, Sequence Analysis</td>
+      <td>nlstradamus</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus</td>
+      <td>0.0.11</td>
+      <td>NLStradamus</td>
+      <td>1.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nmr_annotation</td>
+      <td>NmrAnnotation</td>
+      <td>[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>nmr_annotation</td>
+      <td>marie-tremblay-metatoul</td>
+      <td>https://github.com/workflow4metabolomics/nmr_annotation</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation</td>
+      <td>3.0.0</td>
+      <td>r-batch</td>
+      <td>1.1_4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>49</td>
+      <td>49</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>49</td>
+      <td>49</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nmr_annotation2d</td>
+      <td>2DNmrAnnotation</td>
+      <td>[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>2dnmrannotation</td>
+      <td>marie-tremblay-metatoul</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d</td>
+      <td>2.0.0</td>
+      <td>r-batch</td>
+      <td>1.1_4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nmr_preprocessing</td>
+      <td>NMR_Preprocessing, NMR_Read</td>
+      <td>[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>nmr_preprocessing</td>
+      <td>marie-tremblay-metatoul</td>
+      <td>https://github.com/workflow4metabolomics/nmr_preprocessing</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing</td>
+      <td></td>
+      <td>r-batch</td>
+      <td>1.1_4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>142</td>
+      <td>142</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>335</td>
+      <td>341</td>
+      <td>9</td>
+      <td>9</td>
+      <td>477</td>
+      <td>483</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nonpareil</td>
+      <td>nonpareil</td>
+      <td>Estimate average coverage in metagenomic datasets</td>
+      <td>nonpareil</td>
+      <td>nonpareil</td>
+      <td></td>
+      <td>nonpareil</td>
+      <td>Estimate metagenomic coverage and sequence diversity</td>
+      <td>Operation</td>
+      <td></td>
+      <td>To update</td>
+      <td>http://nonpareil.readthedocs.io</td>
+      <td>Metagenomics</td>
+      <td>nonpareil</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil</td>
+      <td>3.1.1</td>
+      <td>nonpareil</td>
+      <td>3.5.5</td>
+      <td>Operation</td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>107</td>
+      <td>143</td>
+      <td>13</td>
+      <td>15</td>
+      <td>148</td>
+      <td>148</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>255</td>
+      <td>291</td>
+      <td>33</td>
+      <td>35</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>normalization</td>
+      <td>normalization</td>
+      <td>[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>normalization</td>
+      <td>marie-tremblay-metatoul</td>
+      <td>https://github.com/workflow4metabolomics/normalization</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization</td>
+      <td>1.0.7</td>
+      <td>r-batch</td>
+      <td>1.1_4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>152</td>
+      <td>162</td>
+      <td>39</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>233</td>
+      <td>236</td>
+      <td>12</td>
+      <td>12</td>
+      <td>385</td>
+      <td>398</td>
+      <td>51</td>
+      <td>52</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>novoplasty</td>
+      <td>novoplasty</td>
+      <td>NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ndierckx/NOVOPlasty</td>
+      <td>Assembly</td>
+      <td>novoplasty</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty</td>
+      <td>4.3.1</td>
+      <td>novoplasty</td>
+      <td>4.3.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7780</td>
+      <td>7780</td>
+      <td>337</td>
+      <td>337</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2323</td>
+      <td>2323</td>
+      <td>99</td>
+      <td>99</td>
+      <td>10104</td>
+      <td>10104</td>
+      <td>437</td>
+      <td>437</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nucleosome_prediction</td>
+      <td>Nucleosome</td>
+      <td>Prediction of Nucleosomes Positions on the Genome</td>
+      <td>nucleosome_prediction</td>
+      <td>nucleosome_prediction</td>
+      <td></td>
+      <td>nucleosome_prediction</td>
+      <td>Prediction of Nucleosomes Positions on the Genome</td>
+      <td>Prediction and recognition, Nucleosome position prediction, Sequence analysis</td>
+      <td>Structural genomics, Nucleic acid sites, features and motifs</td>
+      <td>Up-to-date</td>
+      <td>https://genie.weizmann.ac.il/software/nucleo_exe.html</td>
+      <td>Sequence Analysis</td>
+      <td>nucleosome_prediction</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction</td>
+      <td>3.0</td>
+      <td>nucleosome_prediction</td>
+      <td>3.0</td>
+      <td>Prediction and recognition, Nucleosome position prediction, Sequence analysis</td>
+      <td>Structural genomics, Nucleic acid sites, features and motifs</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>118</td>
+      <td>863</td>
+      <td>19</td>
+      <td>26</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>118</td>
+      <td>863</td>
+      <td>19</td>
+      <td>26</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nugen_nudup</td>
+      <td>nugen_nudup</td>
+      <td>Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.</td>
+      <td>nudup</td>
+      <td>nudup</td>
+      <td></td>
+      <td>NuDup</td>
+      <td>Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.</td>
+      <td>Duplication detection</td>
+      <td>Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tecangenomics/nudup</td>
+      <td>SAM, Metagenomics, Sequence Analysis, Transcriptomics</td>
+      <td>nugen_nudup</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup</td>
+      <td>2.3.3</td>
+      <td>nudup</td>
+      <td>2.3.3</td>
+      <td>Duplication detection</td>
+      <td>Sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>numeric_clustering</td>
+      <td>numeric_clustering</td>
+      <td>Clustering tool for numberic values</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://scikit-learn.org/stable/index.html</td>
+      <td>Statistics</td>
+      <td>numeric_clustering</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering</td>
+      <td>0.9</td>
+      <td>anaconda</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>391</td>
+      <td>486</td>
+      <td>5</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>391</td>
+      <td>486</td>
+      <td>5</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>oases</td>
+      <td>oasesoptimiserv</td>
+      <td>Short read assembler</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Assembly, RNA</td>
+      <td>oases</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/oases</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/oases</td>
+      <td>1.4.0</td>
+      <td>oases</td>
+      <td>0.2.09</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>obisindicators</td>
+      <td>obisindicators, obis_data</td>
+      <td>Compute biodiveristy indicators for marine data from obis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/Marie59/obisindicators</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators</td>
+      <td>0.0.2</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>352</td>
+      <td>352</td>
+      <td>42</td>
+      <td>42</td>
+      <td>8</td>
+      <td>8</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>360</td>
+      <td>360</td>
+      <td>48</td>
+      <td>48</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>obitools</td>
+      <td>obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq</td>
+      <td>OBITools is a set of programs developed to simplify the manipulation of sequence files</td>
+      <td>obitools</td>
+      <td>obitools</td>
+      <td></td>
+      <td>OBITools</td>
+      <td>Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.</td>
+      <td>Sequence analysis, Sequence analysis</td>
+      <td>Sequence analysis, DNA, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>http://metabarcoding.org/obitools</td>
+      <td>Sequence Analysis</td>
+      <td>obitools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools</td>
+      <td>1.2.13</td>
+      <td>obitools</td>
+      <td>1.2.13</td>
+      <td>Sequence analysis, Sequence analysis</td>
+      <td>Sequence analysis, DNA, Sequencing</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>37598</td>
+      <td>37598</td>
+      <td>1277</td>
+      <td>1277</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3862</td>
+      <td>3862</td>
+      <td>280</td>
+      <td>280</td>
+      <td>41460</td>
+      <td>41460</td>
+      <td>1557</td>
+      <td>1557</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ocean</td>
+      <td>argo_getdata, divand_full_analysis</td>
+      <td>Access, process, visualise oceanographic data for the Earth System</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/Marie59/FE-ft-ESG/tree/main/argo</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean</td>
+      <td>0.1.15</td>
+      <td>julia</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ococo</td>
+      <td>ococo</td>
+      <td>Variant detection of SNVs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/karel-brinda/ococo</td>
+      <td>Variant Analysis</td>
+      <td>ococo</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo</td>
+      <td>0.1.2.6</td>
+      <td>ococo</td>
+      <td>0.1.2.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1850</td>
+      <td>1963</td>
+      <td>79</td>
+      <td>93</td>
+      <td>1370</td>
+      <td>1370</td>
+      <td>194</td>
+      <td>194</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3220</td>
+      <td>3333</td>
+      <td>273</td>
+      <td>287</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>odgi</td>
+      <td>odgi_build, odgi_viz</td>
+      <td>Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/vgteam/odgi</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi</td>
+      <td>0.3</td>
+      <td>odgi</td>
+      <td>0.8.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ogcProcess_otb_bandmath</td>
+      <td>otb_band_math</td>
+      <td>Outputs a monoband image which is the result of a mathematical operation on several multi-band images.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AquaINFRA/galaxy</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath</td>
+      <td>1.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>98</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>98</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ogcProcess_otb_meanShiftSmoothing</td>
+      <td>otb_mean_shift_smoothing</td>
+      <td>This application smooths an image using the MeanShift algorithm.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AquaINFRA/galaxy</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing</td>
+      <td>1.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omark</td>
+      <td>omark</td>
+      <td>Proteome quality assessment software</td>
+      <td>omark</td>
+      <td>omark</td>
+      <td></td>
+      <td>OMArk</td>
+      <td>Proteome quality assessment software</td>
+      <td>Sequence assembly validation, Differential protein expression profiling</td>
+      <td>Proteomics, Sequence analysis, Statistics and probability</td>
+      <td>To update</td>
+      <td>https://github.com/DessimozLab/OMArk</td>
+      <td>Sequence Analysis</td>
+      <td>omark</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark</td>
+      <td>0.3.0</td>
+      <td></td>
+      <td></td>
+      <td>Sequence assembly validation, Differential protein expression profiling</td>
+      <td>Proteomics, Sequence analysis, Statistics and probability</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>12</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omero</td>
+      <td>omero_import, omero_metadata_import, omero_roi_import</td>
+      <td>Import images, region of interest, metadata into an OMERO.server using omero-py</td>
+      <td>omero</td>
+      <td>omero</td>
+      <td></td>
+      <td>OMERO</td>
+      <td>Client-server Java software for visualisation, management and analysis of biological microscope images.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Data visualisation</td>
+      <td>To update</td>
+      <td>https://github.com/ome/omero-py/</td>
+      <td>Imaging</td>
+      <td>omero_upload</td>
+      <td>ufz</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero</td>
+      <td>5.18.0</td>
+      <td>omero-py</td>
+      <td>5.11.1</td>
+      <td>Image analysis</td>
+      <td>Imaging, Data visualisation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omero_clean_rois_tables</td>
+      <td>omero_clean_rois_tables</td>
+      <td>Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>omero_clean_rois_tables</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables</td>
+      <td>20230623</td>
+      <td>fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omero_get_children_ids</td>
+      <td>omero_get_children_ids</td>
+      <td>Get omero id of children of an omero object id</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>omero_get_children_ids</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids</td>
+      <td>0.2.0</td>
+      <td>omero-py</td>
+      <td>5.11.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omero_get_full_images</td>
+      <td>omero_get_full_images</td>
+      <td>Get full images from omero</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>omero_get_full_images</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images</td>
+      <td>20240521</td>
+      <td>fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omero_hyperstack_to_fluo_measurements_on_gastruloid</td>
+      <td>omero_hyperstack_to_fluo_measurements_on_gastruloid</td>
+      <td>Analyse Hyperstack on OMERO server to measure fluorescence levels</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>omero_hyperstack_to_fluo_measurements_on_gastruloid</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid</td>
+      <td>20230809</td>
+      <td>fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omero_hyperstack_to_gastruloid_measurements</td>
+      <td>omero_hyperstack_to_gastruloid_measurements</td>
+      <td>Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>omero_hyperstack_to_gastruloid_measurements</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements</td>
+      <td>20240214</td>
+      <td>fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ont_fast5_api</td>
+      <td>ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5</td>
+      <td>ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/nanoporetech/ont_fast5_api/</td>
+      <td>Nanopore</td>
+      <td>ont_fast5_api</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api</td>
+      <td>3.1.3</td>
+      <td>ont-fast5-api</td>
+      <td>4.1.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>87</td>
+      <td>87</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>87</td>
+      <td>87</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>onto_toolkit</td>
+      <td>onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def</td>
+      <td>ONTO-Toolkit is a collection of tools for managing ontologies.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://search.cpan.org/~easr/ONTO-PERL-1.45/</td>
+      <td>Ontology Manipulation</td>
+      <td>onto_toolkit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit</td>
+      <td>1.45</td>
+      <td>perl-onto-perl</td>
+      <td>1.45</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>582</td>
+      <td>663</td>
+      <td>68</td>
+      <td>69</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>582</td>
+      <td>663</td>
+      <td>68</td>
+      <td>69</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>openlabcds2csv</td>
+      <td>openlabcds2csv</td>
+      <td>Creates a summary of several "Internal Standard Report" OpenLabCDS results.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Metabolomics</td>
+      <td>openlabcds2csv</td>
+      <td>genouest</td>
+      <td></td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv</td>
+      <td>0.1.0</td>
+      <td>openjdk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>openmm</td>
+      <td>pdbfixer</td>
+      <td>OpenMM is a toolkit for molecular simulation using high performance GPU code.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/openmm</td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>openmm</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm</td>
+      <td>1.8.1</td>
+      <td>pdbfixer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>491</td>
+      <td>491</td>
+      <td>52</td>
+      <td>52</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>491</td>
+      <td>491</td>
+      <td>52</td>
+      <td>52</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>openms</td>
+      <td>AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter</td>
+      <td>OpenMS Suite for LC/MS data management and analyses</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.openms.de/</td>
+      <td>Proteomics</td>
+      <td>openms</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms</td>
+      <td>3.1</td>
+      <td>openms</td>
+      <td>3.2.0</td>
+      <td></td>
+      <td></td>
+      <td>8</td>
+      <td>34</td>
+      <td>144</td>
+      <td>0</td>
+      <td>8</td>
+      <td>34</td>
+      <td>144</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>141</td>
+      <td>124</td>
+      <td>0</td>
+      <td>32169</td>
+      <td>108654</td>
+      <td>3316</td>
+      <td>4889</td>
+      <td>50</td>
+      <td>50</td>
+      <td>15</td>
+      <td>15</td>
+      <td>940</td>
+      <td>940</td>
+      <td>245</td>
+      <td>245</td>
+      <td>33159</td>
+      <td>109644</td>
+      <td>3576</td>
+      <td>5149</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>openms</td>
+      <td>AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter</td>
+      <td>OpenMS in version 2.1.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>openms</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/openms</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/openms</td>
+      <td>2.1.0</td>
+      <td>openms</td>
+      <td>3.2.0</td>
+      <td></td>
+      <td></td>
+      <td>7</td>
+      <td>34</td>
+      <td>135</td>
+      <td>0</td>
+      <td>7</td>
+      <td>34</td>
+      <td>135</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>135</td>
+      <td>134</td>
+      <td>0</td>
+      <td>31121</td>
+      <td>108907</td>
+      <td>3369</td>
+      <td>5029</td>
+      <td>50</td>
+      <td>50</td>
+      <td>15</td>
+      <td>15</td>
+      <td>933</td>
+      <td>933</td>
+      <td>242</td>
+      <td>242</td>
+      <td>32104</td>
+      <td>109890</td>
+      <td>3626</td>
+      <td>5286</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>optdoe</td>
+      <td>optdoe</td>
+      <td>Optimal Design Of Experiment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/pablocarb/doebase</td>
+      <td>Synthetic Biology</td>
+      <td>optdoe</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe</td>
+      <td>v2.0.2</td>
+      <td>doebase</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>optitype</td>
+      <td>optitype</td>
+      <td>Precision HLA typing from NGS data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/FRED-2/OptiType</td>
+      <td>Sequence Analysis</td>
+      <td>optitype</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype</td>
+      <td>1.3.5</td>
+      <td>optitype</td>
+      <td>1.3.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>500</td>
+      <td>500</td>
+      <td>45</td>
+      <td>45</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>500</td>
+      <td>500</td>
+      <td>45</td>
+      <td>45</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>orfipy</td>
+      <td>orfipy</td>
+      <td>Galaxy wrapper for ORFIPY</td>
+      <td>orfipy</td>
+      <td>orfipy</td>
+      <td></td>
+      <td>orfipy</td>
+      <td>A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.</td>
+      <td>Coding region prediction, Database search, Transcriptome assembly, De-novo assembly</td>
+      <td>Computer science, RNA-Seq, Transcriptomics, Small molecules</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/urmi-21/orfipy</td>
+      <td>Sequence Analysis</td>
+      <td>orfipy</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy</td>
+      <td>0.0.4</td>
+      <td>orfipy</td>
+      <td>0.0.4</td>
+      <td>Coding region prediction, Database search, Transcriptome assembly, De-novo assembly</td>
+      <td>Computer science, RNA-Seq, Transcriptomics, Small molecules</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>897</td>
+      <td>897</td>
+      <td>99</td>
+      <td>99</td>
+      <td>1792</td>
+      <td>1792</td>
+      <td>239</td>
+      <td>239</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2689</td>
+      <td>2689</td>
+      <td>338</td>
+      <td>338</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>orientationpy</td>
+      <td>orientationpy</td>
+      <td>Compute image orientation</td>
+      <td></td>
+      <td></td>
+      <td>orientationj</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>orientationpy</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy</td>
+      <td>0.2.0.4</td>
+      <td>orientationpy</td>
+      <td>0.2.0.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>orthofinder</td>
+      <td>orthofinder_onlygroups</td>
+      <td>Accurate inference of orthologous gene groups made easy</td>
+      <td>OrthoFinder</td>
+      <td>OrthoFinder</td>
+      <td></td>
+      <td>OrthoFinder</td>
+      <td>OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.</td>
+      <td>Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment</td>
+      <td>Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/davidemms/OrthoFinder</td>
+      <td>Phylogenetics, Sequence Analysis</td>
+      <td>orthofinder</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder</td>
+      <td>2.5.5</td>
+      <td>orthofinder</td>
+      <td>3.0.1b1</td>
+      <td>Genome comparison, Genome alignment</td>
+      <td>Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2018</td>
+      <td>2018</td>
+      <td>419</td>
+      <td>419</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>438</td>
+      <td>438</td>
+      <td>58</td>
+      <td>58</td>
+      <td>2456</td>
+      <td>2456</td>
+      <td>477</td>
+      <td>477</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>overlay_images</td>
+      <td>ip_overlay_images</td>
+      <td>Overlay two images</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis</td>
+      <td>Imaging</td>
+      <td>overlay_images</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images</td>
+      <td>0.0.4</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>149</td>
+      <td>149</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td>167</td>
+      <td>167</td>
+      <td>32</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>packaged_annotation_loader</td>
+      <td>packaged_annotation_loader</td>
+      <td>Tool to make cached genome annotation data available as a list of datasets collection</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader</td>
+      <td>Data Source</td>
+      <td>packaged_annotation_loader</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader</td>
+      <td>0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>packmol</td>
+      <td>packmol</td>
+      <td>PACKMOL is a package for creating starting structures for Molecular Dynamics simulations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://m3g.iqm.unicamp.br/packmol/home.shtml</td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>packmol</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol</td>
+      <td>18.169.1</td>
+      <td>packmol</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>282</td>
+      <td>295</td>
+      <td>32</td>
+      <td>33</td>
+      <td>420</td>
+      <td>420</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>702</td>
+      <td>715</td>
+      <td>40</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pacu</td>
+      <td>pacu_map, pacu_snp</td>
+      <td>PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.</td>
+      <td>pacu</td>
+      <td>pacu</td>
+      <td></td>
+      <td>PACU</td>
+      <td>PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).</td>
+      <td>Clustering</td>
+      <td>Phylogenetics, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BioinformaticsPlatformWIV-ISP/PACU</td>
+      <td>Sequence Analysis, Phylogenetics</td>
+      <td>pacu</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu</td>
+      <td>0.0.5</td>
+      <td>pacu_snp</td>
+      <td>0.0.5</td>
+      <td>Clustering</td>
+      <td>Phylogenetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pairtools</td>
+      <td>pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats</td>
+      <td>Flexible tools for Hi-C data processing</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://pairtools.readthedocs.io</td>
+      <td>Sequence Analysis</td>
+      <td>pairtools</td>
+      <td>iuc</td>
+      <td>https://github.com/open2c/pairtools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools</td>
+      <td>1.1.0</td>
+      <td>pairtools</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>196</td>
+      <td>196</td>
+      <td>16</td>
+      <td>16</td>
+      <td>19</td>
+      <td>19</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>215</td>
+      <td>215</td>
+      <td>30</td>
+      <td>30</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pandas_rolling_window</td>
+      <td>pandas_rolling_window</td>
+      <td>Rolling window calculations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html</td>
+      <td>Statistics</td>
+      <td>pandas_rolling_window</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window</td>
+      <td>0.1</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>261</td>
+      <td>275</td>
+      <td>12</td>
+      <td>12</td>
+      <td>63</td>
+      <td>63</td>
+      <td>22</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>324</td>
+      <td>338</td>
+      <td>34</td>
+      <td>34</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pangolin</td>
+      <td>pangolin</td>
+      <td>Phylogenetic Assignment of Named Global Outbreak LINeages</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/hCoV-2019/pangolin</td>
+      <td>Sequence Analysis</td>
+      <td>pangolin</td>
+      <td>nml</td>
+      <td>https://github.com/hCoV-2019/pangolin</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin</td>
+      <td>1.1.14</td>
+      <td>pangolin</td>
+      <td>4.3</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7457</td>
+      <td>7457</td>
+      <td>508</td>
+      <td>508</td>
+      <td>8518</td>
+      <td>8518</td>
+      <td>377</td>
+      <td>377</td>
+      <td>2760</td>
+      <td>2760</td>
+      <td>259</td>
+      <td>259</td>
+      <td>18735</td>
+      <td>18735</td>
+      <td>1144</td>
+      <td>1144</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pangolin</td>
+      <td>pangolin</td>
+      <td>Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.</td>
+      <td>pangolin_cov-lineages</td>
+      <td>pangolin_cov-lineages</td>
+      <td></td>
+      <td>pangolin</td>
+      <td>Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages</td>
+      <td>Tree-based sequence alignment, Variant classification</td>
+      <td>Virology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cov-lineages/pangolin</td>
+      <td>Sequence Analysis</td>
+      <td>pangolin</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin</td>
+      <td>4.3</td>
+      <td>pangolin</td>
+      <td>4.3</td>
+      <td>Tree-based sequence alignment, Variant classification</td>
+      <td>Virology</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7457</td>
+      <td>7457</td>
+      <td>508</td>
+      <td>508</td>
+      <td>8518</td>
+      <td>8518</td>
+      <td>377</td>
+      <td>377</td>
+      <td>2760</td>
+      <td>2760</td>
+      <td>259</td>
+      <td>259</td>
+      <td>18735</td>
+      <td>18735</td>
+      <td>1144</td>
+      <td>1144</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>paralyzer</td>
+      <td>paralyzer</td>
+      <td>A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/</td>
+      <td>RNA</td>
+      <td>paralyzer</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer</td>
+      <td>1.5</td>
+      <td>paralyzer</td>
+      <td>1.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>322</td>
+      <td>349</td>
+      <td>24</td>
+      <td>29</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>322</td>
+      <td>349</td>
+      <td>24</td>
+      <td>29</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>parse_mito_blast</td>
+      <td>parse_mito_blast</td>
+      <td>Filtering blast out from querying assembly against mitochondrial database.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py</td>
+      <td>Sequence Analysis</td>
+      <td>parse_mito_blast</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast</td>
+      <td>1.0.2</td>
+      <td>parse_mito_blast</td>
+      <td>1.0.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>203</td>
+      <td>203</td>
+      <td>65</td>
+      <td>65</td>
+      <td>288</td>
+      <td>288</td>
+      <td>62</td>
+      <td>62</td>
+      <td>110</td>
+      <td>110</td>
+      <td>20</td>
+      <td>20</td>
+      <td>601</td>
+      <td>601</td>
+      <td>147</td>
+      <td>147</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>partialr_square</td>
+      <td>partialRsq</td>
+      <td>Compute partial R square</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>partialr_square</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square</td>
+      <td>1.0.0</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>142</td>
+      <td>8</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>142</td>
+      <td>8</td>
+      <td>42</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pathifier</td>
+      <td>pathifier</td>
+      <td>pathifier</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://</td>
+      <td>Transcriptomics, Statistics</td>
+      <td>pathifier</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier</td>
+      <td>1.40.0</td>
+      <td>bioconductor-pathifier</td>
+      <td>1.40.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>245</td>
+      <td>245</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>245</td>
+      <td>245</td>
+      <td>10</td>
+      <td>10</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pathview</td>
+      <td>pathview</td>
+      <td>Pathview is a tool set for pathway based data integration and visualization.</td>
+      <td>pathview</td>
+      <td>pathview</td>
+      <td></td>
+      <td>pathview</td>
+      <td>Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.</td>
+      <td>Pathway or network analysis, Pathway or network visualisation</td>
+      <td>Molecular interactions, pathways and networks, Systems biology, Data visualisation</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/pathview.html</td>
+      <td>Statistics, RNA, Micro-array Analysis</td>
+      <td>pathview</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview</td>
+      <td>1.34.0</td>
+      <td>bioconductor-pathview</td>
+      <td>1.42.0</td>
+      <td>Pathway or network analysis, Pathway or network visualisation</td>
+      <td>Molecular interactions, pathways and networks, Systems biology, Data visualisation</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6204</td>
+      <td>6211</td>
+      <td>1261</td>
+      <td>1261</td>
+      <td>6667</td>
+      <td>6667</td>
+      <td>1143</td>
+      <td>1143</td>
+      <td>1160</td>
+      <td>1160</td>
+      <td>189</td>
+      <td>189</td>
+      <td>14031</td>
+      <td>14038</td>
+      <td>2593</td>
+      <td>2593</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pathwaymatcher</td>
+      <td>reactome_pathwaymatcher</td>
+      <td>Reactome Pathway Matcher</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/LuisFranciscoHS/PathwayMatcher</td>
+      <td>Proteomics</td>
+      <td>reactome_pathwaymatcher</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher</td>
+      <td></td>
+      <td>pathwaymatcher</td>
+      <td>1.9.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>174</td>
+      <td>244</td>
+      <td>65</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>174</td>
+      <td>244</td>
+      <td>65</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>patrist</td>
+      <td>patrist</td>
+      <td>Extract Patristic Distance From a Tree</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02</td>
+      <td>Phylogenetics</td>
+      <td>patrist</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/patrist</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist</td>
+      <td>0.1.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pbgcpp</td>
+      <td>pbgcpp</td>
+      <td>Compute genomic consensus and call variants using PacBio reads mapped to a reference</td>
+      <td>genomicconsensus</td>
+      <td>genomicconsensus</td>
+      <td></td>
+      <td>GenomicConsensus</td>
+      <td>The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.</td>
+      <td>Variant calling</td>
+      <td>Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/PacificBiosciences/gcpp</td>
+      <td>Variant Analysis</td>
+      <td>pbgcpp</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp</td>
+      <td>2.0.2</td>
+      <td>pbgcpp</td>
+      <td>2.0.2</td>
+      <td>Variant calling</td>
+      <td>Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pbmm2</td>
+      <td>pbmm2</td>
+      <td>A minimap2 SMRT wrapper for PacBio data.</td>
+      <td>pbmm2</td>
+      <td>pbmm2</td>
+      <td></td>
+      <td>pbmm2</td>
+      <td>pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.</td>
+      <td>Pairwise sequence alignment, Sorting</td>
+      <td>Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/PacificBiosciences/pbmm2</td>
+      <td>Next Gen Mappers</td>
+      <td>pbmm2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2</td>
+      <td>1.14.99</td>
+      <td>pbmm2</td>
+      <td>1.14.99</td>
+      <td>Pairwise sequence alignment, Sorting</td>
+      <td>Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pbtk</td>
+      <td>bam2fastx</td>
+      <td>Convert PacBio Bam File to fasta or fastq file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/PacificBiosciences/pbtk</td>
+      <td>Convert Formats, Fasta Manipulation, Fastq Manipulation</td>
+      <td>bam2fastx</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk</td>
+      <td>3.1.1</td>
+      <td>pbtk</td>
+      <td>3.1.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>22</td>
+      <td>22</td>
+      <td>109</td>
+      <td>109</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>167</td>
+      <td>167</td>
+      <td>41</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pe_histogram</td>
+      <td>pe_histogram</td>
+      <td>Contains a tool that produces an insert size histogram for a paired-end BAM file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram</td>
+      <td>Graphics</td>
+      <td>pe_histogram</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram</td>
+      <td>1.0.2</td>
+      <td>openjdk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5505</td>
+      <td>5505</td>
+      <td>510</td>
+      <td>510</td>
+      <td>7932</td>
+      <td>8582</td>
+      <td>811</td>
+      <td>909</td>
+      <td>736</td>
+      <td>736</td>
+      <td>119</td>
+      <td>119</td>
+      <td>14173</td>
+      <td>14823</td>
+      <td>1440</td>
+      <td>1538</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>peakachu</td>
+      <td>peakachu</td>
+      <td>PEAKachu is a peak-caller for CLIP- and RIP-Seq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, RNA</td>
+      <td>peakachu</td>
+      <td>rnateam</td>
+      <td>https://github.com/tbischler/PEAKachu</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/peakachu</td>
+      <td>0.2.0+galaxy1</td>
+      <td>peakachu</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2807</td>
+      <td>3337</td>
+      <td>178</td>
+      <td>196</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2807</td>
+      <td>3337</td>
+      <td>178</td>
+      <td>196</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>peakzilla</td>
+      <td>peakzilla</td>
+      <td>Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/steinmann/peakzilla</td>
+      <td>ChIP-seq</td>
+      <td>peakzilla</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla</td>
+      <td>1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pear</td>
+      <td>iuc_pear</td>
+      <td>PEAR evaluates all possible paired-end read overlaps</td>
+      <td>pear</td>
+      <td>pear</td>
+      <td></td>
+      <td>PEAR</td>
+      <td>Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.</td>
+      <td>Sequence merging</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://cme.h-its.org/exelixis/web/software/pear/</td>
+      <td>Fastq Manipulation</td>
+      <td>pear</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear</td>
+      <td>0.9.6</td>
+      <td>pear</td>
+      <td>0.9.6</td>
+      <td>Sequence merging</td>
+      <td>Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6269</td>
+      <td>6866</td>
+      <td>260</td>
+      <td>292</td>
+      <td>5530</td>
+      <td>20068</td>
+      <td>467</td>
+      <td>1664</td>
+      <td>5647</td>
+      <td>8471</td>
+      <td>198</td>
+      <td>300</td>
+      <td>17446</td>
+      <td>35405</td>
+      <td>925</td>
+      <td>2256</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pearson_correlation</td>
+      <td>Pearson_and_apos_Correlation1</td>
+      <td>Pearson and apos Correlation between any two numeric columns</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>pearson_correlation</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pep_pointer</td>
+      <td>pep_pointer</td>
+      <td>PepPointer categorizes peptides by their genomic coordinates.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Genomic Interval Operations, Proteomics</td>
+      <td>pep_pointer</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer</td>
+      <td>0.1.3+galaxy1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>506</td>
+      <td>511</td>
+      <td>54</td>
+      <td>55</td>
+      <td>21</td>
+      <td>21</td>
+      <td>12</td>
+      <td>12</td>
+      <td>163</td>
+      <td>163</td>
+      <td>8</td>
+      <td>8</td>
+      <td>690</td>
+      <td>695</td>
+      <td>74</td>
+      <td>75</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pepquery</td>
+      <td>pepquery</td>
+      <td>A peptide-centric MS search engine for novel peptide identification and validation.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pepquery.org</td>
+      <td>Proteomics</td>
+      <td>pepquery</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery</td>
+      <td>1.6.2</td>
+      <td>pepquery</td>
+      <td>2.0.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7047</td>
+      <td>7047</td>
+      <td>76</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7047</td>
+      <td>7047</td>
+      <td>76</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pepquery2</td>
+      <td>pepquery2, pepquery2_index, pepquery2_show_sets</td>
+      <td>PepQuery2 peptide-centric MS search for peptide identification and validation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://pepquery.org</td>
+      <td>Proteomics</td>
+      <td>pepquery2</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2</td>
+      <td>2.0.2</td>
+      <td>pepquery</td>
+      <td>2.0.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1222</td>
+      <td>1222</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1222</td>
+      <td>1222</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>peptide_genomic_coordinate</td>
+      <td>peptide_genomic_coordinate</td>
+      <td>Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>peptide_genomic_coordinate</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate</td>
+      <td>1.0.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>472</td>
+      <td>472</td>
+      <td>56</td>
+      <td>56</td>
+      <td>16</td>
+      <td>16</td>
+      <td>10</td>
+      <td>10</td>
+      <td>149</td>
+      <td>149</td>
+      <td>5</td>
+      <td>5</td>
+      <td>637</td>
+      <td>637</td>
+      <td>71</td>
+      <td>71</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>peptideshaker</td>
+      <td>fasta_cli, ident_params, peptide_shaker, search_gui</td>
+      <td>PeptideShaker and SearchGUI</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://compomics.github.io</td>
+      <td>Proteomics</td>
+      <td>peptideshaker</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker</td>
+      <td></td>
+      <td>searchgui</td>
+      <td>4.3.11</td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>4</td>
+      <td>2</td>
+      <td>0</td>
+      <td>11986</td>
+      <td>17898</td>
+      <td>1046</td>
+      <td>1153</td>
+      <td>1314</td>
+      <td>1314</td>
+      <td>389</td>
+      <td>389</td>
+      <td>3034</td>
+      <td>3034</td>
+      <td>118</td>
+      <td>118</td>
+      <td>16334</td>
+      <td>22246</td>
+      <td>1553</td>
+      <td>1660</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>peptimapper</td>
+      <td>peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag</td>
+      <td>Proteogenomics workflow for the expert annotation of eukaryotic genomes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9</td>
+      <td>Proteomics</td>
+      <td></td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper</td>
+      <td>2.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pepxml_to_xls</td>
+      <td></td>
+      <td>Convert PepXML to Tabular</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>pepxml_to_xls</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>percolator</td>
+      <td>batched_set_list_creator, percolator, percolator_input_converters, pout2mzid</td>
+      <td>Percolator</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>percolator</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator</td>
+      <td>3.5</td>
+      <td>percolator</td>
+      <td>3.7.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>338</td>
+      <td>378</td>
+      <td>15</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1059</td>
+      <td>1059</td>
+      <td>13</td>
+      <td>13</td>
+      <td>1397</td>
+      <td>1437</td>
+      <td>28</td>
+      <td>29</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>perf</td>
+      <td>stats_perf_tool</td>
+      <td>suitable for boolean classification problems</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://osmot.cs.cornell.edu/kddcup/software.html</td>
+      <td></td>
+      <td>stats_perf_tool</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/perf</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/perf</td>
+      <td>5.11.0</td>
+      <td>perf</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>permutate_axis</td>
+      <td>ip_permutate_axis</td>
+      <td>Permutates axes</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>permutate_axis</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis</td>
+      <td>0.2-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>36</td>
+      <td>42</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>36</td>
+      <td>42</td>
+      <td>1</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pfamscan</td>
+      <td>pfamscan</td>
+      <td>Search a FASTA sequence against a library of Pfam HMM.</td>
+      <td>pfamscan</td>
+      <td>pfamscan</td>
+      <td></td>
+      <td>PfamScan</td>
+      <td>This tool is used to search a FASTA sequence against a library of Pfam HMM.</td>
+      <td>Protein sequence analysis</td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/</td>
+      <td>Sequence Analysis</td>
+      <td>pfamscan</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan</td>
+      <td>1.6</td>
+      <td>pfam_scan</td>
+      <td>1.6</td>
+      <td>Protein sequence analysis</td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>773</td>
+      <td>773</td>
+      <td>60</td>
+      <td>60</td>
+      <td>495</td>
+      <td>495</td>
+      <td>72</td>
+      <td>72</td>
+      <td>246</td>
+      <td>246</td>
+      <td>17</td>
+      <td>17</td>
+      <td>1514</td>
+      <td>1514</td>
+      <td>149</td>
+      <td>149</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pg_tools</td>
+      <td>pg_dump, pg_import, pg_query</td>
+      <td>tool suite for dealing with Postgresql databases from Galaxy's history</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.postgresql.org</td>
+      <td>Data Export, Data Source</td>
+      <td>pgtools</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tools/pgtools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools</td>
+      <td></td>
+      <td>postgresql</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pgsnp2gd_snp</td>
+      <td>pgSnp2gd_snp</td>
+      <td>Convert from pgSnp to gd_snp</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>pgsnp2gd_snp</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pharmcat</td>
+      <td>pharmcat</td>
+      <td>Pharmacogenomics Clinical Annotation Tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pharmcat.org/</td>
+      <td>Variant Analysis</td>
+      <td>pharmcat</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>109</td>
+      <td>109</td>
+      <td>29</td>
+      <td>29</td>
+      <td>250</td>
+      <td>250</td>
+      <td>84</td>
+      <td>84</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>359</td>
+      <td>359</td>
+      <td>113</td>
+      <td>113</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pharokka</td>
+      <td>pharokka</td>
+      <td>rapid standardised annotation tool for bacteriophage genomes and metagenomes</td>
+      <td>pharokka</td>
+      <td>pharokka</td>
+      <td></td>
+      <td>Pharokka</td>
+      <td>Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.</td>
+      <td>Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly</td>
+      <td>Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA</td>
+      <td>To update</td>
+      <td>https://github.com/gbouras13/pharokka</td>
+      <td>Genome annotation</td>
+      <td>pharokka</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka</td>
+      <td>1.3.2</td>
+      <td>\n                pharokka\n</td>
+      <td></td>
+      <td>Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly</td>
+      <td>Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5462</td>
+      <td>5462</td>
+      <td>334</td>
+      <td>334</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>309</td>
+      <td>309</td>
+      <td>52</td>
+      <td>52</td>
+      <td>5771</td>
+      <td>5771</td>
+      <td>386</td>
+      <td>386</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>phyloseq</td>
+      <td>phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness</td>
+      <td>Handling and analysis of high-throughput microbiome census data</td>
+      <td>phyloseq</td>
+      <td>phyloseq</td>
+      <td></td>
+      <td>phyloseq</td>
+      <td>Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.</td>
+      <td>Deposition, Analysis, Visualisation</td>
+      <td>Microbiology, Sequence analysis, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html</td>
+      <td>Metagenomics</td>
+      <td>phyloseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq</td>
+      <td>1.46.0</td>
+      <td>bioconductor-phyloseq</td>
+      <td>1.46.0</td>
+      <td>Deposition, Analysis, Visualisation</td>
+      <td>Microbiology, Sequence analysis, Metagenomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1199</td>
+      <td>1199</td>
+      <td>193</td>
+      <td>193</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1205</td>
+      <td>1205</td>
+      <td>194</td>
+      <td>194</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>phyml</td>
+      <td>phyml</td>
+      <td>PhyML is a phylogeny software based on the maximum-likelihood principle.</td>
+      <td>phyml</td>
+      <td>phyml</td>
+      <td></td>
+      <td>PhyML</td>
+      <td>Phylogenetic estimation software using Maximum Likelihood</td>
+      <td>Phylogenetic tree generation (maximum likelihood and Bayesian methods)</td>
+      <td>Phylogenetics, Bioinformatics, Phylogenetics</td>
+      <td>Up-to-date</td>
+      <td>http://www.atgc-montpellier.fr/phyml/</td>
+      <td>Phylogenetics</td>
+      <td>phyml</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml</td>
+      <td>3.3.20220408</td>
+      <td>phyml</td>
+      <td>3.3.20220408</td>
+      <td></td>
+      <td>Phylogenetics, Bioinformatics, Phylogenetics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1975</td>
+      <td>2034</td>
+      <td>246</td>
+      <td>258</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>553</td>
+      <td>564</td>
+      <td>140</td>
+      <td>144</td>
+      <td>2528</td>
+      <td>2598</td>
+      <td>386</td>
+      <td>402</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>physiofit</td>
+      <td>physiofit</td>
+      <td>PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake &amp; production fluxes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>physiofit.readthedocs.io</td>
+      <td>Metabolomics</td>
+      <td>physiofit</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/MetaSys-LISBP/PhysioFit</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit</td>
+      <td>3.4.0</td>
+      <td>physiofit</td>
+      <td>3.4.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>physiofit_manager</td>
+      <td>physiofit_data_manager</td>
+      <td>Handling of physiofit input files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>physiofit.readthedocs.io</td>
+      <td>Metabolomics</td>
+      <td>physiofit_manager</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager</td>
+      <td>1.0.1</td>
+      <td>physiofit_data_manager</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pi_db_tools</td>
+      <td>calc_delta_pi, pi_db_split, pi_dbspec_align</td>
+      <td>HiRIEF tools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>hirieftools</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools</td>
+      <td>1.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>picard</td>
+      <td>picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile</td>
+      <td>Picard SAM/BAM manipulation tools.</td>
+      <td>picard_samtofastq</td>
+      <td>picard_samtofastq, picard_replacesamheader, picard_fastqtosam, picard_reordersam</td>
+      <td></td>
+      <td>picard_samtofastq</td>
+      <td>Create a FASTQ file.</td>
+      <td>Formatting</td>
+      <td>Sequencing</td>
+      <td>To update</td>
+      <td>http://broadinstitute.github.io/picard/</td>
+      <td>SAM</td>
+      <td>picard</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard</td>
+      <td>3.1.1</td>
+      <td>picard</td>
+      <td>3.2.0</td>
+      <td>Formatting</td>
+      <td>Sequencing</td>
+      <td>31</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>4</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>386934</td>
+      <td>399039</td>
+      <td>11024</td>
+      <td>11956</td>
+      <td>366646</td>
+      <td>589980</td>
+      <td>32000</td>
+      <td>57111</td>
+      <td>56622</td>
+      <td>62258</td>
+      <td>2845</td>
+      <td>3398</td>
+      <td>810202</td>
+      <td>1051277</td>
+      <td>45869</td>
+      <td>72465</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pick_value</td>
+      <td>pick_value</td>
+      <td>Compose a text parameter value using text, integer and float values</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>pick_value</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1607</td>
+      <td>1607</td>
+      <td>41</td>
+      <td>41</td>
+      <td>490</td>
+      <td>490</td>
+      <td>53</td>
+      <td>53</td>
+      <td>127</td>
+      <td>127</td>
+      <td>4</td>
+      <td>4</td>
+      <td>2224</td>
+      <td>2224</td>
+      <td>98</td>
+      <td>98</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>picrust</td>
+      <td>picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes</td>
+      <td>PICRUSt wrappers</td>
+      <td>picrust</td>
+      <td>picrust</td>
+      <td></td>
+      <td>PICRUSt</td>
+      <td>PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.</td>
+      <td>Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding</td>
+      <td>Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing</td>
+      <td>To update</td>
+      <td>https://picrust.github.io/picrust/</td>
+      <td>Metagenomics</td>
+      <td>picrust</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust</td>
+      <td>1.1.1</td>
+      <td>picrust</td>
+      <td>1.1.4</td>
+      <td>Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding</td>
+      <td>Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing</td>
+      <td>0</td>
+      <td>6</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>867</td>
+      <td>1128</td>
+      <td>144</td>
+      <td>165</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2106</td>
+      <td>2106</td>
+      <td>121</td>
+      <td>121</td>
+      <td>2973</td>
+      <td>3234</td>
+      <td>265</td>
+      <td>286</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>picrust2</td>
+      <td>picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions</td>
+      <td>PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States</td>
+      <td>picrust2</td>
+      <td>picrust2</td>
+      <td></td>
+      <td>PICRUSt2</td>
+      <td>PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.</td>
+      <td>Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis</td>
+      <td>Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/picrust/picrust2/wiki</td>
+      <td>Metagenomics</td>
+      <td>picrust2</td>
+      <td>iuc</td>
+      <td>https://github.com/picrust/picrust2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2</td>
+      <td>2.5.3</td>
+      <td>picrust2</td>
+      <td>2.5.3</td>
+      <td>Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis</td>
+      <td>Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2532</td>
+      <td>2532</td>
+      <td>382</td>
+      <td>382</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1311</td>
+      <td>1311</td>
+      <td>83</td>
+      <td>83</td>
+      <td>3844</td>
+      <td>3844</td>
+      <td>466</td>
+      <td>466</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pileup_interval</td>
+      <td>pileup_interval</td>
+      <td>Pileup-to-Interval condenses pileup format into ranges of bases</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>SAM</td>
+      <td>pileup_interval</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval</td>
+      <td>1.0.3</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>613</td>
+      <td>640</td>
+      <td>48</td>
+      <td>54</td>
+      <td>1381</td>
+      <td>7804</td>
+      <td>201</td>
+      <td>1552</td>
+      <td>756</td>
+      <td>815</td>
+      <td>22</td>
+      <td>30</td>
+      <td>2750</td>
+      <td>9259</td>
+      <td>271</td>
+      <td>1636</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pileup_parser</td>
+      <td>pileup_parser</td>
+      <td>Filter pileup on coverage and SNPs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-devteam/</td>
+      <td>SAM</td>
+      <td>pileup_parser</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser</td>
+      <td>1.0.2</td>
+      <td>perl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3639</td>
+      <td>3774</td>
+      <td>414</td>
+      <td>461</td>
+      <td>9754</td>
+      <td>52522</td>
+      <td>1247</td>
+      <td>4531</td>
+      <td>1893</td>
+      <td>2433</td>
+      <td>191</td>
+      <td>318</td>
+      <td>15286</td>
+      <td>58729</td>
+      <td>1852</td>
+      <td>5310</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pilon</td>
+      <td>pilon</td>
+      <td>pilon is a tool for assembly improvement and variant analysis in bacteria</td>
+      <td>pilon</td>
+      <td>pilon</td>
+      <td></td>
+      <td>pilon</td>
+      <td>Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.</td>
+      <td>Sequence assembly, Analysis, Read alignment</td>
+      <td>Assembly</td>
+      <td>To update</td>
+      <td>https://github.com/broadinstitute/pilon/wiki</td>
+      <td>Variant Analysis</td>
+      <td>pilon</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon</td>
+      <td>1.20.1</td>
+      <td>pilon</td>
+      <td>1.24</td>
+      <td>Sequence assembly, Analysis</td>
+      <td>Assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9045</td>
+      <td>9458</td>
+      <td>1115</td>
+      <td>1144</td>
+      <td>7989</td>
+      <td>7989</td>
+      <td>1070</td>
+      <td>1070</td>
+      <td>3945</td>
+      <td>4137</td>
+      <td>726</td>
+      <td>741</td>
+      <td>20979</td>
+      <td>21584</td>
+      <td>2911</td>
+      <td>2955</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pindel</td>
+      <td>pindel</td>
+      <td>Pindel detects genome-wide structural variation.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>pindel</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel</td>
+      <td>0.2.5b9</td>
+      <td>pindel</td>
+      <td>0.2.5b9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pipelign</td>
+      <td>pipelign</td>
+      <td>Multipe sequence alignment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/asmmhossain/pipelign/</td>
+      <td>Next Gen Mappers</td>
+      <td>pipelign</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign</td>
+      <td>0.2</td>
+      <td>pipelign</td>
+      <td>0.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1245</td>
+      <td>1245</td>
+      <td>231</td>
+      <td>231</td>
+      <td>9046</td>
+      <td>9046</td>
+      <td>630</td>
+      <td>630</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10291</td>
+      <td>10291</td>
+      <td>861</td>
+      <td>861</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pipmir</td>
+      <td>pipmir</td>
+      <td>A method to identify novel plant miRNA.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/</td>
+      <td>RNA</td>
+      <td>pipmir</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir</td>
+      <td>0.1.0</td>
+      <td>pipmir</td>
+      <td>1.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>238</td>
+      <td>283</td>
+      <td>42</td>
+      <td>45</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>238</td>
+      <td>283</td>
+      <td>42</td>
+      <td>45</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>piranha</td>
+      <td>piranha</td>
+      <td>Piranha is a peak-caller for CLIP- and RIP-Seq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, RNA</td>
+      <td>piranha</td>
+      <td>rnateam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/piranha</td>
+      <td>1.2.1.0</td>
+      <td>piranha</td>
+      <td>1.2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1408</td>
+      <td>2068</td>
+      <td>94</td>
+      <td>119</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1408</td>
+      <td>2068</td>
+      <td>94</td>
+      <td>119</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pizzly</td>
+      <td>pizzly</td>
+      <td>Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/pmelsted/pizzly/</td>
+      <td>Transcriptomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly</td>
+      <td>0.37.3.1</td>
+      <td>pizzly</td>
+      <td>0.37.3</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>201</td>
+      <td>210</td>
+      <td>23</td>
+      <td>24</td>
+      <td>998</td>
+      <td>998</td>
+      <td>76</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1199</td>
+      <td>1208</td>
+      <td>99</td>
+      <td>100</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plantseg</td>
+      <td>plantseg</td>
+      <td>Tool for cell instance aware segmentation in densely packed 3D volumetric images</td>
+      <td>plantseg</td>
+      <td>plantseg</td>
+      <td></td>
+      <td>PlantSeg</td>
+      <td>Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.</td>
+      <td>Network analysis, Quantification, Microscope image visualisation</td>
+      <td>Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>plantseg</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg</td>
+      <td>1.8.1</td>
+      <td>plant-seg</td>
+      <td></td>
+      <td>Network analysis, Quantification, Microscope image visualisation</td>
+      <td>Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plasflow</td>
+      <td>PlasFlow</td>
+      <td>PlasFlow - Prediction of plasmid sequences in metagenomic contigs.</td>
+      <td>plasflow</td>
+      <td>plasflow</td>
+      <td></td>
+      <td>PlasFlow</td>
+      <td>PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.</td>
+      <td>Sequence analysis</td>
+      <td>Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/smaegol/PlasFlow</td>
+      <td>Sequence Analysis</td>
+      <td>plasflow</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow</td>
+      <td>1.1.0</td>
+      <td>plasflow</td>
+      <td>1.1.0</td>
+      <td>Sequence analysis</td>
+      <td>Metagenomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>37086</td>
+      <td>37272</td>
+      <td>711</td>
+      <td>734</td>
+      <td>6346</td>
+      <td>6346</td>
+      <td>583</td>
+      <td>583</td>
+      <td>3065</td>
+      <td>3065</td>
+      <td>61</td>
+      <td>61</td>
+      <td>46497</td>
+      <td>46683</td>
+      <td>1355</td>
+      <td>1378</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plasmid_profiler</td>
+      <td>plasmid_profiler</td>
+      <td>Explores plasmid content in WGS data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>plasmid_profiler</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler</td>
+      <td>0.1.6</td>
+      <td>r</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plasmid_profiler_suite</td>
+      <td></td>
+      <td>Plasmid Profiler suite defining all dependencies for Plasmid Profiler</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>suite_plasmid_profiler</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plasmidfinder</td>
+      <td>plasmidfinder</td>
+      <td>"PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"</td>
+      <td>PlasmidFinder</td>
+      <td>PlasmidFinder</td>
+      <td></td>
+      <td>PlasmidFinder</td>
+      <td>PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).</td>
+      <td>Genome assembly, Scaffolding, Multilocus sequence typing</td>
+      <td>Whole genome sequencing, Sequence assembly, Mapping, Probes and primers</td>
+      <td>Up-to-date</td>
+      <td>https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/</td>
+      <td>Sequence Analysis</td>
+      <td>plasmidfinder</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder</td>
+      <td>2.1.6</td>
+      <td>plasmidfinder</td>
+      <td>2.1.6</td>
+      <td>Genome assembly, Scaffolding, Multilocus sequence typing</td>
+      <td>Whole genome sequencing, Sequence assembly, Mapping, Probes and primers</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14652</td>
+      <td>14652</td>
+      <td>251</td>
+      <td>251</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>101</td>
+      <td>101</td>
+      <td>18</td>
+      <td>18</td>
+      <td>14753</td>
+      <td>14753</td>
+      <td>269</td>
+      <td>269</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plasmidspades</td>
+      <td>plasmidspades</td>
+      <td>Genome assembler for assemblying plasmid</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Assembly</td>
+      <td>plasmidspades</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades</td>
+      <td>1.1</td>
+      <td>spades</td>
+      <td>4.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>platypus</td>
+      <td>bg_platypus</td>
+      <td>efficient and accurate variant-detection in high-throughput sequencing data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.well.ox.ac.uk/platypus</td>
+      <td>Sequence Analysis</td>
+      <td>platypus</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/platypus</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/platypus</td>
+      <td>0.0.11</td>
+      <td>platypus</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plink</td>
+      <td>plink</td>
+      <td>Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.</td>
+      <td>plink</td>
+      <td>plink</td>
+      <td></td>
+      <td>PLINK</td>
+      <td>Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.</td>
+      <td>Genetic variation analysis</td>
+      <td>GWAS study</td>
+      <td>Up-to-date</td>
+      <td>https://www.cog-genomics.org/plink</td>
+      <td>Genome-Wide Association Study</td>
+      <td>plink</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink</td>
+      <td>1.90b6.21</td>
+      <td>plink</td>
+      <td>1.90b6.21</td>
+      <td>Genetic variation analysis</td>
+      <td>GWAS study</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>851</td>
+      <td>851</td>
+      <td>127</td>
+      <td>127</td>
+      <td>249</td>
+      <td>249</td>
+      <td>43</td>
+      <td>43</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1100</td>
+      <td>1100</td>
+      <td>170</td>
+      <td>170</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plot_from_lda</td>
+      <td>plot_for_lda_output1</td>
+      <td>Draw ROC plot on "Perform LDA" output</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Statistics</td>
+      <td>plot_from_lda</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda</td>
+      <td>1.0.1</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>65</td>
+      <td>77</td>
+      <td>19</td>
+      <td>25</td>
+      <td>153</td>
+      <td>886</td>
+      <td>38</td>
+      <td>343</td>
+      <td>142</td>
+      <td>155</td>
+      <td>8</td>
+      <td>10</td>
+      <td>360</td>
+      <td>1118</td>
+      <td>65</td>
+      <td>378</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plotheatmap</td>
+      <td>plotheatmap</td>
+      <td>This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Computational chemistry</td>
+      <td>plotheatmap</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap</td>
+      <td>1.0</td>
+      <td>bioconductor-preprocesscore</td>
+      <td>1.64.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plotly_ml_performance_plots</td>
+      <td>plotly_ml_performance_plots</td>
+      <td>performance plots for machine learning problems</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics</td>
+      <td>Visualization</td>
+      <td>plotly_ml_performance_plots</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots</td>
+      <td>0.4</td>
+      <td>galaxy-ml</td>
+      <td>0.10.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1342</td>
+      <td>1472</td>
+      <td>184</td>
+      <td>197</td>
+      <td>902</td>
+      <td>902</td>
+      <td>156</td>
+      <td>156</td>
+      <td>630</td>
+      <td>630</td>
+      <td>24</td>
+      <td>24</td>
+      <td>2874</td>
+      <td>3004</td>
+      <td>364</td>
+      <td>377</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plotly_parallel_coordinates_plot</td>
+      <td>plotly_parallel_coordinates_plot</td>
+      <td>parallel coordinates plot produced with plotly</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://plot.ly/python/parallel-coordinates-plot/</td>
+      <td>Visualization</td>
+      <td>plotly_parallel_coordinates_plot</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot</td>
+      <td>0.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>408</td>
+      <td>664</td>
+      <td>91</td>
+      <td>122</td>
+      <td>627</td>
+      <td>627</td>
+      <td>118</td>
+      <td>118</td>
+      <td>605</td>
+      <td>605</td>
+      <td>26</td>
+      <td>26</td>
+      <td>1640</td>
+      <td>1896</td>
+      <td>235</td>
+      <td>266</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plotly_regression_performance_plots</td>
+      <td>plotly_regression_performance_plots</td>
+      <td>performance plots for regression problems</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://scikit-learn.org/stable/supervised_learning.html#supervised-learning</td>
+      <td>Visualization</td>
+      <td>plotly_regression_performance_plots</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots</td>
+      <td>0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>764</td>
+      <td>879</td>
+      <td>213</td>
+      <td>237</td>
+      <td>304</td>
+      <td>304</td>
+      <td>95</td>
+      <td>95</td>
+      <td>193</td>
+      <td>193</td>
+      <td>26</td>
+      <td>26</td>
+      <td>1261</td>
+      <td>1376</td>
+      <td>334</td>
+      <td>358</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pmd_fdr</td>
+      <td>pmd_fdr</td>
+      <td>Calculate Precursor Mass Discrepancy (PMD) for MS/MS</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/slhubler/PMD-FDR-for-Galaxy-P</td>
+      <td>Proteomics</td>
+      <td>pmd_fdr</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr</td>
+      <td>1.4.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pneumocat</td>
+      <td>pneumocat</td>
+      <td>Pneumococcal Capsular Typing of illumina fastq reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phe-bioinformatics/PneumoCaT</td>
+      <td>Variant Analysis</td>
+      <td>pneumocat</td>
+      <td>nml</td>
+      <td>https://github.com/phe-bioinformatics/PneumoCaT</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat</td>
+      <td>1.2.1</td>
+      <td>pneumocat</td>
+      <td>1.2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>points2labelimage</td>
+      <td>ip_points_to_label</td>
+      <td>Points to label image</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>points2labelimage</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage</td>
+      <td>0.4</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>points_association_nn</td>
+      <td>ip_points_association_nn</td>
+      <td>Association of points in consecutive frames</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis</td>
+      <td>Imaging</td>
+      <td>points_association_nn</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn</td>
+      <td>0.0.3-2</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>poisson2test</td>
+      <td>poisson2test</td>
+      <td>Poisson two-sample test</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Statistics, Metagenomics</td>
+      <td>poisson2test</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test</td>
+      <td>1.0.0</td>
+      <td>taxonomy</td>
+      <td>0.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>112</td>
+      <td>120</td>
+      <td>16</td>
+      <td>16</td>
+      <td>4</td>
+      <td>562</td>
+      <td>1</td>
+      <td>140</td>
+      <td>320</td>
+      <td>347</td>
+      <td>7</td>
+      <td>8</td>
+      <td>436</td>
+      <td>1029</td>
+      <td>24</td>
+      <td>164</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>polypolish</td>
+      <td>polypolish</td>
+      <td>"Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."</td>
+      <td>Polypolish</td>
+      <td>Polypolish</td>
+      <td></td>
+      <td>Polypolish</td>
+      <td>Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.</td>
+      <td>Genome assembly, Read mapping, Mapping assembly, Sequencing error detection</td>
+      <td>Sequence assembly, Sequence composition, complexity and repeats, Mapping</td>
+      <td>To update</td>
+      <td>https://github.com/rrwick/Polypolish</td>
+      <td>Sequence Analysis</td>
+      <td>polypolish</td>
+      <td>iuc</td>
+      <td>https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish</td>
+      <td>0.5.0</td>
+      <td>polypolish</td>
+      <td>0.6.0</td>
+      <td>Genome assembly, Read mapping, Mapping assembly, Sequencing error detection</td>
+      <td>Sequence assembly, Sequence composition, complexity and repeats, Mapping</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>731</td>
+      <td>731</td>
+      <td>86</td>
+      <td>86</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>4</td>
+      <td>4</td>
+      <td>773</td>
+      <td>773</td>
+      <td>90</td>
+      <td>90</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>porechop</td>
+      <td>porechop</td>
+      <td>Porechop - Finding and removing adapters from Oxford Nanopore reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/rrwick/Porechop</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td>porechop</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop</td>
+      <td></td>
+      <td>porechop</td>
+      <td>0.2.4</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>262015</td>
+      <td>262852</td>
+      <td>2627</td>
+      <td>2711</td>
+      <td>83623</td>
+      <td>83623</td>
+      <td>1918</td>
+      <td>1918</td>
+      <td>52558</td>
+      <td>52558</td>
+      <td>1037</td>
+      <td>1037</td>
+      <td>398196</td>
+      <td>399033</td>
+      <td>5582</td>
+      <td>5666</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>poretools</td>
+      <td>poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot</td>
+      <td>A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.</td>
+      <td>poretools</td>
+      <td>poretools</td>
+      <td></td>
+      <td>Poretools</td>
+      <td>Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>DNA, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://poretools.readthedocs.io/en/latest/</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools</td>
+      <td>0.6.1a1</td>
+      <td>poretools</td>
+      <td>0.6.1a1</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>DNA, Sequencing</td>
+      <td>13</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>13</td>
+      <td>0</td>
+      <td>19942</td>
+      <td>20587</td>
+      <td>1055</td>
+      <td>1245</td>
+      <td>33619</td>
+      <td>40808</td>
+      <td>2183</td>
+      <td>2594</td>
+      <td>9261</td>
+      <td>9261</td>
+      <td>365</td>
+      <td>365</td>
+      <td>62822</td>
+      <td>70656</td>
+      <td>3603</td>
+      <td>4204</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>positions2snv_alignment</td>
+      <td>positions2snv_alignment</td>
+      <td>Generate alignment of SNVs from SNVPhyl variant table.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Variant Analysis</td>
+      <td>positions2snv_alignment</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>positions2snv_invariant_alignment</td>
+      <td>positions2snv_invariant_alignment</td>
+      <td>Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Variant Analysis</td>
+      <td>positions2snv_invariant_alignment</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>predictnls</td>
+      <td>predictnls</td>
+      <td>Python reimplementation of predictNLS for Galaxy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls</td>
+      <td>Sequence Analysis</td>
+      <td>predictnls</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls</td>
+      <td>0.0.10</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>presto</td>
+      <td>presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3</td>
+      <td>pRESTO toolkit for immune repertoire analysis.</td>
+      <td>presto</td>
+      <td>presto</td>
+      <td></td>
+      <td>pRESTO</td>
+      <td>Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Sequencing, DNA, Immunology</td>
+      <td>To update</td>
+      <td>https://presto.readthedocs.io/</td>
+      <td>Sequence Analysis</td>
+      <td>presto</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto</td>
+      <td>0.6.2</td>
+      <td>presto</td>
+      <td>0.7.2</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Sequencing, DNA, Immunology</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>63244</td>
+      <td>65177</td>
+      <td>1392</td>
+      <td>1599</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>63244</td>
+      <td>65177</td>
+      <td>1392</td>
+      <td>1599</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pretext</td>
+      <td>pretext_graph, pretext_map, pretext_snapshot</td>
+      <td>Process genome contacts maps processing images.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/wtsi-hpag/PretextSnapshot</td>
+      <td>Sequence Analysis</td>
+      <td>suite_pretext</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext</td>
+      <td>0.0.6</td>
+      <td>pretextgraph</td>
+      <td>0.0.6</td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3463</td>
+      <td>3463</td>
+      <td>538</td>
+      <td>538</td>
+      <td>1853</td>
+      <td>1853</td>
+      <td>256</td>
+      <td>256</td>
+      <td>1097</td>
+      <td>1097</td>
+      <td>70</td>
+      <td>70</td>
+      <td>6413</td>
+      <td>6413</td>
+      <td>864</td>
+      <td>864</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>principal_component_analysis</td>
+      <td>pca1</td>
+      <td>Principal Component Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>principal_component_analysis</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis</td>
+      <td>1.0.2</td>
+      <td>rpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9788</td>
+      <td>10032</td>
+      <td>207</td>
+      <td>244</td>
+      <td>3072</td>
+      <td>8054</td>
+      <td>607</td>
+      <td>1488</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12860</td>
+      <td>18086</td>
+      <td>814</td>
+      <td>1732</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>prinseq</td>
+      <td>prinseq</td>
+      <td>PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets</td>
+      <td>prinseq</td>
+      <td>prinseq</td>
+      <td></td>
+      <td>PRINSEQ</td>
+      <td>PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.</td>
+      <td>Read pre-processing, Sequence trimming, Sequence contamination filtering</td>
+      <td>Transcriptomics, Metagenomics, Genomics</td>
+      <td>To update</td>
+      <td>http://prinseq.sourceforge.net/manual.html</td>
+      <td>Fastq Manipulation, Metagenomics</td>
+      <td>prinseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq</td>
+      <td>@TOOL_VERSION+galaxy2</td>
+      <td>prinseq</td>
+      <td>0.20.4</td>
+      <td>Read pre-processing, Sequence trimming, Sequence contamination filtering</td>
+      <td>Transcriptomics, Metagenomics</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>10152</td>
+      <td>10626</td>
+      <td>253</td>
+      <td>281</td>
+      <td>10581</td>
+      <td>10581</td>
+      <td>1240</td>
+      <td>1240</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20733</td>
+      <td>21207</td>
+      <td>1493</td>
+      <td>1521</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>probecoverage</td>
+      <td>probecoverage</td>
+      <td>computes and plots read coverage of genomic regions by sequencing datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Sequence Analysis, Genomic Interval Operations, Graphics, Statistics</td>
+      <td>probecoverage</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage</td>
+      <td>0.22.0</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>prodigal</td>
+      <td>prodigal</td>
+      <td>A protein-coding gene prediction software tool for bacterial and archaeal genomes</td>
+      <td>prodigal</td>
+      <td>prodigal</td>
+      <td></td>
+      <td>Prodigal</td>
+      <td>Fast, reliable protein-coding gene prediction for prokaryotic genomes.</td>
+      <td>Genome annotation</td>
+      <td>Genomics, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/hyattpd/Prodigal</td>
+      <td>Genome annotation</td>
+      <td>prodigal</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal</td>
+      <td>2.6.3</td>
+      <td>prodigal</td>
+      <td>2.6.3</td>
+      <td>Genome annotation</td>
+      <td>Genomics, Sequence analysis</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1902</td>
+      <td>1902</td>
+      <td>167</td>
+      <td>167</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1902</td>
+      <td>1902</td>
+      <td>167</td>
+      <td>167</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>progressivemauve</td>
+      <td>progressivemauve, xmfa2gff3</td>
+      <td>Mauve/ProgressiveMauve Multiple Sequence Aligner</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://darlinglab.org/mauve/user-guide/progressivemauve.html</td>
+      <td>Sequence Analysis</td>
+      <td>progressivemauve</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve</td>
+      <td></td>
+      <td>progressivemauve</td>
+      <td>snapshot_2015_02_13</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2064</td>
+      <td>2173</td>
+      <td>678</td>
+      <td>695</td>
+      <td>2900</td>
+      <td>2900</td>
+      <td>1034</td>
+      <td>1034</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4964</td>
+      <td>5073</td>
+      <td>1712</td>
+      <td>1729</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>projective_transformation</td>
+      <td>ip_projective_transformation</td>
+      <td>Projective transformation</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>projective_transformation</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation</td>
+      <td>0.1.2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>40</td>
+      <td>86</td>
+      <td>4</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>86</td>
+      <td>4</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>projective_transformation_points</td>
+      <td>ip_projective_transformation_points</td>
+      <td>Projective transformation of ROIs defined by pixel (point) coordinates</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>projective_transformation_points</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points</td>
+      <td>0.1.1</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20858</td>
+      <td>21444</td>
+      <td>14</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20858</td>
+      <td>21444</td>
+      <td>14</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>prokka</td>
+      <td>prokka</td>
+      <td>Rapid annotation of prokaryotic genomes</td>
+      <td>prokka</td>
+      <td>prokka</td>
+      <td></td>
+      <td>Prokka</td>
+      <td>Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.</td>
+      <td>Gene prediction, Coding region prediction, Genome annotation</td>
+      <td>Genomics, Model organisms, Virology</td>
+      <td>Up-to-date</td>
+      <td>http://github.com/tseemann/prokka</td>
+      <td>Sequence Analysis</td>
+      <td>prokka</td>
+      <td>crs4</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka</td>
+      <td>1.14.6</td>
+      <td>prokka</td>
+      <td>1.14.6</td>
+      <td>Coding region prediction, Genome annotation</td>
+      <td>Genomics, Model organisms, Virology</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>464359</td>
+      <td>476554</td>
+      <td>7475</td>
+      <td>7721</td>
+      <td>313285</td>
+      <td>331256</td>
+      <td>11243</td>
+      <td>12384</td>
+      <td>131211</td>
+      <td>141875</td>
+      <td>4358</td>
+      <td>4947</td>
+      <td>908855</td>
+      <td>949685</td>
+      <td>23076</td>
+      <td>25052</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>promer</td>
+      <td>promer4_substitutions</td>
+      <td>Aligns two sets of contigs and reports amino acid substitutions between them</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/promer</td>
+      <td>Assembly</td>
+      <td>promer</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/promer</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer</td>
+      <td>1.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>prot-scriber</td>
+      <td>prot_scriber</td>
+      <td>Protein annotation of short human readable descriptions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/usadellab/prot-scriber</td>
+      <td>Proteomics</td>
+      <td>prot_scriber</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber</td>
+      <td>0.1.6</td>
+      <td>prot-scriber</td>
+      <td>0.1.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>protease_prediction</td>
+      <td>eden_protease_prediction</td>
+      <td>This tool can learn the cleavage specificity of a given class of proteases.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/fabriziocosta/eden</td>
+      <td>Sequence Analysis, Proteomics</td>
+      <td>protease_prediction</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction</td>
+      <td>0.9</td>
+      <td>eden</td>
+      <td>2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>129</td>
+      <td>155</td>
+      <td>15</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>129</td>
+      <td>155</td>
+      <td>15</td>
+      <td>21</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>protein_analysis</td>
+      <td>promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort</td>
+      <td>TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis</td>
+      <td>Sequence Analysis</td>
+      <td>tmhmm_and_signalp</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis</td>
+      <td>0.0.13</td>
+      <td>promoter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>11743</td>
+      <td>12752</td>
+      <td>1137</td>
+      <td>1278</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11745</td>
+      <td>12754</td>
+      <td>1138</td>
+      <td>1279</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>protein_properties</td>
+      <td>bg_protein_properties</td>
+      <td>Calculation of various properties from given protein sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>protein_properties</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties</td>
+      <td>0.2.0</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>465</td>
+      <td>638</td>
+      <td>81</td>
+      <td>100</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>465</td>
+      <td>638</td>
+      <td>81</td>
+      <td>100</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteinortho</td>
+      <td>proteinortho, proteinortho_grab_proteins, proteinortho_summary</td>
+      <td>Proteinortho is a tool to detect orthologous proteins/genes within different species.</td>
+      <td>proteinortho</td>
+      <td>proteinortho</td>
+      <td></td>
+      <td>Proteinortho</td>
+      <td>Proteinortho is a tool to detect orthologous genes within different species</td>
+      <td>Sequence clustering, Sequence analysis</td>
+      <td>Comparative genomics</td>
+      <td>To update</td>
+      <td>https://gitlab.com/paulklemm_PHD/proteinortho</td>
+      <td>Proteomics</td>
+      <td>proteinortho</td>
+      <td>iuc</td>
+      <td>https://gitlab.com/paulklemm_PHD/proteinortho</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho</td>
+      <td>6.3.1</td>
+      <td>proteinortho</td>
+      <td>6.3.2</td>
+      <td>Sequence clustering, Sequence analysis</td>
+      <td>Comparative genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3962</td>
+      <td>3962</td>
+      <td>501</td>
+      <td>501</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3962</td>
+      <td>3962</td>
+      <td>501</td>
+      <td>501</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteinpilot</td>
+      <td>convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>proteinpilot</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_joinquantpepionswithproteins</td>
+      <td>proteomiqon_joinquantpepionswithproteins</td>
+      <td>The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_joinquantpepionswithproteins</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins</td>
+      <td>0.0.1</td>
+      <td>proteomiqon-joinquantpepionswithproteins</td>
+      <td>0.0.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>366</td>
+      <td>366</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>366</td>
+      <td>366</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_labeledproteinquantification</td>
+      <td>proteomiqon_labeledproteinquantification</td>
+      <td>The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_labeledproteinquantification</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification</td>
+      <td>0.0.1</td>
+      <td>proteomiqon-labeledproteinquantification</td>
+      <td>0.0.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_labelfreeproteinquantification</td>
+      <td>proteomiqon_labelfreeproteinquantification</td>
+      <td>The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_labelfreeproteinquantification</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification</td>
+      <td>0.0.1</td>
+      <td>proteomiqon-labelfreeproteinquantification</td>
+      <td>0.0.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_mzmltomzlite</td>
+      <td>proteomiqon_mzmltomzlite</td>
+      <td>The tool MzMLToMzLite allows to convert mzML files to mzLite files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_mzmltomzlite</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite</td>
+      <td>0.0.8</td>
+      <td>proteomiqon-mzmltomzlite</td>
+      <td>0.0.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>721</td>
+      <td>721</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>721</td>
+      <td>721</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_peptidedb</td>
+      <td>proteomiqon_peptidedb</td>
+      <td>The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_peptidedb</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb</td>
+      <td>0.0.7</td>
+      <td>proteomiqon-peptidedb</td>
+      <td>0.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>96</td>
+      <td>96</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>96</td>
+      <td>96</td>
+      <td>12</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_peptidespectrummatching</td>
+      <td>proteomiqon_peptidespectrummatching</td>
+      <td>Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_peptidespectrummatching</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching</td>
+      <td>0.0.7</td>
+      <td>proteomiqon-peptidespectrummatching</td>
+      <td>0.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>686</td>
+      <td>686</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>686</td>
+      <td>686</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_proteininference</td>
+      <td>proteomiqon_proteininference</td>
+      <td>MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_proteininference</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference</td>
+      <td>0.0.7</td>
+      <td>proteomiqon-proteininference</td>
+      <td>0.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>89</td>
+      <td>89</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>89</td>
+      <td>89</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_psmbasedquantification</td>
+      <td>proteomiqon_psmbasedquantification</td>
+      <td>The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_psmbasedquantification</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification</td>
+      <td>0.0.8</td>
+      <td>proteomiqon-psmbasedquantification</td>
+      <td>0.0.9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>604</td>
+      <td>604</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>604</td>
+      <td>604</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_psmstatistics</td>
+      <td>proteomiqon_psmstatistics</td>
+      <td>The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_psmstatistics</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics</td>
+      <td>0.0.8</td>
+      <td>proteomiqon-psmstatistics</td>
+      <td>0.0.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>694</td>
+      <td>694</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>694</td>
+      <td>694</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteore_venn_diagram</td>
+      <td>proteore_venn_diagram</td>
+      <td>ProteoRE JVenn Diagram</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>proteore_venn_diagram</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram</td>
+      <td>2021.06.08</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>protxml_to_xls</td>
+      <td>protxml_to_xls</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>protxml_to_xls</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls</td>
+      <td>0.1.0</td>
+      <td>trans_proteomic_pipeline</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pseudogenome</td>
+      <td>pseudogenome</td>
+      <td>Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Sequence Analysis</td>
+      <td>pseudogenome</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome</td>
+      <td>1.0.0</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>psiclass</td>
+      <td>psiclass</td>
+      <td>PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.</td>
+      <td>psiclass</td>
+      <td>psiclass</td>
+      <td></td>
+      <td>PsiCLASS</td>
+      <td>Reference-based transcriptome assembler for single or multiple RNA-seq samples</td>
+      <td>Transcriptome assembly</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/splicebox/PsiCLASS</td>
+      <td>Transcriptomics</td>
+      <td>psiclass</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass</td>
+      <td>1.0.3</td>
+      <td>psiclass</td>
+      <td>1.0.3</td>
+      <td>Transcriptome assembly</td>
+      <td>Sequence assembly</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>24</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>24</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>psm2sam</td>
+      <td>PSMtoSAM</td>
+      <td>PSM to SAM</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/proBAMr.html</td>
+      <td>Proteomics</td>
+      <td>psm_to_sam</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam</td>
+      <td>1.3.2.1</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>psm_eval</td>
+      <td>psm_eval</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>psm_eval</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval</td>
+      <td>0.1.0</td>
+      <td>binaries_for_psm_eval</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>psm_validation</td>
+      <td>psmvalidator</td>
+      <td>Validate PSM from Ion Fragmentation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/psm_fragments.git</td>
+      <td>Proteomics</td>
+      <td>psm_validation</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation</td>
+      <td>1.0.3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>20</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>20</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>psy-maps</td>
+      <td>psy_maps</td>
+      <td>Visualization of regular geographical data on a map with psyplot</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/Chilipp/psy-maps</td>
+      <td>Visualization, Climate Analysis</td>
+      <td>psy_maps</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps</td>
+      <td>1.3.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>333</td>
+      <td>502</td>
+      <td>62</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>333</td>
+      <td>502</td>
+      <td>62</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pureclip</td>
+      <td>pureclip</td>
+      <td>PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/skrakau/PureCLIP</td>
+      <td>Sequence Analysis, RNA, CLIP-seq</td>
+      <td>pureclip</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip</td>
+      <td>1.0.4</td>
+      <td>pureclip</td>
+      <td>1.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1319</td>
+      <td>1507</td>
+      <td>81</td>
+      <td>92</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1319</td>
+      <td>1507</td>
+      <td>81</td>
+      <td>92</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>purge_dups</td>
+      <td>purge_dups</td>
+      <td>Purge haplotigs and overlaps in an assembly based on read depth</td>
+      <td>purge_dups</td>
+      <td>purge_dups</td>
+      <td></td>
+      <td>purge_dups</td>
+      <td>Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences</td>
+      <td>Genome assembly, Read binning, Scaffolding</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/dfguan/purge_dups</td>
+      <td>Assembly</td>
+      <td>purge_dups</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups</td>
+      <td>1.2.6</td>
+      <td>purge_dups</td>
+      <td>1.2.6</td>
+      <td>Genome assembly, Read binning, Scaffolding</td>
+      <td>Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17782</td>
+      <td>17782</td>
+      <td>287</td>
+      <td>287</td>
+      <td>853</td>
+      <td>853</td>
+      <td>65</td>
+      <td>65</td>
+      <td>2224</td>
+      <td>2224</td>
+      <td>65</td>
+      <td>65</td>
+      <td>20859</td>
+      <td>20859</td>
+      <td>417</td>
+      <td>417</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pycoqc</td>
+      <td>pycoqc</td>
+      <td>QC metrics for ONT Basecalling</td>
+      <td>pycoqc</td>
+      <td>pycoqc</td>
+      <td></td>
+      <td>pycoQC</td>
+      <td>PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.</td>
+      <td>Sequencing quality control, Statistical calculation</td>
+      <td>Sequence analysis, Data quality management, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tleonardi/pycoQC</td>
+      <td>Nanopore</td>
+      <td>pycoqc</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc</td>
+      <td>2.5.2</td>
+      <td>pycoqc</td>
+      <td>2.5.2</td>
+      <td>Sequencing quality control, Statistical calculation</td>
+      <td>Sequence analysis, Data quality management, Sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22742</td>
+      <td>22742</td>
+      <td>557</td>
+      <td>557</td>
+      <td>2159</td>
+      <td>2159</td>
+      <td>716</td>
+      <td>716</td>
+      <td>776</td>
+      <td>776</td>
+      <td>448</td>
+      <td>448</td>
+      <td>25677</td>
+      <td>25677</td>
+      <td>1721</td>
+      <td>1721</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pyega3</td>
+      <td>pyega3</td>
+      <td>EGA python client uses the EGA REST API to download authorized datasets and files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/EGA-archive/ega-download-client</td>
+      <td>Data Source</td>
+      <td>ega_download_client</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3</td>
+      <td>5.0.2</td>
+      <td>pyega3</td>
+      <td>5.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2716</td>
+      <td>2716</td>
+      <td>104</td>
+      <td>104</td>
+      <td>134</td>
+      <td>134</td>
+      <td>43</td>
+      <td>43</td>
+      <td>40</td>
+      <td>40</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2890</td>
+      <td>2890</td>
+      <td>148</td>
+      <td>148</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pygenometracks</td>
+      <td>pygenomeTracks</td>
+      <td>pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.</td>
+      <td>pygenometracks</td>
+      <td>pygenometracks</td>
+      <td></td>
+      <td>pyGenomeTracks</td>
+      <td>reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.</td>
+      <td>Visualisation, Formatting</td>
+      <td>Model organisms, Imaging, Workflows</td>
+      <td>To update</td>
+      <td>https://github.com/deeptools/pyGenomeTracks</td>
+      <td>Visualization</td>
+      <td>pygenometracks</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks</td>
+      <td>3.8</td>
+      <td>pygenometracks</td>
+      <td>3.9</td>
+      <td>Visualisation, Formatting</td>
+      <td>Model organisms, Imaging, Workflows</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>12858</td>
+      <td>13232</td>
+      <td>986</td>
+      <td>996</td>
+      <td>8092</td>
+      <td>8092</td>
+      <td>943</td>
+      <td>943</td>
+      <td>3238</td>
+      <td>3238</td>
+      <td>124</td>
+      <td>124</td>
+      <td>24188</td>
+      <td>24562</td>
+      <td>2053</td>
+      <td>2063</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pyprophet</td>
+      <td>pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample</td>
+      <td>Semi-supervised learning and scoring of OpenSWATH results.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/PyProphet/pyprophet</td>
+      <td>Proteomics</td>
+      <td></td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet</td>
+      <td>2.1.4</td>
+      <td>pyprophet</td>
+      <td>2.2.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>5</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>2626</td>
+      <td>2626</td>
+      <td>150</td>
+      <td>150</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>609</td>
+      <td>609</td>
+      <td>9</td>
+      <td>9</td>
+      <td>3235</td>
+      <td>3235</td>
+      <td>159</td>
+      <td>159</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pyscenic</td>
+      <td>pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn</td>
+      <td>PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Sequence Analysis</td>
+      <td>suite_pyscenic</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic</td>
+      <td>0.12.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pysradb</td>
+      <td>pysradb_search</td>
+      <td>pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.</td>
+      <td>pysradb</td>
+      <td>pysradb</td>
+      <td></td>
+      <td>pysradb</td>
+      <td>Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.</td>
+      <td>Deposition, Data retrieval</td>
+      <td>Sequencing, Gene transcripts, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/saketkc/pysradb</td>
+      <td>Sequence Analysis</td>
+      <td>pysradb_search</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb</td>
+      <td>1.4.2</td>
+      <td>pysradb</td>
+      <td>2.2.2</td>
+      <td>Deposition, Data retrieval</td>
+      <td>Sequencing, Gene transcripts, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>163</td>
+      <td>163</td>
+      <td>35</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>163</td>
+      <td>163</td>
+      <td>35</td>
+      <td>35</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pyteomics</td>
+      <td>mztab2tsv</td>
+      <td>Tools using the pyteomics library</td>
+      <td>pyteomics</td>
+      <td>pyteomics</td>
+      <td></td>
+      <td>Pyteomics</td>
+      <td>Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.</td>
+      <td>Protein identification</td>
+      <td>Proteomics, Proteomics experiment</td>
+      <td>To update</td>
+      <td>https://pyteomics.readthedocs.io/en/latest/</td>
+      <td>Proteomics, Metabolomics</td>
+      <td>pyteomics</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics</td>
+      <td>4.4.1</td>
+      <td>pyteomics</td>
+      <td>4.7.4</td>
+      <td>Protein identification</td>
+      <td>Proteomics, Proteomics experiment</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>92</td>
+      <td>92</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>92</td>
+      <td>92</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pyvo_integration</td>
+      <td>astronomical_archives</td>
+      <td>Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Data Source</td>
+      <td>astronomicalarchivestool</td>
+      <td>astroteam</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration</td>
+      <td>0.10.0</td>
+      <td>astropy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>53</td>
+      <td>53</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>53</td>
+      <td>53</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qcxms</td>
+      <td>qcxms_getres, qcxms_neutral_run, qcxms_production_run</td>
+      <td>QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/grimme-lab/QCxMS</td>
+      <td>Computational chemistry, Molecular Dynamics</td>
+      <td>QCxMS</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms</td>
+      <td>5.2.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11246</td>
+      <td>11246</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11246</td>
+      <td>11246</td>
+      <td>13</td>
+      <td>13</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qfilt</td>
+      <td>qfilt</td>
+      <td>Filter sequencing data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/veg/qfilt</td>
+      <td>Fastq Manipulation</td>
+      <td>qfilt</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt</td>
+      <td>1.0.0+galaxy1</td>
+      <td>qfilt</td>
+      <td>0.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qiime_add_on</td>
+      <td>qiime_collapse_samples, qiime_make_otu_table</td>
+      <td>QIIME to perform microbial community analysis</td>
+      <td>qiime_add_on</td>
+      <td>qiime_add_on, qiime_core</td>
+      <td></td>
+      <td>qiime_add_on</td>
+      <td>QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.</td>
+      <td>Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control</td>
+      <td>Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics</td>
+      <td>To update</td>
+      <td>http://www.qiime.org</td>
+      <td>Metagenomics</td>
+      <td>qiime</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on</td>
+      <td></td>
+      <td>qiime</td>
+      <td>1.9.1</td>
+      <td>Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control</td>
+      <td>Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2092</td>
+      <td>2342</td>
+      <td>209</td>
+      <td>238</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2094</td>
+      <td>2344</td>
+      <td>210</td>
+      <td>239</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qiime_core</td>
+      <td>qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file</td>
+      <td>QIIME to perform microbial community analysis</td>
+      <td>qiime_core</td>
+      <td>qiime_core</td>
+      <td></td>
+      <td>qiime_core</td>
+      <td>QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.</td>
+      <td>Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control</td>
+      <td>Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics</td>
+      <td>To update</td>
+      <td>http://www.qiime.org</td>
+      <td>Metagenomics</td>
+      <td>qiime</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core</td>
+      <td></td>
+      <td>qiime</td>
+      <td>1.9.1</td>
+      <td>Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control</td>
+      <td>Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>31825</td>
+      <td>34677</td>
+      <td>3375</td>
+      <td>3785</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>14</td>
+      <td>14</td>
+      <td>4</td>
+      <td>4</td>
+      <td>31840</td>
+      <td>34692</td>
+      <td>3380</td>
+      <td>3790</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qiime_extract_viz</td>
+      <td>qiime_extract_viz</td>
+      <td>Extract vizualization from QIIME artifacts</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.qiime.org</td>
+      <td>Metagenomics</td>
+      <td>qiime_extract_viz</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz</td>
+      <td>0.1.0</td>
+      <td>unzip</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qq_tools</td>
+      <td>qq_manhattan</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://CRAN.R-project.org/package=qqman</td>
+      <td>Visualization, Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td></td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools</td>
+      <td>0.1.0</td>
+      <td>r-qqman</td>
+      <td>0.1.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qualimap</td>
+      <td>qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq</td>
+      <td>Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.</td>
+      <td>qualimap</td>
+      <td>qualimap</td>
+      <td></td>
+      <td>QualiMap</td>
+      <td>Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.</td>
+      <td>Sequencing quality control</td>
+      <td>Data quality management</td>
+      <td>Up-to-date</td>
+      <td>http://qualimap.bioinfo.cipf.es/</td>
+      <td>Sequence Analysis, Transcriptomics, SAM</td>
+      <td>qualimap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap</td>
+      <td>2.3</td>
+      <td>qualimap</td>
+      <td>2.3</td>
+      <td>Sequencing quality control</td>
+      <td>Data quality management</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>684820</td>
+      <td>684820</td>
+      <td>3239</td>
+      <td>3239</td>
+      <td>90503</td>
+      <td>90503</td>
+      <td>3881</td>
+      <td>3881</td>
+      <td>29018</td>
+      <td>29018</td>
+      <td>826</td>
+      <td>826</td>
+      <td>804341</td>
+      <td>804341</td>
+      <td>7946</td>
+      <td>7946</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>quality_filter</td>
+      <td>qualityFilter</td>
+      <td>Filter nucleotides based on quality scores</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>quality_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter</td>
+      <td>1.0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>724</td>
+      <td>35</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>724</td>
+      <td>35</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>quantp</td>
+      <td>quantp</td>
+      <td>Correlation between protein and transcript abundance</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>quantp</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp</td>
+      <td>1.1.2</td>
+      <td>r-data.table</td>
+      <td>1.11.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>197</td>
+      <td>241</td>
+      <td>17</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>197</td>
+      <td>241</td>
+      <td>17</td>
+      <td>22</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>quantwiz_iq</td>
+      <td>quantwiz_iq</td>
+      <td>Isobaric Quantitation using QuantWiz-IQ</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://sourceforge.net/projects/quantwiz/</td>
+      <td>Proteomics</td>
+      <td>quantwiz_iq</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq</td>
+      <td>2.0</td>
+      <td>quantwiz-iq</td>
+      <td>2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>32</td>
+      <td>32</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>32</td>
+      <td>32</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>quasitools</td>
+      <td>aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality</td>
+      <td>A collection of tools for analysing Viral Quasispecies</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/quasitools</td>
+      <td>Sequence Analysis</td>
+      <td>quasitools</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/quasitools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools</td>
+      <td>0.7.0</td>
+      <td>quasitools</td>
+      <td>0.7.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13483</td>
+      <td>13483</td>
+      <td>434</td>
+      <td>434</td>
+      <td>13483</td>
+      <td>13483</td>
+      <td>434</td>
+      <td>434</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>quast</td>
+      <td>quast</td>
+      <td>Quast (Quality ASsessment Tool) evaluates genome assemblies.</td>
+      <td>quast</td>
+      <td>quast</td>
+      <td></td>
+      <td>QUAST</td>
+      <td>QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.</td>
+      <td>Visualisation, Sequence assembly validation</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>http://quast.bioinf.spbau.ru/</td>
+      <td>Assembly</td>
+      <td>quast</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast</td>
+      <td>5.2.0</td>
+      <td>quast</td>
+      <td>5.2.0</td>
+      <td>Visualisation, Sequence assembly validation</td>
+      <td>Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>67737</td>
+      <td>69738</td>
+      <td>7787</td>
+      <td>7971</td>
+      <td>51925</td>
+      <td>56602</td>
+      <td>9692</td>
+      <td>10646</td>
+      <td>32003</td>
+      <td>34145</td>
+      <td>3890</td>
+      <td>4127</td>
+      <td>151665</td>
+      <td>160485</td>
+      <td>21369</td>
+      <td>22744</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>query</td>
+      <td>query</td>
+      <td>Execute an SQL statement on a set of tables</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>query</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/query</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/query</td>
+      <td>0.2</td>
+      <td>click</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>query_impc</td>
+      <td>query_impc</td>
+      <td>Contains a tool to query the IMPC database.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc</td>
+      <td>Convert Formats, Web Services</td>
+      <td>query_impc</td>
+      <td>iuc</td>
+      <td>https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc</td>
+      <td>0.9.0</td>
+      <td>requests</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>query_tabular</td>
+      <td>filter_tabular, query_tabular, sqlite_to_tabular</td>
+      <td>Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular</td>
+      <td>Text Manipulation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular</td>
+      <td>3.3.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>130124</td>
+      <td>135361</td>
+      <td>1265</td>
+      <td>1305</td>
+      <td>11135</td>
+      <td>11135</td>
+      <td>922</td>
+      <td>922</td>
+      <td>5939</td>
+      <td>5939</td>
+      <td>153</td>
+      <td>153</td>
+      <td>147198</td>
+      <td>152435</td>
+      <td>2340</td>
+      <td>2380</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>quickmerge</td>
+      <td>quickmerge</td>
+      <td>Merge long-read and hybrid assemblies to increase contiguity</td>
+      <td>quickmerge</td>
+      <td>quickmerge</td>
+      <td></td>
+      <td>quickmerge</td>
+      <td>Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.</td>
+      <td>Genome assembly, Scaffolding, De-novo assembly, Genotyping</td>
+      <td>Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/mahulchak/quickmerge</td>
+      <td>Assembly</td>
+      <td>quickmerge</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge</td>
+      <td>0.3</td>
+      <td>quickmerge</td>
+      <td>0.3</td>
+      <td>Genome assembly, Scaffolding, De-novo assembly, Genotyping</td>
+      <td>Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qupath_roi_splitter</td>
+      <td>qupath_roi_splitter</td>
+      <td>Split ROI coordinates of QuPath TMA annotation by cell type</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/npinter/ROIsplitter</td>
+      <td>Imaging</td>
+      <td>qupath_roi_splitter</td>
+      <td>galaxyp</td>
+      <td>hhttps://github.com/npinter/ROIsplitter</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter</td>
+      <td>0.3.2</td>
+      <td>geojson</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>172</td>
+      <td>172</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>172</td>
+      <td>172</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rRNA</td>
+      <td>meta_rna</td>
+      <td>Identification of ribosomal RNA genes in metagenomic fragments.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://weizhong-lab.ucsd.edu/meta_rna/</td>
+      <td>RNA</td>
+      <td>rrna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rRNA</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA</td>
+      <td>0.1</td>
+      <td>hmmsearch3.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>raceid</td>
+      <td>raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory</td>
+      <td>RaceID3, StemID2, FateID - scRNA analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/dgrun/RaceID3_StemID2_package/</td>
+      <td>Single Cell, Transcriptomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid</td>
+      <td>0.2.3</td>
+      <td>r-raceid</td>
+      <td>0.1.3</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>3077</td>
+      <td>4581</td>
+      <td>395</td>
+      <td>518</td>
+      <td>2856</td>
+      <td>2856</td>
+      <td>1093</td>
+      <td>1093</td>
+      <td>1977</td>
+      <td>1977</td>
+      <td>19</td>
+      <td>19</td>
+      <td>7910</td>
+      <td>9414</td>
+      <td>1507</td>
+      <td>1630</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>racon</td>
+      <td>racon</td>
+      <td>Consensus module for raw de novo DNA assembly of long uncorrected reads.</td>
+      <td>Racon</td>
+      <td>Racon</td>
+      <td></td>
+      <td>Racon</td>
+      <td>Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.</td>
+      <td>Genome assembly, Mapping assembly</td>
+      <td>Whole genome sequencing, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/isovic/racon</td>
+      <td>Sequence Analysis</td>
+      <td>racon</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/racon</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/racon</td>
+      <td>1.5.0</td>
+      <td>racon</td>
+      <td>1.5.0</td>
+      <td>Genome assembly, Mapping assembly</td>
+      <td>Whole genome sequencing, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>27113</td>
+      <td>27315</td>
+      <td>839</td>
+      <td>850</td>
+      <td>9089</td>
+      <td>9089</td>
+      <td>475</td>
+      <td>475</td>
+      <td>5452</td>
+      <td>5452</td>
+      <td>171</td>
+      <td>171</td>
+      <td>41654</td>
+      <td>41856</td>
+      <td>1485</td>
+      <td>1496</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ragtag</td>
+      <td>ragtag</td>
+      <td>Reference-guided scaffolding of draft genomes tool.</td>
+      <td>ragtag</td>
+      <td>ragtag</td>
+      <td></td>
+      <td>ragtag</td>
+      <td>RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.</td>
+      <td>Genome assembly</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/malonge/RagTag</td>
+      <td>Assembly</td>
+      <td>ragtag</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag</td>
+      <td>2.1.0</td>
+      <td>ragtag</td>
+      <td>2.1.0</td>
+      <td>Genome assembly</td>
+      <td>Sequence assembly</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4844</td>
+      <td>4844</td>
+      <td>480</td>
+      <td>480</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>3</td>
+      <td>3</td>
+      <td>4851</td>
+      <td>4851</td>
+      <td>483</td>
+      <td>483</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ramclustr</td>
+      <td>ramclustr, ramclustr_define_experiment</td>
+      <td></td>
+      <td>ramclustr</td>
+      <td>ramclustr</td>
+      <td></td>
+      <td>RAMClustR</td>
+      <td>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</td>
+      <td>Imputation, Standardisation and normalisation, Clustering, Correlation</td>
+      <td>Metabolomics</td>
+      <td>To update</td>
+      <td>https://rdrr.io/cran/RAMClustR/</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr</td>
+      <td>1.3.0</td>
+      <td>r-ramclustr</td>
+      <td>1.3.1</td>
+      <td>Imputation, Standardisation and normalisation, Clustering, Correlation</td>
+      <td>Metabolomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>22</td>
+      <td>22</td>
+      <td>29</td>
+      <td>29</td>
+      <td>14</td>
+      <td>14</td>
+      <td>344</td>
+      <td>344</td>
+      <td>4</td>
+      <td>4</td>
+      <td>431</td>
+      <td>431</td>
+      <td>40</td>
+      <td>40</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rapidnj</td>
+      <td>rapidnj</td>
+      <td>Galaxy wrapper for the RapidNJ tool</td>
+      <td>rapidnj</td>
+      <td>rapidnj</td>
+      <td></td>
+      <td>RapidNJ</td>
+      <td>A tool for fast canonical neighbor-joining tree construction.</td>
+      <td>Phylogenetic tree generation</td>
+      <td>Phylogeny</td>
+      <td>Up-to-date</td>
+      <td>https://birc.au.dk/software/rapidnj/</td>
+      <td>Phylogenetics</td>
+      <td>rapidnj</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj</td>
+      <td>2.3.2</td>
+      <td>rapidnj</td>
+      <td>2.3.2</td>
+      <td></td>
+      <td>Phylogeny</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>339</td>
+      <td>339</td>
+      <td>30</td>
+      <td>30</td>
+      <td>1737</td>
+      <td>1737</td>
+      <td>256</td>
+      <td>256</td>
+      <td>6</td>
+      <td>6</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2082</td>
+      <td>2082</td>
+      <td>287</td>
+      <td>287</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rasusa</td>
+      <td>rasusa</td>
+      <td>Randomly subsample sequencing reads to a specified coverage</td>
+      <td>rasusa</td>
+      <td>rasusa</td>
+      <td></td>
+      <td>rasusa</td>
+      <td>Produces an unbiased subsample of your reads</td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/mbhall88/rasusa</td>
+      <td>Sequence Analysis</td>
+      <td>rasusa</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa</td>
+      <td>2.0.0</td>
+      <td>rasusa</td>
+      <td>2.1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>raven</td>
+      <td>raven</td>
+      <td>Raven is a de novo genome assembler for long uncorrected reads.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lbcb-sci/raven</td>
+      <td>Assembly</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven</td>
+      <td>1.8.3</td>
+      <td>raven-assembler</td>
+      <td>1.8.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9477</td>
+      <td>9477</td>
+      <td>438</td>
+      <td>438</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10585</td>
+      <td>10585</td>
+      <td>182</td>
+      <td>182</td>
+      <td>20062</td>
+      <td>20062</td>
+      <td>620</td>
+      <td>620</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rawtools</td>
+      <td>rawtools</td>
+      <td>Raw Tools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/kevinkovalchik/RawTools</td>
+      <td>Proteomics</td>
+      <td>rawtools</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools</td>
+      <td></td>
+      <td>rawtools</td>
+      <td>2.0.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>166</td>
+      <td>179</td>
+      <td>32</td>
+      <td>33</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>414</td>
+      <td>414</td>
+      <td>13</td>
+      <td>13</td>
+      <td>580</td>
+      <td>593</td>
+      <td>45</td>
+      <td>46</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>raxml</td>
+      <td>raxml</td>
+      <td>RAxML - A Maximum Likelihood based phylogenetic inference</td>
+      <td>raxml</td>
+      <td>raxml</td>
+      <td></td>
+      <td>RAxML</td>
+      <td>A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.</td>
+      <td>Sequence analysis, Phylogenetic tree analysis</td>
+      <td>Phylogenetics, Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.exelixis-lab.org/web/software/raxml/</td>
+      <td>Phylogenetics</td>
+      <td>raxml</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml</td>
+      <td>8.2.12</td>
+      <td>raxml</td>
+      <td>8.2.13</td>
+      <td>Sequence analysis</td>
+      <td>Phylogenetics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>10905</td>
+      <td>10905</td>
+      <td>966</td>
+      <td>966</td>
+      <td>5100</td>
+      <td>5114</td>
+      <td>587</td>
+      <td>587</td>
+      <td>4955</td>
+      <td>6094</td>
+      <td>765</td>
+      <td>892</td>
+      <td>20960</td>
+      <td>22113</td>
+      <td>2318</td>
+      <td>2445</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rbpbench</td>
+      <td>rbpbench</td>
+      <td>Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs</td>
+      <td>rbpbench</td>
+      <td>rbpbench</td>
+      <td></td>
+      <td>RBPBench</td>
+      <td>Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs</td>
+      <td></td>
+      <td>RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/michauhl/RBPBench</td>
+      <td>Sequence Analysis, RNA, CLIP-seq</td>
+      <td>rbpbench</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench</td>
+      <td>0.8.1</td>
+      <td>rbpbench</td>
+      <td>1.0</td>
+      <td></td>
+      <td>RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>90</td>
+      <td>90</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>90</td>
+      <td>90</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rcas</td>
+      <td>rcas</td>
+      <td>RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/BIMSBbioinfo/RCAS</td>
+      <td>RNA</td>
+      <td>rcas</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas</td>
+      <td>1.5.4</td>
+      <td>bioconductor-rcas</td>
+      <td>1.28.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>860</td>
+      <td>1257</td>
+      <td>88</td>
+      <td>98</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>860</td>
+      <td>1257</td>
+      <td>88</td>
+      <td>98</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rcorrector</td>
+      <td>rcorrector</td>
+      <td>Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.</td>
+      <td>rcorrector</td>
+      <td>rcorrector</td>
+      <td></td>
+      <td>Rcorrector</td>
+      <td>This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.</td>
+      <td>Sequencing error detection</td>
+      <td>RNA, RNA-Seq, Sequencing</td>
+      <td>To update</td>
+      <td>https://github.com/mourisl/Rcorrector</td>
+      <td>Fastq Manipulation</td>
+      <td>rcorrector</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector</td>
+      <td>1.0.3+galaxy1</td>
+      <td>rcorrector</td>
+      <td>1.0.7</td>
+      <td>Sequencing error detection</td>
+      <td>RNA, RNA-Seq</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>655</td>
+      <td>655</td>
+      <td>57</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>655</td>
+      <td>655</td>
+      <td>57</td>
+      <td>57</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rcve</td>
+      <td>rcve1</td>
+      <td>Compute RCVE</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>rcve</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve</td>
+      <td>1.0.0</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>49</td>
+      <td>191</td>
+      <td>5</td>
+      <td>46</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>49</td>
+      <td>191</td>
+      <td>5</td>
+      <td>46</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rcx-tk</td>
+      <td>rcx-tk</td>
+      <td>Tools to process metadata or alkane files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/rcx-tk</td>
+      <td>Metabolomics</td>
+      <td>rcx_tk</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk</td>
+      <td>0.1.0+galaxy0</td>
+      <td>rcx-tk</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rdock</td>
+      <td>rdock</td>
+      <td>Docking ligands to proteins and nucleic acids</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rdock.sourceforge.net/</td>
+      <td>Computational chemistry</td>
+      <td>rdock</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock</td>
+      <td>1.0</td>
+      <td>rDock</td>
+      <td>2013.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>read_it_and_keep</td>
+      <td>read_it_and_keep</td>
+      <td>Rapid decontamination of SARS-CoV-2 sequencing reads</td>
+      <td>read_it_and_keep</td>
+      <td>read_it_and_keep</td>
+      <td></td>
+      <td>read_it_and_keep</td>
+      <td>Read contamination removal</td>
+      <td>Filtering, Genome alignment</td>
+      <td>Pathology, Genomics</td>
+      <td>To update</td>
+      <td>https://github.com/GenomePathogenAnalysisService/read-it-and-keep</td>
+      <td>Sequence Analysis</td>
+      <td>read_it_and_keep</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep</td>
+      <td>0.2.2</td>
+      <td>read-it-and-keep</td>
+      <td>0.3.0</td>
+      <td>Filtering, Genome alignment</td>
+      <td>Pathology, Genomics</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3710</td>
+      <td>3710</td>
+      <td>80</td>
+      <td>80</td>
+      <td>7</td>
+      <td>7</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3717</td>
+      <td>3717</td>
+      <td>86</td>
+      <td>86</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>reago</td>
+      <td>reago</td>
+      <td>Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.</td>
+      <td>reago</td>
+      <td>reago</td>
+      <td></td>
+      <td>REAGO</td>
+      <td>This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly, RNA, Metagenomics, Microbiology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/chengyuan/reago-1.1</td>
+      <td>Metagenomics, RNA</td>
+      <td>reago</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago</td>
+      <td>1.1</td>
+      <td>reago</td>
+      <td>1.1</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly, RNA, Metagenomics, Microbiology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>recentrifuge</td>
+      <td>recentrifuge</td>
+      <td>"With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."</td>
+      <td>Recentrifuge</td>
+      <td>Recentrifuge</td>
+      <td></td>
+      <td>Recentrifuge</td>
+      <td>Robust comparative analysis and contamination removal for metagenomics.</td>
+      <td>Taxonomic classification, Expression analysis, Cross-assembly</td>
+      <td>Metagenomics, Microbial ecology, Metagenomic sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/khyox/recentrifuge</td>
+      <td>Metagenomics</td>
+      <td>recentrifuge</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge</td>
+      <td>1.15.0</td>
+      <td>recentrifuge</td>
+      <td>1.15.0</td>
+      <td>Taxonomic classification, Expression analysis, Cross-assembly</td>
+      <td>Metagenomics, Microbial ecology, Metagenomic sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>472</td>
+      <td>472</td>
+      <td>92</td>
+      <td>92</td>
+      <td>32</td>
+      <td>32</td>
+      <td>13</td>
+      <td>13</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td>510</td>
+      <td>510</td>
+      <td>109</td>
+      <td>109</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>recetox_aplcms</td>
+      <td>recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise</td>
+      <td>Peak detection tool for HRMS profile data.</td>
+      <td>recetox-aplcms</td>
+      <td>recetox-aplcms</td>
+      <td></td>
+      <td>recetox-aplcms</td>
+      <td>recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.</td>
+      <td>Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment</td>
+      <td>Metabolomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/recetox-aplcms</td>
+      <td>Metabolomics</td>
+      <td>recetox-aplcms</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms</td>
+      <td>0.13.3</td>
+      <td>r-recetox-aplcms</td>
+      <td>0.13.3</td>
+      <td>Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment</td>
+      <td>Metabolomics</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>862</td>
+      <td>862</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td>910</td>
+      <td>910</td>
+      <td>13</td>
+      <td>13</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>recetox_msfinder</td>
+      <td>recetox_msfinder</td>
+      <td></td>
+      <td>recetox-msfinder</td>
+      <td>recetox-msfinder</td>
+      <td></td>
+      <td>recetox-msfinder</td>
+      <td>This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.</td>
+      <td>Annotation</td>
+      <td>Metabolomics</td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/recetox-msfinder</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder</td>
+      <td>v3.5.2</td>
+      <td></td>
+      <td></td>
+      <td>Annotation</td>
+      <td>Metabolomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>47</td>
+      <td>47</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>47</td>
+      <td>47</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>recetox_xmsannotator</td>
+      <td>recetox_xmsannotator_advanced</td>
+      <td></td>
+      <td>recetox-xmsannotator</td>
+      <td>recetox-xmsannotator</td>
+      <td></td>
+      <td>recetox-xMSannotator</td>
+      <td>Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.</td>
+      <td>Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/recetox-xMSannotator</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator</td>
+      <td>0.10.0</td>
+      <td>r-recetox-xmsannotator</td>
+      <td>0.10.0</td>
+      <td>Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation</td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>93</td>
+      <td>93</td>
+      <td>2</td>
+      <td>2</td>
+      <td>93</td>
+      <td>93</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>red</td>
+      <td>red</td>
+      <td>Red (REpeat Detector)</td>
+      <td>red</td>
+      <td>red</td>
+      <td></td>
+      <td>RED</td>
+      <td>This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.</td>
+      <td>RNA-Seq analysis, Editing</td>
+      <td>RNA, Sequencing, Data visualisation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BioinformaticsToolsmith/Red</td>
+      <td>Sequence Analysis</td>
+      <td>red</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/red</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/red</td>
+      <td>2018.09.10</td>
+      <td>red</td>
+      <td>2018.09.10</td>
+      <td>RNA-Seq analysis, Editing</td>
+      <td>RNA, Sequencing, Data visualisation</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>859</td>
+      <td>859</td>
+      <td>203</td>
+      <td>203</td>
+      <td>305</td>
+      <td>305</td>
+      <td>142</td>
+      <td>142</td>
+      <td>227</td>
+      <td>227</td>
+      <td>58</td>
+      <td>58</td>
+      <td>1391</td>
+      <td>1391</td>
+      <td>403</td>
+      <td>403</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>refseq_masher</td>
+      <td>refseq_masher_contains, refseq_masher_matches</td>
+      <td>Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/refseq_masher</td>
+      <td>Sequence Analysis</td>
+      <td>refseq_masher</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/refseq_masher</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher</td>
+      <td>0.1.2</td>
+      <td>refseq_masher</td>
+      <td>0.1.2</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>428</td>
+      <td>428</td>
+      <td>35</td>
+      <td>35</td>
+      <td>141</td>
+      <td>141</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>569</td>
+      <td>569</td>
+      <td>77</td>
+      <td>77</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>regex_find_replace</td>
+      <td>regex1, regexColumn1</td>
+      <td>Use python regular expressions to find and replace text</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>regex_find_replace</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace</td>
+      <td>1.0.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>78648</td>
+      <td>78834</td>
+      <td>1144</td>
+      <td>1156</td>
+      <td>18063</td>
+      <td>18063</td>
+      <td>870</td>
+      <td>870</td>
+      <td>4455</td>
+      <td>6051</td>
+      <td>194</td>
+      <td>289</td>
+      <td>101166</td>
+      <td>102948</td>
+      <td>2208</td>
+      <td>2315</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>regionalgam</td>
+      <td>regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RetoSchmucki/regionalGAM</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam</td>
+      <td>1.5</td>
+      <td>r-mgcv</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>438</td>
+      <td>542</td>
+      <td>128</td>
+      <td>157</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>438</td>
+      <td>542</td>
+      <td>128</td>
+      <td>157</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rem_complex</td>
+      <td>rem_complex</td>
+      <td>Removes molecular coordination complexes.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools</td>
+      <td>Metabolomics</td>
+      <td>rem_complex</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex</td>
+      <td>1.0.0</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>remove_beginning</td>
+      <td>Remove beginning1</td>
+      <td>Remove lines from the beginning of a file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>remove_beginning</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>148572</td>
+      <td>169964</td>
+      <td>3525</td>
+      <td>3682</td>
+      <td>36694</td>
+      <td>113826</td>
+      <td>3910</td>
+      <td>8163</td>
+      <td>9713</td>
+      <td>10577</td>
+      <td>1475</td>
+      <td>1598</td>
+      <td>194979</td>
+      <td>294367</td>
+      <td>8910</td>
+      <td>13443</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>remurna</td>
+      <td>remurna</td>
+      <td>remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna</td>
+      <td>RNA</td>
+      <td>remurna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna</td>
+      <td>1.0.0</td>
+      <td>remurna</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>39</td>
+      <td>44</td>
+      <td>6</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>44</td>
+      <td>6</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rename_annotated_feature</td>
+      <td>rename_annotated_feature</td>
+      <td>Update column names in an abundance table using a annotation table with spectral matching results</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools/</td>
+      <td>Metabolomics</td>
+      <td>rename_annotated_feature</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature</td>
+      <td>1.0.0</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repeat_channels</td>
+      <td>repeat_channels</td>
+      <td>Convert single-channel to multi-channel image</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>repeat_channels</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels</td>
+      <td>1.26.4</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repeat_masker</td>
+      <td>repeatmasker_wrapper</td>
+      <td>RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.repeatmasker.org/</td>
+      <td>Sequence Analysis</td>
+      <td>repeat_masker</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker</td>
+      <td>0.1.2</td>
+      <td>RepeatMasker</td>
+      <td>4.0.9_p2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5998</td>
+      <td>5998</td>
+      <td>810</td>
+      <td>810</td>
+      <td>7618</td>
+      <td>7618</td>
+      <td>803</td>
+      <td>803</td>
+      <td>3135</td>
+      <td>3135</td>
+      <td>292</td>
+      <td>292</td>
+      <td>16751</td>
+      <td>16751</td>
+      <td>1905</td>
+      <td>1905</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repeatexplorer2</td>
+      <td>repeatexplorer_clustering</td>
+      <td>Tool for annotation of repeats from unassembled shotgun reads.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/repeatexplorer/repex_tarean</td>
+      <td>Genome annotation</td>
+      <td>repeatexplorer2</td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2</td>
+      <td>2.3.8</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>95</td>
+      <td>95</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>95</td>
+      <td>95</td>
+      <td>38</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repeatmasker</td>
+      <td>repeatmasker_wrapper</td>
+      <td>RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.</td>
+      <td>repeatmasker</td>
+      <td>repeatmasker</td>
+      <td></td>
+      <td>RepeatMasker</td>
+      <td>A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).</td>
+      <td>Genome annotation</td>
+      <td>Sequence analysis, Sequence composition, complexity and repeats</td>
+      <td>To update</td>
+      <td>http://www.repeatmasker.org/</td>
+      <td>Sequence Analysis</td>
+      <td>repeat_masker</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker</td>
+      <td>4.1.5</td>
+      <td>repeatmasker</td>
+      <td>4.0.9_p2</td>
+      <td>Genome annotation</td>
+      <td>Sequence composition, complexity and repeats</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5998</td>
+      <td>5998</td>
+      <td>810</td>
+      <td>810</td>
+      <td>7618</td>
+      <td>7618</td>
+      <td>803</td>
+      <td>803</td>
+      <td>3135</td>
+      <td>3135</td>
+      <td>292</td>
+      <td>292</td>
+      <td>16751</td>
+      <td>16751</td>
+      <td>1905</td>
+      <td>1905</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repeatmodeler</td>
+      <td>repeatmodeler</td>
+      <td>RepeatModeler - Model repetitive DNA</td>
+      <td>repeatmodeler</td>
+      <td>repeatmodeler</td>
+      <td></td>
+      <td>RepeatModeler</td>
+      <td>De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.</td>
+      <td>Repeat sequence detection</td>
+      <td>Sequence composition, complexity and repeats, Sequence composition, complexity and repeats</td>
+      <td>To update</td>
+      <td>https://www.repeatmasker.org/RepeatModeler/</td>
+      <td>Genome annotation</td>
+      <td>repeatmodeler</td>
+      <td>csbl</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler</td>
+      <td>2.0.5</td>
+      <td></td>
+      <td></td>
+      <td>Repeat sequence detection</td>
+      <td>Sequence composition, complexity and repeats, Sequence composition, complexity and repeats</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7963</td>
+      <td>7963</td>
+      <td>413</td>
+      <td>413</td>
+      <td>1485</td>
+      <td>1485</td>
+      <td>220</td>
+      <td>220</td>
+      <td>8402</td>
+      <td>8402</td>
+      <td>168</td>
+      <td>168</td>
+      <td>17850</td>
+      <td>17850</td>
+      <td>801</td>
+      <td>801</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repenrich</td>
+      <td>edger-repenrich, repenrich</td>
+      <td>Repeat element profiling</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich</td>
+      <td>Transcriptomics</td>
+      <td>repenrich</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich</td>
+      <td>2.31.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1725</td>
+      <td>1790</td>
+      <td>56</td>
+      <td>57</td>
+      <td>1725</td>
+      <td>1790</td>
+      <td>56</td>
+      <td>57</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repenrich2</td>
+      <td>edger-repenrich2, repenrich2</td>
+      <td>Repeat element profiling using bowtie2 aligner</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2</td>
+      <td>Transcriptomics</td>
+      <td>repenrich2</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2</td>
+      <td>2.31.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>replaceColumn</td>
+      <td>replace_column_with_key_value_file</td>
+      <td>A tool to replace all column entries of a file given by values of a key-value file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>replace_column_by_key_value_file</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn</td>
+      <td>0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>577184</td>
+      <td>577312</td>
+      <td>463</td>
+      <td>492</td>
+      <td>43900</td>
+      <td>44233</td>
+      <td>283</td>
+      <td>373</td>
+      <td>2190</td>
+      <td>2190</td>
+      <td>112</td>
+      <td>112</td>
+      <td>623274</td>
+      <td>623735</td>
+      <td>858</td>
+      <td>977</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>replace_chromosome_names</td>
+      <td>replace_chromosome_names</td>
+      <td>Replace chromosome names</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>replace_chromosome_names</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names</td>
+      <td>0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>514</td>
+      <td>573</td>
+      <td>69</td>
+      <td>83</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>514</td>
+      <td>573</td>
+      <td>69</td>
+      <td>83</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repmatch_gff3</td>
+      <td>repmatch_gff3</td>
+      <td>Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>ChIP-seq</td>
+      <td>repmatch_gff3</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3</td>
+      <td></td>
+      <td>matplotlib</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>415</td>
+      <td>721</td>
+      <td>128</td>
+      <td>219</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>415</td>
+      <td>721</td>
+      <td>128</td>
+      <td>219</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>reshape2</td>
+      <td>cast, melt</td>
+      <td>Flexibly restructure and aggregate data using just the two functions melt and dcast</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/web/packages/reshape2/index.html</td>
+      <td>Text Manipulation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2</td>
+      <td>1.4.2</td>
+      <td>r-reshape2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>3543</td>
+      <td>3619</td>
+      <td>108</td>
+      <td>111</td>
+      <td>536</td>
+      <td>536</td>
+      <td>157</td>
+      <td>157</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4079</td>
+      <td>4155</td>
+      <td>265</td>
+      <td>268</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>resize_coordinate_window</td>
+      <td>resize_coordinate_window</td>
+      <td>Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Genomic Interval Operations</td>
+      <td>resize_coordinate_window</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window</td>
+      <td>1.0.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>75</td>
+      <td>86</td>
+      <td>8</td>
+      <td>9</td>
+      <td>138</td>
+      <td>216</td>
+      <td>30</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>213</td>
+      <td>302</td>
+      <td>38</td>
+      <td>66</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rest_tool</td>
+      <td>pubchem_rest_tool</td>
+      <td>This tool fetches data from pubchem via the PubChem REST API.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html</td>
+      <td>Data Source</td>
+      <td>pubchem_rest_tool</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>retip</td>
+      <td>retip_apply, retip_descriptors, retip_filter_rt, retip_train</td>
+      <td></td>
+      <td>retip</td>
+      <td>retip</td>
+      <td></td>
+      <td>Retip</td>
+      <td>Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.</td>
+      <td>Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition</td>
+      <td>Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry</td>
+      <td>To update</td>
+      <td>https://github.com/PaoloBnn/Retip</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/retip</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/retip</td>
+      <td>0.5.4</td>
+      <td></td>
+      <td></td>
+      <td>Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition</td>
+      <td>Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>retrieve_bold</td>
+      <td>retrieve_bold</td>
+      <td>Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://anaconda.org/conda-forge/r-bold</td>
+      <td>Ecology</td>
+      <td>retrieve_bold</td>
+      <td>ecology</td>
+      <td>https://github.com/wpearman1996/MARES_database_pipeline/tree/master</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold</td>
+      <td>1.3.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>retrieve_ensembl_bed</td>
+      <td>retrieve_ensembl_bed</td>
+      <td>Retrieve cDNA features from Ensembl REST API in BED format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rest.ensembl.org/</td>
+      <td>Data Source</td>
+      <td>retrieve_ensembl_bed</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>revertR2orientationInBam</td>
+      <td>revertR2orientationInBam</td>
+      <td>Revert the mapped orientation of R2 mates in a bam.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>SAM</td>
+      <td>revertr2orientationinbam</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam</td>
+      <td>0.0.2</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>11</td>
+      <td>11</td>
+      <td>520</td>
+      <td>520</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>560</td>
+      <td>560</td>
+      <td>42</td>
+      <td>42</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>revoluzer</td>
+      <td>revoluzer_crex, revoluzer_distmat</td>
+      <td>revoluzer wrappers</td>
+      <td>revoluzer</td>
+      <td>revoluzer</td>
+      <td></td>
+      <td>revoluzer</td>
+      <td>Various tools for genome rearrangement analysis. CREx, TreeREx, etc</td>
+      <td>Structural variation detection</td>
+      <td>Molecular evolution, Phylogeny</td>
+      <td>Up-to-date</td>
+      <td>https://gitlab.com/Bernt/revoluzer/</td>
+      <td>Phylogenetics</td>
+      <td>revoluzer</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer</td>
+      <td>0.1.6</td>
+      <td>revoluzer</td>
+      <td>0.1.6</td>
+      <td>Structural variation detection</td>
+      <td>Molecular evolution, Phylogeny</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2444</td>
+      <td>2444</td>
+      <td>52</td>
+      <td>52</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2444</td>
+      <td>2444</td>
+      <td>52</td>
+      <td>52</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rfove</td>
+      <td>rfove</td>
+      <td>Perform segmentation region-based fitting of overlapping ellipses</td>
+      <td>rfove</td>
+      <td>rfove</td>
+      <td></td>
+      <td>RFOVE</td>
+      <td>RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.</td>
+      <td>Image analysis</td>
+      <td>Cell biology, Biomedical science, Imaging</td>
+      <td>To update</td>
+      <td>https://sites.google.com/site/costaspanagiotakis/research/cs</td>
+      <td>Imaging</td>
+      <td>rfove</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove</td>
+      <td>2023.11.12</td>
+      <td></td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Cell biology, Biomedical science, Imaging</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rgcca</td>
+      <td>rgcca</td>
+      <td>multi-block analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/rgcca-factory/RGCCA</td>
+      <td>Statistics</td>
+      <td>rgcca</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca</td>
+      <td>3.0.2</td>
+      <td>rgccacmd</td>
+      <td>3.0.3</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>44</td>
+      <td>44</td>
+      <td>6</td>
+      <td>6</td>
+      <td>77</td>
+      <td>77</td>
+      <td>35</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>41</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rgrnastar</td>
+      <td>rna_star, rna_starsolo</td>
+      <td>RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper</td>
+      <td>star</td>
+      <td>star</td>
+      <td></td>
+      <td>STAR</td>
+      <td>Ultrafast universal RNA-seq data aligner</td>
+      <td>Sequence alignment</td>
+      <td>RNA-Seq, Transcriptomics</td>
+      <td>To update</td>
+      <td>https://github.com/alexdobin/STAR</td>
+      <td>Next Gen Mappers, Transcriptomics</td>
+      <td>rgrnastar</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar</td>
+      <td>2.7.11a</td>
+      <td>star</td>
+      <td>2.7.11b</td>
+      <td>Sequence alignment</td>
+      <td>RNA-Seq, Transcriptomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>438078</td>
+      <td>473957</td>
+      <td>10142</td>
+      <td>10900</td>
+      <td>325474</td>
+      <td>403925</td>
+      <td>15284</td>
+      <td>18791</td>
+      <td>49662</td>
+      <td>53138</td>
+      <td>1359</td>
+      <td>1449</td>
+      <td>813214</td>
+      <td>931020</td>
+      <td>26785</td>
+      <td>31140</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>riassigner</td>
+      <td>riassigner, riassigner_from_comment</td>
+      <td></td>
+      <td>riassigner</td>
+      <td>riassigner</td>
+      <td></td>
+      <td>RIAssigner</td>
+      <td>RIAssigner is a python tool for retention index (RI) computation for GC-MS data.</td>
+      <td>Standardisation and normalisation</td>
+      <td>Metabolomics, Compound libraries and screening, Data submission, annotation and curation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/RIAssigner</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner</td>
+      <td>0.4.1</td>
+      <td>riassigner</td>
+      <td>0.4.1</td>
+      <td>Standardisation and normalisation</td>
+      <td>Metabolomics, Compound libraries and screening, Data submission, annotation and curation</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>46</td>
+      <td>46</td>
+      <td>19</td>
+      <td>19</td>
+      <td>15</td>
+      <td>15</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>62</td>
+      <td>62</td>
+      <td>24</td>
+      <td>24</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ribotaper</td>
+      <td>ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling</td>
+      <td>A method for defining traslated ORFs using Ribosome Profiling data.</td>
+      <td>ribotaper</td>
+      <td>ribotaper</td>
+      <td></td>
+      <td>RiboTaper</td>
+      <td>New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.</td>
+      <td>Gene expression profiling</td>
+      <td>Functional genomics</td>
+      <td>To update</td>
+      <td>https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/</td>
+      <td>RNA</td>
+      <td>ribotaper</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper</td>
+      <td>1.3.1a</td>
+      <td>ribotaper</td>
+      <td>1.3.1</td>
+      <td>Gene expression profiling</td>
+      <td>Functional genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>661</td>
+      <td>681</td>
+      <td>78</td>
+      <td>78</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>661</td>
+      <td>681</td>
+      <td>78</td>
+      <td>78</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ribowaltz</td>
+      <td>ribowaltz_process, ribowaltz_plot</td>
+      <td>Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data</td>
+      <td>riboWaltz</td>
+      <td>riboWaltz</td>
+      <td></td>
+      <td>riboWaltz</td>
+      <td>riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.</td>
+      <td></td>
+      <td>Computational biology</td>
+      <td>To update</td>
+      <td>https://github.com/LabTranslationalArchitectomics/riboWaltz</td>
+      <td>Transcriptomics, RNA</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz</td>
+      <td>1.2.0</td>
+      <td>ribowaltz</td>
+      <td>2.0</td>
+      <td></td>
+      <td>Computational biology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>171</td>
+      <td>171</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>171</td>
+      <td>171</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rmap</td>
+      <td>rmap_wrapper</td>
+      <td>RMAP for Solexa Short Reads Alignment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Next Gen Mappers</td>
+      <td>rmap</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap</td>
+      <td>1.0.0</td>
+      <td>rmap</td>
+      <td>2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rmapq</td>
+      <td>rmapq_wrapper</td>
+      <td>RMAPQ for Solexa Short Reads Alignment with Quality Scores</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Next Gen Mappers</td>
+      <td>rmapq</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq</td>
+      <td>1.0.0</td>
+      <td>rmap</td>
+      <td>2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rmassbank</td>
+      <td>rmassbank</td>
+      <td>RMassBank is an R package for processing tandem MS files and building of MassBank records.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/MassBank/RMassBank</td>
+      <td>Metabolomics</td>
+      <td>rmassbank</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank</td>
+      <td>3.0.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rna_shapes</td>
+      <td>RNAshapes</td>
+      <td>Compute secondary structures of RNA</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>rnashapes</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes</td>
+      <td>3.3.0</td>
+      <td>@EXECUTABLE@</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>137</td>
+      <td>173</td>
+      <td>40</td>
+      <td>49</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>137</td>
+      <td>173</td>
+      <td>40</td>
+      <td>49</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnabob</td>
+      <td>rbc_rnabob</td>
+      <td>Fast pattern searching for RNA structural motifs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://eddylab.org/software.html</td>
+      <td>RNA</td>
+      <td>rnabob</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob</td>
+      <td>2.2.1.0</td>
+      <td>rnabob</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>90</td>
+      <td>196</td>
+      <td>9</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>90</td>
+      <td>196</td>
+      <td>9</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnacode</td>
+      <td>rbc_rnacode</td>
+      <td>Analyze the protein coding potential in MSA</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>rnacode</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode</td>
+      <td>0.3.2</td>
+      <td>rnacode</td>
+      <td>0.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>878</td>
+      <td>1363</td>
+      <td>29</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>878</td>
+      <td>1363</td>
+      <td>29</td>
+      <td>35</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnacommender</td>
+      <td>rbc_rnacommender</td>
+      <td>RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/gianlucacorrado/RNAcommender</td>
+      <td>RNA</td>
+      <td>rnacommender</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender</td>
+      <td>0.1.1</td>
+      <td>sam</td>
+      <td>3.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1024</td>
+      <td>1077</td>
+      <td>18</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1024</td>
+      <td>1077</td>
+      <td>18</td>
+      <td>21</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnaformer</td>
+      <td>infer_rnaformer</td>
+      <td>RNAformer: RNA secondary structure prediction</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/automl/RNAformer</td>
+      <td>RNA</td>
+      <td>rnaformer</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer</td>
+      <td>1.0.0</td>
+      <td>rnaformer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnalien</td>
+      <td>RNAlien</td>
+      <td>RNAlien unsupervized RNA family model construction</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rna.tbi.univie.ac.at/rnalien/</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>rnalien</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien</td>
+      <td>1.3.6</td>
+      <td>rnalien</td>
+      <td>1.8.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>23</td>
+      <td>33</td>
+      <td>10</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>23</td>
+      <td>33</td>
+      <td>10</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnaquast</td>
+      <td>rna_quast</td>
+      <td>rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.</td>
+      <td>rnaQUAST</td>
+      <td>rnaQUAST</td>
+      <td></td>
+      <td>rnaQUAST</td>
+      <td>Quality assessment tool for de novo transcriptome assemblies.</td>
+      <td>De-novo assembly, Transcriptome assembly, Sequence assembly validation</td>
+      <td>Sequence assembly, Transcriptomics, RNA-seq</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/ablab/rnaquast</td>
+      <td>Assembly, RNA</td>
+      <td>rnaquast</td>
+      <td>iuc</td>
+      <td>https://git.ufz.de/lehmanju/rnaquast</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast</td>
+      <td>2.3.0</td>
+      <td>rnaquast</td>
+      <td>2.3.0</td>
+      <td>De-novo assembly, Transcriptome assembly, Sequence assembly validation</td>
+      <td>Sequence assembly, Transcriptomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1522</td>
+      <td>1522</td>
+      <td>254</td>
+      <td>254</td>
+      <td>372</td>
+      <td>372</td>
+      <td>75</td>
+      <td>75</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1899</td>
+      <td>1899</td>
+      <td>330</td>
+      <td>330</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnasnp</td>
+      <td>rnasnp</td>
+      <td>RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rth.dk/resources/rnasnp/</td>
+      <td>RNA</td>
+      <td>rnasnp</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp</td>
+      <td>1.2.0</td>
+      <td>rnasnp</td>
+      <td>1.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>65</td>
+      <td>89</td>
+      <td>14</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>89</td>
+      <td>14</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnaz</td>
+      <td>rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window</td>
+      <td>RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://www.tbi.univie.ac.at/~wash/RNAz/</td>
+      <td>RNA</td>
+      <td>rnaz</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz</td>
+      <td>2.1.1</td>
+      <td>rnaz</td>
+      <td>2.1.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>1156</td>
+      <td>43309</td>
+      <td>93</td>
+      <td>121</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1156</td>
+      <td>43309</td>
+      <td>93</td>
+      <td>121</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>roary</td>
+      <td>roary</td>
+      <td>Roary the pangenome pipeline</td>
+      <td>roary</td>
+      <td>roary</td>
+      <td></td>
+      <td>Roary</td>
+      <td>A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.</td>
+      <td>Genome assembly</td>
+      <td>DNA, Genomics, Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://sanger-pathogens.github.io/Roary/</td>
+      <td>Sequence Analysis</td>
+      <td>roary</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary</td>
+      <td>3.13.0</td>
+      <td>roary</td>
+      <td>3.13.0</td>
+      <td>Genome assembly</td>
+      <td>DNA, Genomics, Mapping</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15196</td>
+      <td>15685</td>
+      <td>1459</td>
+      <td>1501</td>
+      <td>12188</td>
+      <td>12188</td>
+      <td>1768</td>
+      <td>1768</td>
+      <td>4881</td>
+      <td>5539</td>
+      <td>518</td>
+      <td>555</td>
+      <td>32265</td>
+      <td>33412</td>
+      <td>3745</td>
+      <td>3824</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rp2biosensor</td>
+      <td>rp2biosensor</td>
+      <td>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/rp2biosensor</td>
+      <td>Synthetic Biology</td>
+      <td>rp2biosensor</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor</td>
+      <td>3.2.1</td>
+      <td>rp2biosensor</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rp2paths</td>
+      <td>rp2paths</td>
+      <td>Enumerate and seperate the different pathways generated by RetroPath2.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/rp2paths</td>
+      <td>Synthetic Biology</td>
+      <td>rp2paths</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths</td>
+      <td>1.5.1</td>
+      <td>rp2paths</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rpbasicdesign</td>
+      <td>rpbasicdesign</td>
+      <td>Extracting enzyme IDs from rpSBML files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/rpbasicdesign</td>
+      <td>Synthetic Biology</td>
+      <td>rpbasicdesign</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign</td>
+      <td>1.2.2</td>
+      <td>rpbasicdesign</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rpfba</td>
+      <td>rpfba</td>
+      <td>Perform FBA for the RetroPath2.0 heterologous pathways</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/rptools/releases</td>
+      <td>Synthetic Biology</td>
+      <td>rpfba</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba</td>
+      <td>5.12.3</td>
+      <td>rptools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rptools</td>
+      <td>rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz</td>
+      <td>Suite of tools that work on rpSBML format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/rptools</td>
+      <td>Synthetic Biology</td>
+      <td>rptools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools</td>
+      <td>5.13.1</td>
+      <td>rptools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rrparser</td>
+      <td>rrparser</td>
+      <td>Reaction Rules Parser</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/RRParser</td>
+      <td>Synthetic Biology</td>
+      <td>rrparser</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser</td>
+      <td>2.5.2</td>
+      <td>rrparser</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rsat_filter_snps</td>
+      <td>rsat_filter_snps</td>
+      <td>Filter SNPs in RSAT Matrix Scan output</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/</td>
+      <td>ChIP-seq, Systems Biology</td>
+      <td>rsat_filter_snps</td>
+      <td>earlham</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rsem</td>
+      <td>extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie</td>
+      <td>transcript quantification from RNA-Seq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/deweylab/RSEM</td>
+      <td>Transcriptomics, RNA</td>
+      <td>rsem</td>
+      <td>artbio</td>
+      <td>https://github.com/artbio/tools-artbio/tree/master/tools/rsem</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem</td>
+      <td></td>
+      <td>rsem</td>
+      <td>1.3.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>363</td>
+      <td>430</td>
+      <td>158</td>
+      <td>183</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>67</td>
+      <td>146</td>
+      <td>13</td>
+      <td>39</td>
+      <td>430</td>
+      <td>576</td>
+      <td>171</td>
+      <td>222</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rseqc</td>
+      <td>rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin</td>
+      <td>an RNA-seq quality control package</td>
+      <td>rseqc</td>
+      <td>rseqc</td>
+      <td></td>
+      <td>RSeQC</td>
+      <td>Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.</td>
+      <td>Data handling</td>
+      <td>Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://code.google.com/p/rseqc/</td>
+      <td>Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization</td>
+      <td>rseqc</td>
+      <td>nilesh</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc</td>
+      <td>5.0.3</td>
+      <td>rseqc</td>
+      <td>5.0.3</td>
+      <td>Data handling</td>
+      <td>Sequencing</td>
+      <td>22</td>
+      <td>22</td>
+      <td>22</td>
+      <td>0</td>
+      <td>22</td>
+      <td>22</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22</td>
+      <td>22</td>
+      <td>22</td>
+      <td>0</td>
+      <td>136315</td>
+      <td>147595</td>
+      <td>8341</td>
+      <td>9385</td>
+      <td>138707</td>
+      <td>161046</td>
+      <td>10696</td>
+      <td>12789</td>
+      <td>22718</td>
+      <td>23767</td>
+      <td>1593</td>
+      <td>1695</td>
+      <td>297740</td>
+      <td>332408</td>
+      <td>20630</td>
+      <td>23869</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ruvseq</td>
+      <td>ruvseq</td>
+      <td>Remove Unwanted Variation from RNA-Seq Data</td>
+      <td>ruvseq</td>
+      <td>ruvseq</td>
+      <td></td>
+      <td>RUVSeq</td>
+      <td>This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.</td>
+      <td>Differential gene expression analysis</td>
+      <td>Gene expression, RNA-seq</td>
+      <td>To update</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>ruvseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq</td>
+      <td>1.26.0</td>
+      <td>bioconductor-ruvseq</td>
+      <td>1.36.0</td>
+      <td>Differential gene expression analysis</td>
+      <td>Gene expression</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1286</td>
+      <td>1364</td>
+      <td>178</td>
+      <td>193</td>
+      <td>2220</td>
+      <td>2220</td>
+      <td>299</td>
+      <td>299</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3506</td>
+      <td>3584</td>
+      <td>477</td>
+      <td>492</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sailfish</td>
+      <td>sailfish</td>
+      <td>Sailfish is a tool for transcript quantification from RNA-seq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.cs.cmu.edu/~ckingsf/software/sailfish/</td>
+      <td>Sequence Analysis, RNA</td>
+      <td>sailfish</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sailfish</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sailfish</td>
+      <td>0.10.1.1</td>
+      <td>bzip2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3628</td>
+      <td>4168</td>
+      <td>165</td>
+      <td>199</td>
+      <td>8399</td>
+      <td>14473</td>
+      <td>573</td>
+      <td>1147</td>
+      <td>2710</td>
+      <td>3000</td>
+      <td>151</td>
+      <td>175</td>
+      <td>14737</td>
+      <td>21641</td>
+      <td>889</td>
+      <td>1521</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>salmon</td>
+      <td>alevin, salmon, salmonquantmerge</td>
+      <td>Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.</td>
+      <td>salmon</td>
+      <td>salmon</td>
+      <td></td>
+      <td>Salmon</td>
+      <td>A tool for transcript expression quantification from RNA-seq data</td>
+      <td>Sequence composition calculation, RNA-Seq quantification, Gene expression analysis</td>
+      <td>RNA-Seq, Gene expression, Transcriptomics</td>
+      <td>To update</td>
+      <td>https://github.com/COMBINE-lab/salmon</td>
+      <td>Sequence Analysis, RNA, Transcriptomics</td>
+      <td></td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/salmon</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/salmon</td>
+      <td>1.10.1</td>
+      <td>salmon</td>
+      <td>1.10.3</td>
+      <td>Sequence composition calculation, RNA-Seq quantification, Gene expression analysis</td>
+      <td>RNA-Seq, Transcriptomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>73085</td>
+      <td>77081</td>
+      <td>2243</td>
+      <td>2319</td>
+      <td>90634</td>
+      <td>122835</td>
+      <td>3402</td>
+      <td>4726</td>
+      <td>13371</td>
+      <td>15818</td>
+      <td>513</td>
+      <td>586</td>
+      <td>177090</td>
+      <td>215734</td>
+      <td>6158</td>
+      <td>7631</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>salmon-kallisto-mtx-to-10x</td>
+      <td>_salmon_kallisto_mtx_to_10x</td>
+      <td>Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary</td>
+      <td>Sequence Analysis</td>
+      <td>salmon_kallisto_mtx_to_10x</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x</td>
+      <td>0.0.1+galaxy6</td>
+      <td>scipy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>682</td>
+      <td>682</td>
+      <td>172</td>
+      <td>172</td>
+      <td>322</td>
+      <td>322</td>
+      <td>74</td>
+      <td>74</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1007</td>
+      <td>1007</td>
+      <td>249</td>
+      <td>249</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>salsa2</td>
+      <td>salsa</td>
+      <td>A tool to scaffold long read assemblies with Hi-C</td>
+      <td>SALSA</td>
+      <td>SALSA</td>
+      <td></td>
+      <td>SALSA</td>
+      <td>&gt; VERY_LOW CONFIDENCE! | &gt; CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch</td>
+      <td>Genome assembly, De-novo assembly, Scaffolding</td>
+      <td>Sequence assembly, DNA binding sites, Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/marbl/SALSA</td>
+      <td>Assembly</td>
+      <td>salsa</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2</td>
+      <td>2.3</td>
+      <td>salsa2</td>
+      <td>2.3</td>
+      <td>Genome assembly, De-novo assembly, Scaffolding</td>
+      <td>Sequence assembly, DNA binding sites, Mapping</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>463</td>
+      <td>463</td>
+      <td>119</td>
+      <td>119</td>
+      <td>1038</td>
+      <td>1038</td>
+      <td>87</td>
+      <td>87</td>
+      <td>410</td>
+      <td>410</td>
+      <td>24</td>
+      <td>24</td>
+      <td>1911</td>
+      <td>1911</td>
+      <td>230</td>
+      <td>230</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sam2interval</td>
+      <td>sam2interval</td>
+      <td>Convert SAM to interval.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>SAM</td>
+      <td>sam2interval</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval</td>
+      <td>1.0.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1155</td>
+      <td>1251</td>
+      <td>57</td>
+      <td>63</td>
+      <td>2264</td>
+      <td>18187</td>
+      <td>189</td>
+      <td>1748</td>
+      <td>525</td>
+      <td>590</td>
+      <td>10</td>
+      <td>17</td>
+      <td>3944</td>
+      <td>20028</td>
+      <td>256</td>
+      <td>1828</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sam_bitwise_flag_filter</td>
+      <td>sam_bw_filter</td>
+      <td>Filter SAM on bitwise flag values</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>SAM</td>
+      <td>sam_bitwise_flag_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter</td>
+      <td>1.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>96</td>
+      <td>278</td>
+      <td>12</td>
+      <td>26</td>
+      <td>3554</td>
+      <td>76029</td>
+      <td>450</td>
+      <td>6346</td>
+      <td>229</td>
+      <td>345</td>
+      <td>16</td>
+      <td>29</td>
+      <td>3879</td>
+      <td>76652</td>
+      <td>478</td>
+      <td>6401</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sambamba</td>
+      <td>sambamba_sample_or_filter</td>
+      <td>filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>SAM</td>
+      <td>sambamba</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba</td>
+      <td>0.7.1+galaxy1</td>
+      <td>sambamba</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>684</td>
+      <td>684</td>
+      <td>17</td>
+      <td>17</td>
+      <td>684</td>
+      <td>684</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sambamba</td>
+      <td>sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort</td>
+      <td>Sambamba: process your BAM data faster!</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/biod/sambamba</td>
+      <td>SAM</td>
+      <td>sambamba</td>
+      <td>bgruening</td>
+      <td>https://github.com/biod/sambamba</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sambamba</td>
+      <td>1.0.1</td>
+      <td>sambamba</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>297</td>
+      <td>297</td>
+      <td>51</td>
+      <td>51</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>297</td>
+      <td>297</td>
+      <td>51</td>
+      <td>51</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>samblaster</td>
+      <td>samblaster</td>
+      <td>samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files</td>
+      <td>samblaster</td>
+      <td>samblaster</td>
+      <td></td>
+      <td>SAMBLASTER</td>
+      <td>A tool to mark duplicates and extract discordant and split reads from SAM files.</td>
+      <td>Split read mapping</td>
+      <td>DNA, Sequencing, Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/GregoryFaust/samblaster</td>
+      <td>SAM, Fastq Manipulation, Variant Analysis</td>
+      <td>samblaster</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster</td>
+      <td>0.1.26</td>
+      <td>samblaster</td>
+      <td>0.1.26</td>
+      <td>Split read mapping</td>
+      <td>DNA, Sequencing, Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sample_seqs</td>
+      <td>sample_seqs</td>
+      <td>Sub-sample sequences files (e.g. to reduce coverage)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs</td>
+      <td>Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis</td>
+      <td>sample_seqs</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs</td>
+      <td>0.2.6</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3421</td>
+      <td>3859</td>
+      <td>340</td>
+      <td>382</td>
+      <td>883</td>
+      <td>883</td>
+      <td>109</td>
+      <td>109</td>
+      <td>1138</td>
+      <td>1138</td>
+      <td>15</td>
+      <td>15</td>
+      <td>5442</td>
+      <td>5880</td>
+      <td>464</td>
+      <td>506</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>samtools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/samtools/samtools</td>
+      <td>SAM</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools</td>
+      <td>1.20</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>samtools_depad</td>
+      <td>samtools_depad</td>
+      <td>Re-align a SAM/BAM file with a padded reference (using samtools depad)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.htslib.org/</td>
+      <td>Assembly, SAM, Sequence Analysis</td>
+      <td>samtools_depad</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad</td>
+      <td>0.0.5</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>samtools_depth</td>
+      <td>samtools_depth</td>
+      <td>Coverage depth via samtools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.htslib.org/</td>
+      <td>Assembly, Sequence Analysis, SAM</td>
+      <td>samtools_depth</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth</td>
+      <td>0.0.3</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>6485</td>
+      <td>6549</td>
+      <td>720</td>
+      <td>726</td>
+      <td>10127</td>
+      <td>10127</td>
+      <td>1518</td>
+      <td>1518</td>
+      <td>238</td>
+      <td>238</td>
+      <td>37</td>
+      <td>37</td>
+      <td>16850</td>
+      <td>16914</td>
+      <td>2275</td>
+      <td>2281</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>samtools_idxstats</td>
+      <td>samtools_idxstats</td>
+      <td>BAM mapping statistics (using samtools idxstats)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.htslib.org/</td>
+      <td>Assembly, Next Gen Mappers, SAM</td>
+      <td>samtools_idxstats</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats</td>
+      <td>0.0.6</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>52099</td>
+      <td>55110</td>
+      <td>4053</td>
+      <td>4497</td>
+      <td>73194</td>
+      <td>108684</td>
+      <td>6930</td>
+      <td>9936</td>
+      <td>14771</td>
+      <td>15714</td>
+      <td>1222</td>
+      <td>1419</td>
+      <td>140064</td>
+      <td>179508</td>
+      <td>12205</td>
+      <td>15852</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sansa</td>
+      <td>sansa_annotate</td>
+      <td>Sansa is a tool for structural variant annotation.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/dellytools/sansa</td>
+      <td>Variant Analysis</td>
+      <td>sansa</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa</td>
+      <td>0.2.1</td>
+      <td>sansa</td>
+      <td>0.2.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>138</td>
+      <td>138</td>
+      <td>36</td>
+      <td>36</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>138</td>
+      <td>138</td>
+      <td>36</td>
+      <td>36</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sarscov2formatter</td>
+      <td>sarscov2formatter</td>
+      <td>sarscov2formatter custom script</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/nickeener/sarscov2formatter</td>
+      <td>Sequence Analysis</td>
+      <td>sarscov2formatter</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter</td>
+      <td>1.0</td>
+      <td>sarscov2formatter</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>174</td>
+      <td>174</td>
+      <td>16</td>
+      <td>16</td>
+      <td>399</td>
+      <td>399</td>
+      <td>29</td>
+      <td>29</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>573</td>
+      <td>573</td>
+      <td>45</td>
+      <td>45</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sarscov2summary</td>
+      <td>sarscov2summary</td>
+      <td>sarscov2summary custom script</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/nickeener/sarscov2summary</td>
+      <td>Sequence Analysis</td>
+      <td>sarscov2summary</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary</td>
+      <td>0.1</td>
+      <td>sarscov2summary</td>
+      <td>0.5</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>140</td>
+      <td>140</td>
+      <td>5</td>
+      <td>5</td>
+      <td>253</td>
+      <td>253</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>393</td>
+      <td>393</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sashimi_plot</td>
+      <td>sashimi_plot</td>
+      <td>Generates a sashimi plot from bam files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Transcriptomics, Graphics, Visualization</td>
+      <td>sashimi_plot</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot</td>
+      <td>0.1.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sbml2sbol</td>
+      <td>sbml2sbol</td>
+      <td>Convert SBML to SBOL format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/neilswainston/SbmlToSbol</td>
+      <td>Synthetic Biology</td>
+      <td>sbml2sbol</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol</td>
+      <td>0.1.13</td>
+      <td>sbml2sbol</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sc3</td>
+      <td>sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare</td>
+      <td>De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_sc3</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3</td>
+      <td>1.8.0</td>
+      <td>sc3-scripts</td>
+      <td>0.0.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>10</td>
+      <td>10</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scaffold</td>
+      <td>scaffold, scaffold_export</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>scaffold</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold</td>
+      <td>0.1.0</td>
+      <td>scaffold</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scale_image</td>
+      <td>ip_scale_image</td>
+      <td>Scale image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.</td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>scale_image</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image</td>
+      <td>0.18.3</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>477</td>
+      <td>520</td>
+      <td>13</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>477</td>
+      <td>520</td>
+      <td>13</td>
+      <td>16</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scanpy</td>
+      <td>anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data</td>
+      <td>scanpy-scripts, command-line wrapper scripts around Scanpy.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://scanpy.readthedocs.io</td>
+      <td>Transcriptomics, Sequence Analysis, RNA</td>
+      <td>scanpy_scripts</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy</td>
+      <td>1.9.3</td>
+      <td>scanpy-scripts</td>
+      <td>1.9.301</td>
+      <td></td>
+      <td></td>
+      <td>27</td>
+      <td>27</td>
+      <td>27</td>
+      <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>27</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>13</td>
+      <td>0</td>
+      <td>45501</td>
+      <td>45666</td>
+      <td>4832</td>
+      <td>4868</td>
+      <td>7304</td>
+      <td>7304</td>
+      <td>1846</td>
+      <td>1846</td>
+      <td>3106</td>
+      <td>3106</td>
+      <td>457</td>
+      <td>457</td>
+      <td>55911</td>
+      <td>56076</td>
+      <td>7135</td>
+      <td>7171</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scanpy</td>
+      <td>scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders</td>
+      <td>Scanpy – Single-Cell Analysis in Python</td>
+      <td>scanpy</td>
+      <td>scanpy</td>
+      <td></td>
+      <td>SCANPY</td>
+      <td>Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.</td>
+      <td>Differential gene expression analysis</td>
+      <td>Gene expression, Cell biology, Genetics</td>
+      <td>To update</td>
+      <td>https://scanpy.readthedocs.io</td>
+      <td>Single Cell, Spatial Omics, Transcriptomics</td>
+      <td>scanpy</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy</td>
+      <td>1.10.2</td>
+      <td>scanpy</td>
+      <td>1.7.2</td>
+      <td>Differential gene expression analysis</td>
+      <td>Gene expression, Cell biology, Genetics</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>63789</td>
+      <td>64034</td>
+      <td>2543</td>
+      <td>2547</td>
+      <td>29962</td>
+      <td>29962</td>
+      <td>1185</td>
+      <td>1185</td>
+      <td>18028</td>
+      <td>18028</td>
+      <td>379</td>
+      <td>379</td>
+      <td>111779</td>
+      <td>112024</td>
+      <td>4107</td>
+      <td>4111</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scater</td>
+      <td>scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results</td>
+      <td>De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_scater</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater</td>
+      <td>1.10.0</td>
+      <td>scater-scripts</td>
+      <td>0.0.5</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>2</td>
+      <td>6</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>381</td>
+      <td>388</td>
+      <td>99</td>
+      <td>100</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>297</td>
+      <td>297</td>
+      <td>9</td>
+      <td>9</td>
+      <td>678</td>
+      <td>685</td>
+      <td>108</td>
+      <td>109</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scater</td>
+      <td>scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne</td>
+      <td>Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.</td>
+      <td>scater</td>
+      <td>scater</td>
+      <td></td>
+      <td>scater</td>
+      <td>Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.</td>
+      <td>Read pre-processing, Sequencing quality control, Sequence visualisation</td>
+      <td>RNA-seq, Quality affairs, Molecular genetics</td>
+      <td>To update</td>
+      <td>http://bioconductor.org/packages/scater/</td>
+      <td>Single Cell, Transcriptomics, Visualization</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater</td>
+      <td>1.22.0</td>
+      <td>bioconductor-scater</td>
+      <td>1.30.1</td>
+      <td>Read pre-processing, Sequence visualisation</td>
+      <td>Quality affairs, Molecular genetics</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>1345</td>
+      <td>1371</td>
+      <td>350</td>
+      <td>351</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>903</td>
+      <td>903</td>
+      <td>29</td>
+      <td>29</td>
+      <td>2248</td>
+      <td>2274</td>
+      <td>379</td>
+      <td>380</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scatterplot</td>
+      <td>scatterplot_rpy</td>
+      <td>Scatterplot of two numeric columns</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Statistics</td>
+      <td>scatterplot</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot</td>
+      <td>1.0.3</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1234</td>
+      <td>1752</td>
+      <td>179</td>
+      <td>261</td>
+      <td>680</td>
+      <td>9223</td>
+      <td>231</td>
+      <td>1927</td>
+      <td>0</td>
+      <td>49</td>
+      <td>0</td>
+      <td>18</td>
+      <td>1914</td>
+      <td>11024</td>
+      <td>410</td>
+      <td>2206</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sccaf</td>
+      <td>run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out</td>
+      <td>SCCAF: Single Cell Clustering Assessment Framework.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/sccaf/sccaf</td>
+      <td>Transcriptomics</td>
+      <td>SCCAF</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf</td>
+      <td>0.0.9</td>
+      <td>sccaf</td>
+      <td>0.0.10</td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>3</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>3</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>110</td>
+      <td>110</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>110</td>
+      <td>110</td>
+      <td>19</td>
+      <td>19</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sceasy</td>
+      <td>sceasy_convert</td>
+      <td>Convert scRNA data object between popular formats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics</td>
+      <td>sceasy</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy</td>
+      <td>0.0.5</td>
+      <td>r-sceasy</td>
+      <td>0.0.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1059</td>
+      <td>1059</td>
+      <td>222</td>
+      <td>222</td>
+      <td>426</td>
+      <td>426</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1486</td>
+      <td>1486</td>
+      <td>294</td>
+      <td>294</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sceasy</td>
+      <td>sceasy_convert</td>
+      <td>Converter between difference single-cell formats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cellgeni/sceasy/</td>
+      <td>Single Cell, Spatial Omics, Convert Formats</td>
+      <td>sceasy_convert</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy</td>
+      <td>0.0.7</td>
+      <td>r-sceasy</td>
+      <td>0.0.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1059</td>
+      <td>1059</td>
+      <td>222</td>
+      <td>222</td>
+      <td>426</td>
+      <td>426</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1486</td>
+      <td>1486</td>
+      <td>294</td>
+      <td>294</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>schicexplorer</td>
+      <td>schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol</td>
+      <td>scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/joachimwolff/schicexplorer</td>
+      <td>Sequence Analysis, Transcriptomics, Visualization, Single Cell</td>
+      <td>schicexplorer</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer</td>
+      <td>4</td>
+      <td>schicexplorer</td>
+      <td>7</td>
+      <td></td>
+      <td></td>
+      <td>16</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>809</td>
+      <td>809</td>
+      <td>78</td>
+      <td>78</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>105</td>
+      <td>105</td>
+      <td>16</td>
+      <td>16</td>
+      <td>917</td>
+      <td>917</td>
+      <td>96</td>
+      <td>96</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scikit-bio</td>
+      <td>scikit_bio_diversity_beta_diversity</td>
+      <td>scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://scikit-bio.org/</td>
+      <td>Sequence Analysis</td>
+      <td>scikit_bio</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio</td>
+      <td>0.4.2</td>
+      <td>scikit-bio</td>
+      <td>0.4.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1503</td>
+      <td>1955</td>
+      <td>283</td>
+      <td>402</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1504</td>
+      <td>1956</td>
+      <td>284</td>
+      <td>403</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scmap</td>
+      <td>scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features</td>
+      <td>De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_scmap</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap</td>
+      <td>1.6.4</td>
+      <td>scmap-cli</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>97</td>
+      <td>97</td>
+      <td>41</td>
+      <td>41</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>97</td>
+      <td>97</td>
+      <td>41</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scoary</td>
+      <td>scoary</td>
+      <td>Scoary calculates the assocations between all genes in the accessory genome and the traits.</td>
+      <td>scoary</td>
+      <td>scoary</td>
+      <td></td>
+      <td>Scoary</td>
+      <td>Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 &lt; i &lt; N) and the traits. It reports a list of genes sorted by strength of association per trait.</td>
+      <td>Analysis</td>
+      <td>Genotype and phenotype, Model organisms, GWAS study, Functional genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/AdmiralenOla/Scoary</td>
+      <td>Metagenomics</td>
+      <td>scoary</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary</td>
+      <td>1.6.16</td>
+      <td>scoary</td>
+      <td>1.6.16</td>
+      <td>Analysis</td>
+      <td>Genotype and phenotype, Model organisms, GWAS study, Functional genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>901</td>
+      <td>901</td>
+      <td>90</td>
+      <td>90</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>901</td>
+      <td>901</td>
+      <td>90</td>
+      <td>90</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scpipe</td>
+      <td>scpipe</td>
+      <td>A flexible preprocessing pipeline for single-cell RNA-sequencing data</td>
+      <td>scpipe</td>
+      <td>scpipe</td>
+      <td></td>
+      <td>scPipe</td>
+      <td>A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.</td>
+      <td>Genome annotation, Validation, Alignment, Visualisation</td>
+      <td>Gene expression, RNA-Seq, Sequencing</td>
+      <td>To update</td>
+      <td>http://bioconductor.org/packages/release/bioc/html/scPipe.html</td>
+      <td>Transcriptomics, Single Cell</td>
+      <td>scpipe</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe</td>
+      <td>1.0.0+galaxy2</td>
+      <td>bioconductor-scpipe</td>
+      <td>2.2.0</td>
+      <td>Genome annotation, Validation, Alignment, Visualisation</td>
+      <td>Gene expression, RNA-Seq</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>284</td>
+      <td>632</td>
+      <td>34</td>
+      <td>38</td>
+      <td>786</td>
+      <td>786</td>
+      <td>61</td>
+      <td>61</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1071</td>
+      <td>1419</td>
+      <td>96</td>
+      <td>100</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scpred</td>
+      <td>scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model</td>
+      <td>De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_scpred</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred</td>
+      <td>1.0.2</td>
+      <td>scpred-cli</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25</td>
+      <td>25</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25</td>
+      <td>25</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scripting</td>
+      <td>singularity_scriptrunner</td>
+      <td>suite_scripting</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/</td>
+      <td>Text Manipulation</td>
+      <td>scripting tools</td>
+      <td>mbernt</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sdmpredictors</td>
+      <td>sdmpredictors_list_layers</td>
+      <td>Terrestrial and marine predictors for species distribution modelling.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/web/packages/sdmpredictors/index.html</td>
+      <td>Ecology</td>
+      <td>sdmpredictors</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors</td>
+      <td>0.2.15</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seacr</td>
+      <td>seacr</td>
+      <td>SEACR is intended to call peaks and enriched regions from sparse CUT&amp;RUN or chromatin profiling data in which background is dominated by zeroes.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/FredHutch/SEACR</td>
+      <td>Epigenetics, ChIP-seq</td>
+      <td>seacr</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr</td>
+      <td>1.3</td>
+      <td>seacr</td>
+      <td>1.3</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5106</td>
+      <td>5106</td>
+      <td>116</td>
+      <td>116</td>
+      <td>6419</td>
+      <td>6419</td>
+      <td>241</td>
+      <td>241</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11525</td>
+      <td>11525</td>
+      <td>357</td>
+      <td>357</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sed</td>
+      <td>sed_stream_editor</td>
+      <td>Manipulate your data with the sed command line tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sed</td>
+      <td>Text Manipulation</td>
+      <td>sed_wrapper</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sed</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sed</td>
+      <td>0.0.1</td>
+      <td>sed</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>281</td>
+      <td>2284</td>
+      <td>10</td>
+      <td>53</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>281</td>
+      <td>2284</td>
+      <td>10</td>
+      <td>53</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>segalign</td>
+      <td>segalign</td>
+      <td>A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/gsneha26/SegAlign</td>
+      <td>Next Gen Mappers</td>
+      <td>segalign</td>
+      <td>richard-burhans</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign</td>
+      <td>0.1.2.7</td>
+      <td>segalign-galaxy</td>
+      <td>0.1.2.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>252</td>
+      <td>252</td>
+      <td>47</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>252</td>
+      <td>252</td>
+      <td>47</td>
+      <td>47</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>segemehl</td>
+      <td>segemehl</td>
+      <td>segemehl - short read mapping with gaps</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.bioinf.uni-leipzig.de/Software/segemehl/</td>
+      <td>Next Gen Mappers</td>
+      <td>segemehl</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/segemehl</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/segemehl</td>
+      <td>0.2.0.4</td>
+      <td>segemehl</td>
+      <td>0.3.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1095</td>
+      <td>1306</td>
+      <td>98</td>
+      <td>113</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1095</td>
+      <td>1306</td>
+      <td>98</td>
+      <td>113</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>segmetrics</td>
+      <td>ip_segmetrics</td>
+      <td>Image segmentation and object detection performance measures</td>
+      <td>segmetrics</td>
+      <td>segmetrics</td>
+      <td>segmetrics</td>
+      <td>SegMetrics</td>
+      <td>Image segmentation and object detection performance measures</td>
+      <td>Image analysis</td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>segmetrics</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics</td>
+      <td>1.4</td>
+      <td>segmetrics</td>
+      <td>1.5</td>
+      <td>Image analysis</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>selectsequencesfrommsa</td>
+      <td>selectsequencesfrommsa</td>
+      <td>SelectSequences - selects representative entries from a multiple sequence alignment in clustal format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/eggzilla/SelectSequences</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>selectsequencesfrommsa</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa</td>
+      <td>1.0.5</td>
+      <td>selectsequencesfrommsa</td>
+      <td>1.0.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>305</td>
+      <td>463</td>
+      <td>43</td>
+      <td>50</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>305</td>
+      <td>463</td>
+      <td>43</td>
+      <td>50</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>selenzy_wrapper</td>
+      <td>selenzy_wrapper</td>
+      <td>Performs enzyme selection from a reaction query.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/brsynth/selenzy-wrapper</td>
+      <td>Synthetic Biology</td>
+      <td>selenzy_wrapper</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper</td>
+      <td>0.3.0</td>
+      <td>selenzy_wrapper</td>
+      <td>0.3.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>semibin</td>
+      <td>semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train</td>
+      <td>SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks</td>
+      <td>semibin</td>
+      <td>semibin</td>
+      <td></td>
+      <td>SemiBin</td>
+      <td>Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.</td>
+      <td>Sequence assembly, Read binning</td>
+      <td>Metagenomics, Machine learning, Microbial ecology, Sequence assembly</td>
+      <td>To update</td>
+      <td>https://semibin.readthedocs.io/en/latest/</td>
+      <td>Metagenomics</td>
+      <td>semibin</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin</td>
+      <td>2.0.2</td>
+      <td>semibin</td>
+      <td>2.1.0</td>
+      <td>Sequence assembly, Read binning</td>
+      <td>Metagenomics, Machine learning, Microbial ecology, Sequence assembly</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>931</td>
+      <td>931</td>
+      <td>93</td>
+      <td>93</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>931</td>
+      <td>931</td>
+      <td>93</td>
+      <td>93</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq2hla</td>
+      <td>seq2hla</td>
+      <td>Precision HLA typing and expression from RNAseq data</td>
+      <td>seq2hla</td>
+      <td>seq2hla</td>
+      <td></td>
+      <td>Seq2HLA</td>
+      <td>seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.</td>
+      <td>Read mapping, Genetic variation analysis</td>
+      <td>Transcriptomics, Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/TRON-Bioinformatics/seq2HLA</td>
+      <td>Sequence Analysis</td>
+      <td>seq2hla</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla</td>
+      <td>2.3</td>
+      <td>seq2hla</td>
+      <td>2.3</td>
+      <td>Read mapping, Genetic variation analysis</td>
+      <td>Transcriptomics, Mapping</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>342</td>
+      <td>342</td>
+      <td>40</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>342</td>
+      <td>342</td>
+      <td>40</td>
+      <td>40</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_composition</td>
+      <td>seq_composition</td>
+      <td>Sequence composition</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition</td>
+      <td>Sequence Analysis</td>
+      <td>seq_composition</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition</td>
+      <td>0.0.5</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1053</td>
+      <td>1186</td>
+      <td>137</td>
+      <td>195</td>
+      <td>680</td>
+      <td>680</td>
+      <td>206</td>
+      <td>206</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1733</td>
+      <td>1866</td>
+      <td>343</td>
+      <td>401</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_filter_by_id</td>
+      <td>seq_filter_by_id</td>
+      <td>Filter sequences by ID</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id</td>
+      <td>Fasta Manipulation, Sequence Analysis, Text Manipulation</td>
+      <td>seq_filter_by_id</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id</td>
+      <td>0.2.9</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>30300</td>
+      <td>32553</td>
+      <td>732</td>
+      <td>799</td>
+      <td>21726</td>
+      <td>31891</td>
+      <td>619</td>
+      <td>621</td>
+      <td>2886</td>
+      <td>2886</td>
+      <td>144</td>
+      <td>144</td>
+      <td>54912</td>
+      <td>67330</td>
+      <td>1495</td>
+      <td>1564</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_filter_by_mapping</td>
+      <td>seq_filter_by_mapping</td>
+      <td>Filter sequencing reads using SAM/BAM mapping files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping</td>
+      <td>Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis</td>
+      <td>seq_filter_by_mapping</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping</td>
+      <td>0.0.8</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4322</td>
+      <td>4714</td>
+      <td>180</td>
+      <td>205</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4322</td>
+      <td>4714</td>
+      <td>180</td>
+      <td>205</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_length</td>
+      <td>seq_length</td>
+      <td>Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length</td>
+      <td>Fasta Manipulation, Fastq Manipulation, Sequence Analysis</td>
+      <td>seq_length</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length</td>
+      <td>0.0.5</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_primer_clip</td>
+      <td>seq_primer_clip</td>
+      <td>Trim off 5' or 3' primers</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip</td>
+      <td>Assembly, Fasta Manipulation, Text Manipulation</td>
+      <td>seq_primer_clip</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip</td>
+      <td>0.0.18</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_rename</td>
+      <td>seq_rename</td>
+      <td>Rename sequences with ID mapping from a tabular file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename</td>
+      <td>Fasta Manipulation, Sequence Analysis, Text Manipulation</td>
+      <td>seq_rename</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename</td>
+      <td>0.0.10</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_select_by_id</td>
+      <td>seq_select_by_id</td>
+      <td>Select sequences by ID</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id</td>
+      <td>Fasta Manipulation, Sequence Analysis, Text Manipulation</td>
+      <td>seq_select_by_id</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id</td>
+      <td>0.0.15</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2196</td>
+      <td>3529</td>
+      <td>260</td>
+      <td>289</td>
+      <td>2196</td>
+      <td>3529</td>
+      <td>260</td>
+      <td>289</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqcomplexity</td>
+      <td>seqcomplexity</td>
+      <td>Sequence complexity for raw reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/stevenweaver/seqcomplexity</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity</td>
+      <td>0.1.2</td>
+      <td>seqcomplexity</td>
+      <td>0.1.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>19</td>
+      <td>19</td>
+      <td>109</td>
+      <td>109</td>
+      <td>47</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>179</td>
+      <td>179</td>
+      <td>66</td>
+      <td>66</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqkit</td>
+      <td>seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate</td>
+      <td>A cross-platform and ultrafast toolkit for FASTA/Q file manipulation</td>
+      <td>seqkit</td>
+      <td>seqkit</td>
+      <td></td>
+      <td>seqkit</td>
+      <td>FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.</td>
+      <td>DNA transcription, Sequence trimming, DNA translation, Sequence conversion</td>
+      <td>Database management, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://bioinf.shenwei.me/seqkit/</td>
+      <td>Sequence Analysis</td>
+      <td>seqkit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit</td>
+      <td>2.8.2</td>
+      <td>seqkit</td>
+      <td>2.8.2</td>
+      <td>DNA transcription, Sequence trimming, DNA translation</td>
+      <td>Database management, Sequence analysis</td>
+      <td>0</td>
+      <td>2</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3364</td>
+      <td>3364</td>
+      <td>247</td>
+      <td>247</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>244</td>
+      <td>244</td>
+      <td>33</td>
+      <td>33</td>
+      <td>3608</td>
+      <td>3608</td>
+      <td>280</td>
+      <td>280</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqprep</td>
+      <td>seqprep</td>
+      <td>Tool for merging paired-end Illumina reads and trimming adapters.</td>
+      <td>seqprep</td>
+      <td>seqprep</td>
+      <td></td>
+      <td>SeqPrep</td>
+      <td>Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.</td>
+      <td>Nucleic acid design</td>
+      <td>Genomics, Sequence assembly, Sequencing, Probes and primers</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/jstjohn/SeqPrep</td>
+      <td>Fastq Manipulation, Sequence Analysis</td>
+      <td>seqprep</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep</td>
+      <td>1.3.2</td>
+      <td>seqprep</td>
+      <td>1.3.2</td>
+      <td>Nucleic acid design</td>
+      <td>Genomics, Sequence assembly, Sequencing, Probes and primers</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2424</td>
+      <td>2424</td>
+      <td>102</td>
+      <td>102</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2424</td>
+      <td>2424</td>
+      <td>102</td>
+      <td>102</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqsero2</td>
+      <td>seqsero2</td>
+      <td>Salmonella serotype prediction from genome sequencing data</td>
+      <td>seqsero2</td>
+      <td>seqsero2</td>
+      <td></td>
+      <td>SeqSero2</td>
+      <td>rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode)</td>
+      <td>Genome indexing, Antimicrobial resistance prediction, Genome alignment</td>
+      <td>Whole genome sequencing, Sequence assembly, Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/denglab/SeqSero2</td>
+      <td>Sequence Analysis</td>
+      <td>seqsero2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2</td>
+      <td>1.3.1</td>
+      <td>seqsero2</td>
+      <td>1.3.1</td>
+      <td>Genome indexing, Antimicrobial resistance prediction, Genome alignment</td>
+      <td>Whole genome sequencing, Sequence assembly, Genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4182</td>
+      <td>4182</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4182</td>
+      <td>4182</td>
+      <td>42</td>
+      <td>42</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqtk</td>
+      <td>seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq</td>
+      <td>Toolkit for processing sequences in FASTA/Q formats</td>
+      <td>seqtk</td>
+      <td>seqtk</td>
+      <td></td>
+      <td>seqtk</td>
+      <td>A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.</td>
+      <td>Data handling, Sequence file editing</td>
+      <td>Data management</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lh3/seqtk</td>
+      <td>Sequence Analysis</td>
+      <td>seqtk</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk</td>
+      <td>1.4</td>
+      <td>seqtk</td>
+      <td>1.4</td>
+      <td>Data handling, Sequence file editing</td>
+      <td></td>
+      <td>15</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>0</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>14</td>
+      <td>14</td>
+      <td>72816</td>
+      <td>73514</td>
+      <td>2210</td>
+      <td>2300</td>
+      <td>102777</td>
+      <td>107831</td>
+      <td>2313</td>
+      <td>2669</td>
+      <td>154613</td>
+      <td>154613</td>
+      <td>682</td>
+      <td>682</td>
+      <td>330206</td>
+      <td>335958</td>
+      <td>5205</td>
+      <td>5651</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqtk_nml</td>
+      <td>seqtk_nml_sample</td>
+      <td>Tool to downsample fastq reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/lh3/seqtk</td>
+      <td>Sequence Analysis</td>
+      <td>seqtk_nml</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml</td>
+      <td>1.0.1</td>
+      <td>seqtk</td>
+      <td>1.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sequence_format_converter</td>
+      <td>sequence_format_converter</td>
+      <td>various fasta to tabular conversions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Convert Formats, Fasta Manipulation</td>
+      <td>sequence_format_converter</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter</td>
+      <td>2.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqwish</td>
+      <td>seqwish</td>
+      <td>Alignment to variation graph inducer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/seqwish</td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish</td>
+      <td>0.7.5</td>
+      <td>seqwish</td>
+      <td>0.7.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>271</td>
+      <td>271</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>271</td>
+      <td>271</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seurat</td>
+      <td>seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension</td>
+      <td>Seurat - R toolkit for single cell genomics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://satijalab.org/seurat/</td>
+      <td>Single Cell, Transcriptomics, Sequence Analysis</td>
+      <td>seurat</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat</td>
+      <td>5.0</td>
+      <td>r-seurat</td>
+      <td>3.0.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>7</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>11</td>
+      <td>11</td>
+      <td>32</td>
+      <td>32</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>153</td>
+      <td>153</td>
+      <td>16</td>
+      <td>16</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seurat</td>
+      <td>seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features</td>
+      <td>De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_seurat</td>
+      <td>ebi-gxa</td>
+      <td></td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat</td>
+      <td>4.0.0</td>
+      <td>seurat-scripts</td>
+      <td>4.4.0</td>
+      <td></td>
+      <td></td>
+      <td>14</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2296</td>
+      <td>2328</td>
+      <td>673</td>
+      <td>676</td>
+      <td>141</td>
+      <td>141</td>
+      <td>39</td>
+      <td>39</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2437</td>
+      <td>2469</td>
+      <td>712</td>
+      <td>715</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sgwb</td>
+      <td>sgwb_astro_tool</td>
+      <td>SGWB</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Astronomy</td>
+      <td>sgwb_astro_tool</td>
+      <td>astroteam</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb</td>
+      <td>0.0.1+galaxy0</td>
+      <td>ipython</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>shasta</td>
+      <td>shasta</td>
+      <td>Fast de novo assembly of long read sequencing data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/chanzuckerberg/shasta</td>
+      <td>Assembly, Nanopore</td>
+      <td>shasta</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta</td>
+      <td>0.6.0</td>
+      <td>shasta</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>913</td>
+      <td>913</td>
+      <td>308</td>
+      <td>308</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>568</td>
+      <td>568</td>
+      <td>73</td>
+      <td>73</td>
+      <td>1481</td>
+      <td>1481</td>
+      <td>381</td>
+      <td>381</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>shift-longitudes</td>
+      <td>shyft_longitudes</td>
+      <td>Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/</td>
+      <td>Climate Analysis</td>
+      <td>shift_longitudes</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes</td>
+      <td>0.1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>54</td>
+      <td>64</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>54</td>
+      <td>64</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>shorah</td>
+      <td>shorah_amplicon</td>
+      <td>Reconstruct haplotypes using ShoRAH in amplicon mode</td>
+      <td>shorah</td>
+      <td>shorah</td>
+      <td></td>
+      <td>ShoRAH</td>
+      <td>Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.</td>
+      <td>Haplotype mapping, Variant calling</td>
+      <td>Metagenomics, Sequencing, Genetics</td>
+      <td>To update</td>
+      <td>https://github.com/cbg-ethz/shorah/blob/master/README.md</td>
+      <td>Sequence Analysis</td>
+      <td>shorah_amplicon</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah</td>
+      <td>1.1.3</td>
+      <td>shorah</td>
+      <td>1.99.2</td>
+      <td>Haplotype mapping, Variant calling</td>
+      <td>Metagenomics, Sequencing, Genetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>short_reads_figure_high_quality_length</td>
+      <td>hist_high_quality_score</td>
+      <td>Histogram of high quality score reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Graphics</td>
+      <td>short_reads_figure_high_quality_length</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length</td>
+      <td>1.0.0</td>
+      <td>rpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>short_reads_figure_score</td>
+      <td>quality_score_distribution</td>
+      <td>Build base quality distribution</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Graphics</td>
+      <td>short_reads_figure_score</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score</td>
+      <td>1.0.2</td>
+      <td>fontconfig</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>145</td>
+      <td>163</td>
+      <td>25</td>
+      <td>30</td>
+      <td>196</td>
+      <td>3360</td>
+      <td>23</td>
+      <td>711</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>341</td>
+      <td>3523</td>
+      <td>48</td>
+      <td>741</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>short_reads_trim_seq</td>
+      <td>trim_reads</td>
+      <td>Select high quality segments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fastq Manipulation</td>
+      <td>short_reads_trim_seq</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>175</td>
+      <td>220</td>
+      <td>51</td>
+      <td>60</td>
+      <td>350</td>
+      <td>6657</td>
+      <td>85</td>
+      <td>1602</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>525</td>
+      <td>6877</td>
+      <td>136</td>
+      <td>1662</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>shovill</td>
+      <td>shovill</td>
+      <td>Faster de novo assembly pipeline based around Spades</td>
+      <td>shovill</td>
+      <td>shovill</td>
+      <td></td>
+      <td>shovill</td>
+      <td>Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.</td>
+      <td>Genome assembly</td>
+      <td>Genomics, Microbiology, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tseemann/shovill</td>
+      <td>Assembly</td>
+      <td>shovill</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill</td>
+      <td>1.1.0</td>
+      <td>shovill</td>
+      <td>1.1.0</td>
+      <td>Genome assembly</td>
+      <td>Genomics, Microbiology, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>46125</td>
+      <td>47376</td>
+      <td>2273</td>
+      <td>2356</td>
+      <td>40577</td>
+      <td>40577</td>
+      <td>3971</td>
+      <td>3971</td>
+      <td>19960</td>
+      <td>21130</td>
+      <td>1085</td>
+      <td>1199</td>
+      <td>106662</td>
+      <td>109083</td>
+      <td>7329</td>
+      <td>7526</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>show_beginning</td>
+      <td>Show beginning1</td>
+      <td>Select lines from the beginning of a file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>show_beginning</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>27232</td>
+      <td>36366</td>
+      <td>2184</td>
+      <td>2789</td>
+      <td>16648</td>
+      <td>84460</td>
+      <td>4191</td>
+      <td>18767</td>
+      <td>2785</td>
+      <td>3276</td>
+      <td>373</td>
+      <td>452</td>
+      <td>46665</td>
+      <td>124102</td>
+      <td>6748</td>
+      <td>22008</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>show_tail</td>
+      <td>Show tail1</td>
+      <td>Select lines from the end of a file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>show_tail</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1620</td>
+      <td>2660</td>
+      <td>378</td>
+      <td>589</td>
+      <td>10551</td>
+      <td>24579</td>
+      <td>682</td>
+      <td>1851</td>
+      <td>284</td>
+      <td>398</td>
+      <td>67</td>
+      <td>83</td>
+      <td>12455</td>
+      <td>27637</td>
+      <td>1127</td>
+      <td>2523</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sicer</td>
+      <td>peakcalling_sicer</td>
+      <td>Statistical approach for the Identification of ChIP-Enriched Regions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://home.gwu.edu/~wpeng/Software.htm</td>
+      <td>ChIP-seq</td>
+      <td>sicer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer</td>
+      <td>1.1</td>
+      <td>SICER</td>
+      <td>1.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>276</td>
+      <td>379</td>
+      <td>30</td>
+      <td>42</td>
+      <td>972</td>
+      <td>9053</td>
+      <td>146</td>
+      <td>1008</td>
+      <td>644</td>
+      <td>689</td>
+      <td>5</td>
+      <td>7</td>
+      <td>1892</td>
+      <td>10121</td>
+      <td>181</td>
+      <td>1057</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sickle</td>
+      <td>sickle</td>
+      <td>A windowed adaptive trimming tool for FASTQ files using quality</td>
+      <td>sickle</td>
+      <td>sickle</td>
+      <td></td>
+      <td>sickle</td>
+      <td>A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.</td>
+      <td>Sequence trimming</td>
+      <td>Data quality management</td>
+      <td>To update</td>
+      <td>https://github.com/najoshi/sickle</td>
+      <td>Fastq Manipulation, Sequence Analysis</td>
+      <td>sickle</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle</td>
+      <td>1.33.2</td>
+      <td>sickle-trim</td>
+      <td>1.33</td>
+      <td>Sequence trimming</td>
+      <td>Data quality management</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>18184</td>
+      <td>18937</td>
+      <td>555</td>
+      <td>608</td>
+      <td>10514</td>
+      <td>10514</td>
+      <td>1063</td>
+      <td>1063</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>28698</td>
+      <td>29451</td>
+      <td>1618</td>
+      <td>1671</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>simtext</td>
+      <td>abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix</td>
+      <td>A text mining framework for interactive analysis and visualization of similarities among biomedical entities.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/dlal-group/simtext</td>
+      <td>Text Manipulation</td>
+      <td>simtext</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tools/simtext</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext</td>
+      <td>0.0.2</td>
+      <td>r-argparse</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>2</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>220</td>
+      <td>220</td>
+      <td>68</td>
+      <td>68</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>416</td>
+      <td>416</td>
+      <td>10</td>
+      <td>10</td>
+      <td>636</td>
+      <td>636</td>
+      <td>78</td>
+      <td>78</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sina</td>
+      <td>sina</td>
+      <td>SINA reference based multiple sequence alignment</td>
+      <td>sina</td>
+      <td>sina</td>
+      <td></td>
+      <td>SINA</td>
+      <td>Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment</td>
+      <td>Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment</td>
+      <td>Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy</td>
+      <td>Up-to-date</td>
+      <td>https://sina.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>sina</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina</td>
+      <td>1.7.2</td>
+      <td>sina</td>
+      <td>1.7.2</td>
+      <td>Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment</td>
+      <td>Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1369</td>
+      <td>1369</td>
+      <td>125</td>
+      <td>125</td>
+      <td>2398</td>
+      <td>2398</td>
+      <td>420</td>
+      <td>420</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3767</td>
+      <td>3767</td>
+      <td>545</td>
+      <td>545</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sinto</td>
+      <td>sinto_barcode, sinto_fragments</td>
+      <td>Sinto single-cell analysis tools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/timoast/sinto</td>
+      <td>Single Cell, Epigenetics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto</td>
+      <td>0.10.1</td>
+      <td>sinto</td>
+      <td>0.10.1</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>284</td>
+      <td>284</td>
+      <td>70</td>
+      <td>70</td>
+      <td>165</td>
+      <td>165</td>
+      <td>38</td>
+      <td>38</td>
+      <td>14</td>
+      <td>14</td>
+      <td>2</td>
+      <td>2</td>
+      <td>463</td>
+      <td>463</td>
+      <td>110</td>
+      <td>110</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sistr_cmd</td>
+      <td>sistr_cmd</td>
+      <td>SISTR in silico serotyping tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/sistr_cmd</td>
+      <td>Sequence Analysis</td>
+      <td>sistr_cmd</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd</td>
+      <td>1.1.1</td>
+      <td>sistr_cmd</td>
+      <td>1.1.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3457</td>
+      <td>3457</td>
+      <td>301</td>
+      <td>301</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>556</td>
+      <td>556</td>
+      <td>65</td>
+      <td>65</td>
+      <td>4013</td>
+      <td>4013</td>
+      <td>366</td>
+      <td>366</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sixgill</td>
+      <td>sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge</td>
+      <td>Six-frame Genome-Inferred Libraries for LC-MS/MS</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td></td>
+      <td>Proteomics, MetaProteomics</td>
+      <td>sixgill</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill</td>
+      <td>0.2.4</td>
+      <td>sixgill</td>
+      <td>0.2.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>312</td>
+      <td>312</td>
+      <td>71</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>312</td>
+      <td>312</td>
+      <td>71</td>
+      <td>71</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sklearn</td>
+      <td>sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split</td>
+      <td>Machine Learning tool suite from Scikit-learn</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://scikit-learn.org</td>
+      <td>Machine Learning, Statistics</td>
+      <td>sklearn</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sklearn</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sklearn</td>
+      <td>1.0.11.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>30</td>
+      <td>14</td>
+      <td>31</td>
+      <td>0</td>
+      <td>30</td>
+      <td>14</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>31</td>
+      <td>27</td>
+      <td>0</td>
+      <td>82169</td>
+      <td>116810</td>
+      <td>2402</td>
+      <td>2666</td>
+      <td>18101</td>
+      <td>18101</td>
+      <td>2375</td>
+      <td>2375</td>
+      <td>17549</td>
+      <td>17549</td>
+      <td>321</td>
+      <td>321</td>
+      <td>117819</td>
+      <td>152460</td>
+      <td>5098</td>
+      <td>5362</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>skyline2isocor</td>
+      <td>skyline2isocor</td>
+      <td>Converting skyline output to IsoCor input</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor</td>
+      <td>Metabolomics</td>
+      <td>skyline2isocor</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor</td>
+      <td>1.0.0</td>
+      <td>skyline2isocor</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>slamdunk</td>
+      <td>alleyoop, slamdunk</td>
+      <td>Slamdunk maps and quantifies SLAMseq reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://t-neumann.github.io/slamdunk</td>
+      <td>RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers</td>
+      <td>slamdunk</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk</td>
+      <td>0.4.3</td>
+      <td>slamdunk</td>
+      <td>0.4.3</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>346</td>
+      <td>362</td>
+      <td>16</td>
+      <td>16</td>
+      <td>872</td>
+      <td>872</td>
+      <td>67</td>
+      <td>67</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1218</td>
+      <td>1234</td>
+      <td>83</td>
+      <td>83</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sleuth</td>
+      <td>sleuth</td>
+      <td>Sleuth is a program for differential analysis of RNA-Seq data.</td>
+      <td>sleuth</td>
+      <td>sleuth</td>
+      <td></td>
+      <td>sleuth</td>
+      <td>A statistical model and software application for RNA-seq differential expression analysis.</td>
+      <td>Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation</td>
+      <td>RNA-seq, Gene expression, Statistics and probability</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pachterlab/sleuth</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>sleuth</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth</td>
+      <td>0.30.1</td>
+      <td>r-sleuth</td>
+      <td>0.30.1</td>
+      <td>Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation</td>
+      <td>Gene expression, Statistics and probability</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>141</td>
+      <td>141</td>
+      <td>26</td>
+      <td>26</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>141</td>
+      <td>141</td>
+      <td>26</td>
+      <td>26</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>slice_image</td>
+      <td>ip_slice_image</td>
+      <td>Slice image</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>slice_image</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image</td>
+      <td>0.3-4</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>96</td>
+      <td>103</td>
+      <td>4</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>100</td>
+      <td>107</td>
+      <td>5</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>small_rna_clusters</td>
+      <td>small_rna_clusters</td>
+      <td>clusters small rna reads in alignment BAM files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, SAM, Graphics, Next Gen Mappers</td>
+      <td>small_rna_clusters</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters</td>
+      <td>1.3.0</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>small_rna_maps</td>
+      <td>small_rna_maps</td>
+      <td>Generates small read maps from alignment BAM files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, SAM, Graphics, Next Gen Mappers</td>
+      <td>small_rna_maps</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps</td>
+      <td>3.1.1</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>small_rna_signatures</td>
+      <td>overlapping_reads, signature</td>
+      <td>Computes the tendency of small RNAs to overlap with each other.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA</td>
+      <td>small_rna_signatures</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures</td>
+      <td>3.4.2</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>smallgenomeutilities</td>
+      <td>smgu_frameshift_deletions_checks</td>
+      <td>Set of utilities for manipulating small viral genome data.</td>
+      <td>v-pipe</td>
+      <td>v-pipe</td>
+      <td></td>
+      <td>V-pipe</td>
+      <td>Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.</td>
+      <td>Read pre-processing, Sequence alignment, Genetic variation analysis</td>
+      <td>Genomics, Population genetics, Workflows, Virology, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cbg-ethz/smallgenomeutilities</td>
+      <td>Sequence Analysis</td>
+      <td>smallgenomeutilities</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities</td>
+      <td>0.4.1</td>
+      <td>smallgenomeutilities</td>
+      <td>0.4.1</td>
+      <td>Read pre-processing, Sequence alignment, Genetic variation analysis</td>
+      <td>Genomics, Population genetics, Workflows, Virology, Sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>smalt</td>
+      <td>smalt</td>
+      <td>SMALT aligns DNA sequencing reads with a reference genome.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://www.sanger.ac.uk/science/tools/smalt-0</td>
+      <td>Sequence Analysis</td>
+      <td>smalt</td>
+      <td>nml</td>
+      <td>https://sourceforge.net/projects/smalt/</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt</td>
+      <td>0.7.6</td>
+      <td>smalt</td>
+      <td>0.7.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>smart_domains</td>
+      <td>smart_domains</td>
+      <td>SMART domains</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://smart.embl.de/</td>
+      <td>Sequence Analysis</td>
+      <td>smart_domains</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains</td>
+      <td>0.1.0</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>smina</td>
+      <td>smina</td>
+      <td>smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://sourceforge.net/projects/smina/</td>
+      <td>Computational chemistry</td>
+      <td>smina</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina</td>
+      <td>1.0</td>
+      <td>smina</td>
+      <td>2017.11.9</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>499</td>
+      <td>499</td>
+      <td>16</td>
+      <td>16</td>
+      <td>44</td>
+      <td>44</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>543</td>
+      <td>543</td>
+      <td>26</td>
+      <td>26</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>smithsonian-volcanoes</td>
+      <td>smithsonian_volcanoes</td>
+      <td>Retrieve data from Volcanoes of the World (VOTW) Database</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://volcano.si.edu/gvp_votw.cfm</td>
+      <td>Retrieve Data</td>
+      <td>smithsonian_volcanoes</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes</td>
+      <td>0.1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>smudgeplot</td>
+      <td>smudgeplot</td>
+      <td>Inference of ploidy and heterozygosity structure using whole genome sequencing</td>
+      <td>smudgeplots</td>
+      <td>smudgeplots</td>
+      <td></td>
+      <td>Smudgeplots</td>
+      <td>Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568</td>
+      <td>Sequence trimming, Genotyping, k-mer counting</td>
+      <td>Sequence assembly, Genetic variation, Mathematics</td>
+      <td>To update</td>
+      <td>https://github.com/KamilSJaron/smudgeplot</td>
+      <td>Assembly</td>
+      <td>smudgeplot</td>
+      <td>galaxy-australia</td>
+      <td>https://github.com/galaxyproject/tools-iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot</td>
+      <td>0.2.5</td>
+      <td>smudgeplot</td>
+      <td>0.3.0</td>
+      <td>Sequence trimming, Genotyping, k-mer counting</td>
+      <td>Sequence assembly, Genetic variation, Mathematics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>325</td>
+      <td>325</td>
+      <td>61</td>
+      <td>61</td>
+      <td>137</td>
+      <td>137</td>
+      <td>54</td>
+      <td>54</td>
+      <td>843</td>
+      <td>843</td>
+      <td>63</td>
+      <td>63</td>
+      <td>1305</td>
+      <td>1305</td>
+      <td>178</td>
+      <td>178</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snap</td>
+      <td>snap, snap_training</td>
+      <td>SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.</td>
+      <td>snap</td>
+      <td>snap</td>
+      <td></td>
+      <td>SNAP</td>
+      <td>The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.</td>
+      <td>Gene prediction</td>
+      <td>DNA, DNA polymorphism, Genetics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/KorfLab/SNAP</td>
+      <td>Sequence Analysis</td>
+      <td>snap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap</td>
+      <td>2013_11_29</td>
+      <td>snap</td>
+      <td>2013_11_29</td>
+      <td>Gene prediction</td>
+      <td>DNA polymorphism, Genetics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1499</td>
+      <td>1638</td>
+      <td>331</td>
+      <td>358</td>
+      <td>779</td>
+      <td>779</td>
+      <td>244</td>
+      <td>244</td>
+      <td>467</td>
+      <td>467</td>
+      <td>83</td>
+      <td>83</td>
+      <td>2745</td>
+      <td>2884</td>
+      <td>658</td>
+      <td>685</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snapatac2</td>
+      <td>snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing</td>
+      <td>SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://kzhang.org/SnapATAC2/</td>
+      <td>Single Cell, Epigenetics</td>
+      <td>snapatac2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2</td>
+      <td>2.6.4</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1817</td>
+      <td>1817</td>
+      <td>14</td>
+      <td>14</td>
+      <td>4</td>
+      <td>4</td>
+      <td>2</td>
+      <td>2</td>
+      <td>136</td>
+      <td>136</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1957</td>
+      <td>1957</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sniffles</td>
+      <td>sniffles</td>
+      <td>Galaxy wrapper for sniffles</td>
+      <td>sniffles</td>
+      <td>sniffles</td>
+      <td></td>
+      <td>Sniffles</td>
+      <td>An algorithm for structural variation detection from third generation sequencing alignment.</td>
+      <td>Sequence analysis, Structural variation detection</td>
+      <td>DNA structural variation, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/fritzsedlazeck/Sniffles</td>
+      <td>Sequence Analysis</td>
+      <td>sniffles</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles</td>
+      <td>2.4</td>
+      <td>sniffles</td>
+      <td>2.4</td>
+      <td>Sequence analysis, Structural variation detection</td>
+      <td>Sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1141</td>
+      <td>1141</td>
+      <td>134</td>
+      <td>134</td>
+      <td>606</td>
+      <td>606</td>
+      <td>156</td>
+      <td>156</td>
+      <td>2267</td>
+      <td>2267</td>
+      <td>80</td>
+      <td>80</td>
+      <td>4014</td>
+      <td>4014</td>
+      <td>370</td>
+      <td>370</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snipit</td>
+      <td>snipit</td>
+      <td>Summarise snps relative to a reference sequence</td>
+      <td>snipit</td>
+      <td>snipit</td>
+      <td></td>
+      <td>snipit</td>
+      <td>Summarise snps relative to a reference sequence</td>
+      <td>Base position variability plotting</td>
+      <td>Virology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/aineniamh/snipit</td>
+      <td>Variant Analysis, Sequence Analysis</td>
+      <td>snipit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit</td>
+      <td>1.2</td>
+      <td>snipit</td>
+      <td>1.2</td>
+      <td>Base position variability plotting</td>
+      <td>Virology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>905</td>
+      <td>905</td>
+      <td>44</td>
+      <td>44</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>905</td>
+      <td>905</td>
+      <td>44</td>
+      <td>44</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snippy</td>
+      <td>snippy_core, snippy, snippy_clean_full_aln</td>
+      <td>Contains the snippy tool for characterising microbial snps</td>
+      <td>snippy</td>
+      <td>snippy</td>
+      <td></td>
+      <td>snippy</td>
+      <td>Rapid haploid variant calling and core SNP phylogeny generation.</td>
+      <td>Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling</td>
+      <td>Genomics, Model organisms, DNA polymorphism, Phylogenetics</td>
+      <td>To update</td>
+      <td>https://github.com/tseemann/snippy</td>
+      <td>Sequence Analysis</td>
+      <td>snippy</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy</td>
+      <td></td>
+      <td>snippy</td>
+      <td>4.6.0</td>
+      <td>Phylogenetic tree visualisation, Variant calling</td>
+      <td>Genomics, Model organisms, DNA polymorphism, Phylogenetics</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>0</td>
+      <td>121363</td>
+      <td>124773</td>
+      <td>3448</td>
+      <td>3602</td>
+      <td>92504</td>
+      <td>92504</td>
+      <td>3945</td>
+      <td>3945</td>
+      <td>48068</td>
+      <td>52034</td>
+      <td>2705</td>
+      <td>3073</td>
+      <td>261935</td>
+      <td>269311</td>
+      <td>10098</td>
+      <td>10620</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snp-dists</td>
+      <td>snp_dists</td>
+      <td>Compute pairwise SNP distance matrix from a FASTA sequence alignment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tseemann/snp-dists</td>
+      <td>Variant Analysis</td>
+      <td>snp_dists</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists</td>
+      <td>0.8.2</td>
+      <td>snp-dists</td>
+      <td>0.8.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6555</td>
+      <td>6555</td>
+      <td>807</td>
+      <td>807</td>
+      <td>5336</td>
+      <td>5336</td>
+      <td>171</td>
+      <td>171</td>
+      <td>1143</td>
+      <td>1143</td>
+      <td>182</td>
+      <td>182</td>
+      <td>13034</td>
+      <td>13034</td>
+      <td>1160</td>
+      <td>1160</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snp-sites</td>
+      <td>snp_sites</td>
+      <td>Finds SNP sites from a multi-FASTA alignment file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/sanger-pathogens/snp-sites</td>
+      <td>Variant Analysis</td>
+      <td>snp_sites</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites</td>
+      <td>2.5.1</td>
+      <td>snp-sites</td>
+      <td>2.5.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6597</td>
+      <td>6597</td>
+      <td>663</td>
+      <td>663</td>
+      <td>1467</td>
+      <td>1467</td>
+      <td>256</td>
+      <td>256</td>
+      <td>1279</td>
+      <td>1279</td>
+      <td>114</td>
+      <td>114</td>
+      <td>9343</td>
+      <td>9343</td>
+      <td>1033</td>
+      <td>1033</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpeff</td>
+      <td>snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names</td>
+      <td>SnpEff is a genetic variant annotation and effect prediction toolbox</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://snpeff.sourceforge.net/</td>
+      <td>Genome-Wide Association Study, Variant Analysis</td>
+      <td>snpeff</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff</td>
+      <td></td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>103826</td>
+      <td>108296</td>
+      <td>7181</td>
+      <td>7908</td>
+      <td>115727</td>
+      <td>178110</td>
+      <td>15871</td>
+      <td>22769</td>
+      <td>11817</td>
+      <td>13155</td>
+      <td>2148</td>
+      <td>2321</td>
+      <td>231370</td>
+      <td>299561</td>
+      <td>25200</td>
+      <td>32998</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpeff-covid19</td>
+      <td>snpeff_sars_cov_2</td>
+      <td>SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox</td>
+      <td>snpeff</td>
+      <td>snpeff</td>
+      <td></td>
+      <td>snpEff</td>
+      <td>Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).</td>
+      <td>SNP detection</td>
+      <td>DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs</td>
+      <td>To update</td>
+      <td>http://snpeff.sourceforge.net/</td>
+      <td>Genome-Wide Association Study, Variant Analysis</td>
+      <td>snpeff_sars_cov_2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>SNP detection</td>
+      <td>DNA polymorphism, Nucleic acid sites, features and motifs</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>764895</td>
+      <td>764895</td>
+      <td>1276</td>
+      <td>1276</td>
+      <td>94572</td>
+      <td>94572</td>
+      <td>1636</td>
+      <td>1636</td>
+      <td>26990</td>
+      <td>26990</td>
+      <td>561</td>
+      <td>561</td>
+      <td>886457</td>
+      <td>886457</td>
+      <td>3473</td>
+      <td>3473</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpfreq</td>
+      <td>hgv_snpFreq</td>
+      <td>snpFreq significant SNPs in case-control data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis, Statistics</td>
+      <td>snpfreq</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq</td>
+      <td>1.0.1</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>35</td>
+      <td>44</td>
+      <td>10</td>
+      <td>12</td>
+      <td>307</td>
+      <td>649</td>
+      <td>68</td>
+      <td>181</td>
+      <td>227</td>
+      <td>260</td>
+      <td>16</td>
+      <td>23</td>
+      <td>569</td>
+      <td>953</td>
+      <td>94</td>
+      <td>216</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpfreqplot</td>
+      <td>snpfreqplot</td>
+      <td>A plotting app to visualise the SNPs across a region</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/BrownfieldPlantLab/SNPFreqPlot</td>
+      <td>Variant Analysis</td>
+      <td>snpfreqplot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot</td>
+      <td>1.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3683</td>
+      <td>3683</td>
+      <td>338</td>
+      <td>338</td>
+      <td>1401</td>
+      <td>1401</td>
+      <td>433</td>
+      <td>433</td>
+      <td>1029</td>
+      <td>1029</td>
+      <td>95</td>
+      <td>95</td>
+      <td>6113</td>
+      <td>6113</td>
+      <td>866</td>
+      <td>866</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpsift</td>
+      <td>snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck</td>
+      <td>snpEff SnpSift tools from Pablo Cingolani</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://snpeff.sourceforge.net/SnpSift.html</td>
+      <td>Variant Analysis</td>
+      <td>snpsift</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift</td>
+      <td></td>
+      <td>snpsift</td>
+      <td>5.2</td>
+      <td></td>
+      <td></td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>5142904</td>
+      <td>5146618</td>
+      <td>3602</td>
+      <td>4283</td>
+      <td>382391</td>
+      <td>421190</td>
+      <td>7013</td>
+      <td>9678</td>
+      <td>104030</td>
+      <td>105024</td>
+      <td>960</td>
+      <td>1184</td>
+      <td>5629325</td>
+      <td>5672832</td>
+      <td>11575</td>
+      <td>15145</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpsift_dbnsfp</td>
+      <td>snpSift_dbnsfp</td>
+      <td>snpEff SnpSift dbnsfp tool from Pablo Cingolani</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://snpeff.sourceforge.net/SnpSift.html#dbNSFP</td>
+      <td>Variant Analysis</td>
+      <td>snpsift_dbnsfp</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp</td>
+      <td></td>
+      <td>snpsift</td>
+      <td>5.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>52</td>
+      <td>55</td>
+      <td>23</td>
+      <td>24</td>
+      <td>421</td>
+      <td>421</td>
+      <td>75</td>
+      <td>75</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>476</td>
+      <td>98</td>
+      <td>99</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpsift_genesets</td>
+      <td>snpSift_geneSets</td>
+      <td>Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://snpeff.sourceforge.net/SnpSift.html#geneSets</td>
+      <td>Variant Analysis</td>
+      <td>snpsift_genesets</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets</td>
+      <td></td>
+      <td>snpsift</td>
+      <td>5.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>509</td>
+      <td>554</td>
+      <td>107</td>
+      <td>128</td>
+      <td>474</td>
+      <td>474</td>
+      <td>190</td>
+      <td>190</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>983</td>
+      <td>1028</td>
+      <td>297</td>
+      <td>318</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snv_matrix</td>
+      <td>snvmatrix</td>
+      <td>Generate matrix of SNV distances</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>snv_matrix</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snvtocnv</td>
+      <td>sequenzaindex, snvtocnv</td>
+      <td>infer copy number variations from a vcf file with SNVs using R sequenza</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>snvtocnv</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv</td>
+      <td>3.0.0+galaxy1</td>
+      <td>sequenza-utils</td>
+      <td>3.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>socru</td>
+      <td>socru</td>
+      <td>Order and orientation of complete bacterial genomes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/quadram-institute-bioscience/socru</td>
+      <td>Sequence Analysis</td>
+      <td>socru</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru</td>
+      <td>2.1.7</td>
+      <td>socru</td>
+      <td>2.2.4</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>659</td>
+      <td>659</td>
+      <td>42</td>
+      <td>42</td>
+      <td>296</td>
+      <td>296</td>
+      <td>92</td>
+      <td>92</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>955</td>
+      <td>955</td>
+      <td>134</td>
+      <td>134</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sonneityping</td>
+      <td>sonneityping</td>
+      <td>Scripts for parsing Mykrobe predict results for Shigella sonnei.</td>
+      <td>sonneityping</td>
+      <td>sonneityping</td>
+      <td></td>
+      <td>sonneityping</td>
+      <td>Scripts for parsing Mykrobe predict results for Shigella sonnei.</td>
+      <td>Antimicrobial resistance prediction, Variant calling, Genotyping</td>
+      <td>Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/katholt/sonneityping</td>
+      <td>Sequence Analysis</td>
+      <td>sonneityping</td>
+      <td>iuc</td>
+      <td>https://github.com/katholt/sonneityping</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping</td>
+      <td>20210201</td>
+      <td>sonneityping</td>
+      <td>20210201</td>
+      <td>Antimicrobial resistance prediction, Variant calling, Genotyping</td>
+      <td>Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sortmerna</td>
+      <td>bg_sortmerna</td>
+      <td>SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.</td>
+      <td>sortmerna</td>
+      <td>sortmerna</td>
+      <td></td>
+      <td>SortMeRNA</td>
+      <td>Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.</td>
+      <td>Sequence similarity search, Sequence comparison, Sequence alignment analysis</td>
+      <td>Metatranscriptomics, Metagenomics</td>
+      <td>To update</td>
+      <td>http://bioinfo.lifl.fr/RNA/sortmerna/</td>
+      <td>RNA</td>
+      <td>sortmerna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna</td>
+      <td>4.3.6</td>
+      <td>sortmerna</td>
+      <td>4.3.7</td>
+      <td>Sequence similarity search, Sequence alignment analysis</td>
+      <td>Metatranscriptomics, Metagenomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>19865</td>
+      <td>21034</td>
+      <td>1047</td>
+      <td>1126</td>
+      <td>3141</td>
+      <td>3141</td>
+      <td>328</td>
+      <td>328</td>
+      <td>3304</td>
+      <td>3304</td>
+      <td>189</td>
+      <td>189</td>
+      <td>26310</td>
+      <td>27479</td>
+      <td>1564</td>
+      <td>1643</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spades</td>
+      <td>spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades</td>
+      <td>SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.</td>
+      <td>spades</td>
+      <td>spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades</td>
+      <td></td>
+      <td>SPAdes</td>
+      <td>St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.</td>
+      <td>Genome assembly</td>
+      <td>Sequence assembly</td>
+      <td>To update</td>
+      <td>https://github.com/ablab/spades</td>
+      <td>Assembly, RNA, Metagenomics</td>
+      <td>spades</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades</td>
+      <td>3.15.5</td>
+      <td>spades</td>
+      <td>4.0.0</td>
+      <td>Genome assembly</td>
+      <td>Sequence assembly</td>
+      <td>9</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>3</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>9</td>
+      <td>3</td>
+      <td>0</td>
+      <td>82716</td>
+      <td>87113</td>
+      <td>8209</td>
+      <td>8526</td>
+      <td>120471</td>
+      <td>120475</td>
+      <td>14787</td>
+      <td>14790</td>
+      <td>54067</td>
+      <td>61541</td>
+      <td>5817</td>
+      <td>6653</td>
+      <td>257254</td>
+      <td>269129</td>
+      <td>28813</td>
+      <td>29969</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spades_header_fixer</td>
+      <td>spades_header_fixer</td>
+      <td>Fixes Spades Fasta ids</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Fasta Manipulation</td>
+      <td>spades_fasta_header_fixer</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer</td>
+      <td>1.1.2+galaxy1</td>
+      <td>sed</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spaln</td>
+      <td>list_spaln_tables, spaln</td>
+      <td>Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/</td>
+      <td>Sequence Analysis, Genome annotation</td>
+      <td>spaln</td>
+      <td>iuc</td>
+      <td>https://github.com/ogotoh/spaln</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln</td>
+      <td>2.4.9</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>450</td>
+      <td>491</td>
+      <td>91</td>
+      <td>100</td>
+      <td>4270</td>
+      <td>4270</td>
+      <td>288</td>
+      <td>288</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4720</td>
+      <td>4761</td>
+      <td>379</td>
+      <td>388</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spapros</td>
+      <td>spapros_evaluation, spapros_selection</td>
+      <td>Select and evaluate probe sets for targeted spatial transcriptomics.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/theislab/spapros</td>
+      <td>Single Cell, Transcriptomics, Sequence Analysis</td>
+      <td>spapros</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros</td>
+      <td>0.1.5</td>
+      <td>spapros</td>
+      <td>0.1.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spatyper</td>
+      <td>spatyper</td>
+      <td>Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/HCGB-IGTP/spaTyper</td>
+      <td>Sequence Analysis</td>
+      <td>spatyper</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper</td>
+      <td>0.3.3</td>
+      <td>spatyper</td>
+      <td>0.3.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spec2vec</td>
+      <td>spec2vec_similarity, spec2vec_training</td>
+      <td>Mass spectra similarity scoring using a trained Spec2Vec model.</td>
+      <td>spec2vec</td>
+      <td>spec2vec</td>
+      <td></td>
+      <td>Spec2Vec</td>
+      <td>Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.</td>
+      <td>Spectrum calculation, Spectral library search, Database search, Natural product identification</td>
+      <td>Proteomics experiment, Metabolomics, Natural language processing, Proteomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/iomega/spec2vec</td>
+      <td>Metabolomics</td>
+      <td>spec2vec</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec</td>
+      <td>0.8.0</td>
+      <td>spec2vec</td>
+      <td>0.8.0</td>
+      <td>Spectrum calculation, Spectral library search, Database search, Natural product identification</td>
+      <td>Proteomics experiment, Metabolomics, Natural language processing, Proteomics</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spectrast2spectrast_irt</td>
+      <td>gp_spectrast2spectrast_irt</td>
+      <td>Filter from spectraST files to swath input files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>spectrast2spectrast_irt</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt</td>
+      <td>0.1.0</td>
+      <td>msproteomicstools</td>
+      <td>0.11.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spectrast2tsv</td>
+      <td>gp_spectrast2tsv</td>
+      <td>Filter from spectraST files to swath input files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>spectrast2tsv</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv</td>
+      <td>0.1.0</td>
+      <td>msproteomicstools</td>
+      <td>0.11.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>split_file_on_column</td>
+      <td>tp_split_on_column</td>
+      <td>Split a file on a specific column.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>split_file_on_column</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column</td>
+      <td>0.6</td>
+      <td>gawk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5995</td>
+      <td>6261</td>
+      <td>408</td>
+      <td>453</td>
+      <td>2150</td>
+      <td>2150</td>
+      <td>311</td>
+      <td>311</td>
+      <td>26</td>
+      <td>26</td>
+      <td>2</td>
+      <td>2</td>
+      <td>8171</td>
+      <td>8437</td>
+      <td>721</td>
+      <td>766</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>split_file_to_collection</td>
+      <td>split_file_to_collection</td>
+      <td>Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection</td>
+      <td>Text Manipulation</td>
+      <td>split_file_to_collection</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection</td>
+      <td>0.5.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>16415</td>
+      <td>16623</td>
+      <td>968</td>
+      <td>984</td>
+      <td>9133</td>
+      <td>9133</td>
+      <td>672</td>
+      <td>672</td>
+      <td>4140</td>
+      <td>4140</td>
+      <td>148</td>
+      <td>148</td>
+      <td>29688</td>
+      <td>29896</td>
+      <td>1788</td>
+      <td>1804</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>split_labelmap</td>
+      <td>ip_split_labelmap</td>
+      <td>Split Labelmaps</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>split_labelmap</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap</td>
+      <td>0.2-3</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>44</td>
+      <td>51</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>44</td>
+      <td>51</td>
+      <td>2</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>split_paired_reads</td>
+      <td>split_paired_reads</td>
+      <td>Split paired end reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fastq Manipulation</td>
+      <td>split_paired_reads</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>0</td>
+      <td>3</td>
+      <td>200</td>
+      <td>384</td>
+      <td>31</td>
+      <td>66</td>
+      <td>200</td>
+      <td>397</td>
+      <td>31</td>
+      <td>69</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>splitfasta</td>
+      <td>rbc_splitfasta</td>
+      <td>Split a multi-sequence fasta file into files containing single sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>splitfasta</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta</td>
+      <td>0.4.0</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1772</td>
+      <td>1811</td>
+      <td>278</td>
+      <td>294</td>
+      <td>3012</td>
+      <td>3012</td>
+      <td>564</td>
+      <td>564</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4784</td>
+      <td>4823</td>
+      <td>842</td>
+      <td>858</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spocc</td>
+      <td>spocc_occ</td>
+      <td>Get species occurences data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/web/packages/spocc/index.html</td>
+      <td>Ecology</td>
+      <td>spocc_occ</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc</td>
+      <td>1.2.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>789</td>
+      <td>840</td>
+      <td>130</td>
+      <td>134</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>789</td>
+      <td>840</td>
+      <td>130</td>
+      <td>134</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spolpred</td>
+      <td>spolpred</td>
+      <td>A program for predicting the spoligotype from raw sequence reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>spolpred</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred</td>
+      <td>1.0.1</td>
+      <td>spolpred</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spot_detection_2d</td>
+      <td>ip_spot_detection_2d</td>
+      <td>Spot detection in 2D image sequence</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis</td>
+      <td>Imaging</td>
+      <td>spot_detection_2d</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d</td>
+      <td>0.1</td>
+      <td>giatools</td>
+      <td>0.3.1</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spotyping</td>
+      <td>spotyping</td>
+      <td>SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads</td>
+      <td>spotyping</td>
+      <td>spotyping</td>
+      <td></td>
+      <td>SpoTyping</td>
+      <td>Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.</td>
+      <td>Variant pattern analysis</td>
+      <td>Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/xiaeryu/SpoTyping-v2.0</td>
+      <td>Sequence Analysis</td>
+      <td>spotyping</td>
+      <td>iuc</td>
+      <td>https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping</td>
+      <td>2.1</td>
+      <td>spotyping</td>
+      <td>2.1</td>
+      <td>Variant pattern analysis</td>
+      <td>Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1436</td>
+      <td>1436</td>
+      <td>23</td>
+      <td>23</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1436</td>
+      <td>1436</td>
+      <td>23</td>
+      <td>23</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spyboat</td>
+      <td>spyboat</td>
+      <td>Wavelet analysis for 3d-image stacks</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://github.com/tensionhead/spyboat</td>
+      <td>Imaging, Graphics</td>
+      <td>spyboat</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat</td>
+      <td>0.1.2</td>
+      <td>spyboat</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>142</td>
+      <td>142</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>142</td>
+      <td>142</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sr_bowtie</td>
+      <td>bowtieForSmallRNA</td>
+      <td>bowtie wrapper tool to align small RNA sequencing reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Next Gen Mappers</td>
+      <td>sr_bowtie</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie</td>
+      <td>2.3.0</td>
+      <td>bowtie</td>
+      <td>1.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>80</td>
+      <td>80</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>80</td>
+      <td>80</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sr_bowtie_dataset_annotation</td>
+      <td>sr_bowtie_dataset_annotation</td>
+      <td>Maps iteratively small RNA sequencing datasets to reference sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA</td>
+      <td>sr_bowtie_dataset_annotation</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation</td>
+      <td>2.8</td>
+      <td>bowtie</td>
+      <td>1.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sra-tools</td>
+      <td>fasterq_dump, fastq_dump, sam_dump</td>
+      <td>NCBI Sequence Read Archive toolkit utilities</td>
+      <td>sra-tools</td>
+      <td>sra-tools</td>
+      <td></td>
+      <td>SRA Software Toolkit</td>
+      <td>The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.</td>
+      <td>Data handling</td>
+      <td>DNA, Genomics, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/ncbi/sra-tools</td>
+      <td>Data Source, Fastq Manipulation</td>
+      <td>sra_tools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools</td>
+      <td>3.1.1</td>
+      <td>sra-tools</td>
+      <td>3.1.1</td>
+      <td>Data handling</td>
+      <td>DNA, Genomics, Sequencing</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>364871</td>
+      <td>376580</td>
+      <td>16710</td>
+      <td>17342</td>
+      <td>583675</td>
+      <td>678448</td>
+      <td>53271</td>
+      <td>59638</td>
+      <td>48131</td>
+      <td>50455</td>
+      <td>5910</td>
+      <td>6181</td>
+      <td>996677</td>
+      <td>1105483</td>
+      <td>75891</td>
+      <td>83161</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>srs_tools</td>
+      <td>srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata</td>
+      <td>Compute biodiversity indicators for remote sensing data from Sentinel 2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/Marie59/Sentinel_2A/srs_tools</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools</td>
+      <td>0.0.1</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>239</td>
+      <td>239</td>
+      <td>34</td>
+      <td>34</td>
+      <td>44</td>
+      <td>44</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>283</td>
+      <td>283</td>
+      <td>47</td>
+      <td>47</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>srst2</td>
+      <td>srst2</td>
+      <td>Short Read Sequence Typing for Bacterial Pathogens</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>srst2</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2</td>
+      <td>0.3.7</td>
+      <td>srst2</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>297</td>
+      <td>297</td>
+      <td>40</td>
+      <td>40</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>368</td>
+      <td>368</td>
+      <td>41</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>srst2</td>
+      <td>srst2</td>
+      <td>SRST2 Short Read Sequence Typing for Bacterial Pathogens</td>
+      <td>srst2</td>
+      <td>srst2</td>
+      <td></td>
+      <td>srst2</td>
+      <td>Short Read Sequence Typing for Bacterial Pathogens</td>
+      <td>Multilocus sequence typing</td>
+      <td>Whole genome sequencing, Public health and epidemiology</td>
+      <td>To update</td>
+      <td>http://katholt.github.io/srst2/</td>
+      <td>Metagenomics</td>
+      <td>srst2</td>
+      <td>iuc</td>
+      <td>https://github.com/katholt/srst2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2</td>
+      <td>0.2.0</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td>Multilocus sequence typing</td>
+      <td>Whole genome sequencing, Public health and epidemiology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>297</td>
+      <td>297</td>
+      <td>40</td>
+      <td>40</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>368</td>
+      <td>368</td>
+      <td>41</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sshmm</td>
+      <td>sshmm</td>
+      <td>ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.molgen.mpg.de/heller/ssHMM</td>
+      <td>Sequence Analysis, RNA</td>
+      <td>sshmm</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm</td>
+      <td>1.0.7</td>
+      <td>sshmm</td>
+      <td>1.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>214</td>
+      <td>225</td>
+      <td>17</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>214</td>
+      <td>225</td>
+      <td>17</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>stacks</td>
+      <td>stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks</td>
+      <td>Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq</td>
+      <td>stacks</td>
+      <td>stacks</td>
+      <td></td>
+      <td>Stacks</td>
+      <td>Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.</td>
+      <td>Data handling</td>
+      <td>Mapping, Population genetics</td>
+      <td>To update</td>
+      <td>http://catchenlab.life.illinois.edu/stacks/</td>
+      <td>Sequence Analysis</td>
+      <td>stacks</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks</td>
+      <td></td>
+      <td>stacks</td>
+      <td>2.65</td>
+      <td>Data handling</td>
+      <td>Mapping, Population genetics</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>6440</td>
+      <td>11998</td>
+      <td>465</td>
+      <td>593</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4070</td>
+      <td>4070</td>
+      <td>76</td>
+      <td>76</td>
+      <td>10510</td>
+      <td>16068</td>
+      <td>541</td>
+      <td>669</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>stacks2</td>
+      <td>stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks</td>
+      <td>Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://catchenlab.life.illinois.edu/stacks/</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2</td>
+      <td>2.55</td>
+      <td>stacks</td>
+      <td>2.65</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>8437</td>
+      <td>8592</td>
+      <td>626</td>
+      <td>646</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18016</td>
+      <td>18016</td>
+      <td>270</td>
+      <td>270</td>
+      <td>26453</td>
+      <td>26608</td>
+      <td>896</td>
+      <td>916</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>star_fusion</td>
+      <td>star_fusion</td>
+      <td>STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/STAR-Fusion/STAR-Fusion</td>
+      <td>Sequence Analysis, Transcriptomics</td>
+      <td>star_fusion</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion</td>
+      <td>0.5.4-3+galaxy1</td>
+      <td>star-fusion</td>
+      <td>1.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1312</td>
+      <td>1383</td>
+      <td>82</td>
+      <td>95</td>
+      <td>2198</td>
+      <td>3076</td>
+      <td>234</td>
+      <td>303</td>
+      <td>173</td>
+      <td>173</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3683</td>
+      <td>4632</td>
+      <td>319</td>
+      <td>401</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>staramr</td>
+      <td>staramr_search</td>
+      <td>Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/staramr</td>
+      <td>Sequence Analysis</td>
+      <td>staramr</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr</td>
+      <td>0.10.0</td>
+      <td>staramr</td>
+      <td>0.10.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20778</td>
+      <td>20891</td>
+      <td>2030</td>
+      <td>2045</td>
+      <td>9520</td>
+      <td>9520</td>
+      <td>1424</td>
+      <td>1424</td>
+      <td>6753</td>
+      <td>6753</td>
+      <td>864</td>
+      <td>864</td>
+      <td>37051</td>
+      <td>37164</td>
+      <td>4318</td>
+      <td>4333</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>statistics</td>
+      <td>bg_statistical_hypothesis_testing</td>
+      <td>Tool for computing statistical tests.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/statistics</td>
+      <td>Statistics</td>
+      <td>bg_statistical_hypothesis_testing</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/statistics</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/statistics</td>
+      <td>0.3</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>169</td>
+      <td>346</td>
+      <td>46</td>
+      <td>61</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>169</td>
+      <td>346</td>
+      <td>46</td>
+      <td>61</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>stoc</td>
+      <td>stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic</td>
+      <td>Tools to analyse STOC data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Ecology</td>
+      <td>stoceps</td>
+      <td>ecology</td>
+      <td>https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc</td>
+      <td>0.0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>328</td>
+      <td>328</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>328</td>
+      <td>328</td>
+      <td>38</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>straindesign</td>
+      <td>straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion</td>
+      <td>Toolbox to optimize biological model</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/straindesign</td>
+      <td>Systems Biology, Synthetic Biology</td>
+      <td>straindesign</td>
+      <td>iuc</td>
+      <td>https://github.com/brsynth/straindesign</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign</td>
+      <td>3.2.2</td>
+      <td>straindesign</td>
+      <td>3.2.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>strelka</td>
+      <td>strelka_germline, strelka_somatic</td>
+      <td>Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Illumina/strelka/</td>
+      <td>Variant Analysis</td>
+      <td>strelka</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka</td>
+      <td>2.9.10</td>
+      <td>strelka</td>
+      <td>2.9.10</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>669</td>
+      <td>669</td>
+      <td>112</td>
+      <td>112</td>
+      <td>1261</td>
+      <td>1261</td>
+      <td>417</td>
+      <td>417</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1930</td>
+      <td>1930</td>
+      <td>529</td>
+      <td>529</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>stress_ng</td>
+      <td>stress_ng</td>
+      <td>stress test a computer system in various selectable ways</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Web Services</td>
+      <td>stress_ng</td>
+      <td>bgruening-util</td>
+      <td>https://github.com/ColinIanKing/stress-ng</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng</td>
+      <td>0.12.04</td>
+      <td>stress-ng</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>62</td>
+      <td>62</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>62</td>
+      <td>62</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>stringmlst</td>
+      <td>stringmlst</td>
+      <td>Rapid and accurate identification of the sequence type (ST)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>stringmlst</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst</td>
+      <td>1.1.0</td>
+      <td>stringMLST</td>
+      <td>0.6.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>stringtie</td>
+      <td>stringtie, stringtie_merge</td>
+      <td>StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.</td>
+      <td>stringtie</td>
+      <td>stringtie</td>
+      <td></td>
+      <td>StringTie</td>
+      <td>Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.</td>
+      <td>Transcriptome assembly, RNA-Seq analysis</td>
+      <td>Transcriptomics, RNA-seq</td>
+      <td>Up-to-date</td>
+      <td>http://ccb.jhu.edu/software/stringtie/</td>
+      <td>Transcriptomics</td>
+      <td>stringtie</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie</td>
+      <td>2.2.3</td>
+      <td>stringtie</td>
+      <td>2.2.3</td>
+      <td>Transcriptome assembly, RNA-Seq analysis</td>
+      <td>Transcriptomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>178677</td>
+      <td>187728</td>
+      <td>4972</td>
+      <td>5347</td>
+      <td>320780</td>
+      <td>407379</td>
+      <td>10825</td>
+      <td>15171</td>
+      <td>26375</td>
+      <td>28921</td>
+      <td>1032</td>
+      <td>1167</td>
+      <td>525832</td>
+      <td>624028</td>
+      <td>16829</td>
+      <td>21685</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>structure</td>
+      <td>structure</td>
+      <td>for using multi-locus genotype data to investigate population structure.</td>
+      <td>structure</td>
+      <td>structure</td>
+      <td></td>
+      <td>Structure</td>
+      <td>The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.</td>
+      <td>Genetic variation analysis</td>
+      <td>Population genetics</td>
+      <td>Up-to-date</td>
+      <td>https://web.stanford.edu/group/pritchardlab/structure.html</td>
+      <td>Phylogenetics, Variant Analysis</td>
+      <td>structure</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure</td>
+      <td>2.3.4</td>
+      <td>structure</td>
+      <td>2.3.4</td>
+      <td>Genetic variation analysis</td>
+      <td>Population genetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2858</td>
+      <td>3001</td>
+      <td>118</td>
+      <td>123</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2858</td>
+      <td>3001</td>
+      <td>118</td>
+      <td>123</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>structureharvester</td>
+      <td>structureharvester</td>
+      <td>for parsing STRUCTURE outputs and for performing the Evanno method</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/</td>
+      <td>Phylogenetics, Variant Analysis</td>
+      <td>structureharvester</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester</td>
+      <td>0.6.94</td>
+      <td>structureharvester</td>
+      <td>0.6.94</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>substitution_rates</td>
+      <td>subRate1</td>
+      <td>Estimate substitution rates for non-coding regions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>substitution_rates</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>3901</td>
+      <td>34</td>
+      <td>747</td>
+      <td>105</td>
+      <td>114</td>
+      <td>4</td>
+      <td>4</td>
+      <td>226</td>
+      <td>4015</td>
+      <td>38</td>
+      <td>751</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>substitutions</td>
+      <td>substitutions1</td>
+      <td>Fetch substitutions from pairwise alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>substitutions</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions</td>
+      <td>1.0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>93</td>
+      <td>901</td>
+      <td>13</td>
+      <td>84</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>93</td>
+      <td>901</td>
+      <td>13</td>
+      <td>84</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>subtract</td>
+      <td>gops_subtract_1</td>
+      <td>Subtract the intervals of two datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>subtract</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>566512</td>
+      <td>567199</td>
+      <td>410</td>
+      <td>470</td>
+      <td>49985</td>
+      <td>184650</td>
+      <td>1473</td>
+      <td>7631</td>
+      <td>20648</td>
+      <td>20897</td>
+      <td>155</td>
+      <td>188</td>
+      <td>637145</td>
+      <td>772746</td>
+      <td>2038</td>
+      <td>8289</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>subtract_query</td>
+      <td>subtract_query1</td>
+      <td>Subtract Whole Dataset from another dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>subtract_query</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query</td>
+      <td>0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1178</td>
+      <td>1450</td>
+      <td>124</td>
+      <td>141</td>
+      <td>3169</td>
+      <td>40539</td>
+      <td>636</td>
+      <td>3435</td>
+      <td>799</td>
+      <td>950</td>
+      <td>26</td>
+      <td>38</td>
+      <td>5146</td>
+      <td>42939</td>
+      <td>786</td>
+      <td>3614</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__alignment</td>
+      <td>qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-alignment</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>249</td>
+      <td>249</td>
+      <td>32</td>
+      <td>32</td>
+      <td>16</td>
+      <td>16</td>
+      <td>10</td>
+      <td>10</td>
+      <td>102</td>
+      <td>102</td>
+      <td>16</td>
+      <td>16</td>
+      <td>367</td>
+      <td>367</td>
+      <td>58</td>
+      <td>58</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__composition</td>
+      <td>qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-composition</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>117</td>
+      <td>117</td>
+      <td>41</td>
+      <td>41</td>
+      <td>84</td>
+      <td>84</td>
+      <td>24</td>
+      <td>24</td>
+      <td>161</td>
+      <td>161</td>
+      <td>13</td>
+      <td>13</td>
+      <td>362</td>
+      <td>362</td>
+      <td>78</td>
+      <td>78</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__cutadapt</td>
+      <td>qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-cutadapt</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>217</td>
+      <td>217</td>
+      <td>47</td>
+      <td>47</td>
+      <td>42</td>
+      <td>42</td>
+      <td>20</td>
+      <td>20</td>
+      <td>96</td>
+      <td>96</td>
+      <td>12</td>
+      <td>12</td>
+      <td>355</td>
+      <td>355</td>
+      <td>79</td>
+      <td>79</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__dada2</td>
+      <td>qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://benjjneb.github.io/dada2/</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>721</td>
+      <td>721</td>
+      <td>160</td>
+      <td>160</td>
+      <td>350</td>
+      <td>350</td>
+      <td>91</td>
+      <td>91</td>
+      <td>214</td>
+      <td>214</td>
+      <td>35</td>
+      <td>35</td>
+      <td>1285</td>
+      <td>1285</td>
+      <td>286</td>
+      <td>286</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__deblur</td>
+      <td>qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/biocore/deblur</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>125</td>
+      <td>125</td>
+      <td>30</td>
+      <td>30</td>
+      <td>13</td>
+      <td>13</td>
+      <td>9</td>
+      <td>9</td>
+      <td>83</td>
+      <td>83</td>
+      <td>8</td>
+      <td>8</td>
+      <td>221</td>
+      <td>221</td>
+      <td>47</td>
+      <td>47</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__demux</td>
+      <td>qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-demux</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>396</td>
+      <td>396</td>
+      <td>134</td>
+      <td>134</td>
+      <td>121</td>
+      <td>121</td>
+      <td>57</td>
+      <td>57</td>
+      <td>144</td>
+      <td>144</td>
+      <td>39</td>
+      <td>39</td>
+      <td>661</td>
+      <td>661</td>
+      <td>230</td>
+      <td>230</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__diversity</td>
+      <td>qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-diversity</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>21</td>
+      <td>21</td>
+      <td>22</td>
+      <td>0</td>
+      <td>21</td>
+      <td>21</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>964</td>
+      <td>964</td>
+      <td>318</td>
+      <td>318</td>
+      <td>249</td>
+      <td>249</td>
+      <td>118</td>
+      <td>118</td>
+      <td>475</td>
+      <td>475</td>
+      <td>108</td>
+      <td>108</td>
+      <td>1688</td>
+      <td>1688</td>
+      <td>544</td>
+      <td>544</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__diversity_lib</td>
+      <td>qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-diversity-lib</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>12</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>13</td>
+      <td>13</td>
+      <td>11</td>
+      <td>11</td>
+      <td>1302</td>
+      <td>1302</td>
+      <td>19</td>
+      <td>19</td>
+      <td>1323</td>
+      <td>1323</td>
+      <td>38</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__emperor</td>
+      <td>qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://emperor.microbio.me</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>23</td>
+      <td>23</td>
+      <td>24</td>
+      <td>24</td>
+      <td>11</td>
+      <td>11</td>
+      <td>92</td>
+      <td>92</td>
+      <td>11</td>
+      <td>11</td>
+      <td>174</td>
+      <td>174</td>
+      <td>45</td>
+      <td>45</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__feature_classifier</td>
+      <td>qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-feature-classifier</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>863</td>
+      <td>863</td>
+      <td>220</td>
+      <td>220</td>
+      <td>237</td>
+      <td>237</td>
+      <td>98</td>
+      <td>98</td>
+      <td>181</td>
+      <td>181</td>
+      <td>41</td>
+      <td>41</td>
+      <td>1281</td>
+      <td>1281</td>
+      <td>359</td>
+      <td>359</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__feature_table</td>
+      <td>qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-feature-table</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>17</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>983</td>
+      <td>983</td>
+      <td>287</td>
+      <td>287</td>
+      <td>375</td>
+      <td>375</td>
+      <td>144</td>
+      <td>144</td>
+      <td>907</td>
+      <td>907</td>
+      <td>106</td>
+      <td>106</td>
+      <td>2265</td>
+      <td>2265</td>
+      <td>537</td>
+      <td>537</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__fragment_insertion</td>
+      <td>qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-fragment-insertion</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>46</td>
+      <td>46</td>
+      <td>13</td>
+      <td>13</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>55</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__longitudinal</td>
+      <td>qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-longitudinal</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>11</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>37</td>
+      <td>16</td>
+      <td>16</td>
+      <td>22</td>
+      <td>22</td>
+      <td>7</td>
+      <td>7</td>
+      <td>89</td>
+      <td>89</td>
+      <td>14</td>
+      <td>14</td>
+      <td>148</td>
+      <td>148</td>
+      <td>37</td>
+      <td>37</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__metadata</td>
+      <td>qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-metadata</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>615</td>
+      <td>615</td>
+      <td>143</td>
+      <td>143</td>
+      <td>246</td>
+      <td>246</td>
+      <td>75</td>
+      <td>75</td>
+      <td>115</td>
+      <td>115</td>
+      <td>27</td>
+      <td>27</td>
+      <td>976</td>
+      <td>976</td>
+      <td>245</td>
+      <td>245</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__phylogeny</td>
+      <td>qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-phylogeny</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>12</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>330</td>
+      <td>330</td>
+      <td>83</td>
+      <td>83</td>
+      <td>64</td>
+      <td>64</td>
+      <td>40</td>
+      <td>40</td>
+      <td>195</td>
+      <td>195</td>
+      <td>49</td>
+      <td>49</td>
+      <td>589</td>
+      <td>589</td>
+      <td>172</td>
+      <td>172</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__quality_control</td>
+      <td>qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-quality-control</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__quality_filter</td>
+      <td>qiime2__quality_filter__q_score</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-quality-filter</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>14</td>
+      <td>14</td>
+      <td>16</td>
+      <td>16</td>
+      <td>6</td>
+      <td>6</td>
+      <td>37</td>
+      <td>37</td>
+      <td>2</td>
+      <td>2</td>
+      <td>82</td>
+      <td>82</td>
+      <td>22</td>
+      <td>22</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__rescript</td>
+      <td>qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/nbokulich/RESCRIPt</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__sample_classifier</td>
+      <td>qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-sample-classifier</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>15</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>3</td>
+      <td>3</td>
+      <td>14</td>
+      <td>14</td>
+      <td>10</td>
+      <td>10</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>29</td>
+      <td>29</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__taxa</td>
+      <td>qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-taxa</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>664</td>
+      <td>664</td>
+      <td>145</td>
+      <td>145</td>
+      <td>113</td>
+      <td>113</td>
+      <td>43</td>
+      <td>43</td>
+      <td>255</td>
+      <td>255</td>
+      <td>50</td>
+      <td>50</td>
+      <td>1032</td>
+      <td>1032</td>
+      <td>238</td>
+      <td>238</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__vsearch</td>
+      <td>qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-vsearch</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>84</td>
+      <td>84</td>
+      <td>52</td>
+      <td>52</td>
+      <td>25</td>
+      <td>25</td>
+      <td>16</td>
+      <td>16</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>118</td>
+      <td>118</td>
+      <td>73</td>
+      <td>73</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2_core</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics, Metagenomics, Sequence Analysis</td>
+      <td></td>
+      <td>q2d2</td>
+      <td></td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2_core__tools</td>
+      <td>qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://qiime2.org</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools</td>
+      <td>2024.5.0+dist.he540b0b0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14941</td>
+      <td>14941</td>
+      <td>383</td>
+      <td>383</td>
+      <td>25941</td>
+      <td>25941</td>
+      <td>255</td>
+      <td>255</td>
+      <td>2856</td>
+      <td>2856</td>
+      <td>112</td>
+      <td>112</td>
+      <td>43738</td>
+      <td>43738</td>
+      <td>750</td>
+      <td>750</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_snvphyl</td>
+      <td></td>
+      <td>SNVPhyl suite defining all dependencies for SNVPhyl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>suite_snvphyl_1_2_3</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>superdsm</td>
+      <td>ip_superdsm</td>
+      <td>Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</td>
+      <td>superdsm</td>
+      <td>superdsm</td>
+      <td>superdsm</td>
+      <td>SuperDSM</td>
+      <td>SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.</td>
+      <td>Image analysis</td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>superdsm</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm</td>
+      <td>0.2.0</td>
+      <td>superdsm</td>
+      <td>0.4.0</td>
+      <td>Image analysis</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>swift</td>
+      <td>swiftlink</td>
+      <td>Parallel MCMC Linkage Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/ajm/swiftlink</td>
+      <td>Variant Analysis</td>
+      <td>swiftlink</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift</td>
+      <td>1.0</td>
+      <td>swiftlink</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>syndiva</td>
+      <td>syndiva</td>
+      <td>SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>syndiva</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva</td>
+      <td>1.0</td>
+      <td>clustalo</td>
+      <td>1.2.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>30</td>
+      <td>30</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>30</td>
+      <td>30</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>t2ps</td>
+      <td>Draw_phylogram</td>
+      <td>Draw phylogeny</td>
+      <td>t2ps</td>
+      <td>t2ps</td>
+      <td></td>
+      <td>Draw phylogeny</td>
+      <td>"Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format." - Galaxy tool wrapper</td>
+      <td>Phylogenetic tree visualisation</td>
+      <td>Phylogenomics</td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Metagenomics</td>
+      <td>t2ps</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps</td>
+      <td>1.0.0</td>
+      <td>taxonomy</td>
+      <td>0.10.0</td>
+      <td>Phylogenetic tree visualisation</td>
+      <td>Phylogenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>411</td>
+      <td>472</td>
+      <td>68</td>
+      <td>90</td>
+      <td>102</td>
+      <td>7952</td>
+      <td>13</td>
+      <td>1240</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>513</td>
+      <td>8424</td>
+      <td>81</td>
+      <td>1330</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>t2t_report</td>
+      <td>t2t_report</td>
+      <td>Summarize taxonomy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Metagenomics</td>
+      <td>t2t_report</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report</td>
+      <td>1.0.0</td>
+      <td>taxonomy</td>
+      <td>0.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>927</td>
+      <td>959</td>
+      <td>65</td>
+      <td>78</td>
+      <td>130</td>
+      <td>7194</td>
+      <td>18</td>
+      <td>1143</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1057</td>
+      <td>8153</td>
+      <td>83</td>
+      <td>1221</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>t_coffee</td>
+      <td>t_coffee</td>
+      <td>T-Coffee</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.tcoffee.org/</td>
+      <td>Sequence Analysis</td>
+      <td>t_coffee</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee</td>
+      <td>13.45.0.4846264</td>
+      <td>t-coffee</td>
+      <td>13.46.0.919e8c6b</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3783</td>
+      <td>9125</td>
+      <td>211</td>
+      <td>229</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3784</td>
+      <td>9126</td>
+      <td>212</td>
+      <td>230</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>t_test_two_samples</td>
+      <td>t_test_two_samples</td>
+      <td>T Test for Two Samples</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>t_test_two_samples</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples</td>
+      <td>1.0.1</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>141</td>
+      <td>215</td>
+      <td>20</td>
+      <td>31</td>
+      <td>520</td>
+      <td>1166</td>
+      <td>79</td>
+      <td>274</td>
+      <td>1025</td>
+      <td>1118</td>
+      <td>11</td>
+      <td>12</td>
+      <td>1686</td>
+      <td>2499</td>
+      <td>110</td>
+      <td>317</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>table_annovar</td>
+      <td>table_annovar</td>
+      <td>Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>table_annovar</td>
+      <td>devteam</td>
+      <td>Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar</td>
+      <td>0.2</td>
+      <td>annovar</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16526</td>
+      <td>64515</td>
+      <td>2803</td>
+      <td>7456</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16526</td>
+      <td>64515</td>
+      <td>2803</td>
+      <td>7456</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>table_compute</td>
+      <td>table_compute</td>
+      <td>Perform general-purpose table operations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute</td>
+      <td>Text Manipulation</td>
+      <td>table_compute</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute</td>
+      <td>1.2.4</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>216072</td>
+      <td>216115</td>
+      <td>1811</td>
+      <td>1814</td>
+      <td>12326</td>
+      <td>12326</td>
+      <td>1558</td>
+      <td>1558</td>
+      <td>16136</td>
+      <td>16136</td>
+      <td>256</td>
+      <td>256</td>
+      <td>244534</td>
+      <td>244577</td>
+      <td>3625</td>
+      <td>3628</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tables_arithmetic_operations</td>
+      <td>tables_arithmetic_operations</td>
+      <td>Arithmetic Operations on tables</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>tables_arithmetic_operations</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations</td>
+      <td>1.0.0</td>
+      <td>perl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2188</td>
+      <td>2220</td>
+      <td>33</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2188</td>
+      <td>2220</td>
+      <td>33</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tabular_to_fasta</td>
+      <td>tab2fasta</td>
+      <td>Tabular-to-FASTA</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats</td>
+      <td>tabular_to_fasta</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta</td>
+      <td>1.1.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>329032</td>
+      <td>333057</td>
+      <td>1489</td>
+      <td>1702</td>
+      <td>79033</td>
+      <td>215770</td>
+      <td>2441</td>
+      <td>8587</td>
+      <td>27876</td>
+      <td>33727</td>
+      <td>296</td>
+      <td>360</td>
+      <td>435941</td>
+      <td>582554</td>
+      <td>4226</td>
+      <td>10649</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tabular_to_fastq</td>
+      <td>tabular_to_fastq</td>
+      <td>Tabular to FASTQ converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>tabular_to_fastq</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7011</td>
+      <td>8135</td>
+      <td>449</td>
+      <td>482</td>
+      <td>9473</td>
+      <td>28494</td>
+      <td>626</td>
+      <td>2183</td>
+      <td>850</td>
+      <td>1090</td>
+      <td>80</td>
+      <td>104</td>
+      <td>17334</td>
+      <td>37719</td>
+      <td>1155</td>
+      <td>2769</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tag_pileup_frequency</td>
+      <td>tag_pileup_frequency</td>
+      <td>Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup</td>
+      <td>Statistics, SAM, Genomic Interval Operations</td>
+      <td>tag_pileup_frequency</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency</td>
+      <td>1.0.2</td>
+      <td>openjdk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>158</td>
+      <td>164</td>
+      <td>15</td>
+      <td>16</td>
+      <td>722</td>
+      <td>865</td>
+      <td>40</td>
+      <td>73</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>880</td>
+      <td>1029</td>
+      <td>55</td>
+      <td>89</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tapscan</td>
+      <td>tapscan_classify</td>
+      <td>Search for transcription associated proteins (TAPs)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://plantcode.cup.uni-freiburg.de/tapscan/</td>
+      <td>Proteomics</td>
+      <td>tapscan</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tapscan</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tapscan</td>
+      <td>4.76+galaxy0</td>
+      <td>hmmer</td>
+      <td>3.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>19</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>19</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tarfast5</td>
+      <td>tarfast5</td>
+      <td>produces a tar.gz archive of fast5 sequence files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Nanopore</td>
+      <td>tarfast5</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5</td>
+      <td>0.6.1</td>
+      <td>pigz</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>targetfinder</td>
+      <td>targetfinder</td>
+      <td>Plant small RNA target prediction tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/carringtonlab/TargetFinder.git</td>
+      <td>RNA</td>
+      <td>targetfinder</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder</td>
+      <td>1.7</td>
+      <td>targetfinder</td>
+      <td>1.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>827</td>
+      <td>838</td>
+      <td>89</td>
+      <td>92</td>
+      <td>114</td>
+      <td>114</td>
+      <td>41</td>
+      <td>41</td>
+      <td>900</td>
+      <td>900</td>
+      <td>29</td>
+      <td>29</td>
+      <td>1841</td>
+      <td>1852</td>
+      <td>159</td>
+      <td>162</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tasmanian_mismatch</td>
+      <td>tasmanian_mismatch</td>
+      <td>Analysis of positional mismatches</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/nebiolabs/tasmanian-mismatch</td>
+      <td>Sequence Analysis</td>
+      <td>tasmanian_mismatch</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch</td>
+      <td>1.0.7</td>
+      <td>tasmanian-mismatch</td>
+      <td>1.0.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>61</td>
+      <td>61</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>taxonkit</td>
+      <td>name2taxid, profile2cami</td>
+      <td>TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit</td>
+      <td>taxonkit</td>
+      <td>taxonkit</td>
+      <td></td>
+      <td>TaxonKit</td>
+      <td>TaxonKit is a practical and efficient NCBI taxonomy toolkit.</td>
+      <td>Formatting, Data retrieval</td>
+      <td>Taxonomy, Biotechnology, Ecology</td>
+      <td>Up-to-date</td>
+      <td>https://bioinf.shenwei.me/taxonkit/</td>
+      <td>Metagenomics</td>
+      <td>taxonkit</td>
+      <td>iuc</td>
+      <td>https://github.com/shenwei356/taxonkit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit</td>
+      <td>0.17.0</td>
+      <td>taxonkit</td>
+      <td>0.17.0</td>
+      <td>Formatting, Data retrieval</td>
+      <td>Taxonomy, Biotechnology, Ecology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>taxonomy_filter_refseq</td>
+      <td>taxonomy_filter_refseq</td>
+      <td>Filter RefSeq by taxonomy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/pvanheus/ncbitaxonomy</td>
+      <td>Sequence Analysis, Genome annotation</td>
+      <td>taxonomy_filter_refseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq</td>
+      <td>0.3.0</td>
+      <td>rust-ncbitaxonomy</td>
+      <td>1.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>taxonomy_krona_chart</td>
+      <td>taxonomy_krona_chart</td>
+      <td>Krona pie chart from taxonomic profile</td>
+      <td>krona</td>
+      <td>krona</td>
+      <td></td>
+      <td>Krona</td>
+      <td>Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).</td>
+      <td>Visualisation</td>
+      <td>Metagenomics</td>
+      <td>To update</td>
+      <td>http://sourceforge.net/projects/krona/</td>
+      <td>Assembly</td>
+      <td>taxonomy_krona_chart</td>
+      <td>crs4</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart</td>
+      <td>2.7.1+galaxy0</td>
+      <td>krona</td>
+      <td>2.8.1</td>
+      <td>Visualisation</td>
+      <td>Metagenomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>36069</td>
+      <td>36922</td>
+      <td>5257</td>
+      <td>5431</td>
+      <td>25255</td>
+      <td>30822</td>
+      <td>5066</td>
+      <td>5826</td>
+      <td>7949</td>
+      <td>7949</td>
+      <td>1584</td>
+      <td>1584</td>
+      <td>69273</td>
+      <td>75693</td>
+      <td>11907</td>
+      <td>12841</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>taxpasta</td>
+      <td>taxpasta</td>
+      <td>standardise taxonomic profiles</td>
+      <td>taxpasta</td>
+      <td>taxpasta</td>
+      <td></td>
+      <td>taxpasta</td>
+      <td>TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.</td>
+      <td>Standardisation and normalisation, Aggregation, Formatting, Conversion</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://taxpasta.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>taxpasta</td>
+      <td>iuc</td>
+      <td>https://github.com/taxprofiler/taxpasta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta</td>
+      <td>0.7.0</td>
+      <td>taxpasta</td>
+      <td>0.7.0</td>
+      <td>Standardisation and normalisation, Aggregation, Formatting, Conversion</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>34</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>34</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tb-profiler</td>
+      <td>tb_profiler_profile</td>
+      <td>Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.</td>
+      <td>tb-profiler</td>
+      <td>tb-profiler</td>
+      <td></td>
+      <td>tb-profiler</td>
+      <td>A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/jodyphelan/TBProfiler</td>
+      <td>Sequence Analysis</td>
+      <td>tbprofiler</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler</td>
+      <td>6.2.1</td>
+      <td>tb-profiler</td>
+      <td>6.3.0</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6372</td>
+      <td>6395</td>
+      <td>372</td>
+      <td>379</td>
+      <td>7339</td>
+      <td>7339</td>
+      <td>378</td>
+      <td>378</td>
+      <td>6966</td>
+      <td>6966</td>
+      <td>154</td>
+      <td>154</td>
+      <td>20677</td>
+      <td>20700</td>
+      <td>904</td>
+      <td>911</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tb_variant_filter</td>
+      <td>tb_variant_filter</td>
+      <td>M. tuberculosis H37Rv VCF filter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/COMBAT-TB/tb_variant_filter</td>
+      <td>Variant Analysis</td>
+      <td>tb_variant_filter</td>
+      <td>iuc</td>
+      <td>https://github.com/COMBAT-TB/tb_variant_filter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter</td>
+      <td>0.4.0</td>
+      <td>tb_variant_filter</td>
+      <td>0.4.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>22977</td>
+      <td>22977</td>
+      <td>461</td>
+      <td>461</td>
+      <td>3888</td>
+      <td>3888</td>
+      <td>274</td>
+      <td>274</td>
+      <td>3611</td>
+      <td>3611</td>
+      <td>80</td>
+      <td>80</td>
+      <td>30476</td>
+      <td>30476</td>
+      <td>815</td>
+      <td>815</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tbl2gff3</td>
+      <td>tbl2gff3</td>
+      <td>Table to GFF3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3</td>
+      <td>Convert Formats, Sequence Analysis</td>
+      <td>tbl2gff3</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3</td>
+      <td>1.2</td>
+      <td>bcbiogff</td>
+      <td>0.6.6</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1941</td>
+      <td>1941</td>
+      <td>466</td>
+      <td>466</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>463</td>
+      <td>463</td>
+      <td>112</td>
+      <td>112</td>
+      <td>2404</td>
+      <td>2404</td>
+      <td>578</td>
+      <td>578</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tbvcfreport</td>
+      <td>tbvcfreport</td>
+      <td>Generate HTML report from SnpEff M.tuberculosis VCF(s)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/COMBAT-TB/tbvcfreport</td>
+      <td>Variant Analysis</td>
+      <td>tbvcfreport</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport</td>
+      <td>1.0.1</td>
+      <td>tbvcfreport</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2955</td>
+      <td>2955</td>
+      <td>335</td>
+      <td>335</td>
+      <td>6090</td>
+      <td>6090</td>
+      <td>348</td>
+      <td>348</td>
+      <td>2347</td>
+      <td>2347</td>
+      <td>72</td>
+      <td>72</td>
+      <td>11392</td>
+      <td>11392</td>
+      <td>755</td>
+      <td>755</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>te_finder</td>
+      <td>te_finder</td>
+      <td>Transposable element insertions finder</td>
+      <td>tefinder</td>
+      <td>tefinder</td>
+      <td></td>
+      <td>TEfinder</td>
+      <td>A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.</td>
+      <td>Genome indexing, Variant calling, PCR primer design</td>
+      <td>Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation</td>
+      <td>To update</td>
+      <td>https://github.com/VistaSohrab/TEfinder</td>
+      <td>Sequence Analysis</td>
+      <td>te_finder</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder</td>
+      <td>1.0.1</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td>Genome indexing, Variant calling, PCR primer design</td>
+      <td>Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>203</td>
+      <td>203</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>203</td>
+      <td>203</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>telescope</td>
+      <td>telescope_assign</td>
+      <td>Single locus resolution of Transposable ELEment expression.</td>
+      <td>Telescope-expression</td>
+      <td>Telescope-expression</td>
+      <td></td>
+      <td>Telescope</td>
+      <td>Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.</td>
+      <td>Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping</td>
+      <td>RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/mlbendall/telescope/</td>
+      <td>Genome annotation</td>
+      <td>telescope_assign</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope</td>
+      <td>1.0.3</td>
+      <td>telescope</td>
+      <td>1.0.3</td>
+      <td>Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping</td>
+      <td>RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tetoolkit</td>
+      <td>tetoolkit_tetranscripts</td>
+      <td>The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hammelllab.labsites.cshl.edu/software/</td>
+      <td>Sequence Analysis</td>
+      <td>tetoolkit</td>
+      <td>iuc</td>
+      <td>https://github.com/mhammell-laboratory/TEtranscripts</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit</td>
+      <td>2.2.3</td>
+      <td>tetranscripts</td>
+      <td>2.2.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1013</td>
+      <td>1013</td>
+      <td>74</td>
+      <td>74</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1083</td>
+      <td>1083</td>
+      <td>78</td>
+      <td>78</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tetyper</td>
+      <td>tetyper</td>
+      <td>Type a specific transposable element (TE) of interest from paired-end sequencing data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/aesheppard/TETyper</td>
+      <td>Sequence Analysis</td>
+      <td>tetyper</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper</td>
+      <td>1.1</td>
+      <td>tetyper</td>
+      <td>1.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>106</td>
+      <td>106</td>
+      <td>16</td>
+      <td>16</td>
+      <td>155</td>
+      <td>155</td>
+      <td>47</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>261</td>
+      <td>261</td>
+      <td>63</td>
+      <td>63</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>text_processing</td>
+      <td>tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq</td>
+      <td>High performance text processing tools using the GNU coreutils, sed, awk and friends.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.gnu.org/software/</td>
+      <td>Text Manipulation</td>
+      <td>text_processing</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing</td>
+      <td>9.3</td>
+      <td>coreutils</td>
+      <td>8.25</td>
+      <td></td>
+      <td></td>
+      <td>20</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>20</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>1</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>3898014</td>
+      <td>4015573</td>
+      <td>37698</td>
+      <td>42095</td>
+      <td>648268</td>
+      <td>915282</td>
+      <td>47636</td>
+      <td>69828</td>
+      <td>103365</td>
+      <td>105214</td>
+      <td>7778</td>
+      <td>7953</td>
+      <td>4649647</td>
+      <td>5036069</td>
+      <td>93112</td>
+      <td>119876</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tgsgapcloser</td>
+      <td>tgsgapcloser</td>
+      <td>TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.</td>
+      <td>TGS-GapCloser</td>
+      <td>TGS-GapCloser</td>
+      <td></td>
+      <td>TGS-GapCloser</td>
+      <td>TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.</td>
+      <td>Genome assembly, Read mapping, Scaffolding, Localised reassembly</td>
+      <td>Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping</td>
+      <td>To update</td>
+      <td>https://github.com/BGI-Qingdao/TGS-GapCloser</td>
+      <td>Assembly</td>
+      <td>tgsgapcloser</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser</td>
+      <td>1.0.3</td>
+      <td>tgsgapcloser</td>
+      <td>1.2.1</td>
+      <td>Genome assembly, Read mapping, Scaffolding, Localised reassembly</td>
+      <td>Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>547</td>
+      <td>547</td>
+      <td>51</td>
+      <td>51</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>547</td>
+      <td>547</td>
+      <td>51</td>
+      <td>51</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tiara</td>
+      <td>tiara</td>
+      <td>Tool for identification of eukaryotic sequences in the metagenomic datasets.</td>
+      <td>Tiara</td>
+      <td>Tiara</td>
+      <td></td>
+      <td>TIARA</td>
+      <td>Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).</td>
+      <td>Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection</td>
+      <td>Sequencing, Genomics, DNA polymorphism, DNA structural variation</td>
+      <td>To update</td>
+      <td>https://github.com/ibe-uw/tiara</td>
+      <td>Metagenomics, Sequence Analysis</td>
+      <td>tiara</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tiara</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tiara</td>
+      <td>1.0.3</td>
+      <td>tiara</td>
+      <td></td>
+      <td>Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection</td>
+      <td>Sequencing, Genomics, DNA polymorphism</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tn93</td>
+      <td>tn93_readreduce, tn93, tn93_cluster, tn93_filter</td>
+      <td>Compute distances between sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/veg/tn93/</td>
+      <td>Sequence Analysis</td>
+      <td>tn93</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93</td>
+      <td>1.0.14</td>
+      <td>tn93</td>
+      <td>1.0.14</td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1915</td>
+      <td>1915</td>
+      <td>42</td>
+      <td>42</td>
+      <td>1972</td>
+      <td>1972</td>
+      <td>225</td>
+      <td>225</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3887</td>
+      <td>3887</td>
+      <td>267</td>
+      <td>267</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tool_recommendation_model</td>
+      <td>create_tool_recommendation_model</td>
+      <td>Create model to recommend tools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools</td>
+      <td>Machine Learning</td>
+      <td>create_tool_recommendation_model</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model</td>
+      <td>0.0.5</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>445</td>
+      <td>445</td>
+      <td>25</td>
+      <td>25</td>
+      <td>71</td>
+      <td>71</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>516</td>
+      <td>516</td>
+      <td>57</td>
+      <td>57</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tooldistillator</td>
+      <td>tooldistillator, tooldistillator_summarize</td>
+      <td>ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files</td>
+      <td>tooldistillator</td>
+      <td>tooldistillator</td>
+      <td></td>
+      <td>ToolDistillator</td>
+      <td>ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.</td>
+      <td>Data handling, Parsing</td>
+      <td>Microbiology, Bioinformatics, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://gitlab.com/ifb-elixirfr/abromics/tooldistillator</td>
+      <td>Sequence Analysis</td>
+      <td>tooldistillator</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator</td>
+      <td>0.9.1</td>
+      <td>tooldistillator</td>
+      <td>0.9.1</td>
+      <td>Parsing</td>
+      <td>Microbiology, Bioinformatics, Sequence analysis</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>9</td>
+      <td>9</td>
+      <td>6</td>
+      <td>6</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>71</td>
+      <td>71</td>
+      <td>14</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tophat</td>
+      <td>tophat</td>
+      <td>Tophat for Illumina</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA, Next Gen Mappers</td>
+      <td>tophat</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat</td>
+      <td>1.5.0</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>158</td>
+      <td>66524</td>
+      <td>28</td>
+      <td>7228</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>66525</td>
+      <td>28</td>
+      <td>7229</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tophat2</td>
+      <td>tophat2</td>
+      <td>Tophat - fast splice junction mapper for RNA-Seq reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://ccb.jhu.edu/software/tophat/index.shtml</td>
+      <td>RNA, Next Gen Mappers</td>
+      <td>tophat2</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2</td>
+      <td>2.1.1</td>
+      <td>bowtie2</td>
+      <td>2.5.4</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15496</td>
+      <td>26623</td>
+      <td>1076</td>
+      <td>1664</td>
+      <td>83063</td>
+      <td>343017</td>
+      <td>8372</td>
+      <td>27829</td>
+      <td>5388</td>
+      <td>14057</td>
+      <td>508</td>
+      <td>1012</td>
+      <td>103947</td>
+      <td>383697</td>
+      <td>9956</td>
+      <td>30505</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tophat_fusion_post</td>
+      <td>tophat_fusion_post</td>
+      <td>Wrapper for Tophat-Fusion post step</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics</td>
+      <td>tophat_fusion_post</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post</td>
+      <td>0.1</td>
+      <td>blast+</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>220</td>
+      <td>242</td>
+      <td>41</td>
+      <td>46</td>
+      <td>6</td>
+      <td>814</td>
+      <td>2</td>
+      <td>191</td>
+      <td>100</td>
+      <td>120</td>
+      <td>8</td>
+      <td>12</td>
+      <td>326</td>
+      <td>1176</td>
+      <td>51</td>
+      <td>249</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>topologyeditors</td>
+      <td>gromacs_modify_topology, gromacs_extract_topology</td>
+      <td>Set of python scripts and associated tool files that can be used to modify topology files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors</td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>topologyeditors</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors</td>
+      <td>0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>10</td>
+      <td>10</td>
+      <td>20</td>
+      <td>20</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>77</td>
+      <td>77</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tracegroomer</td>
+      <td>tracegroomer</td>
+      <td>TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cbib/TraceGroomer</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer</td>
+      <td>0.1.4</td>
+      <td>tracegroomer</td>
+      <td>0.1.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tracy</td>
+      <td>tracy_align, tracy_assemble, tracy_basecall, tracy_decompose</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy</td>
+      <td>0.6.1</td>
+      <td>tracy</td>
+      <td>0.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3314</td>
+      <td>3314</td>
+      <td>124</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3314</td>
+      <td>3314</td>
+      <td>124</td>
+      <td>124</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>transdecoder</td>
+      <td>transdecoder</td>
+      <td>TransDecoder finds coding regions within transcripts</td>
+      <td>TransDecoder</td>
+      <td>TransDecoder</td>
+      <td></td>
+      <td>TransDecoder</td>
+      <td>TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.</td>
+      <td>Coding region prediction, de Novo sequencing, De-novo assembly</td>
+      <td>Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing</td>
+      <td>To update</td>
+      <td>https://transdecoder.github.io/</td>
+      <td>Transcriptomics, RNA</td>
+      <td>transdecoder</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder</td>
+      <td>5.5.0</td>
+      <td>transdecoder</td>
+      <td>5.7.1</td>
+      <td>Coding region prediction, de Novo sequencing, De-novo assembly</td>
+      <td>Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5964</td>
+      <td>6418</td>
+      <td>944</td>
+      <td>970</td>
+      <td>5450</td>
+      <td>5450</td>
+      <td>1066</td>
+      <td>1066</td>
+      <td>2610</td>
+      <td>2796</td>
+      <td>317</td>
+      <td>344</td>
+      <td>14024</td>
+      <td>14664</td>
+      <td>2327</td>
+      <td>2380</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>transit</td>
+      <td>gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps</td>
+      <td>TRANSIT</td>
+      <td>transit</td>
+      <td>transit</td>
+      <td></td>
+      <td>TRANSIT</td>
+      <td>A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.</td>
+      <td>Transposon prediction</td>
+      <td>DNA, Sequencing, Mobile genetic elements</td>
+      <td>To update</td>
+      <td>https://github.com/mad-lab/transit/</td>
+      <td>Genome annotation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit</td>
+      <td>3.0.2</td>
+      <td>transit</td>
+      <td>3.2.3</td>
+      <td>Transposon prediction</td>
+      <td>DNA, Sequencing, Mobile genetic elements</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>1039</td>
+      <td>1039</td>
+      <td>189</td>
+      <td>189</td>
+      <td>2672</td>
+      <td>3349</td>
+      <td>467</td>
+      <td>485</td>
+      <td>358</td>
+      <td>358</td>
+      <td>47</td>
+      <td>47</td>
+      <td>4069</td>
+      <td>4746</td>
+      <td>703</td>
+      <td>721</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>translate_bed</td>
+      <td>translate_bed</td>
+      <td>Translate BED transcript CDS or cDNA in 3 frames</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rest.ensembl.org/</td>
+      <td>Proteomics</td>
+      <td>translate_bed</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>649</td>
+      <td>685</td>
+      <td>138</td>
+      <td>142</td>
+      <td>473</td>
+      <td>473</td>
+      <td>105</td>
+      <td>105</td>
+      <td>761</td>
+      <td>761</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1883</td>
+      <td>1919</td>
+      <td>261</td>
+      <td>265</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>translate_bed_sequences</td>
+      <td>translate_bed_sequences</td>
+      <td>Perform 3 frame translation of BED file augmented with a sequence column</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>translate_bed_sequences</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences</td>
+      <td>0.2.0</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>57</td>
+      <td>69</td>
+      <td>16</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>57</td>
+      <td>69</td>
+      <td>16</td>
+      <td>21</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>transtermhp</td>
+      <td>transtermhp</td>
+      <td>Finds rho-independent transcription terminators in bacterial genomes</td>
+      <td>transtermhp</td>
+      <td>transtermhp</td>
+      <td></td>
+      <td>TransTermHP</td>
+      <td>TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator</td>
+      <td>Transcriptional regulatory element prediction</td>
+      <td>Transcription factors and regulatory sites</td>
+      <td>To update</td>
+      <td>https://transterm.cbcb.umd.edu</td>
+      <td>Sequence Analysis</td>
+      <td>transtermhp</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp</td>
+      <td></td>
+      <td>transtermhp</td>
+      <td>2.09</td>
+      <td>Transcriptional regulatory element prediction</td>
+      <td>Transcription factors and regulatory sites</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>250</td>
+      <td>254</td>
+      <td>31</td>
+      <td>31</td>
+      <td>174</td>
+      <td>174</td>
+      <td>45</td>
+      <td>45</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>424</td>
+      <td>428</td>
+      <td>76</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tree_relabeler</td>
+      <td>tree_relabel</td>
+      <td>Relabels the tips of a newick formatted tree.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>tree_relabeler</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler</td>
+      <td>1.1.0</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trim_galore</td>
+      <td>trim_galore</td>
+      <td>Trim Galore adaptive quality and adapter trimmer</td>
+      <td>trim_galore</td>
+      <td>trim_galore</td>
+      <td></td>
+      <td>Trim Galore</td>
+      <td>A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.</td>
+      <td>Sequence trimming, Primer removal, Read pre-processing</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/</td>
+      <td>Sequence Analysis, Fastq Manipulation</td>
+      <td>trim_galore</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore</td>
+      <td>0.6.7</td>
+      <td>trim-galore</td>
+      <td>0.6.10</td>
+      <td>Sequence trimming, Primer removal, Read pre-processing</td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>229489</td>
+      <td>275008</td>
+      <td>5733</td>
+      <td>6500</td>
+      <td>228708</td>
+      <td>324716</td>
+      <td>11708</td>
+      <td>16638</td>
+      <td>22644</td>
+      <td>23869</td>
+      <td>1439</td>
+      <td>1527</td>
+      <td>480841</td>
+      <td>623593</td>
+      <td>18880</td>
+      <td>24665</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trimmer</td>
+      <td>trimmer</td>
+      <td>Trim leading or trailing characters.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>trimmer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer</td>
+      <td>0.0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>5304</td>
+      <td>7438</td>
+      <td>447</td>
+      <td>512</td>
+      <td>15698</td>
+      <td>108672</td>
+      <td>658</td>
+      <td>2946</td>
+      <td>266</td>
+      <td>822</td>
+      <td>53</td>
+      <td>81</td>
+      <td>21268</td>
+      <td>116932</td>
+      <td>1158</td>
+      <td>3539</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trimmomatic</td>
+      <td>trimmomatic</td>
+      <td>A flexible read trimming tool for Illumina NGS data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://www.usadellab.org/cms/?page=trimmomatic</td>
+      <td>Fastq Manipulation</td>
+      <td>trimmomatic</td>
+      <td>pjbriggs</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic</td>
+      <td>0.39</td>
+      <td>trimmomatic</td>
+      <td>0.39</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>352353</td>
+      <td>383014</td>
+      <td>14547</td>
+      <td>15408</td>
+      <td>632385</td>
+      <td>839058</td>
+      <td>39323</td>
+      <td>49850</td>
+      <td>125340</td>
+      <td>139097</td>
+      <td>5268</td>
+      <td>5975</td>
+      <td>1110078</td>
+      <td>1361169</td>
+      <td>59138</td>
+      <td>71233</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trinity</td>
+      <td>trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats</td>
+      <td>Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq</td>
+      <td>trinity</td>
+      <td>trinity</td>
+      <td></td>
+      <td>Trinity</td>
+      <td>Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.</td>
+      <td>Transcriptome assembly</td>
+      <td>Transcriptomics, Gene expression, Gene transcripts</td>
+      <td>To update</td>
+      <td>https://github.com/trinityrnaseq/trinityrnaseq</td>
+      <td>Transcriptomics, RNA</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity</td>
+      <td>2.15.1</td>
+      <td>trinity</td>
+      <td>2.15.2</td>
+      <td>Transcriptome assembly</td>
+      <td>Transcriptomics, Gene transcripts</td>
+      <td>9</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>9</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>13</td>
+      <td>12</td>
+      <td>0</td>
+      <td>35698</td>
+      <td>39132</td>
+      <td>4376</td>
+      <td>4632</td>
+      <td>44509</td>
+      <td>44509</td>
+      <td>6714</td>
+      <td>6714</td>
+      <td>21883</td>
+      <td>23889</td>
+      <td>1924</td>
+      <td>2070</td>
+      <td>102090</td>
+      <td>107530</td>
+      <td>13014</td>
+      <td>13416</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trinotate</td>
+      <td>trinotate</td>
+      <td>Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.</td>
+      <td>trinotate</td>
+      <td>trinotate</td>
+      <td></td>
+      <td>Trinotate</td>
+      <td>Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.</td>
+      <td>Gene functional annotation</td>
+      <td>Gene expression, Transcriptomics</td>
+      <td>To update</td>
+      <td>https://trinotate.github.io/</td>
+      <td>Transcriptomics, RNA</td>
+      <td>trinotate</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate</td>
+      <td>3.2.2</td>
+      <td>trinotate</td>
+      <td>4.0.2</td>
+      <td>Gene functional annotation</td>
+      <td>Transcriptomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1968</td>
+      <td>2080</td>
+      <td>374</td>
+      <td>390</td>
+      <td>1825</td>
+      <td>1825</td>
+      <td>527</td>
+      <td>527</td>
+      <td>862</td>
+      <td>1060</td>
+      <td>161</td>
+      <td>195</td>
+      <td>4655</td>
+      <td>4965</td>
+      <td>1062</td>
+      <td>1112</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tripal</td>
+      <td>analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync</td>
+      <td>Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxy-genome-annotation/python-tripal</td>
+      <td>Web Services</td>
+      <td></td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal</td>
+      <td></td>
+      <td>python-tripal</td>
+      <td>3.2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trna_prediction</td>
+      <td>aragorn_trna, trnascan</td>
+      <td>Aragorn predicts tRNA and tmRNA in nucleotide sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://mbioserv2.mbioekol.lu.se/ARAGORN/</td>
+      <td>RNA</td>
+      <td>trna_prediction</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction</td>
+      <td>0.6</td>
+      <td>aragorn</td>
+      <td>1.2.41</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>4361</td>
+      <td>4601</td>
+      <td>741</td>
+      <td>807</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2469</td>
+      <td>2469</td>
+      <td>190</td>
+      <td>190</td>
+      <td>6830</td>
+      <td>7070</td>
+      <td>931</td>
+      <td>997</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trycycler</td>
+      <td>trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample</td>
+      <td>Trycycler toolkit wrappers</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/rrwick/Trycycler</td>
+      <td>Assembly</td>
+      <td>trycycler</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler</td>
+      <td>0.5.5</td>
+      <td>trycycler</td>
+      <td>0.5.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14681</td>
+      <td>14681</td>
+      <td>265</td>
+      <td>265</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4488</td>
+      <td>4488</td>
+      <td>147</td>
+      <td>147</td>
+      <td>19169</td>
+      <td>19169</td>
+      <td>412</td>
+      <td>412</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tsebra</td>
+      <td>tsebra</td>
+      <td>This tool has been developed to combine BRAKER predictions.</td>
+      <td>tsebra</td>
+      <td>tsebra</td>
+      <td></td>
+      <td>TSEBRA</td>
+      <td>TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.</td>
+      <td>Homology-based gene prediction, Alternative splicing prediction</td>
+      <td>Gene expression, RNA-Seq, Gene transcripts, Model organisms</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Gaius-Augustus/TSEBRA</td>
+      <td>Genome annotation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra</td>
+      <td>1.1.2.5</td>
+      <td>tsebra</td>
+      <td>1.1.2.5</td>
+      <td>Homology-based gene prediction, Alternative splicing prediction</td>
+      <td>Gene expression, RNA-Seq, Gene transcripts, Model organisms</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tsne</td>
+      <td>tsne</td>
+      <td>T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/web/packages/Rtsne/</td>
+      <td>Text Manipulation</td>
+      <td>tsne</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne</td>
+      <td>0.0.2</td>
+      <td>r-rtsne</td>
+      <td>0.13</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>255</td>
+      <td>379</td>
+      <td>31</td>
+      <td>37</td>
+      <td>281</td>
+      <td>281</td>
+      <td>64</td>
+      <td>64</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>536</td>
+      <td>660</td>
+      <td>95</td>
+      <td>101</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>twobittofa</td>
+      <td>ucsc-twobittofa</td>
+      <td>twoBitToFa is a tool to convert all or part of .2bit file to FASTA</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://genome.ucsc.edu/goldenpath/help/twoBit.html</td>
+      <td>Convert Formats</td>
+      <td>ucsc_twobittofa</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa</td>
+      <td>469</td>
+      <td>ucsc-twobittofa</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>413</td>
+      <td>511</td>
+      <td>84</td>
+      <td>118</td>
+      <td>441</td>
+      <td>441</td>
+      <td>123</td>
+      <td>123</td>
+      <td>21</td>
+      <td>21</td>
+      <td>2</td>
+      <td>2</td>
+      <td>875</td>
+      <td>973</td>
+      <td>209</td>
+      <td>243</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tximport</td>
+      <td>tximport</td>
+      <td>Wrapper for the Bioconductor package tximport</td>
+      <td>tximport</td>
+      <td>tximport</td>
+      <td></td>
+      <td>tximport</td>
+      <td>An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.</td>
+      <td>Pathway or network analysis, Formatting, RNA-Seq analysis</td>
+      <td>Transcriptomics, Gene transcripts, Workflows</td>
+      <td>Up-to-date</td>
+      <td>http://bioconductor.org/packages/tximport/</td>
+      <td>Transcriptomics</td>
+      <td>tximport</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport</td>
+      <td>1.30.0</td>
+      <td>bioconductor-tximport</td>
+      <td>1.30.0</td>
+      <td>Pathway or network analysis, Formatting, RNA-Seq analysis</td>
+      <td>Transcriptomics, Gene transcripts, Workflows</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1802</td>
+      <td>1802</td>
+      <td>225</td>
+      <td>225</td>
+      <td>6963</td>
+      <td>6963</td>
+      <td>904</td>
+      <td>904</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8765</td>
+      <td>8765</td>
+      <td>1129</td>
+      <td>1129</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc-cell-browser</td>
+      <td>ucsc_cell_browser</td>
+      <td>Python pipeline and Javascript scatter plot library for single-cell datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cells.ucsc.edu/</td>
+      <td>Transcriptomics</td>
+      <td>ucsc_cell_browser</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser</td>
+      <td>1.0.0+galaxy1</td>
+      <td>ucsc-cell-browser</td>
+      <td>1.2.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>965</td>
+      <td>975</td>
+      <td>178</td>
+      <td>181</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>965</td>
+      <td>975</td>
+      <td>178</td>
+      <td>181</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_axtchain</td>
+      <td>ucsc_axtchain</td>
+      <td>Chain together genome alignments</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_axtchain</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain</td>
+      <td>469</td>
+      <td>ucsc-axtchain</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_axttomaf</td>
+      <td>ucsc_axtomaf</td>
+      <td>Convert dataset from axt to MAF format.</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Convert Formats</td>
+      <td>ucsc_axttomaf</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf</td>
+      <td>469</td>
+      <td>ucsc-axttomaf</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_blat</td>
+      <td>ucsc_blat</td>
+      <td>Standalone blat sequence search command line tool</td>
+      <td>blat</td>
+      <td>blat</td>
+      <td></td>
+      <td>BLAT</td>
+      <td>Fast, accurate spliced alignment of DNA sequences.</td>
+      <td>Sequence alignment</td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://genome.ucsc.edu/goldenPath/help/blatSpec.html</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_blat</td>
+      <td>yating-l</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat</td>
+      <td>469</td>
+      <td>ucsc-blat</td>
+      <td>469</td>
+      <td>Sequence alignment</td>
+      <td>Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_chainnet</td>
+      <td>ucsc_chainnet</td>
+      <td>Make alignment nets out of chains</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_chainnet</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet</td>
+      <td>469</td>
+      <td>ucsc-chainnet</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_chainprenet</td>
+      <td>ucsc_chainprenet</td>
+      <td>Remove chains that don't have a chance of being netted</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_chainprenet</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet</td>
+      <td>469</td>
+      <td>ucsc-chainprenet</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_chainsort</td>
+      <td>ucsc_chainsort</td>
+      <td>Sort chains. By default sorts by score.</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_chainsort</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort</td>
+      <td>469</td>
+      <td>ucsc-chainsort</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_custom_track</td>
+      <td>build_ucsc_custom_track_1</td>
+      <td>Build custom track for UCSC genome browser</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_custom_track</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track</td>
+      <td>1.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>373</td>
+      <td>463</td>
+      <td>134</td>
+      <td>151</td>
+      <td>2249</td>
+      <td>18611</td>
+      <td>638</td>
+      <td>4080</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2622</td>
+      <td>19074</td>
+      <td>772</td>
+      <td>4231</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_netfilter</td>
+      <td>ucsc_netfilter</td>
+      <td>Filter out parts of net</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_netfilter</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter</td>
+      <td>469</td>
+      <td>ucsc-netfilter</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_netsyntenic</td>
+      <td>ucsc_netsyntenic</td>
+      <td>Add synteny info to a net dataset</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_netsyntenic</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic</td>
+      <td>469</td>
+      <td>ucsc-netsyntenic</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_nettoaxt</td>
+      <td>ucsc_nettoaxt</td>
+      <td>Convert net (and chain) to axt format.</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Convert Formats</td>
+      <td>ucsc_nettoaxt</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt</td>
+      <td>469</td>
+      <td>ucsc-nettoaxt</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>umi_tools</td>
+      <td>umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist</td>
+      <td>UMI-tools extract - Extract UMIs from fastq</td>
+      <td>umi-tools</td>
+      <td>umi-tools</td>
+      <td></td>
+      <td>UMI-tools</td>
+      <td>Tools for handling Unique Molecular Identifiers in NGS data sets.</td>
+      <td>Sequencing quality control</td>
+      <td>NGS, Sequence sites, features and motifs, Quality affairs</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/CGATOxford/UMI-tools</td>
+      <td>Sequence Analysis, Transcriptomics, Single Cell</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools</td>
+      <td>1.1.5</td>
+      <td>umi_tools</td>
+      <td>1.1.5</td>
+      <td>Sequencing quality control</td>
+      <td>Sequence sites, features and motifs, Quality affairs</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>55050</td>
+      <td>68123</td>
+      <td>1090</td>
+      <td>1223</td>
+      <td>9001</td>
+      <td>9001</td>
+      <td>906</td>
+      <td>906</td>
+      <td>12444</td>
+      <td>12444</td>
+      <td>187</td>
+      <td>187</td>
+      <td>76495</td>
+      <td>89568</td>
+      <td>2183</td>
+      <td>2316</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>unicycler</td>
+      <td>unicycler</td>
+      <td>Unicycler is a hybrid assembly pipeline for bacterial genomes.</td>
+      <td>unicycler</td>
+      <td>unicycler</td>
+      <td></td>
+      <td>Unicycler</td>
+      <td>A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.</td>
+      <td>Genome assembly, Aggregation</td>
+      <td>Microbiology, Genomics, Sequencing, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/rrwick/Unicycler</td>
+      <td>Assembly</td>
+      <td>unicycler</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler</td>
+      <td>0.5.1</td>
+      <td>unicycler</td>
+      <td>0.5.1</td>
+      <td>Genome assembly, Aggregation</td>
+      <td>Microbiology, Genomics, Sequencing, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>74120</td>
+      <td>77648</td>
+      <td>3798</td>
+      <td>3963</td>
+      <td>64946</td>
+      <td>90075</td>
+      <td>5451</td>
+      <td>7380</td>
+      <td>19516</td>
+      <td>20422</td>
+      <td>2010</td>
+      <td>2080</td>
+      <td>158582</td>
+      <td>188145</td>
+      <td>11259</td>
+      <td>13423</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>unipept</td>
+      <td>unipept</td>
+      <td>Unipept retrieves metaproteomics information</td>
+      <td>unipept</td>
+      <td>unipept</td>
+      <td></td>
+      <td>Unipept</td>
+      <td>Metaproteomics data analysis with a focus on interactive data visualizations.</td>
+      <td>Prediction and recognition, Visualisation</td>
+      <td>Proteomics, Proteogenomics, Biodiversity, Workflows</td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp</td>
+      <td>Proteomics</td>
+      <td>unipept</td>
+      <td>galaxyp</td>
+      <td>https://unipept.ugent.be/apidocs</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept</td>
+      <td>4.5.1</td>
+      <td>python</td>
+      <td></td>
+      <td>Prediction and recognition, Visualisation</td>
+      <td>Proteomics, Proteogenomics, Biodiversity, Workflows</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4900</td>
+      <td>5146</td>
+      <td>257</td>
+      <td>270</td>
+      <td>251</td>
+      <td>251</td>
+      <td>81</td>
+      <td>81</td>
+      <td>1069</td>
+      <td>1069</td>
+      <td>29</td>
+      <td>29</td>
+      <td>6220</td>
+      <td>6466</td>
+      <td>367</td>
+      <td>380</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>uniprot_rest_interface</td>
+      <td>uniprot</td>
+      <td>UniProt ID mapping and sequence retrieval</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/jdrudolph/uniprot</td>
+      <td>Proteomics, Sequence Analysis</td>
+      <td>uniprot_rest_interface</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface</td>
+      <td>0.6</td>
+      <td>requests</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2117</td>
+      <td>2725</td>
+      <td>341</td>
+      <td>412</td>
+      <td>3111</td>
+      <td>5779</td>
+      <td>594</td>
+      <td>1011</td>
+      <td>806</td>
+      <td>806</td>
+      <td>50</td>
+      <td>50</td>
+      <td>6034</td>
+      <td>9310</td>
+      <td>985</td>
+      <td>1473</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>uniprotxml_downloader</td>
+      <td>uniprotxml_downloader</td>
+      <td>Download UniProt proteome in XML or fasta format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>uniprotxml_downloader</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader</td>
+      <td>2.4.0</td>
+      <td>requests</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1488</td>
+      <td>1596</td>
+      <td>230</td>
+      <td>266</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>743</td>
+      <td>743</td>
+      <td>35</td>
+      <td>35</td>
+      <td>2231</td>
+      <td>2339</td>
+      <td>265</td>
+      <td>301</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>unzip</td>
+      <td>unzip</td>
+      <td>Unzip file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Convert Formats</td>
+      <td>unzip</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip</td>
+      <td>6.0</td>
+      <td>unzip</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6942</td>
+      <td>7024</td>
+      <td>1345</td>
+      <td>1356</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2461</td>
+      <td>2461</td>
+      <td>266</td>
+      <td>266</td>
+      <td>9404</td>
+      <td>9486</td>
+      <td>1612</td>
+      <td>1623</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>upload_roi_and_measures_to_omero</td>
+      <td>uploadROIandMeasuresToOMERO</td>
+      <td>Upload the ROI coordinates and the measurements to the omero server</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>upload_roi_and_measures_to_omero</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero</td>
+      <td>0.0.5</td>
+      <td>omero-py</td>
+      <td>5.11.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>usher</td>
+      <td>usher_matutils, usher</td>
+      <td>UShER toolkit wrappers</td>
+      <td>usher</td>
+      <td>usher</td>
+      <td></td>
+      <td>usher</td>
+      <td>The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.</td>
+      <td>Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)</td>
+      <td>Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics</td>
+      <td>To update</td>
+      <td>https://github.com/yatisht/usher</td>
+      <td>Phylogenetics</td>
+      <td>usher</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher</td>
+      <td>0.2.1</td>
+      <td>usher</td>
+      <td>0.6.3</td>
+      <td>Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)</td>
+      <td>Cladistics, Genotype and phenotype, Phylogenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1060</td>
+      <td>1060</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1060</td>
+      <td>1060</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>valet</td>
+      <td>valet</td>
+      <td>A pipeline for detecting mis-assemblies in metagenomic assemblies.</td>
+      <td>valet</td>
+      <td>valet</td>
+      <td></td>
+      <td>VALET</td>
+      <td>VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.</td>
+      <td>Sequence assembly, Sequence assembly visualisation</td>
+      <td>Metagenomics, Sequence assembly</td>
+      <td>To update</td>
+      <td>https://github.com/marbl/VALET</td>
+      <td>Metagenomics</td>
+      <td>valet</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet</td>
+      <td></td>
+      <td>valet</td>
+      <td>1.0</td>
+      <td>Sequence assembly, Sequence assembly visualisation</td>
+      <td>Metagenomics, Sequence assembly</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>518</td>
+      <td>677</td>
+      <td>75</td>
+      <td>87</td>
+      <td>234</td>
+      <td>234</td>
+      <td>65</td>
+      <td>65</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>752</td>
+      <td>911</td>
+      <td>140</td>
+      <td>152</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>validate_fasta_database</td>
+      <td>validate_fasta_database</td>
+      <td>runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation, Proteomics</td>
+      <td>validate_fasta_database</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database</td>
+      <td>0.1.5</td>
+      <td>validate-fasta-database</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>112</td>
+      <td>112</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>112</td>
+      <td>112</td>
+      <td>38</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vapor</td>
+      <td>vapor</td>
+      <td>Classify Influenza samples from raw short read sequence data</td>
+      <td>vapor</td>
+      <td>vapor</td>
+      <td></td>
+      <td>VAPOR</td>
+      <td>VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (&gt; 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.</td>
+      <td>Data retrieval, De-novo assembly, Read mapping</td>
+      <td>Whole genome sequencing, Mapping, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/connor-lab/vapor</td>
+      <td>Sequence Analysis</td>
+      <td>vapor</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor</td>
+      <td>1.0.2</td>
+      <td>vapor</td>
+      <td>1.0.2</td>
+      <td>Data retrieval, De-novo assembly, Read mapping</td>
+      <td>Whole genome sequencing, Mapping, Sequence assembly</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5936</td>
+      <td>5936</td>
+      <td>147</td>
+      <td>147</td>
+      <td>523</td>
+      <td>523</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6459</td>
+      <td>6459</td>
+      <td>162</td>
+      <td>162</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vardict</td>
+      <td>vardict_java</td>
+      <td>VarDict - calls SNVs and indels for tumour-normal pairs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AstraZeneca-NGS/VarDictJava</td>
+      <td>Variant Analysis</td>
+      <td>vardict_java</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict</td>
+      <td>1.8.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>381</td>
+      <td>381</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>381</td>
+      <td>381</td>
+      <td>37</td>
+      <td>37</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>variant_analyzer</td>
+      <td>mut2read, mut2sscs, read2mut</td>
+      <td>Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>variant_analyzer</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer</td>
+      <td>2.0.0</td>
+      <td>matplotlib</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>95</td>
+      <td>95</td>
+      <td>14</td>
+      <td>14</td>
+      <td>516</td>
+      <td>516</td>
+      <td>67</td>
+      <td>67</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>611</td>
+      <td>611</td>
+      <td>81</td>
+      <td>81</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>varscan</td>
+      <td>varscan_copynumber, varscan_mpileup, varscan_somatic</td>
+      <td>VarScan is a variant caller for high-throughput sequencing data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://dkoboldt.github.io/varscan/</td>
+      <td>Variant Analysis</td>
+      <td>varscan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/iuc/tree/master/tools/varscan</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan</td>
+      <td>2.4.3</td>
+      <td>varscan</td>
+      <td>2.4.6</td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>10711</td>
+      <td>11502</td>
+      <td>1442</td>
+      <td>1560</td>
+      <td>16705</td>
+      <td>16705</td>
+      <td>3135</td>
+      <td>3135</td>
+      <td>1036</td>
+      <td>1036</td>
+      <td>100</td>
+      <td>100</td>
+      <td>28452</td>
+      <td>29243</td>
+      <td>4677</td>
+      <td>4795</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>varscan_vaf</td>
+      <td>varscan_vaf</td>
+      <td>Compute variant allele frequency in vcf files generated by varscan.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>varscan_vaf</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf</td>
+      <td>0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>varscan_version_2</td>
+      <td>varscan</td>
+      <td>VarScan wrapper</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://dkoboldt.github.io/varscan/</td>
+      <td>Variant Analysis</td>
+      <td>varscan_version_2</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2</td>
+      <td>2.4.2</td>
+      <td>varscan</td>
+      <td>2.4.6</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5058</td>
+      <td>6139</td>
+      <td>606</td>
+      <td>699</td>
+      <td>17232</td>
+      <td>53268</td>
+      <td>2965</td>
+      <td>5686</td>
+      <td>2298</td>
+      <td>2656</td>
+      <td>424</td>
+      <td>482</td>
+      <td>24588</td>
+      <td>62063</td>
+      <td>3995</td>
+      <td>6867</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>varvamp</td>
+      <td>varvamp</td>
+      <td>Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses</td>
+      <td>varvamp</td>
+      <td>varvamp</td>
+      <td></td>
+      <td>varVAMP</td>
+      <td>variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.</td>
+      <td>PCR primer design</td>
+      <td>Virology, Probes and primers</td>
+      <td>To update</td>
+      <td>https://github.com/jonas-fuchs/varVAMP/</td>
+      <td>Sequence Analysis</td>
+      <td>varvamp</td>
+      <td>iuc</td>
+      <td>https://github.com/jonas-fuchs/varVAMP</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp</td>
+      <td>1.2.0</td>
+      <td>varvamp</td>
+      <td>1.2.1</td>
+      <td>PCR primer design</td>
+      <td>Virology, Probes and primers</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>273</td>
+      <td>273</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>273</td>
+      <td>273</td>
+      <td>12</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf2maf</td>
+      <td>vcf2maf</td>
+      <td>vcf2maf: Convert VCF into MAF</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/mskcc/vcf2maf</td>
+      <td>Convert Formats</td>
+      <td>vcf2maf</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf</td>
+      <td>1.6.21</td>
+      <td>vcf2maf</td>
+      <td>1.6.22</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1097</td>
+      <td>1097</td>
+      <td>46</td>
+      <td>46</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1162</td>
+      <td>1162</td>
+      <td>51</td>
+      <td>51</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf2pgsnp</td>
+      <td>vcf2pgSnp</td>
+      <td>VCF to pgSnp</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>vcf2pgsnp</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>191</td>
+      <td>221</td>
+      <td>57</td>
+      <td>65</td>
+      <td>1399</td>
+      <td>2700</td>
+      <td>209</td>
+      <td>584</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1590</td>
+      <td>2921</td>
+      <td>266</td>
+      <td>649</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf2snvalignment</td>
+      <td>vcf2snvalignment</td>
+      <td>Generates multiple alignment of variant calls</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>vcf2snvalignment</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf2tsv</td>
+      <td>vcf2tsv</td>
+      <td>Converts VCF files into tab-delimited format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis, Convert Formats</td>
+      <td>vcf2tsv</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>169090</td>
+      <td>169679</td>
+      <td>823</td>
+      <td>874</td>
+      <td>16304</td>
+      <td>42215</td>
+      <td>1141</td>
+      <td>2594</td>
+      <td>2485</td>
+      <td>2511</td>
+      <td>169</td>
+      <td>172</td>
+      <td>187879</td>
+      <td>214405</td>
+      <td>2133</td>
+      <td>3640</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf_annotate</td>
+      <td>vcf_annotate</td>
+      <td>Annotate a VCF file (dbSNP, hapmap)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>vcf_annotate</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>263</td>
+      <td>340</td>
+      <td>31</td>
+      <td>54</td>
+      <td>263</td>
+      <td>342</td>
+      <td>31</td>
+      <td>56</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf_extract</td>
+      <td>vcf_extract</td>
+      <td>Extract reads from a specified region</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>vcf_extract</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>513</td>
+      <td>569</td>
+      <td>6</td>
+      <td>9</td>
+      <td>513</td>
+      <td>569</td>
+      <td>6</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf_filter</td>
+      <td>vcf_filter</td>
+      <td>Filter a VCF file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>vcf_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>400</td>
+      <td>455</td>
+      <td>129</td>
+      <td>140</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>238</td>
+      <td>606</td>
+      <td>19</td>
+      <td>56</td>
+      <td>638</td>
+      <td>1061</td>
+      <td>148</td>
+      <td>196</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf_intersect</td>
+      <td>vcf_intersect</td>
+      <td>Generate the intersection of two VCF files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>vcf_intersect</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>335</td>
+      <td>463</td>
+      <td>19</td>
+      <td>28</td>
+      <td>335</td>
+      <td>482</td>
+      <td>19</td>
+      <td>31</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfaddinfo</td>
+      <td>vcfaddinfo</td>
+      <td>Adds info fields from the second dataset which are not present in the first dataset.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfaddinfo</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>882</td>
+      <td>888</td>
+      <td>30</td>
+      <td>32</td>
+      <td>6118</td>
+      <td>8261</td>
+      <td>36</td>
+      <td>114</td>
+      <td>175</td>
+      <td>184</td>
+      <td>6</td>
+      <td>6</td>
+      <td>7175</td>
+      <td>9333</td>
+      <td>72</td>
+      <td>152</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfallelicprimitives</td>
+      <td>vcfallelicprimitives</td>
+      <td>Splits alleleic primitives (gaps or mismatches) into multiple VCF lines</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfallelicprimitives</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6879</td>
+      <td>17157</td>
+      <td>897</td>
+      <td>1219</td>
+      <td>7585</td>
+      <td>14509</td>
+      <td>1245</td>
+      <td>1925</td>
+      <td>1648</td>
+      <td>1681</td>
+      <td>225</td>
+      <td>229</td>
+      <td>16112</td>
+      <td>33347</td>
+      <td>2367</td>
+      <td>3373</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfanno</td>
+      <td>vcfanno</td>
+      <td>Annotate VCF files</td>
+      <td>vcfanno</td>
+      <td>vcfanno</td>
+      <td></td>
+      <td>vcfanno</td>
+      <td>Fast, flexible annotation of genetic variants.</td>
+      <td>SNP annotation</td>
+      <td>Genetic variation, Data submission, annotation and curation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/brentp/vcfanno</td>
+      <td>Variant Analysis</td>
+      <td>vcfanno</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/vcfanno/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno</td>
+      <td>0.3.5</td>
+      <td>vcfanno</td>
+      <td>0.3.5</td>
+      <td>SNP annotation</td>
+      <td>Genetic variation, Data submission, annotation and curation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>174</td>
+      <td>174</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>174</td>
+      <td>174</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfannotate</td>
+      <td>vcfannotate</td>
+      <td>Intersect VCF records with BED annotations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfannotate</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2797</td>
+      <td>2850</td>
+      <td>157</td>
+      <td>181</td>
+      <td>3668</td>
+      <td>14532</td>
+      <td>652</td>
+      <td>1392</td>
+      <td>494</td>
+      <td>507</td>
+      <td>61</td>
+      <td>63</td>
+      <td>6959</td>
+      <td>17889</td>
+      <td>870</td>
+      <td>1636</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfannotategenotypes</td>
+      <td>vcfannotategenotypes</td>
+      <td>Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfannotategenotypes</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>189</td>
+      <td>203</td>
+      <td>62</td>
+      <td>66</td>
+      <td>497</td>
+      <td>1828</td>
+      <td>155</td>
+      <td>387</td>
+      <td>184</td>
+      <td>197</td>
+      <td>11</td>
+      <td>11</td>
+      <td>870</td>
+      <td>2228</td>
+      <td>228</td>
+      <td>464</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfbedintersect</td>
+      <td>vcfbedintersect</td>
+      <td>Intersect VCF and BED datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfbedintersect</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3017</td>
+      <td>4049</td>
+      <td>185</td>
+      <td>210</td>
+      <td>4709</td>
+      <td>20250</td>
+      <td>406</td>
+      <td>1147</td>
+      <td>507</td>
+      <td>527</td>
+      <td>40</td>
+      <td>42</td>
+      <td>8233</td>
+      <td>24826</td>
+      <td>631</td>
+      <td>1399</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfbreakcreatemulti</td>
+      <td>vcfbreakcreatemulti</td>
+      <td>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfbreakcreatemulti</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>416</td>
+      <td>478</td>
+      <td>35</td>
+      <td>40</td>
+      <td>3969</td>
+      <td>10457</td>
+      <td>82</td>
+      <td>309</td>
+      <td>362</td>
+      <td>378</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4747</td>
+      <td>11313</td>
+      <td>125</td>
+      <td>357</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfcheck</td>
+      <td>vcfcheck</td>
+      <td>Verify that the reference allele matches the reference genome</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfcheck</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>745</td>
+      <td>767</td>
+      <td>96</td>
+      <td>106</td>
+      <td>803</td>
+      <td>1895</td>
+      <td>222</td>
+      <td>627</td>
+      <td>241</td>
+      <td>256</td>
+      <td>16</td>
+      <td>17</td>
+      <td>1789</td>
+      <td>2918</td>
+      <td>334</td>
+      <td>750</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfcombine</td>
+      <td>vcfcombine</td>
+      <td>Combine multiple VCF datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfcombine</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1422</td>
+      <td>2020</td>
+      <td>284</td>
+      <td>505</td>
+      <td>4951</td>
+      <td>19530</td>
+      <td>1021</td>
+      <td>2669</td>
+      <td>493</td>
+      <td>516</td>
+      <td>60</td>
+      <td>62</td>
+      <td>6866</td>
+      <td>22066</td>
+      <td>1365</td>
+      <td>3236</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfcommonsamples</td>
+      <td>vcfcommonsamples</td>
+      <td>Output records belonging to samples commong between two datasets.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfcommonsamples</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>233</td>
+      <td>253</td>
+      <td>37</td>
+      <td>42</td>
+      <td>234</td>
+      <td>1839</td>
+      <td>79</td>
+      <td>287</td>
+      <td>199</td>
+      <td>214</td>
+      <td>11</td>
+      <td>12</td>
+      <td>666</td>
+      <td>2306</td>
+      <td>127</td>
+      <td>341</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfdistance</td>
+      <td>vcfdistance</td>
+      <td>Calculate distance to the nearest variant.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfdistance</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>572</td>
+      <td>585</td>
+      <td>90</td>
+      <td>92</td>
+      <td>2063</td>
+      <td>2427</td>
+      <td>139</td>
+      <td>296</td>
+      <td>272</td>
+      <td>290</td>
+      <td>19</td>
+      <td>22</td>
+      <td>2907</td>
+      <td>3302</td>
+      <td>248</td>
+      <td>410</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcffilter</td>
+      <td>vcffilter2</td>
+      <td>Tool for filtering VCF files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcffilter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>37489</td>
+      <td>47142</td>
+      <td>2113</td>
+      <td>2218</td>
+      <td>75128</td>
+      <td>162296</td>
+      <td>5730</td>
+      <td>10533</td>
+      <td>2626</td>
+      <td>2736</td>
+      <td>320</td>
+      <td>331</td>
+      <td>115243</td>
+      <td>212174</td>
+      <td>8163</td>
+      <td>13082</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcffixup</td>
+      <td>vcffixup</td>
+      <td>Count the allele frequencies across alleles present in each record in the VCF file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcffixup</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>926</td>
+      <td>957</td>
+      <td>155</td>
+      <td>173</td>
+      <td>2291</td>
+      <td>5323</td>
+      <td>313</td>
+      <td>985</td>
+      <td>251</td>
+      <td>265</td>
+      <td>28</td>
+      <td>31</td>
+      <td>3468</td>
+      <td>6545</td>
+      <td>496</td>
+      <td>1189</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfflatten</td>
+      <td>vcfflatten2</td>
+      <td>Removes multi-allelic sites by picking the most common alternate</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfflatten</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>172</td>
+      <td>183</td>
+      <td>21</td>
+      <td>25</td>
+      <td>351</td>
+      <td>879</td>
+      <td>67</td>
+      <td>201</td>
+      <td>312</td>
+      <td>342</td>
+      <td>15</td>
+      <td>16</td>
+      <td>835</td>
+      <td>1404</td>
+      <td>103</td>
+      <td>242</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfgeno2haplo</td>
+      <td>vcfgeno2haplo</td>
+      <td>Convert genotype-based phased alleles into haplotype alleles</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfgeno2haplo</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>778</td>
+      <td>794</td>
+      <td>107</td>
+      <td>112</td>
+      <td>2414</td>
+      <td>3721</td>
+      <td>179</td>
+      <td>508</td>
+      <td>209</td>
+      <td>225</td>
+      <td>20</td>
+      <td>21</td>
+      <td>3401</td>
+      <td>4740</td>
+      <td>306</td>
+      <td>641</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfgenotypes</td>
+      <td>vcfgenotypes</td>
+      <td>Convert numerical representation of genotypes to allelic.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfgenotypes</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>502</td>
+      <td>555</td>
+      <td>134</td>
+      <td>143</td>
+      <td>3428</td>
+      <td>6338</td>
+      <td>266</td>
+      <td>858</td>
+      <td>220</td>
+      <td>235</td>
+      <td>23</td>
+      <td>24</td>
+      <td>4150</td>
+      <td>7128</td>
+      <td>423</td>
+      <td>1025</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfhethom</td>
+      <td>vcfhethom</td>
+      <td>Count the number of heterozygotes and alleles, compute het/hom ratio.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfhethom</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1964</td>
+      <td>1991</td>
+      <td>182</td>
+      <td>186</td>
+      <td>1937</td>
+      <td>3846</td>
+      <td>188</td>
+      <td>644</td>
+      <td>567</td>
+      <td>601</td>
+      <td>26</td>
+      <td>27</td>
+      <td>4468</td>
+      <td>6438</td>
+      <td>396</td>
+      <td>857</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfleftalign</td>
+      <td>vcfleftalign</td>
+      <td>Left-align indels and complex variants in VCF dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfleftalign</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>269</td>
+      <td>310</td>
+      <td>38</td>
+      <td>42</td>
+      <td>358</td>
+      <td>1071</td>
+      <td>89</td>
+      <td>287</td>
+      <td>179</td>
+      <td>213</td>
+      <td>12</td>
+      <td>14</td>
+      <td>806</td>
+      <td>1594</td>
+      <td>139</td>
+      <td>343</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfprimers</td>
+      <td>vcfprimers</td>
+      <td>Extract flanking sequences for each VCF record</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfprimers</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>590</td>
+      <td>711</td>
+      <td>28</td>
+      <td>33</td>
+      <td>403</td>
+      <td>831</td>
+      <td>75</td>
+      <td>200</td>
+      <td>190</td>
+      <td>214</td>
+      <td>10</td>
+      <td>12</td>
+      <td>1183</td>
+      <td>1756</td>
+      <td>113</td>
+      <td>245</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfrandomsample</td>
+      <td>vcfrandomsample</td>
+      <td>Randomly sample sites from VCF dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfrandomsample</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>161</td>
+      <td>168</td>
+      <td>13</td>
+      <td>15</td>
+      <td>153</td>
+      <td>350</td>
+      <td>27</td>
+      <td>75</td>
+      <td>184</td>
+      <td>192</td>
+      <td>6</td>
+      <td>6</td>
+      <td>498</td>
+      <td>710</td>
+      <td>46</td>
+      <td>96</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfselectsamples</td>
+      <td>vcfselectsamples</td>
+      <td>Select samples from a VCF file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfselectsamples</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>830</td>
+      <td>900</td>
+      <td>69</td>
+      <td>88</td>
+      <td>1315</td>
+      <td>6257</td>
+      <td>237</td>
+      <td>959</td>
+      <td>344</td>
+      <td>363</td>
+      <td>20</td>
+      <td>21</td>
+      <td>2489</td>
+      <td>7520</td>
+      <td>326</td>
+      <td>1068</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfsort</td>
+      <td>vcfsort</td>
+      <td>Sort VCF dataset by coordinate</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfsort</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1868</td>
+      <td>1904</td>
+      <td>174</td>
+      <td>185</td>
+      <td>18378</td>
+      <td>24175</td>
+      <td>422</td>
+      <td>1279</td>
+      <td>537</td>
+      <td>674</td>
+      <td>70</td>
+      <td>73</td>
+      <td>20783</td>
+      <td>26753</td>
+      <td>666</td>
+      <td>1537</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_annotate</td>
+      <td>vcftools_annotate</td>
+      <td>Annotate VCF using custom/user-defined annotations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_annotate</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate</td>
+      <td>0.1</td>
+      <td>echo</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>155</td>
+      <td>192</td>
+      <td>81</td>
+      <td>90</td>
+      <td>1853</td>
+      <td>3943</td>
+      <td>581</td>
+      <td>1280</td>
+      <td>144</td>
+      <td>156</td>
+      <td>13</td>
+      <td>16</td>
+      <td>2152</td>
+      <td>4291</td>
+      <td>675</td>
+      <td>1386</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_compare</td>
+      <td>vcftools_compare</td>
+      <td>Compare VCF files to get overlap and uniqueness statistics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_compare</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare</td>
+      <td>0.1</td>
+      <td>tabix</td>
+      <td>1.11</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>440</td>
+      <td>594</td>
+      <td>127</td>
+      <td>142</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>0</td>
+      <td>12</td>
+      <td>440</td>
+      <td>610</td>
+      <td>127</td>
+      <td>154</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_consensus</td>
+      <td>vcftools_consensus</td>
+      <td>Apply VCF variants to a fasta file to create consensus sequence</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_consensus</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus</td>
+      <td>0.1.11</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_isec</td>
+      <td>vcftools_isec</td>
+      <td>Intersect multiple VCF datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_isec</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec</td>
+      <td>0.1.1</td>
+      <td>tabix</td>
+      <td>1.11</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>379</td>
+      <td>537</td>
+      <td>104</td>
+      <td>118</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>39</td>
+      <td>496</td>
+      <td>28</td>
+      <td>48</td>
+      <td>418</td>
+      <td>1034</td>
+      <td>132</td>
+      <td>167</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_merge</td>
+      <td>vcftools_merge</td>
+      <td>Merge multiple VCF datasets into a single dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_merge</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge</td>
+      <td>0.1.11</td>
+      <td>tabix</td>
+      <td>1.11</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>817</td>
+      <td>1084</td>
+      <td>244</td>
+      <td>273</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>93</td>
+      <td>448</td>
+      <td>44</td>
+      <td>60</td>
+      <td>910</td>
+      <td>1532</td>
+      <td>288</td>
+      <td>333</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_slice</td>
+      <td>vcftools_slice</td>
+      <td>Subset VCF dataset by genomic regions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_slice</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice</td>
+      <td>0.1</td>
+      <td>echo</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>410</td>
+      <td>423</td>
+      <td>56</td>
+      <td>60</td>
+      <td>6261</td>
+      <td>8115</td>
+      <td>133</td>
+      <td>362</td>
+      <td>127</td>
+      <td>157</td>
+      <td>10</td>
+      <td>19</td>
+      <td>6798</td>
+      <td>8695</td>
+      <td>199</td>
+      <td>441</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_subset</td>
+      <td>vcftools_subset</td>
+      <td>Select samples from a VCF dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_subset</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset</td>
+      <td>0.1</td>
+      <td>tabix</td>
+      <td>1.11</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>134</td>
+      <td>142</td>
+      <td>46</td>
+      <td>49</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>120</td>
+      <td>142</td>
+      <td>12</td>
+      <td>19</td>
+      <td>254</td>
+      <td>284</td>
+      <td>58</td>
+      <td>68</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfvcfintersect</td>
+      <td>vcfvcfintersect</td>
+      <td>Intersect two VCF datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfvcfintersect</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>976544</td>
+      <td>977015</td>
+      <td>703</td>
+      <td>748</td>
+      <td>64155</td>
+      <td>81830</td>
+      <td>981</td>
+      <td>2103</td>
+      <td>11044</td>
+      <td>11069</td>
+      <td>225</td>
+      <td>229</td>
+      <td>1051743</td>
+      <td>1069914</td>
+      <td>1909</td>
+      <td>3080</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vegan</td>
+      <td>vegan_diversity, vegan_fisher_alpha, vegan_rarefaction</td>
+      <td>an R package fo community ecologist</td>
+      <td>vegan</td>
+      <td>vegan</td>
+      <td></td>
+      <td>vegan</td>
+      <td>Ordination methods, diversity analysis and other functions for community and vegetation ecologists</td>
+      <td>Standardisation and normalisation, Analysis</td>
+      <td>Ecology, Phylogenetics, Environmental science</td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/package=vegan</td>
+      <td>Metagenomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan</td>
+      <td>2.4-3</td>
+      <td>r-vegan</td>
+      <td>2.3_4</td>
+      <td>Standardisation and normalisation, Analysis</td>
+      <td>Ecology, Phylogenetics, Environmental science</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>2157</td>
+      <td>2287</td>
+      <td>198</td>
+      <td>209</td>
+      <td>3930</td>
+      <td>5591</td>
+      <td>446</td>
+      <td>744</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6087</td>
+      <td>7878</td>
+      <td>644</td>
+      <td>953</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>velocyto</td>
+      <td>velocyto_cli</td>
+      <td>Velocyto is a library for the analysis of RNA velocity.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://velocyto.org/</td>
+      <td>Transcriptomics, Single Cell</td>
+      <td>velocyto</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto</td>
+      <td>0.17.17</td>
+      <td>velocyto.py</td>
+      <td>0.17.17</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>4</td>
+      <td>4</td>
+      <td>22</td>
+      <td>22</td>
+      <td>6</td>
+      <td>6</td>
+      <td>16</td>
+      <td>16</td>
+      <td>1</td>
+      <td>1</td>
+      <td>45</td>
+      <td>45</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>velvet</td>
+      <td>velvetg, velveth</td>
+      <td>de novo genomic assembler specially designed for short read sequencing technologies</td>
+      <td>velvet</td>
+      <td>velvet</td>
+      <td></td>
+      <td>Velvet</td>
+      <td>A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.</td>
+      <td>Formatting, De-novo assembly</td>
+      <td>Sequence assembly</td>
+      <td>To update</td>
+      <td>https://www.ebi.ac.uk/~zerbino/velvet/</td>
+      <td>Assembly</td>
+      <td>velvet</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet</td>
+      <td></td>
+      <td>velvet</td>
+      <td>1.2.10</td>
+      <td>Formatting, De-novo assembly</td>
+      <td>Sequence assembly</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25171</td>
+      <td>27943</td>
+      <td>3899</td>
+      <td>4270</td>
+      <td>51187</td>
+      <td>51187</td>
+      <td>7557</td>
+      <td>7557</td>
+      <td>28546</td>
+      <td>28619</td>
+      <td>3585</td>
+      <td>3613</td>
+      <td>104904</td>
+      <td>107749</td>
+      <td>15041</td>
+      <td>15440</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>velvet_optimiser</td>
+      <td>velvetoptimiser</td>
+      <td>Automatically optimize Velvet assemblies</td>
+      <td>velvetoptimiser</td>
+      <td>velvetoptimiser</td>
+      <td></td>
+      <td>VelvetOptimiser</td>
+      <td>This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.</td>
+      <td>Optimisation and refinement, Sequence assembly</td>
+      <td>Genomics, Sequence assembly</td>
+      <td>To update</td>
+      <td></td>
+      <td>Assembly</td>
+      <td>velvetoptimiser</td>
+      <td>simon-gladman</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser</td>
+      <td>2.2.6+galaxy2</td>
+      <td>velvet</td>
+      <td>1.2.10</td>
+      <td>Optimisation and refinement, Sequence assembly</td>
+      <td>Genomics, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4715</td>
+      <td>5343</td>
+      <td>888</td>
+      <td>965</td>
+      <td>9575</td>
+      <td>9576</td>
+      <td>2117</td>
+      <td>2117</td>
+      <td>3271</td>
+      <td>5524</td>
+      <td>1050</td>
+      <td>1397</td>
+      <td>17561</td>
+      <td>20443</td>
+      <td>4055</td>
+      <td>4479</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>venn_list</td>
+      <td>venn_list</td>
+      <td>Draw Venn Diagram (PDF) from lists, FASTA files, etc</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list</td>
+      <td>Graphics, Sequence Analysis, Visualization</td>
+      <td>venn_list</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list</td>
+      <td>0.1.2</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4519</td>
+      <td>5476</td>
+      <td>667</td>
+      <td>730</td>
+      <td>9858</td>
+      <td>18420</td>
+      <td>986</td>
+      <td>2010</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14377</td>
+      <td>23896</td>
+      <td>1653</td>
+      <td>2740</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>verify_map</td>
+      <td>verify_map</td>
+      <td>Checks the mapping quality of all BAM(s)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>verify_map</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>verkko</td>
+      <td>verkko</td>
+      <td>Telomere-to-telomere assembly pipeline</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/marbl/verkko</td>
+      <td>Assembly</td>
+      <td>verkko</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko</td>
+      <td>1.3.1</td>
+      <td>verkko</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>25</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>25</td>
+      <td>25</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vg</td>
+      <td>vg_convert, vg_deconstruct, vg_view</td>
+      <td>Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/vgteam/vg</td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg</td>
+      <td>1.23.0</td>
+      <td>vg</td>
+      <td>1.59.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>478</td>
+      <td>478</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>478</td>
+      <td>478</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vibrant</td>
+      <td>vibrant</td>
+      <td>Virus Identification By iteRative ANnoTation</td>
+      <td>VIBRANT</td>
+      <td>VIBRANT</td>
+      <td></td>
+      <td>VIBRANT</td>
+      <td>Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions</td>
+      <td>Sequence trimming, Scaffolding, Genome annotation</td>
+      <td>Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/AnantharamanLab/VIBRANT</td>
+      <td>Metagenomics</td>
+      <td>vibrant</td>
+      <td>ufz</td>
+      <td>https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant</td>
+      <td>1.2.1</td>
+      <td>vibrant</td>
+      <td>1.2.1</td>
+      <td>Sequence trimming, Scaffolding, Genome annotation</td>
+      <td>Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vienna_rna</td>
+      <td>viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup</td>
+      <td>ViennaRNA - Prediction and comparison of RNA secondary structures</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.tbi.univie.ac.at/RNA/</td>
+      <td>RNA</td>
+      <td>viennarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna</td>
+      <td>2.2.10</td>
+      <td>viennarna</td>
+      <td>2.6.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21</td>
+      <td>21</td>
+      <td>0</td>
+      <td>3197</td>
+      <td>8107</td>
+      <td>344</td>
+      <td>415</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3197</td>
+      <td>8107</td>
+      <td>344</td>
+      <td>415</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vigiechiro</td>
+      <td>vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid</td>
+      <td>Tools created by the vigiechiro team to analyses and identify chiro sounds files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro</td>
+      <td>Ecology</td>
+      <td>vigiechiro</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro</td>
+      <td>0.1.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>14412</td>
+      <td>14590</td>
+      <td>722</td>
+      <td>732</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14412</td>
+      <td>14590</td>
+      <td>722</td>
+      <td>732</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>virAnnot</td>
+      <td>virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv</td>
+      <td>virAnnot wrappers</td>
+      <td>virannot</td>
+      <td>virannot</td>
+      <td></td>
+      <td>virAnnot</td>
+      <td>VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project "Plant Health Bioinformatics Network". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy.</td>
+      <td>Sequence annotation, Sequence clustering, Sequence cluster visualisation</td>
+      <td>Metagenomics, Virology, Microbial ecology</td>
+      <td>To update</td>
+      <td>https://github.com/marieBvr/virAnnot</td>
+      <td>Metagenomics</td>
+      <td>virannot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot</td>
+      <td>1.1.0+galaxy0</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td>Sequence annotation, Sequence clustering, Sequence cluster visualisation</td>
+      <td>Metagenomics, Virology, Microbial ecology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>94</td>
+      <td>94</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>94</td>
+      <td>94</td>
+      <td>16</td>
+      <td>16</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>virheat</td>
+      <td>virheat</td>
+      <td>generates a heatmap of allele frequencies from vcf files</td>
+      <td>virheat</td>
+      <td>virheat</td>
+      <td></td>
+      <td>virHEAT</td>
+      <td>VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.</td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/jonas-fuchs/virHEAT</td>
+      <td>Visualization, Variant Analysis</td>
+      <td>virheat</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat</td>
+      <td>0.7.1</td>
+      <td>virheat</td>
+      <td>0.7.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>virhunter</td>
+      <td>virhunter</td>
+      <td>Deep Learning method for novel virus detection in sequencing data</td>
+      <td>virhunter</td>
+      <td>virhunter</td>
+      <td></td>
+      <td>VirHunter</td>
+      <td>VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).</td>
+      <td>Sequence classification</td>
+      <td>Virology</td>
+      <td>To update</td>
+      <td>https://github.com/cbib/virhunter</td>
+      <td>Machine Learning</td>
+      <td>virhunter</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter</td>
+      <td>1.0.0</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Sequence classification</td>
+      <td>Virology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>574</td>
+      <td>574</td>
+      <td>76</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>574</td>
+      <td>574</td>
+      <td>76</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>virsorter</td>
+      <td>virsorter</td>
+      <td>VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.</td>
+      <td>virsorter</td>
+      <td>virsorter</td>
+      <td></td>
+      <td>virsorter</td>
+      <td>Identify DNA and RNA virus sequences.</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/jiarong/VirSorter2/</td>
+      <td>Metagenomics</td>
+      <td>virsorter</td>
+      <td>ufz</td>
+      <td>https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter</td>
+      <td>2.2.4</td>
+      <td>virsorter</td>
+      <td>2.2.4</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>visceral_evaluatesegmentation</td>
+      <td>ip_visceral_evaluatesegmentation</td>
+      <td>Visceral Project - Evaluate Segmentation Tool</td>
+      <td></td>
+      <td></td>
+      <td>evaluatesegmentation-tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>visceral_evaluatesegmentation</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation</td>
+      <td>0.5-2</td>
+      <td>visceral-evaluatesegmentation</td>
+      <td>2015.07.03</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20</td>
+      <td>25</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>25</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vmd</td>
+      <td></td>
+      <td>vmd is a package for  visualizing and analyzing trajectories from molecular dynamics (MD) simulations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.ks.uiuc.edu/Research/vmd/</td>
+      <td>Computational chemistry</td>
+      <td>vmd</td>
+      <td>chemteam</td>
+      <td>https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>volcanoplot</td>
+      <td>volcanoplot</td>
+      <td>Tool to create a Volcano Plot</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://ggplot2.tidyverse.org/</td>
+      <td>Visualization, Transcriptomics, Statistics</td>
+      <td>volcanoplot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot</td>
+      <td>0.0.6</td>
+      <td>r-ggplot2</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>34917</td>
+      <td>36852</td>
+      <td>3670</td>
+      <td>3786</td>
+      <td>54931</td>
+      <td>54931</td>
+      <td>5597</td>
+      <td>5597</td>
+      <td>7183</td>
+      <td>7183</td>
+      <td>905</td>
+      <td>905</td>
+      <td>97031</td>
+      <td>98966</td>
+      <td>10172</td>
+      <td>10288</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>voronoi_tessellation</td>
+      <td>voronoi_tessellation</td>
+      <td>Compute Voronoi tesselation</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.</td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>voronoi_tesselation</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation</td>
+      <td>0.22.0</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vsearch</td>
+      <td>vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting</td>
+      <td>VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.</td>
+      <td>vsearch</td>
+      <td>vsearch</td>
+      <td></td>
+      <td>VSEARCH</td>
+      <td>High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.</td>
+      <td>DNA mapping, Chimera detection</td>
+      <td>Metagenomics, Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/torognes/vsearch</td>
+      <td>Sequence Analysis</td>
+      <td>vsearch</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch</td>
+      <td>2.8.3</td>
+      <td>vsearch</td>
+      <td>2.29.0</td>
+      <td>DNA mapping, Chimera detection</td>
+      <td>Metagenomics, Sequence analysis</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>9694</td>
+      <td>10338</td>
+      <td>559</td>
+      <td>628</td>
+      <td>12282</td>
+      <td>53546</td>
+      <td>1031</td>
+      <td>2007</td>
+      <td>5334</td>
+      <td>5672</td>
+      <td>246</td>
+      <td>277</td>
+      <td>27310</td>
+      <td>69556</td>
+      <td>1836</td>
+      <td>2912</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vsnp</td>
+      <td>vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics</td>
+      <td>The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/USDA-VS/vSNP</td>
+      <td>Sequence Analysis</td>
+      <td>vsnp</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp</td>
+      <td>3.0.6</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vt</td>
+      <td>vt_@BINARY@, vt_@BINARY@</td>
+      <td>A tool set for short variant discovery in genetic sequence data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>vt</td>
+      <td>bgruening</td>
+      <td>https://github.com/atks/vt</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/vt</td>
+      <td>0.2</td>
+      <td>vt</td>
+      <td>2015.11.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>w4mclassfilter</td>
+      <td>w4mclassfilter</td>
+      <td>Filter W4M data by values or metadata</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper</td>
+      <td>Metabolomics</td>
+      <td>w4mclassfilter</td>
+      <td>eschen42</td>
+      <td>https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master</td>
+      <td>https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter</td>
+      <td>0.98.19</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2370</td>
+      <td>2836</td>
+      <td>9</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1482</td>
+      <td>1509</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3852</td>
+      <td>4345</td>
+      <td>13</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>w4mconcatenate</td>
+      <td>W4Mconcatenate</td>
+      <td>[W4M][Utils] concatenate two Metadata tables</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>w4mconcatenate</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate</td>
+      <td>1.0.0+galaxy0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>w4mcorcov</td>
+      <td>w4mcorcov</td>
+      <td>OPLS-DA Contrasts of Univariate Results</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper</td>
+      <td>Metabolomics</td>
+      <td>w4mcorcov</td>
+      <td>eschen42</td>
+      <td>https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master</td>
+      <td>https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov</td>
+      <td>0.98.18</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>238</td>
+      <td>375</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>2</td>
+      <td>2</td>
+      <td>248</td>
+      <td>385</td>
+      <td>12</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>w4mjoinpn</td>
+      <td>w4mjoinpn</td>
+      <td>Join positive- and negative-mode W4M datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper</td>
+      <td>Metabolomics</td>
+      <td>w4mjoinpn</td>
+      <td>eschen42</td>
+      <td>https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master</td>
+      <td>https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn</td>
+      <td>0.98.2</td>
+      <td>coreutils</td>
+      <td>8.25</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>150</td>
+      <td>171</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>2</td>
+      <td>2</td>
+      <td>157</td>
+      <td>178</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>wade</td>
+      <td>wade</td>
+      <td>identify regions of interest</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/wade</td>
+      <td>Sequence Analysis</td>
+      <td>wade</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/wade</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade</td>
+      <td>0.2.5+galaxy1</td>
+      <td>wade</td>
+      <td>0.2.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>waveica</td>
+      <td>waveica</td>
+      <td>Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.</td>
+      <td>waveica</td>
+      <td>waveica</td>
+      <td></td>
+      <td>WaveICA</td>
+      <td>Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.</td>
+      <td>Standardisation and normalisation</td>
+      <td>Metabolomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/WaveICA</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/waveica</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/waveica</td>
+      <td>0.2.0</td>
+      <td>r-recetox-waveica</td>
+      <td>0.2.0</td>
+      <td>Standardisation and normalisation</td>
+      <td>Metabolomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>39</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>weather_app</td>
+      <td>simple_weather</td>
+      <td>provides simple weather in text format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://wttr.in/</td>
+      <td>Visualization, Web Services</td>
+      <td>simpleweather</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app</td>
+      <td>0.1.2</td>
+      <td>curl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>weblogo3</td>
+      <td>rgweblogo3</td>
+      <td>Sequence Logo generator for fasta</td>
+      <td>weblogo</td>
+      <td>weblogo</td>
+      <td></td>
+      <td>WebLogo</td>
+      <td>Web-based application designed to make generate sequence logos.</td>
+      <td>Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition</td>
+      <td>Nucleic acid sites, features and motifs, Sequence analysis</td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics</td>
+      <td>weblogo3</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3</td>
+      <td>3.5.0</td>
+      <td>weblogo</td>
+      <td>3.7.9</td>
+      <td>Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition</td>
+      <td>Nucleic acid sites, features and motifs, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2720</td>
+      <td>2818</td>
+      <td>206</td>
+      <td>228</td>
+      <td>10299</td>
+      <td>30578</td>
+      <td>1354</td>
+      <td>3657</td>
+      <td>1226</td>
+      <td>1285</td>
+      <td>50</td>
+      <td>59</td>
+      <td>14245</td>
+      <td>34681</td>
+      <td>1610</td>
+      <td>3944</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>weightedaverage</td>
+      <td>wtavg</td>
+      <td>Assign weighted-average of the values of features overlapping an interval</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>weightedaverage</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage</td>
+      <td>1.0.1</td>
+      <td>galaxy-ops</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>227</td>
+      <td>2307</td>
+      <td>17</td>
+      <td>75</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>227</td>
+      <td>2307</td>
+      <td>17</td>
+      <td>75</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>whisper</td>
+      <td>whisper</td>
+      <td>Transcribe audio or video files to text using the OpenAI Whisper.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/whisper</td>
+      <td>Machine Learning</td>
+      <td>whisper</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/whisper</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/whisper</td>
+      <td>20231117</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>96</td>
+      <td>96</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>96</td>
+      <td>96</td>
+      <td>13</td>
+      <td>13</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>wigtobigwig</td>
+      <td>ucsc_wigtobigwig</td>
+      <td>converts bedGraph (wig) files into binary bigwig</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://genome.ucsc.edu/goldenPath/help/bigWig.html</td>
+      <td>Convert Formats</td>
+      <td>ucsc_wigtobigwig</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig</td>
+      <td>469</td>
+      <td>ucsc-wigtobigwig</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1601</td>
+      <td>1601</td>
+      <td>106</td>
+      <td>106</td>
+      <td>1108</td>
+      <td>1108</td>
+      <td>172</td>
+      <td>172</td>
+      <td>200</td>
+      <td>200</td>
+      <td>15</td>
+      <td>15</td>
+      <td>2909</td>
+      <td>2909</td>
+      <td>293</td>
+      <td>293</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>windowmasker</td>
+      <td>windowmasker_mkcounts, windowmasker_ustat</td>
+      <td>Identify repetitive regions using WindowMasker</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/</td>
+      <td>Sequence Analysis</td>
+      <td>windowmasker</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker</td>
+      <td>1.0</td>
+      <td>blast</td>
+      <td>2.16.0</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>537</td>
+      <td>537</td>
+      <td>19</td>
+      <td>19</td>
+      <td>12</td>
+      <td>12</td>
+      <td>7</td>
+      <td>7</td>
+      <td>297</td>
+      <td>297</td>
+      <td>2</td>
+      <td>2</td>
+      <td>846</td>
+      <td>846</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>windowsplitter</td>
+      <td>winSplitter</td>
+      <td>Make windows</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>windowsplitter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter</td>
+      <td>1.0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>2</td>
+      <td>171</td>
+      <td>3961</td>
+      <td>34</td>
+      <td>328</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>171</td>
+      <td>3972</td>
+      <td>34</td>
+      <td>330</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>winnowmap</td>
+      <td>winnowmap</td>
+      <td>A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/marbl/Winnowmap</td>
+      <td>Next Gen Mappers</td>
+      <td>winnowmap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap</td>
+      <td>2.03</td>
+      <td>winnowmap</td>
+      <td>2.03</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>279</td>
+      <td>279</td>
+      <td>46</td>
+      <td>46</td>
+      <td>12</td>
+      <td>12</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>291</td>
+      <td>291</td>
+      <td>50</td>
+      <td>50</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>woundhealing</td>
+      <td>woundhealing_scratch_assay</td>
+      <td>Tool to automate quantification of wound healing in high-throughput microscopy scratch assays</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://git.embl.de/grp-cba/wound-healing-htm-screen</td>
+      <td>Imaging</td>
+      <td>Wound healing scratch assay image analysis</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing</td>
+      <td>1.6.1</td>
+      <td>fiji-morpholibj</td>
+      <td>1.6.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>wsi_extract_top_view</td>
+      <td>ip_wsi_extract_top_view</td>
+      <td>WSI Extract Top View</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>wsi_extract_top_view</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view</td>
+      <td>0.2-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>32</td>
+      <td>38</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>32</td>
+      <td>38</td>
+      <td>2</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>wtdbg</td>
+      <td>wtdbg</td>
+      <td>WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.</td>
+      <td>wtdbg2</td>
+      <td>wtdbg2</td>
+      <td></td>
+      <td>wtdbg2</td>
+      <td>Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.</td>
+      <td>Genome assembly, De-novo assembly</td>
+      <td>Sequence assembly, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/ruanjue/wtdbg2</td>
+      <td>Assembly</td>
+      <td>wtdbg</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg</td>
+      <td>2.5</td>
+      <td>wtdbg</td>
+      <td>2.5</td>
+      <td>Genome assembly, De-novo assembly</td>
+      <td>Sequence assembly, Sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1619</td>
+      <td>1715</td>
+      <td>337</td>
+      <td>376</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1619</td>
+      <td>1715</td>
+      <td>337</td>
+      <td>376</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xarray</td>
+      <td>timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select</td>
+      <td>xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://xarray.pydata.org</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray</td>
+      <td>2022.3.0</td>
+      <td>xarray</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>2</td>
+      <td>6</td>
+      <td>0</td>
+      <td>5</td>
+      <td>2</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>2</td>
+      <td>0</td>
+      <td>5995</td>
+      <td>5995</td>
+      <td>275</td>
+      <td>275</td>
+      <td>66</td>
+      <td>66</td>
+      <td>23</td>
+      <td>23</td>
+      <td>295</td>
+      <td>295</td>
+      <td>3</td>
+      <td>3</td>
+      <td>6356</td>
+      <td>6356</td>
+      <td>301</td>
+      <td>301</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xcms</td>
+      <td>abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw</td>
+      <td></td>
+      <td>XCMS</td>
+      <td>XCMS</td>
+      <td></td>
+      <td>xcms</td>
+      <td>Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data.  The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling.</td>
+      <td>Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation</td>
+      <td>Biological imaging, Data visualisation, Metabolomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/sneumann/xcms</td>
+      <td>Metabolomics</td>
+      <td>xcms</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms</td>
+      <td>4.0.0</td>
+      <td>bioconductor-xcms</td>
+      <td>4.0.0</td>
+      <td>Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation</td>
+      <td>Data visualisation, Metabolomics</td>
+      <td>9</td>
+      <td>11</td>
+      <td>12</td>
+      <td>0</td>
+      <td>9</td>
+      <td>11</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>10</td>
+      <td>9</td>
+      <td>0</td>
+      <td>31909</td>
+      <td>35790</td>
+      <td>1357</td>
+      <td>1384</td>
+      <td>7099</td>
+      <td>7099</td>
+      <td>413</td>
+      <td>413</td>
+      <td>5333</td>
+      <td>5357</td>
+      <td>330</td>
+      <td>330</td>
+      <td>44341</td>
+      <td>48246</td>
+      <td>2100</td>
+      <td>2127</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xmlstarlet</td>
+      <td>xmlstarlet</td>
+      <td>Tool to convert a xml file from one metadata standard to another</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats</td>
+      <td>xmlstarlet</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet</td>
+      <td>1.6.1</td>
+      <td>xmlstarlet</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59</td>
+      <td>59</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59</td>
+      <td>59</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xpath</td>
+      <td>xpath</td>
+      <td>XPath XML querying tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://search.cpan.org/dist/XML-XPath/</td>
+      <td>Text Manipulation</td>
+      <td>xpath</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath</td>
+      <td></td>
+      <td>perl-xml-xpath</td>
+      <td>1.47</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>128</td>
+      <td>235</td>
+      <td>7</td>
+      <td>8</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>128</td>
+      <td>236</td>
+      <td>7</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xpore</td>
+      <td>xpore_dataprep, xpore_diffmod</td>
+      <td>Identification and quantification of differential RNA modifications from direct RNA sequencing</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/GoekeLab/xpore</td>
+      <td>Nanopore</td>
+      <td>xpore</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore</td>
+      <td>2.1+galaxy0</td>
+      <td>xpore</td>
+      <td>2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xtb</td>
+      <td>xtb_molecular_optimization</td>
+      <td>Performs semiempirical molecular optimization.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/grimme-lab/xtb</td>
+      <td>Metabolomics</td>
+      <td>xtb_molecular_optimization</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/xtb</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/xtb</td>
+      <td>6.6.1</td>
+      <td>xtb</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>143</td>
+      <td>143</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>143</td>
+      <td>143</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xy_plot</td>
+      <td>XY_Plot_1</td>
+      <td>Plotting tool for multiple series and graph types</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Statistics</td>
+      <td>xy_plot</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot</td>
+      <td>1.0.2</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4490</td>
+      <td>6169</td>
+      <td>768</td>
+      <td>889</td>
+      <td>6120</td>
+      <td>15516</td>
+      <td>1921</td>
+      <td>3653</td>
+      <td>2033</td>
+      <td>2212</td>
+      <td>556</td>
+      <td>590</td>
+      <td>12643</td>
+      <td>23897</td>
+      <td>3245</td>
+      <td>5132</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>yac_clipper</td>
+      <td>yac</td>
+      <td>Clips 3' adapters for small RNA sequencing reads.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Fastq Manipulation</td>
+      <td>yac_clipper</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper</td>
+      <td>2.5.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>yahs</td>
+      <td>yahs</td>
+      <td>Yet Another Hi-C scaffolding tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/c-zhou/yahs</td>
+      <td>Assembly</td>
+      <td>yahs</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs</td>
+      <td>1.2a.2</td>
+      <td>yahs</td>
+      <td>1.2.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>618</td>
+      <td>618</td>
+      <td>176</td>
+      <td>176</td>
+      <td>336</td>
+      <td>336</td>
+      <td>62</td>
+      <td>62</td>
+      <td>588</td>
+      <td>588</td>
+      <td>25</td>
+      <td>25</td>
+      <td>1542</td>
+      <td>1542</td>
+      <td>263</td>
+      <td>263</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>zeiss_lmd_converter</td>
+      <td>ZeissLMDconverter</td>
+      <td>Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter</td>
+      <td>Proteomics</td>
+      <td></td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter</td>
+      <td>2.0.4</td>
+      <td>shapely</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>zerone</td>
+      <td>zerone</td>
+      <td>ChIP-seq discretization and quality control</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/nanakiksc/zerone</td>
+      <td>ChIP-seq</td>
+      <td>zerone</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone</td>
+      <td>1.0</td>
+      <td>zerone</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>83</td>
+      <td>96</td>
+      <td>9</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>83</td>
+      <td>96</td>
+      <td>9</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>zoo_project_ogc_api_processes</td>
+      <td>zoo_project_ogc_api_processes</td>
+      <td>This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AquaINFRA/galaxy</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes</td>
+      <td>0.1.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+  </tbody>
+</table>
+
+</div>
\ No newline at end of file
diff --git a/communities/genome/resources/tools.tsv b/communities/genome/resources/tools.tsv
new file mode 100644
index 00000000..e8073b86
--- /dev/null
+++ b/communities/genome/resources/tools.tsv
@@ -0,0 +1,1470 @@
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+10x_bamtofastq	10x_bamtofastq	Converts 10x Genomics BAM to FASTQ								Up-to-date	https://github.com/10XGenomics/bamtofastq	Convert Formats	10x_bamtofastq	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	1.4.1	10x_bamtofastq	1.4.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	307	307	80	80	8	8	3	3	3	3	1	1	318	318	84	84	False		
+2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1434	6746	120	122	0	0	0	0	305	305	11	11	1739	7051	131	133	False		
+2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1156	13842	40	42	0	0	0	0	121	121	4	4	1277	13963	44	46	False		
+2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	591	6863	38	40	0	0	0	0	119	119	3	3	710	6982	41	43	False		
+2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	762	782	100	101	0	0	0	0	230	230	14	14	992	1012	114	115	False		
+2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	948	6261	98	100	0	0	0	0	153	153	13	13	1101	6414	111	113	False		
+AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	119	14	17	0	0	0	0	0	0	0	0	45	119	14	17	False		
+AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	189	3094	23	25	0	0	0	0	0	0	0	0	189	3094	23	25	False		
+CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25532	50045	45	57	0	0	0	0	0	0	0	0	25532	50045	45	57	False		
+CollectResults	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1119	2115	50	62	0	0	0	0	0	0	0	0	1119	2115	50	62	False		
+CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	108	1	3	0	0	0	0	0	0	0	0	37	108	1	3	False		
+EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	516	516	128	128	0	0	0	0	0	0	0	0	516	516	128	128	False		
+Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	352	352	36	36	0	0	0	0	0	0	0	0	352	352	36	36	False		
+Ensembl-REST	get_feature_info, get_genetree, get_sequences	A suite of Galaxy tools designed to work with Ensembl REST API.								To update	https://rest.ensembl.org	Data Source		earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	0.1.2	requests				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	474	2914	132	163	0	0	0	0	0	0	0	0	474	2914	132	163	False		
+GAFA	gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	47	6	6	0	0	0	0	0	0	0	0	40	47	6	6	False		
+GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	80	150	18	23	0	0	0	0	0	0	0	0	80	150	18	23	False		
+Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	53	53	18	18	0	0	0	0	0	0	0	0	53	53	18	18	False		
+LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25572	50177	45	57	0	0	0	0	0	0	0	0	25572	50177	45	57	False		
+NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	3210	62854	96	124	0	0	0	0	0	0	0	0	3210	62854	96	124	False		
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	1038	1038	146	146	0	0	0	0	849	849	38	38	1887	1887	184	184	False		
+Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	71	9	10	0	0	0	0	0	0	0	0	45	71	9	10	False		
+PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1202	2121	48	62	0	0	0	0	0	0	0	0	1202	2121	48	62	False		
+Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1116	1897	57	71	0	0	0	0	0	0	0	0	1116	1897	57	71	False		
+Structure_GSPAN	structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	991	3060	50	62	0	0	0	0	0	0	0	0	991	3060	50	62	False		
+ThermoRawFileParser	thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2467	2959	88	124	0	0	0	0	1097	1097	18	18	3564	4056	106	142	False		
+TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1003	1022	48	52	0	0	0	0	0	0	0	0	1003	1022	48	52	False		
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	43	43	20	20	0	0	0	0	0	0	0	0	43	43	20	20	False		
+ab1_fastq	ab1_fastq_converter	Tool to convert ab1 files into FASTQ files								To update		Convert Formats	ab1fastq	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq	1.20.0	bioconductor-sangerseqr	1.38.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	49465	49465	281	281	0	0	0	0	0	0	0	0	49465	49465	281	281	False		
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	619817	622353	4097	4130	320454	320454	2915	2915	496156	503743	2012	2227	1436427	1446550	9024	9272	False		
+abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1139	1139	109	109	0	0	0	0	0	0	0	0	1139	1139	109	109	False		
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5543	5543	1042	1042	1301	1305	413	414	2030	2030	299	299	8874	8878	1754	1755	False		
+adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	348	348	62	62	0	0	0	0	0	0	0	0	348	348	62	62	False		
+add_input_name_as_column	addName	Add input name as column on an existing tabular file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	Text Manipulation	add_input_name_as_column	mvdbeek	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	76834	86002	227	246	20174	20953	312	395	11	11	2	2	97019	106966	541	643	False		
+add_line_to_file	add_line_to_file	Adds a text line to the beginning or end of a file.								To update		Text Manipulation	add_line_to_file	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	0.1.0	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	15933	15933	378	378	1736	1736	214	214	380	380	28	28	18049	18049	620	620	False		
+add_value	addValue	Add a value as a new column.								To update		Text Manipulation	add_value	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value	https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value	1.0.1	perl				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	37860	374587	1293	1610	17588	293713	1243	6197	3873	4397	202	229	59321	672697	2738	8036	False		
+aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	200	200	77	77	83	83	39	39	1747	1747	44	44	2030	2030	160	160	False		
+agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	244	244	0	0	0	0	119	119	10	10	1555	1555	254	254	False		
+aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	262	36	36	0	0	0	0	0	0	0	0	262	262	36	36	False		
+align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	511	541	32	35	0	0	0	0	0	0	0	0	511	541	32	35	False		
+allegro	allegro	Linkage and haplotype analysis from deCODE	allegro	allegro		Allegro	It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	To update	http://www.decode.com/software/	Variant Analysis	allegro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro	@VER@.0	allegro	3	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ambertools	ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap	Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.								To update	http://ambermd.org/AmberTools.php	Molecular Dynamics, Computational chemistry	ambertools	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools	21.10	ambertools				7	2	7	0	7	2	7	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	5	0	41793	41881	510	511	1126	1126	159	159	1552	1552	85	85	44471	44559	754	755	False		
+amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	81	81	17	17	0	0	0	0	0	0	0	0	81	81	17	17	False		
+ampvis2	ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.9			Analysis, Visualisation	Biodiversity	0	0	19	0	0	0	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	1213	1213	155	155	0	0	0	0	0	0	0	0	1213	1213	155	155	False		
+amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5734	5734	334	334	1035	1035	106	106	0	0	0	0	6769	6769	440	440	False		
+ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	7	7	0	0	0	0	0	0	0	0	26	26	7	7	False		
+anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	41	2	2	0	0	0	0	0	0	0	0	36	41	2	2	False		
+anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	43047	43139	1826	1827	17240	17240	878	878	9309	9309	298	298	69596	69688	3002	3003	False		
+annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	29266	30655	2849	2973	59299	66180	5917	6355	5644	5644	1049	1049	94209	102479	9815	10377	False		
+antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	292	306	5	7	0	0	0	0	0	0	0	0	292	306	5	7	False		
+antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15949	16490	726	811	5113	5113	649	649	6043	6043	169	169	27105	27646	1544	1629	False		
+apoc	apoc	Large-scale structural comparison of protein pockets								To update	http://cssb.biology.gatech.edu/APoc	Computational chemistry	apoc	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc	1.0+galaxy1	apoc	1b16			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	4	4	4	1	1	1	1	0	0	0	0	5	5	5	5	False		
+apollo	create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism	Access an Apollo instance from Galaxy								To update	https://github.com/galaxy-genome-annotation/python-apollo	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo		apollo	4.2.13			0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	0	3600	3760	883	911	6	6	4	4	0	0	0	0	3606	3766	887	915	False		
+appendfdr	append_fdr									To update			appendfdr	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr	0.2.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	75	75	9	9	0	0	0	0	0	0	0	0	75	75	9	9	False		
+aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	59	74	10	12	0	0	0	0	0	0	0	0	59	74	10	12	False		
+argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3670	3670	71	71	3	3	2	2	234	234	10	10	3907	3907	83	83	False		
+art	art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/	Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	Conversion	Bioinformatics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	140	140	9	9	0	0	0	0	0	0	0	0	140	140	9	9	False		
+artbio_bam_cleaning	artbio_bam_cleaning	filter bam files before somatic-varscan or lumpy-smoove analysis								To update	http://artbio.fr	SAM, Variant Analysis	artbio_bam_cleaning	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	1.10+galaxy0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	9021	9021	238	238	0	0	0	0	0	0	0	0	9021	9021	238	238	False		
+askomics	askomics_integrate	Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/								To update	https://github.com/askomics/	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics		askocli	0.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+askor	askor_de	AskoR links EdgeR and AskOmics								To update	https://github.com/askomics/askoR	Transcriptomics	askor_de	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	0.2	bioconductor-limma	3.58.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+astral	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees								Up-to-date	https://github.com/smirarab/ASTRAL	Phylogenetics	astral	iuc	https://github.com/usegalaxy-be/galaxytools/tree/main/astral	https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral	5.7.8	astral-tree	5.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	151	151	5	5	151	151	5	5	False		
+astropytools	astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo	AstropyTools library contains Galaxy tools for elementary Astrophysical operations								To update	https://github.com/astropy/astropy	Astronomy	astropytools	volodymyrss	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	0.1.0+galaxy0	astropy				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	13	13	5	5	0	0	0	0	0	0	0	0	13	13	5	5	False		
+atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	232	279	62	72	0	0	0	0	0	0	0	0	232	279	62	72	False		
+augustus	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	12890	13988	1826	1988	14901	14901	2633	2633	6187	6187	511	511	33978	35076	4970	5132	False		
+augustus	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10109	11052	1378	1509	12573	12573	2206	2206	5274	5274	369	369	27956	28899	3953	4084	False		
+b2btools	b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.7	Protein disorder prediction, Protein secondary structure prediction		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	369	369	19	19	0	0	0	0	0	0	0	0	369	369	19	19	False		
+background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1	False		
+bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11117	11117	534	534	19	19	1	1	9601	9601	167	167	20737	20737	702	702	False		
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bam_to_scidx	bam_to_scidx	Contains a tool that converts a BAM file to an ScIdx file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx	Convert Formats	bam_to_scidx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	83	131	15	20	329	785	50	210	0	0	0	0	412	916	65	230	False		
+bamclipper	bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bamhash	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	158	181	40	44	0	0	0	0	0	0	0	0	158	181	40	44	False		
+bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	14693	15620	653	721	61872	101400	1656	5678	39	39	3	3	76604	117059	2312	6402	False		
+bamtools_filter	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115954	124795	2994	3180	95433	142254	6712	10660	5793	5793	497	497	217180	272842	10203	14337	False		
+bamtools_split	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	9073	9073	401	401	2746	2746	224	224	103	103	10	10	11922	11922	635	635	False		
+bamutil	bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	45	45	20	20	69	69	21	21	258	258	1	1	372	372	42	42	False		
+bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	55392	56095	4951	5035	47603	47603	4916	4916	18089	18089	3121	3121	121084	121787	12988	13072	False		
+barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	111	111	8	8	29	29	10	10	21	21	4	4	161	161	22	22	False		
+baric_archive	baric_archive_rennes, baric_archive_toulouse	A data source tool to fetch data from a BARIC Archive server.								To update	https://www.cesgo.org/catibaric/	Data Source		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	1.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+barrnap	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update	https://github.com/tseemann/barrnap	Sequence Analysis	barrnap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	Gene prediction	Genomics, Model organisms, Model organisms	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6041	6041	316	316	0	0	0	0	6723	7273	240	322	12764	13314	556	638	False		
+basecoverage	gops_basecoverage_1	Base Coverage of all intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	basecoverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	226	308	27	35	2615	45557	302	2284	482	522	32	36	3323	46387	361	2355	False		
+baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+basil	basil	Breakpoint detection, including large insertions								Up-to-date	https://github.com/seqan/anise_basil	Variant Analysis	basil	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil	1.2.0	anise_basil	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	306	311	82	83	467	467	99	99	0	0	0	0	773	778	181	182	False		
+batched_lastz	batched_lastz	Galaxy wrapper for the batching Lastz runs								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	batched_lastz	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	1.04.22	lastz	1.04.22			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	123	123	5	5	0	0	0	0	123	123	5	5	False		
+bax2bam	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	208	208	26	26	210	210	30	30	0	0	0	0	418	418	56	56	False		
+bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	90	90	28	28	0	0	0	0	0	0	0	0	90	90	28	28	False		
+bbgbigwig	bbgtobigwig	Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://www.encodeproject.org/software/bedgraphtobigwig/	Convert Formats	bbgbigwig	iuc	https://www.encodeproject.org/software/bedgraphtobigwig/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig	0.1	ucsc-bedgraphtobigwig	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	42	42	7	7	175	175	26	26	0	0	0	0	217	217	33	33	False		
+bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.09	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	4	0	0	11989	11989	768	768	4458	4458	652	652	2507	2507	80	80	18954	18954	1500	1500	False		
+bcftools	bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@	BCFtools toolkit wrappers	bcftools	bcftools		BCFtools	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.	Data handling, Variant calling	Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment	To update	https://samtools.github.io/bcftools/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools	1.15.1	bcftools	1.21	Data handling, Variant calling	DNA polymorphism, GWAS study, Genotyping experiment	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	7	0	2352	3092	234	265	0	0	0	0	0	0	0	0	2352	3092	234	265	False		
+beacon2	beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff	beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://github.com/EGA-archive/beacon2-ri-tools/tree/main	Variant Analysis	beacon2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2	2.0.0	beacon2-ri-tools	2.0.0	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	33	33	9	9	0	0	0	0	0	0	0	0	33	33	9	9	False		
+beacon2-import	beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence	Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants.	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://pypi.org/project/beacon2-import/	Variant Analysis	Beacon2_Import	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import	2.2.4	beacon2-import	2.2.4	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22	22	7	7	0	0	0	0	0	0	0	0	22	22	7	7	False		
+beagle	beagle	Beagle is a program for phasing and imputing missing genotypes.								To update	https://faculty.washington.edu/browning/beagle/beagle.html	Variant Analysis	beagle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle	5.2_21Apr21.304	beagle	5.4_22Jul22.46e			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	88	88	28	28	0	0	0	0	0	0	0	0	88	88	28	28	False		
+bed_to_protein_map	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	410	419	134	137	363	363	99	99	158	158	13	13	931	940	246	249	False		
+bedops	bedops-sort-bed	BEDOPS: high-performance genomic feature operations								Up-to-date	https://bedops.readthedocs.io/en/latest/	Genomic Interval Operations	bedops_sortbed	iuc	https://bedops.readthedocs.io/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops	2.4.41	bedops	2.4.41			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	93	93	36	36	181	181	62	62	0	0	0	0	274	274	98	98	False		
+bedtools	bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed	bedtools is a powerful toolset for genome arithmetic	bedtools	bedtools		BEDTools	BEDTools is an extensive suite of utilities for comparing genomic features in BED format.	Mapping	Genomics	Up-to-date	https://github.com/arq5x/bedtools2	Genomic Interval Operations, Text Manipulation	bedtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools	2.31.1	bedtools	2.31.1	Mapping	Genomics	37	37	37	0	37	37	37	0	0	0	0	0	0	0	0	0	0	37	6	37	0	0	37	0	0	0	37	0	0	0	0	0	0	37	37	37	0	916111	962278	13235	14525	407944	647621	25849	41751	84008	89233	2486	2832	1408063	1699132	41570	59108	False		
+bellerophon	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1611	1611	262	262	763	763	67	67	543	543	30	30	2917	2917	359	359	False		
+berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	617	617	63	63	617	617	63	63	False		
+best_regression_subsets	BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3	4	3	4	14	253	7	72	0	0	0	0	17	257	10	76	False		
+bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1635	1671	123	124	0	0	0	0	334	334	21	21	1969	2005	144	145	False		
+bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	2	0	0	0	0	0	0	0	0	3	3	2	2	False		
+bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	544	544	20	20	0	0	0	0	0	0	0	0	544	544	20	20	False		
+bigwig_outlier_bed	bigwig_outlier_bed	pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files	bigtools	bigtools		bigtools	Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.			To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	Sequence Analysis	bigwig_outlier_bed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed	0.2.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	218	218	5	5	0	0	0	0	0	0	0	0	218	218	5	5	False		
+bigwig_to_bedgraph	bigwig_to_bedgraph	Convert from bigWig to bedGraph format								To update		Convert Formats	bigwig_to_bedgraph	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	0.1.0	ucsc_tools				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5769	6802	567	650	0	0	0	0	0	3	0	1	5769	6805	567	651	False		
+bigwig_to_bedgraph	bigwig_to_bedgraph	Converts a bigWig file to bedGraph format								To update	http://artbio.fr	Convert Formats	bigwig_to_bedgraph	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	377+galaxy1	ucsc-bigwigtobedgraph	469			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5769	6802	567	650	0	0	0	0	0	3	0	1	5769	6805	567	651	False		
+bigwig_to_wig	bigwig_to_wig	Converts a bigWig file to Wiggle (WIG) format								To update	https://artbio.fr	Convert Formats	bigwig_to_wig	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	3+galaxy0	ucsc-bigwiginfo	469			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	401	1385	87	88	0	0	0	0	188	188	9	9	589	1573	96	97	False		
+binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	29	1	1	0	0	0	0	0	0	0	0	24	29	1	1	False		
+binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	126	126	42	42	0	0	0	0	0	0	0	0	126	126	42	42	False		
+bio3d	bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize	Bio3d is a program that can be used to analyse molecular dynamics trajectories.								To update	http://thegrantlab.org/bio3d/index.php	Computational chemistry	bio3d	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	2.4_1	r-bio3d	2.3_3			5	4	5	0	5	4	5	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	5	5	0	10600	10729	1150	1159	1042	1042	255	255	2756	2756	215	215	14398	14527	1620	1629	False		
+bioext	bioext_bam2msa, bioext_bealign	A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!								Up-to-date	https://pypi.python.org/pypi/biopython-extensions/	Next Gen Mappers		iuc	https://github.com/davebx/bioext-gx/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext	0.21.9	python-bioext	0.21.9			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	17413	17413	822	822	15349	15349	2020	2020	2	2	1	1	32764	32764	2843	2843	False		
+bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	61	61	4	4	0	0	0	0	0	0	0	0	61	61	4	4	False		
+biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+biohansel_bionumeric_converter	bionumeric_convert	Convert BioHansel output data to a Bionumerics friendly form								To update	https://github.com/phac-nml/galaxy_tools	Text Manipulation	biohansel_bionumeric_converter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter	0.2.0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	1	0	0	0	0	0	0	0	0	2	2	1	1	False		
+bioinformatics_cafe	fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1137	1137	97	97	1029	1029	71	71	0	0	0	0	2166	2166	168	168	False		
+biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12725	12725	297	297	2851	5049	450	638	2171	2371	214	239	17747	20145	961	1174	False		
+biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	25	11	11	0	0	0	0	0	0	0	0	25	25	11	11	False		
+biomoldyn	biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering	Tools for MD analysis								To update	https://github.com/moldyn/	Molecular Dynamics, Computational chemistry	biomoldyn	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn	1.5.2	scipy				4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	3	0	493	493	119	119	441	441	148	148	0	0	0	0	934	934	267	267	False		
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	151	151	143	143	43	43	596	596	22	22	1286	1286	216	216	False		
+bioperl	bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	Data handling, Service invocation	Genomics, Software engineering	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7738	7931	478	508	8301	8301	849	849	1369	1369	154	154	17408	17601	1481	1511	False		
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6243	6243	375	375	0	0	0	0	6243	6243	375	375	False		
+biotransformer	biotransformer	BioTransformer is a tool for prediction of small molecule metabolism in mammals.	biotransformer	biotransformer		BioTransformer	BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	Up-to-date	https://bitbucket.org/djoumbou/biotransformerjar/src/master/	Metabolomics	biotransformer	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	3.0.20230403	biotransformer	3.0.20230403	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	48	48	1	1	48	48	1	1	False		
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	3	1	1	0	0	0	0	0	0	0	0	3	3	1	1	False		
+bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	4	4	4	0	13715	14997	992	1099	0	0	0	0	197	197	22	22	13912	15194	1014	1121	False		
+blast	magicblast	Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome								Up-to-date	https://ncbi.github.io/magicblast/	Next Gen Mappers	magicblast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast	1.7.0	magicblast	1.7.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	738	738	151	151	0	0	0	0	2	2	1	1	740	740	152	152	False		
+blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1063	1237	257	300	0	0	0	0	0	0	0	0	1063	1237	257	300	False		
+blast_parser	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	417	438	99	104	0	0	0	0	0	0	0	0	417	438	99	104	False		
+blast_plus_remote_blastp	blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.16.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24916	27120	283	347	0	0	0	0	0	0	0	0	24916	27120	283	347	False		
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blastxml_to_gapped_gff3	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	585	585	102	102	172	172	63	63	135	135	16	16	892	892	181	181	False		
+blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	264392	265217	483	552	0	0	0	0	0	0	0	0	264392	265217	483	552	False		
+blat_coverage_report	generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blat_mapping	blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1527	1527	79	79	6	6	1	1	317	317	26	26	1850	1850	106	106	False		
+blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	768	3043	97	119	14	14	11	11	276	276	9	9	1058	3333	117	139	False		
+blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	811	1501	54	79	64	64	29	29	561	561	15	15	1436	2126	98	123	False		
+bowtie2	bowtie2	Bowtie2: Fast and sensitive read alignment	bowtie2	bowtie2		Bowtie 2	Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.	Read mapping	Mapping, Genomics, Mapping	To update	http://bowtie-bio.sourceforge.net/bowtie2	Next Gen Mappers	bowtie2	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2	2.5.3	bowtie2	2.5.4	Read mapping	Mapping, Genomics, Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	1	1	1	0	397893	427447	12133	13176	577209	903193	33086	52020	60105	67495	3779	4271	1035207	1398135	48998	69467	False		
+bowtie_wrappers	bowtie_wrapper	Galaxy wrappers for the Bowtie short read mapping tools.								To update	http://bowtie-bio.sourceforge.net/	Next Gen Mappers	bowtie_wrappers	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers	https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers	1.2.0	bowtie	1.3.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	24164	25149	1320	1480	17537	203397	1330	17491	15654	15992	291	351	57355	244538	2941	19322	False		
+bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	51378	51378	775	775	3298	3298	160	160	1660	1660	63	63	56336	56336	998	998	False		
+braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	165	165	48	48	0	0	0	0	0	0	0	0	165	165	48	48	False		
+braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1938	1938	294	294	0	0	0	0	412	412	71	71	2350	2350	365	365	False		
+breseq	breseq	Predicts mutations in microbial genomes	breseq	breseq		breseq	Runs Breseq software on a set of fastq files.	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	To update	https://github.com/barricklab/breseq	Variant Analysis	breseq	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq	0.35.5	breseq	0.39.0	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	2976	2976	98	98	0	0	0	0	884	884	70	70	3860	3860	168	168	False		
+brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template	brew3r.r	brew3r.r		BREW3R.r	This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.	Genome annotation	Transcriptomics, Genomics	To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2			Genome annotation	Transcriptomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6	6	2	2	0	0	0	0	7	7	3	3	False		
+bumbershoot	idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	1186	1356	21	32	0	0	0	0	0	0	0	0	1186	1356	21	32	False		
+bundle_collections	bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.58			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	1	1518	1526	73	76	1520	1528	74	77	False		
+busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	102717	103051	3877	3926	34251	34251	3506	3506	33192	34369	2439	2525	170160	171671	9822	9957	False		
+bwa	bwa_mem, bwa	Wrapper for bwa mem, aln, sampe, and samse	bwa	bwa		BWA	Fast, accurate, memory-efficient aligner for short and long sequencing reads	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	Up-to-date	http://bio-bwa.sourceforge.net/	Next Gen Mappers	bwa	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa	0.7.18	bwa	0.7.18	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	2	0	0	0	2	0	0	0	0	0	0	2	2	2	2	976935	1017671	13526	14401	474702	681286	32627	47624	79802	87191	4219	4954	1531439	1786148	50372	66979	False		
+bwa_mem2	bwa_mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.	bwa-mem2	bwa-mem2		Bwa-mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,  dataset and the running machine.	Sequence alignment	Mapping	Up-to-date	https://github.com/bwa-mem2/bwa-mem2	Next Gen Mappers	bwa_mem2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2	2.2.1	bwa-mem2	2.2.1	Sequence alignment	Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	56619	56619	2324	2324	36631	36631	2808	2808	18121	18121	713	713	111371	111371	5845	5845	False		
+bwameth	bwameth	Fast and accurate alignment of BS-seq reads								Up-to-date	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.7	bwameth	0.2.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7970	11724	643	826	5524	5524	611	611	1242	1242	114	114	14736	18490	1368	1551	False		
+c3s	c3s	Copernicus Climate Change Service (C3S)								To update	https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset	Climate Analysis	c3s	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	0.3.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	234	234	11	11	4	4	4	4	92	92	3	3	330	330	18	18	False		
+cactus	cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			Multiple sequence alignment, Genome alignment	Genomics, Sequence assembly, Mapping, Phylogenetics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	299	299	61	61	0	0	0	0	1339	1339	95	95	1638	1638	156	156	False		
+cads	cads	Copernicus Atmosphere Data Store (ADS)								To update	https://ads.atmosphere.copernicus.eu/#!/home	Climate Analysis	cads	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	52	52	1	1	0	0	0	0	0	0	0	0	52	52	1	1	False		
+calculate_contrast_threshold	calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+calculate_numeric_param	calculate_numeric_param	Calculate a numeric parameter value using integer and float values.								To update		Text Manipulation	calculate_numeric_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param	0.1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1393	1393	10	10	0	0	0	0	0	0	0	0	1393	1393	10	10	False		
+calisp	calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	False		
+camera	abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos									To update		Metabolomics	camera	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera	1.48.0	r-snow	0.4_1			1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	2	0	677	787	114	120	60	60	30	30	734	746	26	26	1471	1593	170	176	False		
+cami_amber	biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert	Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments								Up-to-date	https://github.com/CAMI-challenge/AMBER	Metagenomics	cami_amber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber	2.0.7	cami-amber	2.0.7			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	195	195	4	4	0	0	0	0	0	0	0	0	195	195	4	4	False		
+canonical_correlation_analysis	cca1	Canonical Correlation Analysis								To update		Statistics	canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis	1.0.0	R				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	66	75	16	18	141	505	31	147	0	0	0	0	207	580	47	165	False		
+canu	canu	Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).	canu	canu		CANU	De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.	De-novo assembly	Genomics	Up-to-date	https://github.com/marbl/canu		canu	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/canu	https://github.com/bgruening/galaxytools/tree/master/tools/canu	2.2	canu	2.2	De-novo assembly	Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13360	14618	1383	1444	0	0	0	0	3542	3542	385	385	16902	18160	1768	1829	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	9869	9869	158	158	0	0	0	0	6886	6886	146	146	16755	16755	304	304	False		
+cardinal	cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								Up-to-date	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	3.4.3	bioconductor-cardinal	3.4.3			0	9	11	0	0	9	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	0	9	11	9	0	41875	50702	663	713	12	12	1	1	7512	7512	231	231	49399	58226	895	945	False		
+cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3835	3835	597	597	1359	1359	467	467	646	646	98	98	5840	5840	1162	1162	False		
+categorize_elements_satisfying_criteria	categorize_elements_satisfying_criteria	Categorize Elements satisfying criteria.								To update		Statistics	categorize_elements_satisfying_criteria	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria	https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	41	4	5	0	0	0	0	168	186	12	14	205	227	16	19	False		
+ccat	peakcalling_ccat	Control-based ChIP-seq Analysis Tool								To update		ChIP-seq	ccat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat	0.0.2	ccat	3.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	175	28	39	0	0	0	0	0	0	0	0	88	175	28	39	False		
+cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5946	7379	407	628	0	0	0	0	5946	7379	407	628	False		
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10414	10414	510	510	2	2	1	1	2	2	1	1	10418	10418	512	512	False		
+cdo	cdo_info, cdo_operations	CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.								To update	https://code.mpimet.mpg.de/projects/cdo/	Climate Analysis		climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	2.0.0					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	218	218	17	17	0	0	0	0	0	0	0	0	218	218	17	17	False		
+cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	4	4	0	0	0	0	0	0	0	0	8	8	4	4	False		
+cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	4	4	0	0	0	0	0	0	0	0	14	14	4	4	False		
+cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	0	0	23	23	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	0	4773	4773	749	749	0	0	0	0	5688	5688	94	94	10461	10461	843	843	False		
+cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55	55	11	11	0	0	0	0	0	0	0	0	55	55	11	11	False		
+cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	225	225	32	32	271	271	61	61	0	0	0	0	496	496	93	93	False		
+cesm	cesm	Community Earth System Model (CESM)								Up-to-date	https://www.cesm.ucar.edu/	Climate Analysis	cesm	climate	https://github.com/ESCOMP/CESM	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm	2.1.3	cesm	2.1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	14	2	2	0	0	0	0	0	0	0	0	14	14	2	2	False		
+cfm	cfmid	Competitive Fragmentation Modeling (CFM)								Up-to-date	https://sourceforge.net/p/cfm-id/	Metabolomics	cfmid	computational-metabolomics	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	33	cfm	33			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+chado	analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree	Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado								To update	https://github.com/galaxy-genome-annotation/python-chado	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado		python-chado	2.3.9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	183	183	20	20	0	0	0	0	0	0	0	0	183	183	20	20	False		
+change_case	ChangeCase	Convert column case.								To update		Text Manipulation	change_case	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case	https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case	1.0.1	perl				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	0	1	1	1	1	10606	12531	2204	2547	9044	17167	1748	2394	923	938	240	245	20573	30636	4192	5186	False		
+charts	charts	Enables advanced visualization options in Galaxy Charts								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3383	4001	1576	1822	7870	13727	3823	6880	249	350	108	145	11502	18078	5507	8847	False		
+chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	62	12	12	0	0	0	0	0	0	0	0	62	62	12	12	False		
+checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	7500	7500	930	930	0	0	0	0	0	0	0	0	7500	7500	930	930	False		
+checkv	checkv_end_to_end	Assess quality of single-contig viral genomes	checkv	checkv		CheckV	CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	Up-to-date	https://bitbucket.org/berkeleylab/checkv/	Metagenomics	checkv	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv	1.0.3	checkv	1.0.3	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	207	207	1	1	0	0	0	0	0	0	0	0	207	207	1	1	False		
+cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+chewbbaca	chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema	BSR-Based Allele Calling Algorithm								To update	https://github.com/B-UMMI/chewBBACA/tree/master	Variant Analysis	chewbbaca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca		chewbbaca	3.3.10			0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	727	727	76	76	0	0	0	0	0	0	0	0	727	727	76	76	False		
+chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	16468	18344	956	991	33692	34453	2559	2625	2948	2948	104	104	53108	55745	3619	3720	False		
+chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	16542	16542	287	287	1061	1061	102	102	27	27	5	5	17630	17630	394	394	False		
+chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	6	6	0	0	0	0	14	14	6	6	False		
+chromeister	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2696	2696	398	398	0	0	0	0	1235	1235	186	186	3931	3931	584	584	False		
+chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+circexplorer	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	211	263	32	40	0	0	0	0	209	209	6	6	420	472	38	46	False		
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	524	524	32	32	0	0	0	0	0	0	0	0	524	524	32	32	False		
+circos	circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile	Build Circos Plots in Galaxy	galactic_circos	galactic_circos		Galactic Circos	Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.	Sequence visualisation		To update	http://circos.ca/	Graphics	circos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos	0.69.8	circos	0.69.9	Sequence visualisation		11	11	11	0	11	11	11	0	0	0	0	0	0	0	0	0	0	0	11	11	0	0	0	0	0	0	11	0	0	0	0	0	0	11	11	11	0	26265	26265	2483	2483	31332	31332	3535	3535	26359	26359	999	999	83956	83956	7017	7017	False		
+cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	21	4	4	9	9	5	5	18	18	1	1	48	48	10	10	False		
+clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3388	3388	187	187	1	1	1	1	1	1	1	1	3390	3390	189	189	False		
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+climate-stripes	climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	239	239	35	35	16	16	2	2	182	182	3	3	437	437	40	40	False		
+clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	548	548	18	18	0	0	0	0	548	548	18	18	False		
+clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	79867	80817	1675	1785	49493	87884	3703	7380	8797	9713	670	728	138157	178414	6048	9893	False		
+cluster	gops_cluster_1	Cluster the intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	cluster	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	513	813	18	35	2406	30579	156	1547	1353	1393	17	20	4272	32785	191	1602	False		
+clustering_from_distmat	clustering_from_distmat	Distance matrix-based hierarchical clustering using SciPy								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	Statistics	clustering_from_distmat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat	1.1.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	5	5	0	0	0	0	0	0	0	0	12	12	5	5	False		
+cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2609	2609	3	3	0	0	0	0	0	0	0	0	2609	2609	3	3	False		
+cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	90	112	11	14	0	0	0	0	0	0	0	0	90	112	11	14	False		
+cnv-phenopacket	cnv_phenopacket	cnv-phenopacket Converts TSV metadata file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv_phenopacket	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket	1.0.2	cnv-phenopacket				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	False		
+cnv-vcf2json	cnv_vcf2json	cnv-vcf2json Converts structural variants VCF file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv-vcf2json	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json	1.1.0	cnv-vcf2json				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5	False		
+cnvkit	cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target	detecting copy number variants and alterations genome-wide from high-throughput sequencing	cnvkit	cnvkit		CNVkit	CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.	Variant calling	DNA structural variation	Up-to-date	https://github.com/etal/cnvkit	Variant Analysis	cnvkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit	0.9.11	cnvkit	0.9.11	Variant calling		0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	618	618	177	177	0	0	0	0	0	0	0	0	618	618	177	177	False		
+codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	61197	61220	64	65	0	0	0	0	0	0	0	0	61197	61220	64	65	False		
+cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	316	355	25	29	0	0	0	0	0	0	0	0	316	355	25	29	False		
+cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2758	2758	22	22	20	20	10	10	0	0	0	0	2778	2778	32	32	False		
+colabfold	colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6771	6771	50	50	0	0	0	0	6771	6771	50	50	False		
+colibread	commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								Up-to-date	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14	commet	24.7.14			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	273	273	40	40	0	0	0	0	0	0	0	0	273	273	40	40	False		
+collapse_collection	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	39518	40471	3555	3629	22007	24841	3536	4045	3969	4101	814	835	65494	69413	7905	8509	False		
+collection_column_join	collection_column_join	Column Join on Collections								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	Text Manipulation	collection_column_join	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join	0.0.3	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	23979	25337	3827	4011	21671	25163	4645	5045	2939	3036	688	701	48589	53536	9160	9757	False		
+collection_element_identifiers	collection_element_identifiers	Extract element identifiers of a collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	Text Manipulation	collection_element_identifiers	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers	0.0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6905	7102	1620	1630	7761	7761	1897	1897	1157	1157	243	243	15823	16020	3760	3770	False		
+color_deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	16	2	3	0	0	0	0	0	0	0	0	15	16	2	3	False		
+colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	40	40	2	2	0	0	0	0	0	0	0	0	40	40	2	2	False		
+column_arrange_by_header	bg_column_arrange_by_header	Column arrange by header name								To update		Text Manipulation	column_arrange_by_header	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5356	5636	446	484	2026	2026	375	375	1400	1531	117	138	8782	9193	938	997	False		
+column_maker	Add_a_column1	Compute an expression on every row								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	Text Manipulation	column_maker	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker	2.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2940752	3907183	5422	6121	263254	737503	6095	13728	96478	97667	884	974	3300484	4742353	12401	20823	False		
+column_order_header_sort	column_order_header_sort	Sort Column Order by heading								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	Text Manipulation	column_order_header_sort	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort	0.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3735	3891	268	297	1923	1923	381	381	0	0	0	0	5658	5814	649	678	False		
+column_remove_by_header	column_remove_by_header	Remove columns by header								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	Text Manipulation	column_remove_by_header	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header	1.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8331	8917	613	662	5206	5206	716	716	1976	1976	27	27	15513	16099	1356	1405	False		
+combineJSON	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	530	530	65	65	8	8	6	6	0	0	0	0	538	538	71	71	False		
+combine_tabular_collection	combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	221	5	28	0	0	0	0	0	0	0	0	39	221	5	28	False		
+compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	332	28	32	0	0	0	0	0	0	0	0	306	332	28	32	False		
+compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	266	266	39	39	28	28	15	15	0	0	0	0	294	294	54	54	False		
+complement	gops_complement_1	Complement intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	complement	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	187	233	15	20	495	4810	165	836	405	451	7	7	1087	5494	187	863	False		
+compose_text_param	compose_text_param	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	compose_text_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param	0.1.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	0	0	0	45827	45831	689	691	7721	7721	303	303	1481	1481	121	121	55029	55033	1113	1115	False		
+compress_file	compress_file	Compress files.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	Text Manipulation	compress_file	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file	0.1.0	gzip				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6343	6343	290	290	3674	3674	286	286	11832	11832	59	59	21849	21849	635	635	False		
+compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	85	96	9	10	0	0	0	0	316	334	8	8	401	430	17	18	False		
+compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	55	65	2	2	0	0	0	0	317	335	5	5	372	400	7	7	False		
+compute_q_values	compute_q_values	Compute q-values based on multiple simultaneous tests p-values								To update		Statistics	compute_q_values	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values	1.0.1	R				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	35	0	3	0	0	0	0	0	0	0	0	0	35	0	3	False		
+concat	gops_concat_1	Concatenate two bed files								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	concat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat	1.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	575128	575441	694	783	43420	85345	629	3508	19330	19418	104	117	637878	680204	1427	4408	False		
+concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	76	82	11	12	0	0	0	0	0	0	0	0	76	82	11	12	False		
+concat_multi_datasets	cat_multi_datasets	Concatenate multiple datasets tail-to-head, including collection datasets.								To update	http://artbio.fr	Text Manipulation	concatenate_multiple_datasets	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	1.4.3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	4822	4824	613	614	1317	1317	204	204	3088	3795	252	289	9227	9936	1069	1107	False		
+concat_paired	concat_fastqs	Concatenate paired datasets								To update	https://github.com/phac-nml/concat	Text Manipulation	concat_paired	nml	https://github.com/phac-nml/concat	https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	2105	2105	155	155	0	0	0	0	0	0	0	0	2105	2105	155	155	False		
+condense_characters	Condense characters1	Condense consecutive characters.								To update		Text Manipulation	condense_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters	1.0.0					1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47	2173	28	368	195	205	8	8	242	2378	36	376	False		
+consensus_from_alignments	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1184	1184	154	154	0	0	0	0	0	0	0	0	1184	1184	154	154	False		
+consolidate_vcfs	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+convert_characters	Convert characters1	Convert delimiters to tab.								To update		Text Manipulation	convert_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters	1.0.1	python				1	1	1	0	1	1	1	0	1	1	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	23589	28986	1061	1200	23507	160693	2302	8699	5413	6446	251	329	52509	196125	3614	10228	False		
+convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cooler	cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify	cooler different tools to process Hi-C from mirnylab								To update	https://github.com/open2c/cooler	Epigenetics	cooler	lldelisle	https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler	0.9.3	htslib	1.21			4	0	5	0	4	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	170	170	26	26	195	195	39	39	0	0	0	0	365	365	65	65	False		
+coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16077	16547	11	11	0	0	0	0	0	0	0	0	16077	16547	11	11	False		
+coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+correlation	cor2	Correlation for numeric columns								To update		Statistics	correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation	1.0.0	rpy				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	398	876	106	134	412	5568	105	755	192	239	21	27	1002	6683	232	916	False		
+correlation_analysis	correlation_analysis	[Metabolomics][W4M] Metabolites Correlation Analysis								To update	http://workflow4metabolomics.org	Metabolomics	correlation_analysis	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis	1.0.1+galaxy0	r-batch	1.1_4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	280	307	110	124	712	1277	332	628	476	541	55	79	1468	2125	497	831	False		
+count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	314	326	73	75	0	0	0	0	129	129	6	6	443	455	79	81	False		
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage	gops_coverage_1	Coverage of a set of intervals on second set of intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	coverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1560	1725	43	58	4328	44209	193	2113	283	316	16	18	6171	46250	252	2189	False		
+coverage_report	CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1081	1081	151	151	0	0	0	0	0	0	0	0	1081	1081	151	151	False		
+cpat	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.								Up-to-date	https://github.com/liguowang/cpat	Transcriptomics	cpat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	3.0.5	cpat	3.0.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	204	204	47	47	165	165	40	40	125	125	7	7	494	494	94	94	False		
+cpm_tpm_rpk	cpm_tpm_rpk	Generate CPM,TPM or RPK from raw counts								To update	http://artbio.fr	Transcriptomics	cpm_tpm_rpk	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	0.6.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+crispr_studio	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	Visualisation	Sequence analysis, Genomics, Data visualisation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1052	1053	75	76	0	0	0	0	0	0	0	0	1052	1053	75	76	False		
+crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	276	390	61	76	131	131	42	42	0	0	0	0	407	521	103	118	False		
+crossmap	crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig	CrossMap converts genome coordinates or annotation files between genome assemblies								Up-to-date	http://crossmap.sourceforge.net/	Convert Formats, Genomic Interval Operations	crossmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap	0.7.0	crossmap	0.7.0			5	0	6	0	5	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	5	6	5	0	2182	2182	331	331	5251	5251	903	903	0	0	0	0	7433	7433	1234	1234	False		
+crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4066	4139	166	180	0	0	0	0	0	0	0	0	4066	4139	166	180	False		
+cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9942	9942	26	26	0	0	0	0	0	0	0	0	9942	9942	26	26	False		
+csvtk	csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq	Rapid data investigation and manipulation of csv/tsv files								To update	https://bioinf.shenwei.me/csvtk/	Text Manipulation	csvtk	nml	https://github.com/shenwei356/csvtk	https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk	0.20.0	csvtk	0.30.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	20	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cta	cta_astro_tool	Basic simulation of CTA telescope observations using gammapy package								To update		Astronomy	cta_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta	0.0.1+galaxy0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	196	211	41	48	1	447	1	161	0	0	0	0	197	658	42	209	False		
+cuffcompare	cuffcompare	Galaxy wrappers for the Cuffcompare tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffcompare	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1	1	0	768	1199	171	300	2205	24981	754	5750	251	493	46	98	3224	26673	971	6148	False		
+cuffdiff	cuffdiff	Galaxy wrappers for the Cuffdiff tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffdiff	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff	2.2.1	cufflinks	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	4176	6065	564	725	24284	117007	4952	20249	971	4231	193	616	29431	127303	5709	21590	False		
+cufflinks	cufflinks	Galaxy wrappers for the Cufflinks tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cufflinks	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	1	1	1	0	26122	33320	870	1213	70653	349091	6984	27076	3963	10315	440	836	100738	392726	8294	29125	False		
+cuffmerge	cuffmerge	Galaxy wrappers for the Cuffmerge tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffmerge	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1	1	0	2406	3448	351	637	20978	67769	3641	13764	1209	3057	227	573	24593	74274	4219	14974	False		
+cuffnorm	cuffnorm	The Cuffnorm tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffnorm	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	374	701	81	114	1032	13499	273	1166	262	322	53	70	1668	14522	407	1350	False		
+cuffquant	cuffquant	The Cuffquant tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffquant	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	408	732	54	71	1964	15883	267	1310	308	422	26	46	2680	17037	347	1427	False		
+cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1251	1803	98	166	3461	15159	486	2044	2425	3338	57	159	7137	20300	641	2369	False		
+cummerbund_to_tabular	cummerbund_to_cuffdiff	Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.								To update		Convert Formats, Next Gen Mappers	cummerbund_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular	1.0.1					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	888	1208	43	97	1334	2683	101	479	0	0	0	0	2222	3891	144	576	False		
+curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	12	2	2	0	0	0	0	0	0	0	0	12	12	2	2	False		
+custom_pro_db	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1729	1744	144	146	450	450	72	72	361	361	12	12	2540	2555	228	230	False		
+custom_pro_db_annotation_data_manager		CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cut_columns	Cut1	Select columns from a dataset.								To update		Text Manipulation	cut_columns	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns	1.0.2					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	0	1	1	1	1	1973168	2034965	11939	12833	352364	803522	12967	30199	128777	133584	2341	2572	2454309	2972071	27247	45604	False		
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	259754	272370	11716	12601	334550	362356	18618	20162	64377	65986	3507	3627	658681	700712	33841	36390	False		
+cutesv	cutesv	Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.	cuteSV	cuteSV		cuteSV	Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis	Split read mapping, Genotyping, Structural variation detection	DNA structural variation, Sequencing, Computer science	To update	https://github.com/tjiangHIT/cuteSV	Variant Analysis	cutesv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv	1.0.8	cutesv	2.1.1	Split read mapping, Genotyping, Structural variation detection	Sequencing, Computer science	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	260	260	43	43	0	0	0	0	119	119	8	8	379	379	51	51	False		
+cwpair2	cwpair2	Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.								To update		ChIP-seq	cwpair2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2	1.1.1	matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	173	280	41	83	0	0	0	0	173	280	41	83	False		
+dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	0	10	10	10	0	92240	92240	2716	2716	179176	179176	5317	5317	12478	12478	394	394	283894	283894	8427	8427	False		
+das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1323	1323	47	47	0	0	0	0	0	0	0	0	1323	1323	47	47	False		
+data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	441	451	83	87	3	3	2	2	0	0	0	0	444	454	85	89	False		
+data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	867	877	213	216	339	339	94	94	64	64	5	5	1270	1280	312	315	False		
+data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	967	967	308	308	0	0	0	0	0	0	0	0	967	967	308	308	False		
+data_manager_eggnog_mapper		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+data_manager_eggnog_mapper_abspath		download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+data_source_iris_tcga	data_source_iris_tcga	IRIS-TCGA Data source tool								To update		Data Source	data_source_iris_tcga	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga	https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+datamash	datamash_ops, datamash_reverse, datamash_transpose	GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.								To update	https://www.gnu.org/software/datamash/	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash	1.8	datamash	1.1.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	1	3	3	0	0	1	0	0	0	1	0	0	0	0	0	0	3	3	3	0	748586	760943	7066	7307	98089	112831	5306	6131	16235	16317	2161	2171	862910	890091	14533	15609	False		
+dbbuilder	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4813	5555	687	805	0	0	0	0	961	961	87	87	5774	6516	774	892	False		
+decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	121	121	28	28	0	0	0	0	0	0	0	0	121	121	28	28	False		
+decoupler	score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk	decoupler - Ensemble of methods to infer biological activities								To update	https://decoupler-py.readthedocs.io/en/latest/	Transcriptomics	suite_decoupler	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler	1.4.0+galaxy3	decoupler	1.5.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	54	6	6	0	0	0	0	0	0	0	0	54	54	6	6	False		
+decoyfasta		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	558	558	7	7	0	0	0	0	0	0	0	0	558	558	7	7	False		
+deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	37	37	0	0	0	0	0	0	0	0	65	65	37	37	False		
+deepvariant	deepvariant	DeepVariant is a deep learning-based variant caller								To update	https://github.com/google/deepvariant	Variant Analysis	deepvariant	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant	1.5.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2561	2561	325	325	2916	2916	460	460	0	0	0	0	5477	5477	785	785	False		
+deg_annotate	deg_annotate	Annotate DESeq2/DEXSeq output tables								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	Transcriptomics	deg_annotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate	1.1.0	bedtools	2.31.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22774	23146	4084	4155	33972	33972	5372	5372	4236	4236	846	846	60982	61354	10302	10373	False		
+delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	40	6	7	0	0	0	0	0	0	0	0	33	40	6	7	False		
+delly	delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge	Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.	delly2	delly2		Delly2	Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.	Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis	DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases	To update	https://github.com/dellytools/delly	Variant Analysis	delly	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly	https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly	0.9.1	delly	1.2.9	Indel detection, Structural variation detection, Genotyping	Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	6	0	0	0	0	0	0	6	6	0	0	1451	1451	288	288	0	0	0	0	0	0	0	0	1451	1451	288	288	False		
+deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	97434	109474	11355	12514	183905	246475	24951	31957	18551	20166	2647	2905	299890	376115	38953	47376	False		
+deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	43	48	8	8	0	0	0	0	0	0	0	0	43	48	8	8	False		
+dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	18	18	0	0	0	0	0	0	0	0	89	89	18	18	False		
+dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	14874	16927	533	837	18475	28854	1403	2568	3854	4271	141	163	37203	50052	2077	3568	False		
+dgidb_annotator	dgidb_annotate	Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)								To update		Systems Biology, Variant Analysis	dgidb_annotator	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator	0.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	69	26	30	0	304	0	133	0	0	0	0	59	373	26	163	False		
+dia_umpire	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	28	33	4	4	0	0	0	0	134	134	4	4	162	167	8	8	False		
+dialignr	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	40	2	2	0	0	0	0	0	0	0	0	40	40	2	2	False		
+diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	0	3	3	0	61376	61746	1847	1895	23164	28729	1140	1556	63034	63034	522	522	147574	153509	3509	3973	False		
+diann	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	72	72	14	14	0	0	0	0	171	171	14	14	243	243	28	28	False		
+diapysef	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	262	262	38	38	0	0	0	0	256	256	6	6	518	518	44	44	False		
+diff	diff	GNU diff tool that calculates the differences between two files.								To update	http://www.gnu.org/software/diffutils/	Text Manipulation	diff	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diff	https://github.com/bgruening/galaxytools/tree/master/tools/diff	3.7	diffutils				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	362	362	99	99	23	23	17	17	0	0	0	0	385	385	116	116	False		
+diffacto	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	11	7	7	0	0	0	0	0	0	0	0	11	11	7	7	False		
+diffbind	diffbind	Diffbind provides functions for  processing  ChIP-Seq  data.	diffbind	diffbind		DiffBind	Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.	Differential binding analysis	ChIP-seq	Up-to-date	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind	3.12.0	bioconductor-diffbind	3.12.0	Differential binding analysis	ChIP-seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7092	7663	606	652	14367	18624	1360	1916	1477	1640	69	84	22936	27927	2035	2652	False		
+diffbind		Diffbind provides functions for  processing  ChIP-Seq  data.								To update	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+digestdb	digestdb									To update			digestdb	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dimet	dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@	DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.								Up-to-date	https://github.com/cbib/DIMet	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet	0.2.4	dimet	0.2.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+directag_and_tagrecon										To update			directag_and_tagrecon	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	358	406	124	139	1361	1361	384	384	0	0	0	0	1719	1767	508	523	False		
+divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26	32	8	9	86	172	20	53	0	0	0	0	112	204	28	62	False		
+dnabot	dnabot	DNA assembly using BASIC on OpenTrons								To update	https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT	Synthetic Biology	dnabot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot	3.1.0	dnabot				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dnaweaver	dnaweaver	Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.								Up-to-date	https://github.com/Edinburgh-Genome-Foundry/DnaWeaver	Synthetic Biology	dnaweaver	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver	1.0.2	dnaweaver_synbiocad	1.0.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	921	1626	4	31	0	0	0	0	0	0	0	0	921	1626	4	31	False		
+dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	74	88	12	15	0	0	0	0	0	0	0	0	74	88	12	15	False		
+dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	7358	7358	88	88	0	0	0	0	0	0	0	0	7358	7358	88	88	False		
+draw_stacked_barplots	draw_stacked_barplots	Draw Stacked Bar Plots for different categories and different criteria								To update		Graphics, Statistics	draw_stacked_barplots	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots	https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots	1.0.0	R				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	216	47	52	0	0	0	0	183	213	22	31	372	429	69	83	False		
+drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	916	916	113	113	0	0	0	0	0	0	0	0	916	916	113	113	False		
+droplet-barcode-plot	_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1151	1151	184	184	356	356	77	77	3	3	1	1	1510	1510	262	262	False		
+dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1900	1901	412	413	609	609	131	131	0	0	0	0	2509	2510	543	544	False		
+dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4413	4442	430	431	4403	4403	255	255	1816	1816	33	33	10632	10661	718	719	False		
+dwt_cor_ava_perclass	compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Feature Occurrences								To update		Statistics	dwt_cor_ava_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	141	8	11	136	141	8	11	False		
+dwt_cor_avb_all	compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features								To update		Statistics	dwt_cor_avb_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	124	124	7	7	124	124	7	7	False		
+dwt_ivc_all	compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Second Moments for Feature Occurrences								To update		Statistics	dwt_ivc_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	121	123	5	7	121	123	5	7	False		
+dwt_var_perclass	compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom	Compute P-values and Max Variances for Feature Occurrences								To update		Statistics	dwt_var_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	131	132	7	8	131	132	7	8	False		
+dwt_var_perfeature	dwt_var1	Wavelet variance using Discrete Wavelet Transfoms								To update		Statistics	dwt_var_perfeature	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature	1.0.2	r-bitops				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	30	36	2	4	11	11	4	4	206	220	6	7	247	267	12	15	False		
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	28	28	2	2	0	0	0	0	0	0	0	0	28	28	2	2	False		
+ebi_tools	ebi_search_rest_results	Tools to query and download data from several EMBL-EBI databases								To update	http://www.ebi.ac.uk/services/all	Web Services, Data Source	ebi_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools	0.1.1	six				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	276	406	133	163	1421	1421	547	547	0	0	0	0	1697	1827	680	710	False		
+ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12996	12996	137	137	10	10	1	1	0	0	0	0	13006	13006	138	138	False		
+edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	19294	20905	2423	2618	48876	58723	6341	7527	8010	8705	846	892	76180	88333	9610	11037	False		
+edta	edta	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. 	edta	edta		The Extensive de novo TE Annotator (EDTA)	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	To update	https://github.com/oushujun/EDTA	Variant Analysis	edta	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta	https://github.com/bgruening/galaxytools/tree/master/tools/edta		edta	2.2.0	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4495	4495	111	111	0	0	0	0	0	0	0	0	4495	4495	111	111	False		
+effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	1	3	1	0	34432	34437	1149	1152	42	42	2	2	21027	21027	413	413	55501	55506	1564	1567	False		
+egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2809	3060	371	402	5179	5179	759	759	1931	1931	226	226	9919	10170	1356	1387	False		
+embl2fa	embl2fa	Converts EMBL flat format to fasta format								To update	http://artbio.fr	Text Manipulation	embl2fa	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	0	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	107	107	107	0	143762	148864	4481	5039	151989	296028	13224	31140	24955	27001	2397	2705	320706	471893	20102	38884	False		
+ena_upload	ena_upload	Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 								To update	https://github.com/usegalaxy-eu/ena-upload-cli	Data Export	ena_upload	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload	0.7.3	ena-upload-cli	0.7.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	366	366	41	41	0	0	0	0	1302	1302	14	14	1668	1668	55	55	False		
+enasearch	enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data	A Python library for interacting with ENA's API								To update	https://github.com/bebatut/enasearch	Data Source	enasearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch		enasearch	0.2.2			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	1989	2302	367	453	0	0	0	0	0	0	0	0	1989	2302	367	453	False		
+encyclopedia	encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30			2	4	7	0	2	4	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	738	738	98	98	1	1	1	1	42	42	4	4	781	781	103	103	False		
+ensembl_vep	ensembl_vep	Ensembl VEP: Annotate VCFs with variant effect predictions								Up-to-date	https://github.com/Ensembl/ensembl-vep	Variant Analysis	ensembl_vep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep	112.0	ensembl-vep	112.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3051	3051	171	171	0	0	0	0	0	0	0	0	3051	3051	171	171	False		
+eodie	eodie	Earth Observation Data Information Extractor								To update	https://eodie.readthedocs.io/	Climate Analysis	eodie	climate	https://gitlab.com/eetun-tiimi/EODIE	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie	1.0.2	eodie				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	45	45	4	4	0	0	0	0	0	0	0	0	45	45	4	4	False		
+epicseg	epicseg_segment	EpiCSeg is a tool for conducting chromatin segmentation.								To update	https://github.com/lamortenera/epicseg	Epigenetics	epicseg	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	@VERSION_STRING@	epicseg	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	160	252	17	21	0	0	0	0	0	0	0	0	160	252	17	21	False		
+episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	880	880	80	80	221	221	37	37	49	49	3	3	1150	1150	120	120	False		
+essential_climate_variables	cds_essential_variability	Get Copernicus Essential Climate Variables for assessing climate variability								To update	https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview	Climate Analysis, Data Source	cds_essential_variability	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	232	336	39	40	0	0	0	0	0	0	0	0	232	336	39	40	False		
+ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	820	966	89	106	0	0	0	0	0	0	0	0	820	966	89	106	False		
+evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+exomedepth	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	517	517	61	61	2995	2995	184	184	0	0	0	0	3512	3512	245	245	False		
+exonerate	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1030	1072	185	188	1058	1058	189	189	922	922	35	35	3010	3052	409	412	False		
+exparna	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5396	5938	580	607	628	628	168	168	519	519	107	107	6543	7085	855	882	False		
+export_to_cluster	export_to_cluster	Export datasets to cluster								To update	https://github.com/TGAC/earlham-galaxytools/	Data Export	export_to_cluster	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster	0.0.2	EXPORT_DIR_PREFIX				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+express	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	278	337	34	45	0	1184	0	117	2402	2844	23	60	2680	4365	57	222	False		
+extract_genomic_dna	Extract genomic DNA 1	Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.								To update		Genomic Interval Operations	extract_genomic_dna	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna	https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna	3.0.3+galaxy2	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	1	0	0	0	1	1	1	1	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	9409	12735	813	923	20180	259099	2072	11791	168	611	20	63	29757	272445	2905	12777	False		
+ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+falco	falco	A high throughput sequence QC analysis tool	falco	falco		Falco	A high-speed FastQC emulation for quality control of sequencing data.	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	Up-to-date	https://github.com/smithlabcode/falco/	Sequence Analysis	falco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco	https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco	1.2.4	falco	1.2.4	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4298	4298	34	34	0	0	0	0	0	0	0	0	4298	4298	34	34	False		
+fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	601	601	128	128	1165	1165	232	232	0	0	0	0	1766	1766	360	360	False		
+fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	469	ucsc-fasplit	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3278	3361	460	478	6144	6144	595	595	1139	1139	183	183	10561	10644	1238	1256	False		
+fasta2bed	fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5191	5367	104	130	5191	5367	104	130	False		
+fasta_compute_length	fasta_compute_length	Compute sequence length								To update	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.4	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	8547	9136	978	1129	17748	51150	1404	5670	4239	4404	162	190	30534	64690	2544	6989	False		
+fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39695	39742	242	255	13660	19007	600	1398	1521	1603	92	112	54876	60352	934	1765	False		
+fasta_extract	fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	10	10	1	1	0	0	0	0	1286	1827	144	181	1296	1837	145	182	False		
+fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	47494	51924	889	997	50663	101663	1488	3742	3919	5601	241	276	102076	159188	2618	5015	False		
+fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	1	5235	5486	237	288	4060	25609	480	2039	816	1093	73	89	10111	32188	790	2416	False		
+fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	30917	32191	1142	1257	36869	36869	1346	1346	5236	5236	230	230	73022	74296	2718	2833	False		
+fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	497	808	71	108	2249	5479	216	703	415	437	18	20	3161	6724	305	831	False		
+fasta_nucleotide_color_plot	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	164	179	42	47	758	905	128	170	0	0	0	0	922	1084	170	217	False		
+fasta_stats	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	43726	44512	3104	3259	19941	19941	3693	3693	16788	18589	2467	2650	80455	83042	9264	9602	False		
+fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	108876	113638	1572	1793	82527	192112	2209	8565	5711	7649	275	334	197114	313399	4056	10692	False		
+fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6685	6685	603	603	0	0	0	0	0	0	0	0	6685	6685	603	603	False		
+fastg2protlib	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	29	29	8	8	0	0	0	0	0	0	0	0	29	29	8	8	False		
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	136	11	11	0	0	0	0	0	0	0	0	136	136	11	11	False		
+fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	1	1126086	1127111	6847	6909	422259	422259	10722	10722	76462	76462	2242	2242	1624807	1625832	19811	19873	False		
+fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8604	8799	215	240	54200	75329	919	2957	1562	1680	76	85	64366	85808	1210	3282	False		
+fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15582	18350	690	771	40489	121585	2715	9239	4657	5793	214	287	60728	145728	3619	10297	False		
+fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	92594	102535	2576	2995	179461	897457	9437	44701	15434	25533	664	1073	287489	1025525	12677	48769	False		
+fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7560	7560	1266	1266	6539	6539	1581	1581	0	0	0	0	14099	14099	2847	2847	False		
+fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2488	3132	215	267	6241	14508	834	2121	4121	4592	131	158	12850	22232	1180	2546	False		
+fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	234	249	43	44	2648	8092	288	983	442	466	12	17	3324	8807	343	1044	False		
+fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5873	8936	532	657	14738	20229	1889	2366	2316	2711	225	261	22927	31876	2646	3284	False		
+fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18216	19573	2348	2492	23484	25936	3482	3851	6207	6551	1402	1442	47907	52060	7232	7785	False		
+fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15628	17130	536	679	24157	58368	1954	5716	1941	2266	172	214	41726	77764	2662	6609	False		
+fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3169	3521	459	535	19309	30747	1410	3441	807	1023	219	247	23285	35291	2088	4223	False		
+fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1271	1393	131	176	12763	58819	2073	8850	430	479	32	51	14464	60691	2236	9077	False		
+fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	335	352	44	47	1583	9696	269	2229	1131	1254	15	27	3049	11302	328	2303	False		
+fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	17279	18386	3826	4062	55268	136888	6055	12590	7685	9356	1854	2043	80232	164630	11735	18695	False		
+fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_stats	fastq_stats	FASTQ Summary Statistics by column								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3858	4595	680	815	15213	81513	3159	14109	3855	4163	184	256	22926	90271	4023	15180	False		
+fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	36069	37805	1151	1234	45213	99852	2691	6370	8457	13335	408	609	89739	150992	4250	8213	False		
+fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	12895	14110	269	297	13315	30673	612	1810	5125	5373	64	87	31335	50156	945	2194	False		
+fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10114	11383	582	665	23906	92351	1986	8818	1588	2607	108	212	35608	106341	2676	9695	False		
+fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								To update		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4881	6165	859	967	29458	99179	3455	11369	2171	2678	259	338	36510	108022	4573	12674	False		
+fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	1	0	1784056	1913280	41344	43940	2269843	3195869	90828	140008	410004	445555	14195	16026	4463903	5554704	146367	199974	False		
+fastqc_stats	FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5162	5162	2350	2350	10176	10176	4714	4714	2610	2610	991	991	17948	17948	8055	8055	False		
+fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	3	0	0	0	0	0	8	0	3	False		
+fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	208349	217568	3421	3732	131388	245005	5108	13227	18655	18655	679	679	358392	481228	9208	17638	False		
+fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	65542	65631	1049	1071	25992	25992	2147	2147	6733	7339	649	745	98267	98962	3845	3963	False		
+fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1769	2020	88	101	6948	24960	358	2424	623	998	32	50	9340	27978	478	2575	False		
+fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	16957	18124	225	260	37001	89126	919	2720	863	989	56	68	54821	108239	1200	3048	False		
+fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3140	3520	178	212	13975	117900	1198	6006	409	712	36	55	17524	122132	1412	6273	False		
+fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	64187	67981	326	349	87477	185555	781	3067	16563	17125	58	78	168227	270661	1165	3494	False		
+fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	174	272	61	92	4295	25068	1056	4180	1127	1171	70	89	5596	26511	1187	4361	False		
+fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2218	2344	168	206	20551	60032	3784	9866	2347	2460	234	256	25116	64836	4186	10328	False		
+fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2364	2526	180	214	6572	11745	303	1024	462	696	49	64	9398	14967	532	1302	False		
+fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10707	12597	356	415	21568	67304	574	1527	719	861	61	78	32994	80762	991	2020	False		
+fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	13584	14557	550	641	123676	206733	2034	8390	2819	4757	229	267	140079	226047	2813	9298	False		
+fates-emerald	ctsm_fates	EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model								To update	https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api	Climate Analysis	ctsm_fates	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	2.0	fates-emerald				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	264	264	69	69	34	34	11	11	103	103	1	1	401	401	81	81	False		
+fatovcf	fatovcf	Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_fatovcf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	448	ucsc-fatovcf	448		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	385	385	46	46	587	587	107	107	58	58	5	5	1030	1030	158	158	False		
+feature_alignment	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	18	18	1	1	0	0	0	0	0	0	0	0	18	18	1	1	False		
+featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22308	22388	16	19	350	13711	54	349	0	0	0	0	22658	36099	70	368	False		
+featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	740719	770524	11699	12547	643892	784396	23272	27598	66108	68867	2348	2463	1450719	1623787	37319	42608	False		
+feelnc	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	Annotation, Classification	Functional, regulatory and non-coding RNA	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1375	1500	95	99	797	797	116	116	59	59	3	3	2231	2356	214	218	False		
+feelnc2asko	feelnc2asko	Convert FeelNC GTF to GFF3								To update	https://github.com/tderrien/FEELnc	Convert Formats	feelnc2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+feht	feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	1	1	1	1	False		
+fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5618	5820	582	607	21673	21673	938	938	869	869	110	110	28160	28362	1630	1655	False		
+file_manipulation	bg_uniq	This tool returns all unique lines from a tab-separated file.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	Text Manipulation	unique	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	0.4	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	6690	8818	554	612	0	0	0	0	0	0	0	0	6690	8818	554	612	False		
+filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	26717	29932	1026	1072	42990	42990	1176	1176	9619	9619	230	230	79326	82541	2432	2478	False		
+filter_compounds	filter_orgmet_anorg	Tool for filtering organometallics/anorganic compounds from a list of compounds.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	filter_compounds	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	3.1.1	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_density	filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_stats	filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_transcripts_via_tracking	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23	24	9	10	62	635	26	241	2	2	2	2	87	661	37	253	False		
+filter_vcf	filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	53310	53944	1499	1575	25043	25043	726	726	10824	10824	593	593	89177	89811	2818	2894	False		
+find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	62	70	10	12	3	1787	1	204	0	0	0	0	65	1857	11	216	False		
+find_repeats	findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+find_subsequences	bg_find_subsequences									To update			find_subsequences	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences	0.3	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	554	784	69	79	2820	3047	323	361	20	20	1	1	3394	3851	393	441	False		
+fisher_test	fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	1985	1985	41	41	0	0	0	0	0	0	0	0	1985	1985	41	41	False		
+flanking_features	flanking_features_1	Fetch closest non-overlapping feature for every interval								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	flanking_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features	4.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	589	731	51	63	2445	32847	304	2549	1214	1294	15	22	4248	34872	370	2634	False		
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22017	22304	239	255	9399	14886	462	709	4	4	1	1	31420	37194	702	965	False		
+flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	661	715	52	54	0	0	0	0	167	167	15	15	828	882	67	69	False		
+flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	2	2	0	0	0	0	0	0	0	0	9	9	2	2	False		
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32514	32675	3379	3422	19434	19434	2537	2537	9843	9843	1624	1624	61791	61952	7540	7583	False		
+footprint	footprint	Find transcription factor footprints								To update	https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/	Epigenetics	footprint	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	1.0.0	footprint	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	57	5	5	0	0	0	0	0	0	0	0	57	57	5	5	False		
+format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	189	203	57	60	0	0	0	0	0	0	0	0	189	203	57	60	False		
+format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5940	6474	558	608	0	0	0	0	0	0	0	0	5940	6474	558	608	False		
+fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1257	1450	150	162	0	0	0	0	1052	1052	45	45	2309	2502	195	207	False		
+fragpipe	fragpipe	Data analysis for mass spectrometry-based proteomics.								Up-to-date	https://fragpipe.nesvilab.org/	Proteomics	fragpipe	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	20.0	fragpipe	20.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	64	64	9	9	0	0	0	0	0	0	0	0	64	64	9	9	False		
+free_energy		Free energy tools of BRIDGE.								To update		Molecular Dynamics, Computational chemistry	freeenergy	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+freebayes	freebayes, bamleftalign	Galaxy Freebayes Bayesian genetic variant detector tool	freebayes	freebayes		FreeBayes	Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	To update	https://github.com/ekg/freebayes	Variant Analysis	freebayes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes	1.3.6	freebayes	1.3.8	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	149715	171093	8158	8794	144708	256315	15996	25107	19156	21936	2251	2571	313579	449344	26405	36472	False		
+freec	control_freec	Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.	freec	freec		FREEC	A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.	Copy number estimation, Variant calling, Genome alignment	DNA structural variation, Oncology, Human genetics, Data mining	To update	http://boevalab.inf.ethz.ch/FREEC/	Variant Analysis	control_freec	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec	11.6	gawk		Copy number estimation, Variant calling, Genome alignment	Oncology, Human genetics, Data mining	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	748	748	91	91	0	0	0	0	12	12	1	1	760	760	92	92	False		
+freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	21757	21757	101	101	217	217	21	21	0	0	0	0	21974	21974	122	122	False		
+frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fromHicupToJuicebox	fromHicupToJuicebox	Convert the output of hicup (as sam or bam) to the input of juicebox.								To update		Epigenetics	from_hicup_to_juicebox	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fromgtfTobed12	fromgtfTobed12	Convert GTF files to BED12 format								To update	https://pythonhosted.org/gffutils/contents.html	Convert Formats	fromgtftobed12	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	0.11.1+galaxy1	gffutils	0.13			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fsd	fsd, fsd_beforevsafter, fsd_regions, td	Tool that plots a histogram of sizes of read families								To update		Graphics	duplex_family_size_distribution	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd	1.0.2	matplotlib				4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	578	578	34	34	0	0	0	0	578	578	34	34	False		
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	8648	8648	1408	1408	32	32	6	6	6406	6406	597	597	15086	15086	2011	2011	False		
+garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	11	11	0	0	0	0	0	0	0	0	27	27	11	11	False		
+gatk4	filtermutectcalls, mergemutectstats, mutect2	Find somatic variations								To update	http://artbio.fr	Variant Analysis	gatk4	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gatk4	gatk4_mutect2	A Galaxy wrapper for Mutect2 from GATK								To update	https://software.broadinstitute.org/gatk/gatk4	Variant Analysis	gatk4_mutect2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3463	3463	452	452	9040	9040	1639	1639	0	0	0	0	12503	12503	2091	2091	False		
+gblocks	gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	466	466	62	62	466	466	62	62	False		
+gc_derivatization	gc_derivatization	In silico derivatization for GC.								Up-to-date	https://github.com/RECETOX/gc-meox-tms	Metabolomics	gc_derivatization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	1.0.1	gc-meox-tms	1.0.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gcms2isocor	gcms2isocor	Conversion from GCMS PostRun Analysis to Isocor								To update		Metabolomics	gcms2isocor	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gcms2isocor	gcms2isocor	Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs								To update	https://github.com/p2m2/p2m2tools	Metabolomics	gcms2isocor	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor	0.2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	1409	1498	39	42	0	0	0	0	0	0	0	0	1409	1498	39	42	False		
+gdcwebapp	data_source_gdcwebapp	GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format								To update	http://bioinf.iasi.cnr.it/gdcwebapp/	Data Source, Convert Formats	gdcwebapp	iuc	https://github.com/fabio-cumbo/GDCWebApp4Galaxy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp	1.0.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gecko	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	723	723	235	235	0	0	0	0	786	786	95	95	1509	1509	330	330	False		
+gemini	gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	Sequence analysis, Genetic variation analysis	Sequence analysis	1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	4967	5475	1863	1992	992	1118	279	370	3756	3811	423	425	9715	10404	2565	2787	False		
+genebed_maf_to_fasta	GeneBed_Maf_Fasta2	Stitch gene blocks given a set of coding exon intervals								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	Genomic Interval Operations	genebed_maf_to_fasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta	1.0.1+galaxy0					1	1	1	0	1	1	1	0	0	1	0	0	0	1	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	1	0	4	4	2	2	221	2905	23	279	0	0	0	0	225	2909	25	281	False		
+genehunter_modscore	genehunter_modscore	Maximised LOD score pedigree analysis utility								To update	https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1	Variant Analysis	genehunter_modscore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore	3.0.0	ghm	3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+geneiobio	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	101	101	25	25	0	0	0	0	59	59	6	6	160	160	31	31	False		
+genenotebook	genenotebook_build	Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io								Up-to-date	https://genenotebook.github.io	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	0.4.16	genoboo	0.4.16			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+generate_pc_lda_matrix	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115	124	29	30	518	1029	102	261	184	198	14	17	817	1351	145	308	False		
+genetrack	genetrack	"Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand."								To update		ChIP-seq	genetrack	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack		numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	445	660	104	197	0	0	0	0	445	660	104	197	False		
+genform	genform	genform: generation of molecular formulas by high-resolution MS and MS/MS data								To update	https://sourceforge.net/projects/genform/	Metabolomics	genform	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform		genform	r8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	68	68	4	4	0	0	0	0	0	0	0	0	68	68	4	4	False		
+genomad	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	genomad	genomad		geNomad	geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.	Sequence annotation, Taxonomic classification	Sequence analysis	To update	https://github.com/apcamargo/genomad/	Metagenomics	genomad	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad	1.8.0	genomad	1.8.1	Sequence annotation, Taxonomic classification	Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+genomescope	genomescope	Analyze unassembled short reads								Up-to-date	https://github.com/tbenavi1/genomescope2.0	Statistics	genomescope	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope	2.0.1	genomescope2	2.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3181	3181	665	665	2112	2112	435	435	1622	1622	148	148	6915	6915	1248	1248	False		
+genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	47	47	13	13	0	0	0	0	0	0	0	0	47	47	13	13	False		
+genrich	genrich	Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).								To update	https://github.com/jsh58/Genrich	ChIP-seq	genrich	iuc	https://github.com/jsh58/Genrich	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich	0.5+galaxy2	genrich	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3534	3577	402	405	2840	2840	419	419	571	571	31	31	6945	6988	852	855	False		
+getTn5ExtendedCoverage	getTn5ExtendedCoverage	Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension								To update		Epigenetics	gettn5extendedcoverage	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+get_flanks	get_flanks1	Get flanks returns flanking region/s for every gene								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	get_flanks	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3768	325011	1462	2044	9350	242043	2201	6583	787	1070	119	146	13905	568124	3782	8773	False		
+get_hrun	get_hrun	Annotate indel variants with homopolymer context								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	Variant Analysis	get_hrun	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun	0.5.9.2	pyfaidx	0.8.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5	False		
+get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	746	746	136	136	0	0	0	0	1504	1504	244	244	2250	2250	380	380	False		
+get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+getindelrates_3way	indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	290	20	86	0	0	0	0	70	290	20	86	False		
+getindels_2way	getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	74	237	24	61	0	0	0	0	74	237	24	61	False		
+getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1542	1542	159	159	0	0	0	0	587	587	64	64	2129	2129	223	223	False		
+gfa_to_fa	gfa_to_fa	gfa_to_fa - Converting GFA format to Fasta format								To update	http://gfa-spec.github.io/GFA-spec/	Convert Formats	gfa_to_fa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa	0.1.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9664	9775	763	765	5623	5623	493	493	1000	1000	135	135	16287	16398	1391	1393	False		
+gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	To update	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.7	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11748	11748	767	767	6560	6560	397	397	2556	2556	106	106	20864	20864	1270	1270	False		
+gff3_rebase	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	806	812	68	68	197	197	37	37	132	132	12	12	1135	1141	117	117	False		
+gffcompare	gffcompare	Galaxy wrappers for Geo Pertea's GffCompare package.	gffcompare	gffcompare		gffcompare	Program for comparing, annotating, merging and tracking transcripts in GFF files.	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	https://github.com/gpertea/gffcompare/	Transcriptomics	gffcompare	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare	0.12.6	gffcompare	0.12.6	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3560	3980	916	999	5281	8000	1713	2521	1468	1642	208	225	10309	13622	2837	3745	False		
+gffcompare_to_bed	gffcompare_to_bed	Filter and convert a gffCompare GTF to BED								To update	https://github.com/gpertea/gffcompare/	Convert Formats	gffcompare_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	0.2.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1375	2230	329	347	1071	1071	362	362	492	492	64	64	2938	3793	755	773	False		
+gffread	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12828	13716	1740	1829	15217	23818	2588	3486	4423	4423	732	732	32468	41957	5060	6047	False		
+ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	0	5	5	5	0	24606	25662	3463	3630	26805	26808	5143	5144	8174	8237	1259	1279	59585	60707	9865	10053	False		
+ggupset	emc-ggupset	Create Upset Plots with ggupset								To update	https://github.com/const-ae/ggupset	Graphics	ggupset	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset	1.0	r-ggupset				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	490	682	74	109	127	14058	20	1798	0	0	0	0	617	14740	94	1907	False		
+glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	0	4343	4343	407	407	0	0	0	0	0	0	0	0	4343	4343	407	407	False		
+glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	11	6	6	85	984	29	230	10	11	7	8	106	1006	42	244	False		
+gnali	gnali	A tool to find nonessential, loss-of-function gene variants								Up-to-date	https://github.com/phac-nml/gnali/	Variant Analysis	gnali	nml	https://github.com/phac-nml/gnali/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali	1.1.0	gnali	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	5800	6212	826	871	7756	7756	1048	1048	1149	1149	215	215	14705	15117	2089	2134	False		
+goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	20207	21960	2807	3139	24488	26198	3066	3321	4155	4155	545	545	48850	52313	6418	7005	False		
+gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	72	5	7	0	0	0	0	0	0	0	0	34	72	5	7	False		
+gprofiler	gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense	functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more								To update	https://biit.cs.ut.ee/gprofiler	Statistics, Web Services	gprofiler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler	@TOOL_VERSION@+galaxy11	r-gprofiler2				5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	4001	4001	614	614	7882	7882	1238	1238	0	0	0	0	11883	11883	1852	1852	False		
+graph_converter	graph_converter	Convert between different graph formats								To update		Convert Formats	graph_converter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+graphclust	graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	1	0	0	0	0	0	0	0	0	0	6	0	1	False		
+graphembed	graphembed	Compute a 2D embedding of a data matrix given supervised class information								Up-to-date	https://github.com/fabriziocosta/GraphEmbed	Statistics, Graphics	graphembed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed	2.4	graph_embed	2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	78	78	6	6	120	120	43	43	0	0	0	0	198	198	49	49	False		
+graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1725	2708	97	99	2	2	2	2	0	0	0	0	1727	2710	99	101	False		
+graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	9816	10927	1285	1350	1273	1273	368	368	1104	1104	242	242	12193	13304	1895	1960	False		
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	7012	7344	323	338	0	0	0	0	0	0	0	0	7012	7344	323	338	False		
+graphprot	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy2	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	463	484	18	19	0	0	0	0	0	0	0	0	463	484	18	19	False		
+gromacs	gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj	GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.								To update	https://github.com/gromacs	Molecular Dynamics, Computational chemistry	gromacs	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	2022	gromacs	2021.3			14	8	15	0	14	8	15	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	15	9	0	184067	184203	3441	3451	9382	9382	1438	1438	10325	10325	648	648	203774	203910	5527	5537	False		
+gsc_center_scale	center_scale	Center or scale (standardize) data								To update	http://artbio.fr	Statistics	gsc_center_scale	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_filter_cells	filter_cells	Filter single cell RNAseq data on libray depth and number of detected genes								To update	http://artbio.fr	Transcriptomics	gsc_filter_cells	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_filter_genes	filter_genes	Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_filter_genes	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_gene_expression_correlations	single_cell_gene_expression_correlations	Compute single-cell paire-wise gene expressions correlations								To update	http://artbio.fr	Transcriptomics	gsc_gene_expression_correlations	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_mannwhitney_de	mannwhitney_de	Perform a mann-whitney differential testing between two sets of gene expression data								To update	http://artbio.fr	Transcriptomics	gsc_mannwhitney_de	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	4.1.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_scran_normalize	scran_normalize	Normalize raw counts using scran								To update	http://artbio.fr	Transcriptomics	gsc_scran_normalize	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	1.28.1+galaxy0	bioconductor-scran	1.30.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	24	24	3	3	2	2	10	10	2	2	102	102	28	28	False		
+gsc_signature_score	signature_score	Compute signature scores from single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_signature_score	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	2.3.9+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gstf_preparation	gstf_preparation	GeneSeqToFamily preparation converts data for the workflow								To update	https://github.com/TGAC/earlham-galaxytools/	Convert Formats	gstf_preparation	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	0.4.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	377	400	17	17	0	0	0	0	0	0	0	0	377	400	17	17	False		
+gtdb_to_taxdump	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	gtdb_to_taxdump	gtdb_to_taxdump		gtdb_to_taxdump	Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.	Data handling, Mapping, Generation	Computational biology	Up-to-date	https://github.com/nick-youngblut/gtdb_to_taxdump	Metagenomics	gtdb_to_taxdump	iuc	https://github.com/nick-youngblut/gtdb_to_taxdump	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	0.1.9	Data handling, Mapping, Generation	Computational biology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	Up-to-date	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.4.0	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	476	476	87	87	0	0	0	0	588	588	74	74	1064	1064	161	161	False		
+gtf-2-gene-list	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1982	1983	323	324	1040	1040	343	343	205	205	38	38	3227	3228	704	705	False		
+gtfToBed12	gtftobed12	Convert GTF files to BED12 format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README	Convert Formats	gtftobed12	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12	357	ucsc-gtftogenepred	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	8329	9363	3336	3828	8009	8009	3130	3130	1577	1577	344	344	17915	18949	6810	7302	False		
+gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3690	3811	326	336	3323	3323	235	235	1895	2429	234	258	8908	9563	795	829	False		
+guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	1	1	7	7	1	1	False		
+gvcftools	gvcftools_extract_variants	gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf.								To update	https://github.com/sequencing/gvcftools	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools	0.1	gvcftools	0.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gwastools	gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	Deposition, Analysis, Annotation	GWAS study	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	7303	7303	222	222	20	20	2	2	0	0	0	0	7323	7323	224	224	False		
+hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	349	359	32	33	364	364	53	53	0	0	0	0	713	723	85	86	False		
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	103	103	4	4	103	103	4	4	False		
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	502	502	66	66	0	0	0	0	0	0	0	0	502	502	66	66	False		
+happy	som.py	A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.	hap.py	hap.py		hap.py	This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	To update	https://github.com/Illumina/hap.py	Variant Analysis	happy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy	0.3.14	hap.py	0.3.15	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hardklor	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	98	111	5	8	0	0	0	0	0	0	0	0	98	111	5	8	False		
+hclust2	hclust2	Plots heatmaps								To update	https://bitbucket.org/nsegata/hclust2/	Data Visualization	hclust2	rnateam	https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2	https://github.com/bgruening/galaxytools/tree/master/tools/hclust2	0.99	hclust2	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hcluster_sg	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	243	263	54	57	0	0	0	0	0	0	0	0	243	263	54	57	False		
+hcluster_sg_parser	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	266	293	22	25	0	0	0	0	0	0	0	0	266	293	22	25	False		
+heatmap2	ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	0	46700	50808	4645	5114	64214	70429	5799	6830	7783	7912	704	724	118697	129149	11148	12668	False		
+heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	bionet, heinz		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	1281	1434	367	442	1559	1559	636	636	678	678	52	52	3518	3671	1055	1130	False		
+helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	267	267	39	39	0	0	0	0	80	80	7	7	347	347	46	46	False		
+hess	hess_astro_tool	Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope								To update		Astronomy	hess_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess	0.0.2+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+hgv_fundo	hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	145	1794	33	397	0	0	0	0	145	1794	33	397	False		
+hgv_hilbertvis	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	119	265	16	60	0	0	0	0	119	265	16	60	False		
+hgvsparser	hgvsparser	Parsing and building variant descriptor strings compliant with the HGVS standard								To update	https://github.com/VariantEffect/hgvsParseR/tree/master	Variant Analysis	hgvsparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6346	6346	2	2	0	0	0	0	0	0	0	0	6346	6346	2	2	False		
+hicexplorer	hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								Up-to-date	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.5	hicexplorer	3.7.5			38	38	38	0	38	38	38	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	33	36	33	0	44449	68602	3236	4177	46	46	21	21	1328	1328	67	67	45823	69976	3324	4265	False		
+hicstuff	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices								To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hictk	hictk	Convert cooler to juicebox_hic								Up-to-date	https://github.com/paulsengroup/hictk	Convert Formats, Epigenetics	hictk	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	1.0.0	hictk	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	9	9	0	0	0	0	0	0	0	0	17	17	9	9	False		
+hicup	hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater	The HiCUP-Pipeline from the Bioinformatics Babraham Institute.								To update	https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html	Epigenetics	hicup	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	0.9.2					7	0	7	0	7	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	6	0	901	1020	160	184	440	440	111	111	0	0	0	0	1341	1460	271	295	False		
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1819	1819	539	539	1334	1334	389	389	2472	2472	137	137	5625	5625	1065	1065	False		
+hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	156	156	20	20	0	0	0	0	220	220	11	11	376	376	31	31	False		
+high_dim_heatmap	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	2	2	0	0	0	0	0	0	0	0	18	18	2	2	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	0	12	0	0	0	0	0	0	0	0	0	228	0	12	False		
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	337151	353499	10046	10719	699868	896164	26656	34018	87016	94859	5302	5695	1124035	1344522	42004	50432	False		
+histogram	histogram_rpy	Histogram of a numeric column								To update		Graphics, Statistics	histogram	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram	https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram	1.0.4	rpy2	2.7.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3748	4661	866	1002	5993	48272	1507	7101	549	746	152	253	10290	53679	2525	8356	False		
+hivclustering	hivclustering	Infers transmission networks from pairwise distances inferred by tn93								To update	https://pypi.org/project/hivclustering/	Next Gen Mappers	hivclustering	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering	1.3.1	python-hivclustering	1.8.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	0	0	12	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	12	0	35919	36952	1283	1321	0	0	0	0	3023	3023	180	180	38942	39975	1463	1501	False		
+homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+homer	homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	Sequence motif discovery		0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	5	0	0	8531	8531	633	633	0	0	0	0	0	0	0	0	8531	8531	633	633	False		
+htseq-clip	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	98	98	19	19	0	0	0	0	0	0	0	0	98	98	19	19	False		
+htseq_count	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	Nucleic acid sequence analysis	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	144907	168824	3703	4366	213407	346792	10798	16485	27209	33124	2613	2854	385523	548740	17114	23705	False		
+humann	humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.9	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	10	10	0	6	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	26659	26659	2067	2067	865	865	174	174	3238	3238	351	351	30762	30762	2592	2592	False		
+hybpiper	hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.3.0	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1571	1571	3	3	0	0	0	0	144	144	4	4	1715	1715	7	7	False		
+hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	0	17	2	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	12	17	12	0	11429	11429	428	428	7751	7751	676	676	715	715	58	58	19895	19895	1162	1162	False		
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	473	473	93	93	0	0	0	0	0	0	0	0	473	473	93	93	False		
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	1200	1220	187	195	1588	1588	267	267	0	0	0	0	2788	2808	454	462	False		
+idconvert	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	241	276	24	33	0	0	0	0	0	0	0	0	241	276	24	33	False		
+idr	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2953	3027	109	114	1710	1710	199	199	0	0	0	0	4663	4737	308	313	False		
+idr_download	idr_download_by_ids	Image Data Resource downloading tool								To update	https://idr.openmicroscopy.org	Data Source	idr_download_by_ids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download	0.45	omero-py	5.11.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	404	404	37	37	0	0	0	0	24	24	1	1	428	428	38	38	False		
+iedb_api	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1539	1539	35	35	0	0	0	0	0	0	0	0	1539	1539	35	35	False		
+illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	273	659	101	102	0	0	0	0	153	153	15	15	426	812	116	117	False		
+image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	2	2	0	0	0	0	0	0	0	0	58	58	2	2	False		
+image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	5	5	0	0	0	0	0	0	0	0	16	16	5	5	False		
+imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21409	21849	10	12	0	0	0	0	0	0	0	0	21409	21849	10	12	False		
+imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20240614			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	1731	1731	109	109	0	0	0	0	0	0	0	0	1731	1731	109	109	False		
+improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	22	1	1	44	292	3	21	0	0	0	0	62	314	4	22	False		
+infercnv	infercnv	Infer Copy Number Variation from Single-Cell RNA-Seq Data								Up-to-date	https://github.com/broadinstitute/infercnv	Transcriptomics, Variant Analysis	infercnv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv	1.20.0	bioconductor-infercnv	1.20.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	2	2	0	0	0	0	0	0	0	0	10	10	2	2	False		
+infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	59700	112582	223	282	0	0	0	0	1157	1221	34	35	60857	113803	257	317	False		
+influx_data_manager	influx_data_manager	Handling influx_si data inputs in Galaxy workflows								To update	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/	Metabolomics	influx_si_data_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager	1.0.2	influx-si-data-manager	1.0.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+influx_si	influx_si	metabolic flux estimation based on [in]stationary labeling								To update	https://github.com/sgsokol/influx	Metabolomics	influx_si	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si	7.0.1	influx_si	7.0.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+inforna		INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	157	157	14	14	0	0	0	0	0	0	0	0	157	157	14	14	False		
+instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	102	102	16	16	0	0	0	0	0	0	0	0	102	102	16	16	False		
+intarna	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.1	intarna	3.4.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3071	7652	41	47	0	0	0	0	0	0	0	0	3071	7652	41	47	False		
+integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55149	55149	161	161	0	0	0	0	6085	6085	73	73	61234	61234	234	234	False		
+intermine_galaxy_exchange	galaxy_intermine_exchange	InterMine Exporter								To update	https://github.com/intermine	Convert Formats	intermine_galaxy_exchange	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange	0.0.1	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	46	6	12	72	87	13	15	108	108	1	1	217	241	20	28	False		
+interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	70	7	7	0	0	0	0	0	0	0	0	70	70	7	7	False		
+interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34689	55189	1634	1713	65	65	15	15	10897	10897	607	607	45651	66151	2256	2335	False		
+intersect	gops_intersect_1	Intersect the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	20472	349984	2351	3007	45587	778988	4359	14116	6087	7417	484	561	72146	1136389	7194	17684	False		
+interval2maf	Interval2Maf1	Extract MAF blocks given a set of intervals	bx-python	bx-python		bx-python	Tools for manipulating biological data, particularly multiple sequence alignments.		Sequence analysis	To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	interval2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf	1.0.1+galaxy1	bx-python	0.13.0		Sequence analysis	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	32	107	7	10	758	19538	87	1246	16	24	2	2	806	19669	96	1258	False		
+intervene	intervene_pairwise, intervene_upset	Create pairwise and upset plots	intervene	intervene		Intervene	Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.	Sequence comparison, Sequence visualisation	Computational biology	Up-to-date	https://intervene.readthedocs.io	Statistics	intervene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene	0.6.5	intervene	0.6.5	Sequence comparison, Sequence visualisation	Computational biology	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1557	1607	278	292	4458	4458	458	458	0	0	0	0	6015	6065	736	750	False		
+ipo	ipo4retgroup, ipo4xcmsSet	[W4M][LC-MS] IPO								To update	https://github.com/rietho/IPO	Metabolomics	ipo	lecorguille	https://github.com/rietho/IPO	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo	1.10.0	bioconductor-ipo	1.28.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	28279	28481	1623	1646	24662	24662	2093	2093	9780	10086	979	992	62721	63229	4695	4731	False		
+irissv	irissv	Refine insertion sequences								To update	https://github.com/mkirsche/Iris	Variant Analysis	irissv	iuc	https://github.com/galaxyproject/tools-iuc/tools/irissv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv	1.0.5	samtools	1.21			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	29	29	8	8	0	0	0	0	0	0	0	0	29	29	8	8	False		
+isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	59386	59386	151	151	56	56	1	1	4741	4741	59	59	64183	64183	211	211	False		
+isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1301	1301	59	59	1331	1331	60	60	507	507	9	9	3139	3139	128	128	False		
+isolib	isolib	Create an isotopic pattern library for given compounds and adducts.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	isolib	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	1.0.1+galaxy0	bioconductor-metabocoreutils	1.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+isoplot	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	4	3	3	0	0	0	0	0	0	0	0	4	4	3	3	False		
+itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1426	1426	71	71	0	0	0	0	0	0	0	0	1426	1426	71	71	False		
+ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	0	5	5	5	0	1252220	1252220	2366	2366	126027	126027	2496	2496	41901	41901	993	993	1420148	1420148	5855	5855	False		
+iwtomics	iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot	Interval-Wise Testing for Omics Data	iwtomics	iwtomics		IWTomics	"Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset."	Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison	Statistics and probability	To update	https://bioconductor.org/packages/release/bioc/html/IWTomics.html	Statistics	iwtomics	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics	1.0.0	bioconductor-iwtomics	1.26.0	Differential gene expression analysis, Peak calling, Genome annotation, Comparison	Statistics and probability	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	675	690	27	28	159	251	29	49	383	383	12	12	1217	1324	68	89	False		
+jasminesv	jasminesv	Merge structural variants across samples								To update	https://github.com/mkirsche/Jasmine/	Variant Analysis	jasminesv	iuc	https://github.com/galaxyproject/tools-iuc/jasminesv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv	1.0.11	jasminesv	1.1.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32	32	9	9	53	53	19	19	0	0	0	0	85	85	28	28	False		
+jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	21153	22174	5514	5779	17428	17428	6458	6458	15673	17267	3248	3786	54254	56869	15220	16023	False		
+jbrowse	jbrowse_to_container	A tool allowing to export a JBrowse dataset into a JBrowse docker container								To update	https://jbrowse.org	Web Services	jbrowse_to_container	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse		python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse_2	jbrowse_2		JBrowse 2	Modular genome browser with views of synteny and structural variation.	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.15.4	jbrowse2	2.15.4	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1312	1312	219	219	116	116	58	58	37	37	6	6	1465	1465	283	283	False		
+jcvi_gff_stats	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.16			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2747	2926	596	637	2311	2311	741	741	1145	1145	469	469	6203	6382	1806	1847	False		
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1825	1825	237	237	0	0	0	0	971	971	56	56	2796	2796	293	293	False		
+join	gops_join_1	Join the intervals of two datasets side-by-side								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	join	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	15624	330820	1864	2438	52317	513688	10198	39421	1329	1645	213	289	69270	846153	12275	42148	False		
+join_files_by_id	join_files_by_id	This tool will join datasets according to a column with identifier								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	Text Manipulation	join_files_by_id	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id	1.0	r-data.table	1.11.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+join_files_on_column_fuzzy	join_files_on_column_fuzzy	Join two files on a common column, allowing a certain difference.								To update		Text Manipulation	join_files_on_column_fuzzy	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	1.0.1	python				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1980	2697	345	410	0	0	0	0	1081	1081	44	44	3061	3778	389	454	False		
+jq	jq	JQ is a lightweight and flexible command-line JSON processor								To update	https://stedolan.github.io/jq/	Text Manipulation	jq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq	1.0	jq	1.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	660	2374	61	63	336	336	82	82	281	281	11	11	1277	2991	154	156	False		
+jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	30	30	2	2	0	0	0	0	0	0	0	0	30	30	2	2	False		
+justdiff	justdiff	Unix diff								To update	http://artbio.fr	Text Manipulation	justdiff	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	3.10+galaxy0	diffutils				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+justgzip	justgzip	Compress fastq sequence files								To update	http://artbio.fr	Convert Formats	justgzip	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	2.8+galaxy0	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+jvarkit	jvarkit_wgscoverageplotter	Jvarkit : Java utilities for Bioinformatics								Up-to-date	https://lindenb.github.io/jvarkit/	SAM	jvarkit	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit	20201223	jvarkit-wgscoverageplotter	20201223			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7179	7179	509	509	11138	11138	1145	1145	0	0	0	0	18317	18317	1654	1654	False		
+kallisto	kallisto_pseudo, kallisto_quant	kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.	kallisto	kallisto		kallisto	A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.	Gene expression profiling	Transcriptomics, RNA-seq, Gene expression	To update	https://pachterlab.github.io/kallisto/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto	0.48.0	kallisto	0.51.1	Gene expression profiling	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	28398	29031	932	965	73705	80087	2603	3025	5333	5567	218	230	107436	114685	3753	4220	False		
+kaptive	kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kat_sect	kat_@EXECUTABLE@	SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.								To update			kat_sect	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	379	379	53	53	8259	8259	271	271	0	0	0	0	8638	8638	324	324	False		
+kegalign	kegalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	kegalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	0.1.2.7	kegalign-full	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	5	5	1	1	False		
+kernel_canonical_correlation_analysis	kcca1	Kernel Canonical Correlation Analysis								To update		Statistics	kernel_canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis	1.0.0	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	62	70	4	4	207	334	27	71	0	0	0	0	269	404	31	75	False		
+kernel_principal_component_analysis	kpca1	Kernel Principal Component Analysis								To update		Statistics	kernel_principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis	1.0.0	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	144	157	26	30	268	707	83	248	0	0	0	0	412	864	109	278	False		
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	8	8	8	0	1995	2091	174	193	1430	1430	389	389	1580	1580	56	56	5005	5101	619	638	False		
+king	king	Kinship-based INference for Gwas								Up-to-date	http://people.virginia.edu/~wc9c/KING/	Variant Analysis	king	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/king	2.2.7	king	2.2.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	8	4	4	0	0	0	0	0	0	0	0	8	8	4	4	False		
+kinwalker		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.1.0	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	503	503	58	58	0	0	0	0	0	0	0	0	503	503	58	58	False		
+kma	kma_map	Map with KMA								To update	https://bitbucket.org/genomicepidemiology/kma	Next Gen Mappers	kma	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma	1.4.14	kma	1.4.15			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+kmd_hmdb_data_plot	kmd_hmdb_data_plot	retrieves data from KMD HMDB API and produce plot and csv file								To update	https://github.com/workflow4metabolomics/tools-metabolomics	Metabolomics	kmd_hmdb_data_plot	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1342	1342	63	63	0	0	0	0	0	0	0	0	1342	1342	63	63	False		
+kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	5	5	5	0	48136	48164	2754	2760	59952	130398	5869	8654	29008	31148	1936	2200	137096	209710	10559	13614	False		
+kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	271367	271786	6384	6409	101752	101752	4662	4662	53562	53562	1663	1663	426681	427100	12709	12734	False		
+kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23008	23014	1060	1061	16194	24490	1719	2168	14898	14898	436	436	54100	62402	3215	3665	False		
+kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3185	3185	495	495	0	0	0	0	385	385	48	48	3570	3570	543	543	False		
+kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3981	3986	769	771	4087	5610	991	1284	88	88	41	41	8156	9684	1801	2096	False		
+krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	48516	48516	2373	2373	8787	8787	943	943	4369	4369	393	393	61672	61672	3709	3709	False		
+krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	38	2	2	0	0	0	0	0	0	0	0	34	38	2	2	False		
+labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	887	927	13	15	4	4	3	3	0	0	0	0	891	931	16	18	False		
+last	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1584	Sequence alignment	Comparative genomics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	329	329	94	94	0	0	0	0	0	0	0	0	329	329	94	94	False		
+lastz	lastz_wrapper_2, lastz_d_wrapper	Galaxy wrappers for the Lastz and Lastz_d	lastz	lastz		LASTZ	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.	Sequence alignment, Read mapping	Genomics	Up-to-date	https://github.com/lastz/lastz	Next Gen Mappers	lastz	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz	1.04.22	lastz	1.04.22	Sequence alignment, Read mapping	Genomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	77409	84356	447	475	156658	193590	870	3511	38579	38780	173	203	272646	316726	1490	4189	False		
+lastz_paired_reads	lastz_paired_reads_wrapper	Galaxy wrapper for the Lastz alignment tool on paired reads								To update		Next Gen Mappers	lastz_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads	1.1.1	lastz	1.04.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	9	3	4	0	0	0	0	8	10	5	5	15	19	8	9	False		
+lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	89	137	4	20	118	6136	15	1112	0	0	0	0	207	6273	19	1132	False		
+lcrgenie	lcrgenie	Ligase Chain Reaction Genie								To update	https://github.com/neilswainston/LCRGenie	Synthetic Biology	lcrgenie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie	1.0.2	lcr_genie				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lda_analysis	lda_analy1	Perform Linear Discriminant Analysis								To update		Graphics, Statistics	lda_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis	1.0.1	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	147	159	46	48	793	1538	101	314	0	4	0	3	940	1701	147	365	False		
+legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	92	92	8	8	0	0	0	0	0	0	0	0	92	92	8	8	False		
+length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	4349	4466	666	698	2093	2286	928	998	201	201	77	77	6643	6953	1671	1773	False		
+lfq_protein_quant	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	78	116	12	19	0	0	0	0	0	0	0	0	78	116	12	19	False		
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	171	27	30	0	0	0	0	0	0	0	0	149	171	27	30	False		
+limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23442	24466	2379	2475	45734	49342	4565	5032	9327	9517	835	842	78503	83325	7779	8349	False		
+lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	39	4	4	0	0	0	0	0	0	0	0	39	39	4	4	False		
+linear_regression	LinearRegression1	Perform Linear Regression								To update		Statistics	linear_regression	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression	https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression	1.0.1	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	146	1103	31	271	0	0	0	0	146	1103	31	271	False		
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	512	512	126	126	0	0	0	0	480	480	65	65	992	992	191	191	False		
+locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								Up-to-date	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	2.0.1	locarna	2.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	314	350	36	46	0	0	0	0	0	0	0	0	314	350	36	46	False		
+lofreq	lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi	LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.								Up-to-date	https://csb5.github.io/lofreq/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq	2.1.5	lofreq	2.1.5			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	0	0	0	4	0	0	0	0	0	0	5	5	5	0	4176367	4176367	4301	4301	509615	509615	8213	8213	106342	106342	1815	1815	4792324	4792324	14329	14329	False		
+logistic_regression_vif	LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	64	173	12	48	0	0	0	0	64	173	12	48	False		
+logol	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+longorf	longORF	obtain longest ORF in six-frame translations								To update		Sequence Analysis	longorf	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf	0.3.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	822	822	14	14	0	0	0	0	0	0	0	0	822	822	14	14	False		
+lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1219	1219	182	182	0	0	0	0	37	37	4	4	1256	1256	186	186	False		
+ltq_iquant_cli										To update			ltq_iquant_cli	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lumpy_smoove	lumpy_smoove, vcf2hrdetect	Galaxy wrapper of the lumpy-using smoove workflow								To update	http://artbio.fr	Variant Analysis	lumpy_smoove	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	0.2.8+galaxy1	svtyper	0.7.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lumpy_sv	lumpy_prep, lumpy_sv	LUMPY - a general probabilistic framework for structural variant discovery								Up-to-date	http://layerlab.org/software/	Variant Analysis	lumpy_sv	iuc	https://github.com/arq5x/lumpy-sv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv	0.3.1	lumpy-sv	0.3.1			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	1534	1534	199	199	0	0	0	0	0	0	0	0	1534	1534	199	199	False		
+lumpy_sv	lumpy	Find structural variations								To update	http://artbio.fr	Variant Analysis	lumpy_sv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv	1.3	lumpy-sv	0.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	44	44	11	11	0	0	0	0	0	0	0	0	44	44	11	11	False		
+maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2835	2835	59	59	0	0	0	0	0	0	0	0	2835	2835	59	59	False		
+macs2	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	0	0	9	0	0	0	0	0	0	9	9	9	0	87810	96069	4980	5629	153500	227569	12946	18825	10988	12301	692	807	252298	335939	18618	25261	False		
+maf_cpg_filter	cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	85	356	6	28	0	0	0	0	85	356	6	28	False		
+maf_stats	maf_stats1	MAF Coverage statistics								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	maf_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats	1.0.2+galaxy0					1	1	1	0	1	1	1	0	0	1	0	0	0	1	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	1	0	15	21	7	9	227	2470	52	464	1	1	1	1	243	2492	60	474	False		
+mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	0	2	2	2	0	172433	174456	1865	1951	108640	122790	4266	5521	20027	20027	1172	1172	301100	317273	7303	8644	False		
+maftoaxt	maftoaxt	Convert dataset from MAF to axt format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_maftoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	469	ucsc-maftoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mageck	mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test	Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	mageck	mageck		MAGeCK	Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	Genetic variation analysis	Genetics, Genetic variation, Genomics	To update	https://sourceforge.net/projects/mageck/	Genome editing		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck	0.5.9.2	mageck	0.5.9.5	Genetic variation analysis	Genetics, Genetic variation, Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	11761	12093	873	889	5762	5762	473	473	5610	5610	343	343	23133	23465	1689	1705	False		
+mahotas_features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	44	6	6	0	0	0	0	0	0	0	0	39	44	6	6	False		
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6417	6861	1315	1366	7235	7235	1858	1858	4112	4112	902	902	17764	18208	4075	4126	False		
+maldiquant	maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base				0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1452	3822	61	68	0	0	0	0	1065	1065	39	39	2517	4887	100	107	False		
+malt	malt_run	Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.								To update	https://github.com/husonlab/malt	Next Gen Mappers	malt_run	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt	0.5.3	malt	0.62			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	24	9	9	0	0	0	0	0	0	0	0	24	24	9	9	False		
+manta	manta	Structural variant and indel caller for mapped sequencing data								To update	http://artbio.fr	Variant Analysis	manta	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/manta	https://github.com/ARTbio/tools-artbio/tree/main/tools/manta	1.6	manta	1.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	218	218	34	34	0	0	0	0	0	0	0	0	218	218	34	34	False		
+map_param_value	map_param_value	Map a parameter value to another value								To update		Text Manipulation	map_param_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3780	3780	67	67	1012	1012	57	57	105	105	3	3	4897	4897	127	127	False		
+map_peptides_to_bed	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	38	44	6	7	0	0	0	0	0	0	0	0	38	44	6	7	False		
+mapping_quality_stats	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mapping_to_ucsc	mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7871	7871	32	32	0	0	0	0	0	0	0	0	7871	7871	32	32	False		
+marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	51	51	4	4	0	0	0	0	0	0	0	0	51	51	4	4	False		
+mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	10119	10119	61	61	19	19	9	9	647	647	7	7	10785	10785	77	77	False		
+mashmap	mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	894	894	12	12	81	81	5	5	0	0	0	0	975	975	17	17	False		
+masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	471	582	35	40	589	589	80	80	0	0	0	0	1060	1171	115	120	False		
+matchms	matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting	Searching, filtering and converting mass spectral libraries.	matchms	matchms		Matchms	Tool to import, process, clean, and compare mass spectrometry data.	Spectral library search, Format validation, Filtering	Metabolomics	Up-to-date	https://github.com/matchms/matchms	Metabolomics	matchms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	0.27.0	matchms	0.27.0	Spectral library search, Format validation, Filtering	Metabolomics	2	14	14	0	2	14	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	1620	1620	70	70	27	27	8	8	1685	1685	12	12	3332	3332	90	90	False		
+mauve_contig_mover	mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mavedb	mavedb_importer	data source for MaveDB								To update		Data Source	mavedb_importer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb	0.9					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	2	2	0	0	0	0	0	0	0	0	8	8	2	2	False		
+maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	1	0	2798	2798	314	314	2452	2452	508	508	914	914	89	89	6164	6164	911	911	False		
+maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6863	7021	1251	1264	2798	2798	543	543	3189	3189	352	352	12850	13008	2146	2159	False		
+mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	35	13	13	0	0	0	0	0	0	0	0	35	35	13	13	False		
+mdanalysis	mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf	MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations								To update	https://github.com/MDAnalysis/mdanalysis	Computational chemistry	mdanalysis	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis	1.0.0	mdanalysis				10	5	10	0	10	5	10	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	3209	3268	318	326	182	182	51	51	397	397	39	39	3788	3847	408	416	False		
+mdfileconverter	md_converter	A tool for interconverting between different MD structure and trajectory file formats.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter	1.9.7	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26720	26762	251	253	784	784	54	54	977	977	53	53	28481	28523	358	360	False		
+mdslicer	md_slicer	A tool for slicing trajectory files using MDTraj.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer	1.9.9	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	174	174	19	19	6	6	4	4	441	441	7	7	621	621	30	30	False		
+mdtraj	traj_selections_and_merge	MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories								To update	https://github.com/mdtraj/mdtraj	Computational chemistry	mdtraj	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj	1.9.7	mdtraj				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	36	8	8	63	63	4	4	0	0	0	0	99	99	12	12	False		
+mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	73	86	5	5	0	0	0	0	0	0	0	0	73	86	5	5	False		
+mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	3	3	0	0	0	0	0	0	0	0	20	25	3	3	False		
+measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	0	3	3	3	0	117975	117975	1693	1693	55063	55063	796	796	9325	9325	639	639	182363	182363	3128	3128	False		
+medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	9	9	0	0	0	0	0	0	0	0	27	27	9	9	False		
+megablast_xml_parser	megablast_xml_parser	Parse blast XML output								To update		Next Gen Mappers, Convert Formats	megablast_xml_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	743	816	103	141	292	2868	82	459	0	0	0	0	1035	3684	185	600	False		
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	12692	13292	1349	1400	16645	16645	2140	2140	6214	6214	431	431	35551	36151	3920	3971	False		
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	513	557	152	155	74	74	35	35	10	10	4	4	597	641	191	194	False		
+megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	4130	4130	447	447	0	0	0	0	0	0	0	0	4130	4130	447	447	False		
+meme	meme_dreme, meme_fimo, meme_meme, meme_psp_gen	The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.	meme_meme	meme_fimo, meme_meme		meme_meme	An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	To update	http://meme-suite.org/	ChIP-seq	meme	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme	5.5.6	meme	5.5.7	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	3	0	4	0	3	0	4	0	0	0	0	0	0	0	0	0	0	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	4	4	0	20990	22979	762	892	10975	25929	1551	3249	0	0	0	0	31965	48908	2313	4141	False		
+meme_chip	meme_chip	Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.								To update	http://meme-suite.org/	ChIP-seq	meme_chip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip	4.11.2	graphicsmagick	1.3.26			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6413	7000	705	743	7260	7260	1171	1171	0	0	0	0	13673	14260	1876	1914	False		
+meneco	meneco	Meneco computes minimal completions to your draft network with reactions from a repair network								Up-to-date	http://bioasp.github.io/meneco/	Systems Biology	meneco	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	1.5.2	meneco	1.5.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+merge	gops_merge_1	Merge the overlapping intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	565922	566630	418	441	45844	107523	671	4353	19828	19994	100	137	631594	694147	1189	4931	False		
+merge_cols	mergeCols1	Merge columns together.								To update		Text Manipulation	merge_cols	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols	https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols	1.0.3	python				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	20905	31051	1906	2128	21780	132833	885	3172	1524	1925	122	152	44209	165809	2913	5452	False		
+mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	25	2	3	0	0	0	0	0	0	0	0	18	25	2	3	False		
+merlin	merlin	Pedigree Analysis package	merlin	merlin		Merlin	Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation	Haplotype mapping, Genetic mapping	GWAS study, Mapping	Up-to-date	http://csg.sph.umich.edu/abecasis/Merlin/	Variant Analysis	merlin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin	1.1.2	merlin	1.1.2	Haplotype mapping	GWAS study, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3150	3150	477	477	730	730	196	196	1183	1183	151	151	5063	5063	824	824	False		
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+meta_proteome_analyzer	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	126	126	20	20	0	0	0	0	0	0	0	0	126	126	20	20	False		
+metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	0	2	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	6135	6135	382	382	881	881	151	151	1094	1094	104	104	8110	8110	637	637	False		
+metabuli	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	metabuli	metabuli		metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid	Taxonomic classification	Taxonomy	To update	https://github.com/steineggerlab/Metabuli	Sequence Analysis, Metagenomics	metabuli	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli	1.0.5	metabuli	1.0.8	Taxonomic classification	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	7.bba0d80	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	312	312	40	40	0	0	0	0	0	0	0	0	312	312	40	40	False		
+metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	980	980	323	323	0	0	0	0	0	0	0	0	980	980	323	323	False		
+metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	556	756	17	21	310	514	35	55	0	0	0	0	866	1270	52	76	False		
+metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4471	4471	29	29	0	0	0	0	0	0	0	0	4471	4471	29	29	False		
+metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	0	1	2	4	0	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	16629	16648	1183	1187	3983	3983	572	572	4747	4747	278	278	25359	25378	2033	2037	False		
+metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	2730	2831	260	262	0	0	0	0	1540	1540	71	71	4270	4371	331	333	False		
+metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	142	142	32	32	0	0	0	0	379	379	47	47	521	521	79	79	False		
+metfrag	metfrag	[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity)								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag	2.4.5+galaxy3	metfrag	2.4.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	192	192	20	20	0	0	0	0	0	0	0	0	192	192	20	20	False		
+metfrag-vis	metfrag_vis	[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis	2.4.5+galaxy0	metfrag	2.4.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	50	14	14	0	0	0	0	0	0	0	0	50	50	14	14	False		
+methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	632	5461	155	453	0	0	0	0	0	0	0	0	632	5461	155	453	False		
+methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	14907	18971	638	894	2677	2677	230	230	2313	2313	83	83	19897	23961	951	1207	False		
+methylkit	methylkit	A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.								To update	http://bioconductor.org/packages/release/bioc/html/methylKit.html	Epigenetics	methylkit	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	0.99.2	bioconductor-methylkit	1.28.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3209	4572	312	442	479	479	79	79	315	315	51	51	4003	5366	442	572	False		
+mfassignr	mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot	The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements	mfassignr	mfassignr		MFAssignR	Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements.	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	Up-to-date	https://github.com/RECETOX/MFAssignR	Metabolomics	MFAssignR	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	1.1.1	r-mfassignr	1.1.1	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	8	8	0	0	0	0	0	0	0	0	10	10	8	8	False		
+mg_toolkit	mg_toolkit_bulk_download, mg_toolkit_original_metadata	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	mg-toolkit	mg-toolkit		mg-toolkit	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	Data retrieval	Metagenomics	Up-to-date	https://github.com/EBI-Metagenomics/emg-toolkit	Metagenomics	mg_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	0.10.4	mg-toolkit	0.10.4	Data retrieval	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+mgf_formatter	mgf_formatter									Up-to-date			mgf_formatter	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter	1.0.0	mgf-formatter	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	573	573	3	3	0	0	0	0	0	0	0	0	573	573	3	3	False		
+miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+microsatbed	microsatbed	Select microsatellites for a bed file								To update	https://github.com/lmdu/pytrf	Sequence Analysis	microsatbed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed	1.3.3	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	228	4	4	18	18	1	1	0	0	0	0	246	246	5	5	False		
+microsatellite_birthdeath	microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+microsats_alignment_level	microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	135	973	50	140	0	0	0	0	135	973	50	140	False		
+microsats_mutability	microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	34	312	22	87	0	0	0	0	34	312	22	87	False		
+migmap	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	Sequence analysis, Read mapping	Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1082	1229	25	33	1153	1376	70	89	0	0	0	0	2235	2605	95	122	False		
+minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1213	1309	115	124	0	0	0	0	0	0	0	0	1213	1309	115	124	False		
+mine	maximal_information_based_nonparametric_exploration	Maximal Information-based Nonparametric Exploration								To update		Variant Analysis	mine	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine	0.0.1	MINE				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	11	8	8	17	63	6	19	0	0	0	0	26	74	14	27	False		
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7116	7116	256	256	0	0	0	0	278	278	60	60	7394	7394	316	316	False		
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13357	13479	554	562	8416	8416	448	448	898	898	85	85	22671	22793	1087	1095	False		
+minimap2	minimap2	A fast pairwise aligner for genomic and spliced nucleotide sequences	minimap2	minimap2		Minimap2	Pairwise aligner for genomic and spliced nucleotide sequences	Pairwise sequence alignment	Mapping	Up-to-date	https://github.com/lh3/minimap2	Next Gen Mappers	minimap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2	2.28	minimap2	2.28	Pairwise sequence alignment	Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	346530	349075	4323	4419	108535	108535	4075	4075	22331	22331	1166	1166	477396	479941	9564	9660	False		
+minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	229	229	32	32	0	0	0	0	0	0	0	0	229	229	32	32	False		
+miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1244	1244	86	86	24	24	15	15	0	0	0	0	1268	1268	101	101	False		
+miranda	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6408	6514	94	99	0	0	0	0	0	0	0	0	6408	6514	94	99	False		
+miranda2asko	miranda2asko	Converts miRanda output into AskOmics format								To update		Convert Formats	miranda2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	0.2	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1458	1458	36	36	1458	1458	36	36	False		
+mirmachine	mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	False		
+mirnature	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	18	18	9	9	0	0	0	0	0	0	0	0	18	18	9	9	False		
+misc	target_screen, use_theoretical_mz_annotations									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	1.0.0	pandas				0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	2	2	0	0	0	0	0	0	0	0	6	6	2	2	False		
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1117	1117	116	116	0	0	0	0	295	295	25	25	1412	1412	141	141	False		
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1020	1020	176	176	414	414	73	73	277	277	20	20	1711	1711	269	269	False		
+mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	0	191295	191295	1111	1111	42265	42265	320	320	10904	10904	83	83	244464	244464	1514	1514	False		
+mixmodel4repeated_measures	mixmodel4repeated_measures	[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model								To update	http://workflow4metabolomics.org	Metabolomics	mixmodel4repeated_measures	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures	3.1.0	r-lme4				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	13300	13471	1480	1501	6532	6532	1167	1167	10334	11841	1083	1300	30166	31844	3730	3968	False		
+moFF	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	331	762	20	34	0	0	0	0	137	137	4	4	468	899	24	38	False		
+moabs	moabs	MOABS for differential methylation analysis on Bisulfite sequencing data.								To update	https://github.com/sunnyisgalaxy/moabs	Epigenetics	moabs	iuc	https://github.com/sunnyisgalaxy/moabs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs	1.3.4.6	moabs	1.3.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	339	339	56	56	0	0	0	0	0	0	0	0	339	339	56	56	False		
+mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	119024	119024	628	628	42	42	2	2	36310	36310	191	191	155376	155376	821	821	False		
+molecule2gspan	bg_mol2gspan	converter								To update	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	Convert Formats	molecule_to_gspan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	0.2	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3610	3610	559	559	1728	1728	434	434	0	0	0	0	5338	5338	993	993	False		
+morpheus	morpheus	Morpheus MS Search Application	morpheus	morpheus		Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.	Peptide database search	Proteomics	To update	https://cwenger.github.io/Morpheus	Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	288	morpheus	290	Peptide database search	Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	105	153	12	19	0	0	0	0	833	833	93	93	938	986	105	112	False		
+morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mosdepth	mosdepth	fast and flexible BAM/CRAM depth calculation								Up-to-date	https://github.com/brentp/mosdepth	SAM	mosdepth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth	0.3.8	mosdepth	0.3.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1278	1278	87	87	168	168	24	24	102	102	5	5	1548	1548	116	116	False		
+mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	0	129	129	129	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	126	129	129	0	297546	326056	37506	41763	565218	682083	72163	89926	167400	182490	26963	28404	1030164	1190629	136632	160093	False		
+motus	mereg_mOTUs_tables, motus_profiler	Tool for profiling the abundance of microbial taxa.	mOTUs	mOTUs		Metagenomic operational taxonomic units (mOTUs)	Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/motu-tool/mOTUs	Metagenomics	motus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs	https://github.com/bgruening/galaxytools/tree/master/tools/motus	3.1.0	motus	3.1.0	Taxonomic classification	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	76	9	9	0	0	0	0	0	0	0	0	71	76	9	9	False		
+mqppep	mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	13	13	3	3	0	0	0	0	0	0	0	0	13	13	3	3	False		
+mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ms2deepscore	ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training	Mass spectra similarity scoring using a trained ms2deepscore model.	ms2deepscore	ms2deepscore		MS2DeepScore	MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	To update	https://github.com/matchms/ms2deepscore	Metabolomics	ms2deepscore	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	2.0.0	ms2deepscore	2.1.0	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ms2snoop	ms2snoop	[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.								To update	http://workflow4metabolomics.org	Metabolomics	ms2snoop	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop	2.2.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+msPurity	mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								Up-to-date	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity	1.28.0	bioconductor-mspurity	1.28.0			0	0	10	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	848	848	91	91	0	0	0	0	0	0	0	0	848	848	91	91	False		
+msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	864	929	91	101	1100	1100	175	175	0	0	0	0	1964	2029	266	276	False		
+msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20749	22184	455	469	1239	1239	71	71	2666	2666	53	53	24654	26089	579	593	False		
+msgfplus	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	473	529	33	43	0	0	0	0	0	0	0	0	473	529	33	43	False		
+msmetaenhancer	msmetaenhancer		msmetaenhancer	msmetaenhancer		MSMetaEnhancer	Tool for mass spectra metadata annotation.	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/MSMetaEnhancer	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	0.4.0	msmetaenhancer	0.4.0	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	10	10	0	0	0	0	48	48	1	1	251	251	11	11	False		
+msms_extractor	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	110	110	11	11	0	0	0	0	0	0	0	0	110	110	11	11	False		
+msp_merge	msp_merge									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	0.1.0	matchms	0.27.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+msp_split	msp_split	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								To update	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		tomnl	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split	0.0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+msstats	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2353	2353	559	559	1122	1122	211	211	1091	1091	35	35	4566	4566	805	805	False		
+msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	795	795	104	104	0	0	0	0	461	461	12	12	1256	1256	116	116	False		
+mt2mq	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	275	275	38	38	0	0	0	0	0	0	0	0	275	275	38	38	False		
+multigps	multigps	Analyzes collections of multi-condition ChIP-seq data.								To update	http://mahonylab.org/software/multigps/	ChIP-seq	multigps	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps	0.74.0	fonts-conda-ecosystem				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	485	871	159	298	0	0	0	0	485	871	159	298	False		
+multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	106	106	25	25	0	0	0	0	0	0	0	0	106	106	25	25	False		
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	182221	192389	19343	20494	163961	182413	26449	29758	40663	41855	5974	6157	386845	416657	51766	56409	False		
+multispecies_orthologous_microsats	multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mummer	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	883	921	199	211	730	730	199	199	136	202	34	49	1749	1853	432	459	False		
+mummer4	mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1			6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	6	3	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	21587	22119	1940	2033	29284	29284	3626	3626	8194	8194	545	545	59065	59597	6111	6204	False		
+music_deconvolution	music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)								Up-to-date	https://github.com/xuranw/MuSiC	Transcriptomics	music	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/	https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution	0.1.1	music-deconvolution	0.1.1			5	5	4	0	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	2801	2801	289	289	364	364	80	80	1357	1357	21	21	4522	4522	390	390	False		
+mutate_snp_codon	mutate_snp_codon_1	Mutate Codons with SNPs								To update		Variant Analysis	mutate_snp_codon	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	44	49	5	5	81	417	23	118	0	0	0	0	125	466	28	123	False		
+mutational_patterns	mutational_patterns	Mutational patterns and signatures in base substitution catalogs								Up-to-date	http://artbio.fr	Variant Analysis	mutational_patterns	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	3.12.0	bioconductor-mutationalpatterns	3.12.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	854	860	110	111	79	79	15	15	274	274	13	13	1207	1213	138	139	False		
+mzmine	mzmine_batch	mass-spectrometry data processing, with the main focus on LC-MS data	mzmine	mzmine		MZmine	Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	Up-to-date	http://mzmine.github.io/	Metabolomics	mzmine_batch	iuc	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine	3.9.0	mzmine	3.9.0	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5	False		
+mzml_validator	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mzxmlshaper	mzxmlshaper	Convert mzML, mzXML or netCDF files to mzML or mzXML								To update	https://rdrr.io/bioc/mzR/	Metabolomics	mzxmlshaper	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper	1.0.0+galaxy0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+naltorfs	bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2			3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	204	204	75	75	0	0	0	0	204	204	75	75	False		
+nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	839	839	12	12	0	0	0	0	269	269	5	5	1108	1108	17	17	False		
+nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	99052	100009	5671	5755	40386	40386	3371	3371	17919	17919	2188	2188	157357	158314	11230	11314	False		
+nanopolish	nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants	Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.								Up-to-date	https://github.com/jts/nanopolish		nanopolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	0.14.0	nanopolish	0.14.0			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	9284	9694	215	229	0	0	0	0	2358	2358	49	49	11642	12052	264	278	False		
+nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1091	1091	44	44	0	0	0	0	0	0	0	0	1091	1091	44	44	False		
+nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	40	1	1	0	0	0	0	0	0	0	0	36	40	1	1	False		
+ncbi_acc_download	ncbi_acc_download	Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API								Up-to-date	https://github.com/kblin/ncbi-acc-download	Data Source	ncbi_acc_download	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download	0.2.8	ncbi-acc-download	0.2.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6873	6873	1664	1664	17651	17651	4513	4513	6228	6228	972	972	30752	30752	7149	7149	False		
+ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	15	16	16	15	0	391141	443752	9760	10546	306361	350178	11767	13684	227235	244814	3192	3617	924737	1038744	24719	27847	False		
+ncbi_datasets	datasets_download_gene, datasets_download_genome	NCBI datasets downloads biological sequence data across all domains of life from NCBI.	ncbi_datasets	ncbi_datasets		NCBI Datasets	NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.	Data handling, Sequence database search, Data retrieval	Biological databases	To update	https://github.com/ncbi/datasets	Data Source	ncbi_datasets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets	16.20.0	ncbi-datasets-cli		Data handling, Sequence database search, Data retrieval	Biological databases	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	1	2	2	0	4417	4417	1024	1024	6940	6940	2275	2275	1	1	1	1	11358	11358	3300	3300	False		
+ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	6	6	0	0	0	0	15	15	6	6	False		
+ncbi_entrez_direct	ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch	NCBI Entrez Direct allow fetching data from NCBI Databases								Up-to-date	http://www.ncbi.nlm.nih.gov/books/NBK179288/	Data Source	ncbi_entrez_direct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct	22.4	entrez-direct	22.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	2	0	0	0	0	0	3	0	2	False		
+ncbi_entrez_eutils	ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary	NCBI Entrez E-Utilties allow fetching data from NCBI Databases								To update	https://www.ncbi.nlm.nih.gov/books/NBK25501/	Data Source	ncbi_entrez_eutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils	1.70	python				0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	4	0	0	0	2	0	0	0	0	0	0	0	7	7	0	2794	3191	533	664	0	0	0	0	0	0	0	0	2794	3191	533	664	False		
+ncbi_fcs_adaptor	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	842	842	93	93	0	0	0	0	842	842	93	93	False		
+ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	125	125	26	26	2489	2489	139	139	0	0	0	0	2614	2614	165	165	False		
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	790	790	160	160	0	0	0	0	0	0	0	0	790	790	160	160	False		
+netboxr	netboxr	netboxr enables automated discovery of biological process modules by network analysis								To update		Systems Biology	netboxr	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/netboxr	1.6.0	bioconductor-netboxr	1.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	12	6	6	0	0	0	0	0	0	0	0	12	12	6	6	False		
+newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33637	34195	1113	1172	16257	16257	1816	1816	7582	7582	899	899	57476	58034	3828	3887	False		
+nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	0	2	0	0	4411	4411	396	396	9708	9708	279	279	2099	2099	212	212	16218	16218	887	887	False		
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	391	391	158	158	0	0	0	0	0	0	0	0	391	391	158	158	False		
+ngmlr	ngmlr	CoNvex Gap-cost alignMents for Long Reads	ngmlr	ngmlr		NGMLR	An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping, DNA structural variation	Up-to-date	https://github.com/philres/ngmlr	Next Gen Mappers	ngmlr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr	0.2.7	ngmlr	0.2.7	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1403	1403	49	49	0	0	0	0	0	0	0	0	1403	1403	49	49	False		
+ngsutils	ngsutils_bam_filter	NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.	ngsutils	ngsutils		NGSUtils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets	Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering	Genomics, Transcriptomics	To update	https://github.com/ngsutils/ngsutils	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils		ngsutils	0.5.9	Read pre-processing, Variant calling, Formatting, Sequence contamination filtering	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	24611	29662	633	716	15523	21395	740	1128	7751	8972	125	145	47885	60029	1498	1989	False		
+nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+nmr_annotation	NmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation								To update	http://workflow4metabolomics.org	Metabolomics	nmr_annotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_annotation	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation	3.0.0	r-batch	1.1_4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	49	49	5	5	0	0	0	0	0	0	0	0	49	49	5	5	False		
+nmr_annotation2d	2DNmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra								To update	http://workflow4metabolomics.org	Metabolomics	2dnmrannotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d	2.0.0	r-batch	1.1_4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+nmr_preprocessing	NMR_Preprocessing, NMR_Read	[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction								To update	http://workflow4metabolomics.org	Metabolomics	nmr_preprocessing	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_preprocessing	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing		r-batch	1.1_4			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	142	142	8	8	0	0	0	0	335	341	9	9	477	483	17	17	False		
+nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	107	143	13	15	148	148	20	20	0	0	0	0	255	291	33	35	False		
+normalization	normalization	[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data								To update	http://workflow4metabolomics.org	Metabolomics	normalization	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/normalization	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization	1.0.7	r-batch	1.1_4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	152	162	39	40	0	0	0	0	233	236	12	12	385	398	51	52	False		
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	7780	7780	337	337	1	1	1	1	2323	2323	99	99	10104	10104	437	437	False		
+nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	118	863	19	26	0	0	0	0	0	0	0	0	118	863	19	26	False		
+nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+numeric_clustering	numeric_clustering	Clustering tool for numberic values								To update	http://scikit-learn.org/stable/index.html	Statistics	numeric_clustering	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	0.9	anaconda				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	391	486	5	11	0	0	0	0	0	0	0	0	391	486	5	11	False		
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	352	352	42	42	8	8	6	6	0	0	0	0	360	360	48	48	False		
+obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	37598	37598	1277	1277	0	0	0	0	3862	3862	280	280	41460	41460	1557	1557	False		
+ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	54	6	6	0	0	0	0	0	0	0	0	54	54	6	6	False		
+ococo	ococo	Variant detection of SNVs								To update	https://github.com/karel-brinda/ococo	Variant Analysis	ococo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo	0.1.2.6	ococo	0.1.2.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1850	1963	79	93	1370	1370	194	194	0	0	0	0	3220	3333	273	287	False		
+odgi	odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	26	26	6	6	0	0	0	0	0	0	0	0	26	26	6	6	False		
+ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	98	6	6	0	0	0	0	0	0	0	0	98	98	6	6	False		
+ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	57	57	4	4	0	0	0	0	0	0	0	0	57	57	4	4	False		
+omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	158	158	12	12	0	0	0	0	0	0	0	0	158	158	12	12	False		
+omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	3051	3051	87	87	0	0	0	0	0	0	0	0	3051	3051	87	87	False		
+onto_toolkit	onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def	ONTO-Toolkit is a collection of tools for managing ontologies.								Up-to-date	http://search.cpan.org/~easr/ONTO-PERL-1.45/	Ontology Manipulation	onto_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit	1.45	perl-onto-perl	1.45			0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	0	582	663	68	69	0	0	0	0	0	0	0	0	582	663	68	69	False		
+openlabcds2csv	openlabcds2csv	"Creates a summary of several ""Internal Standard Report"" OpenLabCDS results."								To update		Metabolomics	openlabcds2csv	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+openmm	pdbfixer	OpenMM is a toolkit for molecular simulation using high performance GPU code.								To update	https://github.com/openmm	Molecular Dynamics, Computational chemistry	openmm	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	1.8.1	pdbfixer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	491	491	52	52	0	0	0	0	0	0	0	0	491	491	52	52	False		
+openms	AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	3.1	openms	3.2.0			8	34	144	0	8	34	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	141	124	0	32169	108654	3316	4889	50	50	15	15	940	940	245	245	33159	109644	3576	5149	False		
+openms	AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.2.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	135	134	0	31121	108907	3369	5029	50	50	15	15	933	933	242	242	32104	109890	3626	5286	False		
+optdoe	optdoe	Optimal Design Of Experiment								To update	https://github.com/pablocarb/doebase	Synthetic Biology	optdoe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe	v2.0.2	doebase				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+optitype	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	500	500	45	45	0	0	0	0	0	0	0	0	500	500	45	45	False		
+orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	897	897	99	99	1792	1792	239	239	0	0	0	0	2689	2689	338	338	False		
+orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	To update	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	3.0.1b1	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2018	2018	419	419	0	0	0	0	438	438	58	58	2456	2456	477	477	False		
+overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	149	149	31	31	0	0	0	0	18	18	1	1	167	167	32	32	False		
+packaged_annotation_loader	packaged_annotation_loader	Tool to make cached genome annotation data available as a list of datasets collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	Data Source	packaged_annotation_loader	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+packmol	packmol	PACKMOL is a package for creating starting structures for Molecular Dynamics simulations								To update	http://m3g.iqm.unicamp.br/packmol/home.shtml	Molecular Dynamics, Computational chemistry	packmol	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol	18.169.1	packmol				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	282	295	32	33	420	420	8	8	0	0	0	0	702	715	40	41	False		
+pacu	pacu_map, pacu_snp	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.	pacu	pacu		PACU	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).	Clustering	Phylogenetics, Sequence analysis	Up-to-date	https://github.com/BioinformaticsPlatformWIV-ISP/PACU	Sequence Analysis, Phylogenetics	pacu	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu	0.0.5	pacu_snp	0.0.5	Clustering	Phylogenetics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pairtools	pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0			5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	196	196	16	16	19	19	14	14	0	0	0	0	215	215	30	30	False		
+pandas_rolling_window	pandas_rolling_window	Rolling window calculations								To update	https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html	Statistics	pandas_rolling_window	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	0.1	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	261	275	12	12	63	63	22	22	0	0	0	0	324	338	34	34	False		
+pangolin	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	0	0	7457	7457	508	508	8518	8518	377	377	2760	2760	259	259	18735	18735	1144	1144	False		
+pangolin	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	Tree-based sequence alignment, Variant classification	Virology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	0	0	7457	7457	508	508	8518	8518	377	377	2760	2760	259	259	18735	18735	1144	1144	False		
+paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	322	349	24	29	0	0	0	0	0	0	0	0	322	349	24	29	False		
+parse_mito_blast	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	65	65	288	288	62	62	110	110	20	20	601	601	147	147	False		
+partialr_square	partialRsq	Compute partial R square								To update		Statistics	partialr_square	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square	https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	55	142	8	42	0	0	0	0	55	142	8	42	False		
+pathifier	pathifier	pathifier								Up-to-date	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	1.40.0	bioconductor-pathifier	1.40.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	245	245	10	10	0	0	0	0	0	0	0	0	245	245	10	10	False		
+pathview	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6204	6211	1261	1261	6667	6667	1143	1143	1160	1160	189	189	14031	14038	2593	2593	False		
+pathwaymatcher	reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	174	244	65	76	0	0	0	0	0	0	0	0	174	244	65	76	False		
+patrist	patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pbgcpp	pbgcpp	Compute genomic consensus and call variants using PacBio reads mapped to a reference	genomicconsensus	genomicconsensus		GenomicConsensus	The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.	Variant calling	Mapping	Up-to-date	https://github.com/PacificBiosciences/gcpp	Variant Analysis	pbgcpp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp	2.0.2	pbgcpp	2.0.2	Variant calling	Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pbmm2	pbmm2	A minimap2 SMRT wrapper for PacBio data.	pbmm2	pbmm2		pbmm2	pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.	Pairwise sequence alignment, Sorting	Mapping	Up-to-date	https://github.com/PacificBiosciences/pbmm2	Next Gen Mappers	pbmm2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2	1.14.99	pbmm2	1.14.99	Pairwise sequence alignment, Sorting	Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	70	17	17	0	0	0	0	0	0	0	0	70	70	17	17	False		
+pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	22	22	109	109	19	19	0	0	0	0	167	167	41	41	False		
+pe_histogram	pe_histogram	Contains a tool that produces an insert size histogram for a paired-end BAM file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram	Graphics	pe_histogram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram	1.0.2	openjdk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	5505	5505	510	510	7932	8582	811	909	736	736	119	119	14173	14823	1440	1538	False		
+peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2807	3337	178	196	0	0	0	0	0	0	0	0	2807	3337	178	196	False		
+peakzilla	peakzilla	Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.								To update	https://github.com/steinmann/peakzilla	ChIP-seq	peakzilla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla	1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	9	9	0	0	0	0	0	0	0	0	18	18	9	9	False		
+pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	6269	6866	260	292	5530	20068	467	1664	5647	8471	198	300	17446	35405	925	2256	False		
+pearson_correlation	Pearson_and_apos_Correlation1	Pearson and apos Correlation between any two numeric columns								To update		Statistics	pearson_correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	2	0	2	False		
+pep_pointer	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	506	511	54	55	21	21	12	12	163	163	8	8	690	695	74	75	False		
+pepquery	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7047	7047	76	76	0	0	0	0	0	0	0	0	7047	7047	76	76	False		
+pepquery2	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2			0	1	3	0	0	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1222	1222	28	28	0	0	0	0	0	0	0	0	1222	1222	28	28	False		
+peptide_genomic_coordinate	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	472	472	56	56	16	16	10	10	149	149	5	5	637	637	71	71	False		
+peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.11			4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	2	0	11986	17898	1046	1153	1314	1314	389	389	3034	3034	118	118	16334	22246	1553	1660	False		
+peptimapper	peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pepxml_to_xls		Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+percolator	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.7.1			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	338	378	15	16	0	0	0	0	1059	1059	13	13	1397	1437	28	29	False		
+perf	stats_perf_tool	suitable for boolean classification problems								To update	http://osmot.cs.cornell.edu/kddcup/software.html		stats_perf_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/perf	https://github.com/bgruening/galaxytools/tree/master/tools/perf	5.11.0	perf				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	42	1	2	0	0	0	0	0	0	0	0	36	42	1	2	False		
+pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	773	773	60	60	495	495	72	72	246	246	17	17	1514	1514	149	149	False		
+pg_tools	pg_dump, pg_import, pg_query	tool suite for dealing with Postgresql databases from Galaxy's history								To update	https://www.postgresql.org	Data Export, Data Source	pgtools	bgruening	https://github.com/bgruening/galaxytools/tools/pgtools	https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools		postgresql				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pgsnp2gd_snp	pgSnp2gd_snp	Convert from pgSnp to gd_snp								To update		Variant Analysis	pgsnp2gd_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pharmcat	pharmcat	Pharmacogenomics Clinical Annotation Tool								To update	https://pharmcat.org/	Variant Analysis	pharmcat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat						1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	109	109	29	29	250	250	84	84	0	0	0	0	359	359	113	113	False		
+pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
+                pharokka
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	5462	5462	334	334	0	0	0	0	309	309	52	52	5771	5771	386	386	False		
+phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	0	0	1	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	1199	1199	193	193	0	0	0	0	6	6	1	1	1205	1205	194	194	False		
+phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1975	2034	246	258	0	0	0	0	553	564	140	144	2528	2598	386	402	False		
+physiofit	physiofit	PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit	workflow4metabolomics	https://github.com/MetaSys-LISBP/PhysioFit	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit	3.4.0	physiofit	3.4.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+physiofit_manager	physiofit_data_manager	Handling of physiofit input files								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager	1.0.1	physiofit_data_manager	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pi_db_tools	calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+picard	picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile	Picard SAM/BAM manipulation tools.	picard_samtofastq	picard_samtofastq, picard_replacesamheader, picard_fastqtosam, picard_reordersam		picard_samtofastq	Create a FASTQ file.	Formatting	Sequencing	To update	http://broadinstitute.github.io/picard/	SAM	picard	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard	3.1.1	picard	3.2.0	Formatting	Sequencing	31	31	31	0	31	31	31	0	0	0	0	0	0	0	0	0	0	31	4	31	0	0	31	0	0	0	31	0	0	0	0	0	0	31	31	31	0	386934	399039	11024	11956	366646	589980	32000	57111	56622	62258	2845	3398	810202	1051277	45869	72465	False		
+pick_value	pick_value	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	pick_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1607	1607	41	41	490	490	53	53	127	127	4	4	2224	2224	98	98	False		
+picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	867	1128	144	165	0	0	0	0	2106	2106	121	121	2973	3234	265	286	False		
+picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	2532	2532	382	382	1	1	1	1	1311	1311	83	83	3844	3844	466	466	False		
+pileup_interval	pileup_interval	Pileup-to-Interval condenses pileup format into ranges of bases								To update		SAM	pileup_interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval	1.0.3	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	613	640	48	54	1381	7804	201	1552	756	815	22	30	2750	9259	271	1636	False		
+pileup_parser	pileup_parser	Filter pileup on coverage and SNPs								To update	https://github.com/galaxyproject/tools-devteam/	SAM	pileup_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser	1.0.2	perl				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3639	3774	414	461	9754	52522	1247	4531	1893	2433	191	318	15286	58729	1852	5310	False		
+pilon	pilon	pilon is a tool for assembly improvement and variant analysis in bacteria	pilon	pilon		pilon	Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.	Sequence assembly, Analysis, Read alignment	Assembly	To update	https://github.com/broadinstitute/pilon/wiki	Variant Analysis	pilon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon	1.20.1	pilon	1.24	Sequence assembly, Analysis	Assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9045	9458	1115	1144	7989	7989	1070	1070	3945	4137	726	741	20979	21584	2911	2955	False		
+pindel	pindel	Pindel detects genome-wide structural variation.								Up-to-date	http://artbio.fr	Variant Analysis	pindel	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel	https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel	0.2.5b9	pindel	0.2.5b9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pipelign	pipelign	Multipe sequence alignment								Up-to-date	https://github.com/asmmhossain/pipelign/	Next Gen Mappers	pipelign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign	0.2	pipelign	0.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1245	1245	231	231	9046	9046	630	630	0	0	0	0	10291	10291	861	861	False		
+pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	238	283	42	45	0	0	0	0	0	0	0	0	238	283	42	45	False		
+piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1408	2068	94	119	0	0	0	0	0	0	0	0	1408	2068	94	119	False		
+pizzly	pizzly	Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.								To update	https://github.com/pmelsted/pizzly/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly	0.37.3.1	pizzly	0.37.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	201	210	23	24	998	998	76	76	0	0	0	0	1199	1208	99	100	False		
+plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37086	37272	711	734	6346	6346	583	583	3065	3065	61	61	46497	46683	1355	1378	False		
+plasmid_profiler	plasmid_profiler	Explores plasmid content in WGS data								To update			plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler	0.1.6	r				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plasmid_profiler_suite		Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14652	14652	251	251	0	0	0	0	101	101	18	18	14753	14753	269	269	False		
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plink	plink	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	plink	plink		PLINK	Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	Genetic variation analysis	GWAS study	Up-to-date	https://www.cog-genomics.org/plink	Genome-Wide Association Study	plink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink	1.90b6.21	plink	1.90b6.21	Genetic variation analysis	GWAS study	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	851	851	127	127	249	249	43	43	0	0	0	0	1100	1100	170	170	False		
+plot_from_lda	plot_for_lda_output1	"Draw ROC plot on ""Perform LDA"" output"								To update		Graphics, Statistics	plot_from_lda	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda	https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda	1.0.1	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	65	77	19	25	153	886	38	343	142	155	8	10	360	1118	65	378	False		
+plotheatmap	plotheatmap	This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output.								To update		Computational chemistry	plotheatmap	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	1.0	bioconductor-preprocesscore	1.64.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.4	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1342	1472	184	197	902	902	156	156	630	630	24	24	2874	3004	364	377	False		
+plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	408	664	91	122	627	627	118	118	605	605	26	26	1640	1896	235	266	False		
+plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	764	879	213	237	304	304	95	95	193	193	26	26	1261	1376	334	358	False		
+pmd_fdr	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pneumocat	pneumocat	Pneumococcal Capsular Typing of illumina fastq reads								Up-to-date	https://github.com/phe-bioinformatics/PneumoCaT	Variant Analysis	pneumocat	nml	https://github.com/phe-bioinformatics/PneumoCaT	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat	1.2.1	pneumocat	1.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	33	33	2	2	0	0	0	0	0	0	0	0	33	33	2	2	False		
+points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	4	4	0	0	0	0	0	0	0	0	29	29	4	4	False		
+poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	112	120	16	16	4	562	1	140	320	347	7	8	436	1029	24	164	False		
+polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	731	731	86	86	0	0	0	0	42	42	4	4	773	773	90	90	False		
+porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	262015	262852	2627	2711	83623	83623	1918	1918	52558	52558	1037	1037	398196	399033	5582	5666	False		
+poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	13	0	19942	20587	1055	1245	33619	40808	2183	2594	9261	9261	365	365	62822	70656	3603	4204	False		
+positions2snv_alignment	positions2snv_alignment	Generate alignment of SNVs from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+positions2snv_invariant_alignment	positions2snv_invariant_alignment	Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_invariant_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+presto	presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	63244	65177	1392	1599	0	0	0	0	63244	65177	1392	1599	False		
+pretext	pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6			3	2	3	0	3	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	3463	3463	538	538	1853	1853	256	256	1097	1097	70	70	6413	6413	864	864	False		
+principal_component_analysis	pca1	Principal Component Analysis								To update		Statistics	principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis	1.0.2	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9788	10032	207	244	3072	8054	607	1488	0	0	0	0	12860	18086	814	1732	False		
+prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10152	10626	253	281	10581	10581	1240	1240	0	0	0	0	20733	21207	1493	1521	False		
+probecoverage	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1902	1902	167	167	0	0	0	0	0	0	0	0	1902	1902	167	167	False		
+progressivemauve	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update	http://darlinglab.org/mauve/user-guide/progressivemauve.html	Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2064	2173	678	695	2900	2900	1034	1034	0	0	0	0	4964	5073	1712	1729	False		
+projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	86	4	6	0	0	0	0	0	0	0	0	40	86	4	6	False		
+projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20858	21444	14	18	0	0	0	0	0	0	0	0	20858	21444	14	18	False		
+prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	464359	476554	7475	7721	313285	331256	11243	12384	131211	141875	4358	4947	908855	949685	23076	25052	False		
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+prot-scriber	prot_scriber	Protein annotation of short human readable descriptions								Up-to-date	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.6	prot-scriber	0.1.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	10	7	7	0	0	0	0	0	0	0	0	10	10	7	7	False		
+protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	129	155	15	21	0	0	0	0	0	0	0	0	129	155	15	21	False		
+protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	11743	12752	1137	1278	2	2	1	1	0	0	0	0	11745	12754	1138	1279	False		
+protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	465	638	81	100	0	0	0	0	0	0	0	0	465	638	81	100	False		
+proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3962	3962	501	501	0	0	0	0	0	0	0	0	3962	3962	501	501	False		
+proteinpilot	convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml									To update			proteinpilot	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+proteomiqon_joinquantpepionswithproteins	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	366	366	4	4	0	0	0	0	0	0	0	0	366	366	4	4	False		
+proteomiqon_labeledproteinquantification	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	8	8	0	0	0	0	0	0	0	0	16	16	8	8	False		
+proteomiqon_labelfreeproteinquantification	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	6	4	4	0	0	0	0	0	0	0	0	6	6	4	4	False		
+proteomiqon_mzmltomzlite	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	721	721	8	8	0	0	0	0	0	0	0	0	721	721	8	8	False		
+proteomiqon_peptidedb	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	96	96	12	12	0	0	0	0	0	0	0	0	96	96	12	12	False		
+proteomiqon_peptidespectrummatching	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	686	686	5	5	0	0	0	0	0	0	0	0	686	686	5	5	False		
+proteomiqon_proteininference	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	6	6	0	0	0	0	0	0	0	0	89	89	6	6	False		
+proteomiqon_psmbasedquantification	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	604	604	4	4	0	0	0	0	0	0	0	0	604	604	4	4	False		
+proteomiqon_psmstatistics	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	694	694	6	6	0	0	0	0	0	0	0	0	694	694	6	6	False		
+proteore_venn_diagram	proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	1	1	0	0	0	0	0	0	0	0	15	15	1	1	False		
+protxml_to_xls	protxml_to_xls									To update			protxml_to_xls	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pseudogenome	pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+psiclass	psiclass	PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.	psiclass	psiclass		PsiCLASS	Reference-based transcriptome assembler for single or multiple RNA-seq samples	Transcriptome assembly	Sequence assembly	Up-to-date	https://github.com/splicebox/PsiCLASS	Transcriptomics	psiclass	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass	https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass	1.0.3	psiclass	1.0.3	Transcriptome assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	24	5	5	0	0	0	0	0	0	0	0	24	24	5	5	False		
+psm2sam	PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+psm_eval	psm_eval									To update			psm_eval	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval	0.1.0	binaries_for_psm_eval				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+psm_validation	psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	20	20	4	4	0	0	0	0	0	0	0	0	20	20	4	4	False		
+psy-maps	psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.3.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	333	502	62	62	0	0	0	0	0	0	0	0	333	502	62	62	False		
+pureclip	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1319	1507	81	92	0	0	0	0	0	0	0	0	1319	1507	81	92	False		
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17782	17782	287	287	853	853	65	65	2224	2224	65	65	20859	20859	417	417	False		
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22742	22742	557	557	2159	2159	716	716	776	776	448	448	25677	25677	1721	1721	False		
+pyega3	pyega3	EGA python client uses the EGA REST API to download authorized datasets and files.								To update	https://github.com/EGA-archive/ega-download-client	Data Source	ega_download_client	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3	5.0.2	pyega3	5.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2716	2716	104	104	134	134	43	43	40	40	1	1	2890	2890	148	148	False		
+pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12858	13232	986	996	8092	8092	943	943	3238	3238	124	124	24188	24562	2053	2063	False		
+pyprophet	pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5			0	5	6	0	0	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	6	6	0	2626	2626	150	150	0	0	0	0	609	609	9	9	3235	3235	159	159	False		
+pyscenic	pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/								To update		Transcriptomics, RNA, Sequence Analysis	suite_pyscenic	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic	0.12.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pysradb	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.2	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	163	163	35	35	0	0	0	0	0	0	0	0	163	163	35	35	False		
+pyteomics	mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.4	Protein identification	Proteomics, Proteomics experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	92	92	4	4	0	0	0	0	0	0	0	0	92	92	4	4	False		
+pyvo_integration	astronomical_archives	Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy								To update		Data Source	astronomicalarchivestool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration	0.10.0	astropy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	53	6	6	0	0	0	0	0	0	0	0	53	53	6	6	False		
+qcxms	qcxms_getres, qcxms_neutral_run, qcxms_production_run	QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).								To update	https://github.com/grimme-lab/QCxMS	Computational chemistry, Molecular Dynamics	QCxMS	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	5.2.1					0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11246	11246	13	13	0	0	0	0	0	0	0	0	11246	11246	13	13	False		
+qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2092	2342	209	238	0	0	0	0	2	2	1	1	2094	2344	210	239	False		
+qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	0	0	0	32	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	31825	34677	3375	3785	1	1	1	1	14	14	4	4	31840	34692	3380	3790	False		
+qiime_extract_viz	qiime_extract_viz	Extract vizualization from QIIME artifacts								To update	http://www.qiime.org	Metagenomics	qiime_extract_viz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz	0.1.0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	8	8	0	0	0	0	0	0	0	0	17	17	8	8	False		
+qq_tools	qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	0	4	4	4	0	684820	684820	3239	3239	90503	90503	3881	3881	29018	29018	826	826	804341	804341	7946	7946	False		
+quality_filter	qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.13.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	724	35	62	0	0	0	0	98	724	35	62	False		
+quantp	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	197	241	17	22	0	0	0	0	0	0	0	0	197	241	17	22	False		
+quantwiz_iq	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	32	3	3	0	0	0	0	0	0	0	0	32	32	3	3	False		
+quasitools	aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0			0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13483	13483	434	434	13483	13483	434	434	False		
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	67737	69738	7787	7971	51925	56602	9692	10646	32003	34145	3890	4127	151665	160485	21369	22744	False		
+query	query	Execute an SQL statement on a set of tables								To update		Text Manipulation	query	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/query	https://github.com/RECETOX/galaxytools/tree/master/tools/query	0.2	click				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+query_impc	query_impc	Contains a tool to query the IMPC database.								To update	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	Convert Formats, Web Services	query_impc	iuc	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc	0.9.0	requests				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	2	0	0	0	0	0	0	0	0	3	3	2	2	False		
+query_tabular	filter_tabular, query_tabular, sqlite_to_tabular	Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular	3.3.1	python				3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	3	2	0	0	0	0	0	0	1	0	0	0	0	0	0	3	3	3	0	130124	135361	1265	1305	11135	11135	922	922	5939	5939	153	153	147198	152435	2340	2380	False		
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	172	172	9	9	0	0	0	0	0	0	0	0	172	172	9	9	False		
+rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3077	4581	395	518	2856	2856	1093	1093	1977	1977	19	19	7910	9414	1507	1630	False		
+racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	27113	27315	839	850	9089	9089	475	475	5452	5452	171	171	41654	41856	1485	1496	False		
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4844	4844	480	480	0	0	0	0	7	7	3	3	4851	4851	483	483	False		
+ramclustr	ramclustr, ramclustr_define_experiment		ramclustr	ramclustr		RAMClustR	A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	To update	https://rdrr.io/cran/RAMClustR/	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	1.3.0	r-ramclustr	1.3.1	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	58	58	22	22	29	29	14	14	344	344	4	4	431	431	40	40	False		
+rapidnj	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2		Phylogeny	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	339	339	30	30	1737	1737	256	256	6	6	1	1	2082	2082	287	287	False		
+rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	42	42	9	9	0	0	0	0	0	0	0	0	42	42	9	9	False		
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9477	9477	438	438	0	0	0	0	10585	10585	182	182	20062	20062	620	620	False		
+rawtools	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	166	179	32	33	0	0	0	0	414	414	13	13	580	593	45	46	False		
+raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10905	10905	966	966	5100	5114	587	587	4955	6094	765	892	20960	22113	2318	2445	False		
+rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	1.0		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	90	90	6	6	0	0	0	0	0	0	0	0	90	90	6	6	False		
+rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	860	1257	88	98	0	0	0	0	0	0	0	0	860	1257	88	98	False		
+rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	655	655	57	57	0	0	0	0	0	0	0	0	655	655	57	57	False		
+rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	49	191	5	46	0	0	0	0	49	191	5	46	False		
+rcx-tk	rcx-tk	Tools to process metadata or alkane files.								To update	https://github.com/RECETOX/rcx-tk	Metabolomics	rcx_tk	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk	0.1.0+galaxy0	rcx-tk	0.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rdock	rdock	Docking ligands to proteins and nucleic acids								To update	http://rdock.sourceforge.net/	Computational chemistry	rdock	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock	1.0	rDock	2013.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3710	3710	80	80	7	7	6	6	0	0	0	0	3717	3717	86	86	False		
+reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.15.0	recentrifuge	1.15.0	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	472	472	92	92	32	32	13	13	6	6	4	4	510	510	109	109	False		
+recetox_aplcms	recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise	Peak detection tool for HRMS profile data.	recetox-aplcms	recetox-aplcms		recetox-aplcms	recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	Up-to-date	https://github.com/RECETOX/recetox-aplcms	Metabolomics	recetox-aplcms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	0.13.3	r-recetox-aplcms	0.13.3	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	862	862	12	12	0	0	0	0	48	48	1	1	910	910	13	13	False		
+recetox_msfinder	recetox_msfinder		recetox-msfinder	recetox-msfinder		recetox-msfinder	This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.	Annotation	Metabolomics	To update	https://github.com/RECETOX/recetox-msfinder	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	v3.5.2			Annotation	Metabolomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47	47	4	4	0	0	0	0	0	0	0	0	47	47	4	4	False		
+recetox_xmsannotator	recetox_xmsannotator_advanced		recetox-xmsannotator	recetox-xmsannotator		recetox-xMSannotator	Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		Up-to-date	https://github.com/RECETOX/recetox-xMSannotator	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator	0.10.0	r-recetox-xmsannotator	0.10.0	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	93	93	2	2	93	93	2	2	False		
+red	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	859	859	203	203	305	305	142	142	227	227	58	58	1391	1391	403	403	False		
+refseq_masher	refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	428	428	35	35	141	141	42	42	0	0	0	0	569	569	77	77	False		
+regex_find_replace	regex1, regexColumn1	Use python regular expressions to find and replace text								To update		Text Manipulation	regex_find_replace	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	1.0.3	python				2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	78648	78834	1144	1156	18063	18063	870	870	4455	6051	194	289	101166	102948	2208	2315	False		
+regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	438	542	128	157	0	0	0	0	0	0	0	0	438	542	128	157	False		
+rem_complex	rem_complex	Removes molecular coordination complexes.								To update	https://github.com/RECETOX/galaxytools	Metabolomics	rem_complex	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	2	2	0	0	0	0	0	0	0	0	18	18	2	2	False		
+remove_beginning	Remove beginning1	Remove lines from the beginning of a file.								To update		Text Manipulation	remove_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	148572	169964	3525	3682	36694	113826	3910	8163	9713	10577	1475	1598	194979	294367	8910	13443	False		
+remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	44	6	7	0	0	0	0	0	0	0	0	39	44	6	7	False		
+rename_annotated_feature	rename_annotated_feature	Update column names in an abundance table using a annotation table with spectral matching results								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	rename_annotated_feature	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1	False		
+repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.0.9_p2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5998	5998	810	810	7618	7618	803	803	3135	3135	292	292	16751	16751	1905	1905	False		
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	95	38	38	0	0	0	0	0	0	0	0	95	95	38	38	False		
+repeatmasker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.0.9_p2	Genome annotation	Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5998	5998	810	810	7618	7618	803	803	3135	3135	292	292	16751	16751	1905	1905	False		
+repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7963	7963	413	413	1485	1485	220	220	8402	8402	168	168	17850	17850	801	801	False		
+repenrich	edger-repenrich, repenrich	Repeat element profiling								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	Transcriptomics	repenrich	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	2.31.1					0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1725	1790	56	57	1725	1790	56	57	False		
+repenrich2	edger-repenrich2, repenrich2	Repeat element profiling using bowtie2 aligner								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	Transcriptomics	repenrich2	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	2.31.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+replaceColumn	replace_column_with_key_value_file	A tool to replace all column entries of a file given by values of a key-value file.								To update		Text Manipulation	replace_column_by_key_value_file	bgruening	https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn	https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn	0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	577184	577312	463	492	43900	44233	283	373	2190	2190	112	112	623274	623735	858	977	False		
+replace_chromosome_names	replace_chromosome_names	Replace chromosome names								To update		Text Manipulation	replace_chromosome_names	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names	0.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	514	573	69	83	0	0	0	0	0	0	0	0	514	573	69	83	False		
+repmatch_gff3	repmatch_gff3	Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.								To update		ChIP-seq	repmatch_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3		matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	415	721	128	219	0	0	0	0	415	721	128	219	False		
+reshape2	cast, melt	Flexibly restructure and aggregate data using just the two functions melt and dcast								To update	https://cran.r-project.org/web/packages/reshape2/index.html	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2	1.4.2	r-reshape2				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	3543	3619	108	111	536	536	157	157	0	0	0	0	4079	4155	265	268	False		
+resize_coordinate_window	resize_coordinate_window	Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.								To update		Genomic Interval Operations	resize_coordinate_window	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window	https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window	1.0.2	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	75	86	8	9	138	216	30	57	0	0	0	0	213	302	38	66	False		
+rest_tool	pubchem_rest_tool	This tool fetches data from pubchem via the PubChem REST API.								To update	https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html	Data Source	pubchem_rest_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+retip	retip_apply, retip_descriptors, retip_filter_rt, retip_train		retip	retip		Retip	Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.	Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	To update	https://github.com/PaoloBnn/Retip	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	0.5.4			Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+retrieve_ensembl_bed	retrieve_ensembl_bed	Retrieve cDNA features from Ensembl REST API in BED format								To update	http://rest.ensembl.org/	Data Source	retrieve_ensembl_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+revertR2orientationInBam	revertR2orientationInBam	Revert the mapped orientation of R2 mates in a bam.								To update		SAM	revertr2orientationinbam	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	0.0.2	samtools	1.21			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	40	11	11	520	520	31	31	0	0	0	0	560	560	42	42	False		
+revoluzer	revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	Structural variation detection	Molecular evolution, Phylogeny	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2444	2444	52	52	0	0	0	0	0	0	0	0	2444	2444	52	52	False		
+rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	7	7	0	0	0	0	0	0	0	0	15	15	7	7	False		
+rgcca	rgcca	multi-block analysis								To update	https://github.com/rgcca-factory/RGCCA	Statistics	rgcca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca	3.0.2	rgccacmd	3.0.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	44	44	6	6	77	77	35	35	0	0	0	0	121	121	41	41	False		
+rgrnastar	rna_star, rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	star	star		STAR	Ultrafast universal RNA-seq data aligner	Sequence alignment	RNA-Seq, Transcriptomics	To update	https://github.com/alexdobin/STAR	Next Gen Mappers, Transcriptomics	rgrnastar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar	2.7.11a	star	2.7.11b	Sequence alignment	RNA-Seq, Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	2	0	0	0	2	0	0	0	0	0	1	2	2	2	0	438078	473957	10142	10900	325474	403925	15284	18791	49662	53138	1359	1449	813214	931020	26785	31140	False		
+riassigner	riassigner, riassigner_from_comment		riassigner	riassigner		RIAssigner	RIAssigner is a python tool for retention index (RI) computation for GC-MS data.	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/RIAssigner	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	0.4.1	riassigner	0.4.1	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	46	46	19	19	15	15	4	4	1	1	1	1	62	62	24	24	False		
+ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	661	681	78	78	0	0	0	0	0	0	0	0	661	681	78	78	False		
+ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	171	171	20	20	0	0	0	0	0	0	0	0	171	171	20	20	False		
+rmap	rmap_wrapper	RMAP for Solexa Short Reads Alignment								To update		Next Gen Mappers	rmap	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rmapq	rmapq_wrapper	RMAPQ for Solexa Short Reads Alignment with Quality Scores								To update		Next Gen Mappers	rmapq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rmassbank	rmassbank	RMassBank is an R package for processing tandem MS files and building of MassBank records.								To update	https://github.com/MassBank/RMassBank	Metabolomics	rmassbank	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	3.0.0	python				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	48	48	1	1	48	48	1	1	False		
+rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	137	173	40	49	0	0	0	0	0	0	0	0	137	173	40	49	False		
+rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	90	196	9	11	0	0	0	0	0	0	0	0	90	196	9	11	False		
+rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	878	1363	29	35	0	0	0	0	0	0	0	0	878	1363	29	35	False		
+rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1024	1077	18	21	0	0	0	0	0	0	0	0	1024	1077	18	21	False		
+rnaformer	infer_rnaformer	RNAformer: RNA secondary structure prediction								To update	https://github.com/automl/RNAformer	RNA	rnaformer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	1.0.0	rnaformer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	6	6	0	0	0	0	0	0	0	0	26	26	6	6	False		
+rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	33	10	14	0	0	0	0	0	0	0	0	23	33	10	14	False		
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1522	1522	254	254	372	372	75	75	5	5	1	1	1899	1899	330	330	False		
+rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	65	89	14	18	0	0	0	0	0	0	0	0	65	89	14	18	False		
+rnaz	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	1156	43309	93	121	0	0	0	0	0	0	0	0	1156	43309	93	121	False		
+roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15196	15685	1459	1501	12188	12188	1768	1768	4881	5539	518	555	32265	33412	3745	3824	False		
+rp2biosensor	rp2biosensor	Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output								To update	https://github.com/brsynth/rp2biosensor	Synthetic Biology	rp2biosensor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor	3.2.1	rp2biosensor				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rp2paths	rp2paths	Enumerate and seperate the different pathways generated by RetroPath2.0								To update	https://github.com/brsynth/rp2paths	Synthetic Biology	rp2paths	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths	1.5.1	rp2paths				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rpbasicdesign	rpbasicdesign	Extracting enzyme IDs from rpSBML files								To update	https://github.com/brsynth/rpbasicdesign	Synthetic Biology	rpbasicdesign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign	1.2.2	rpbasicdesign				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rpfba	rpfba	Perform FBA for the RetroPath2.0 heterologous pathways								To update	https://github.com/brsynth/rptools/releases	Synthetic Biology	rpfba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba	5.12.3	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rptools	rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz	Suite of tools that work on rpSBML format								To update	https://github.com/brsynth/rptools	Synthetic Biology	rptools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools	5.13.1	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rrparser	rrparser	Reaction Rules Parser								To update	https://github.com/brsynth/RRParser	Synthetic Biology	rrparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser	2.5.2	rrparser				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rsat_filter_snps	rsat_filter_snps	Filter SNPs in RSAT Matrix Scan output								To update	https://github.com/TGAC/earlham-galaxytools/	ChIP-seq, Systems Biology	rsat_filter_snps	earlham	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	1	1	0	363	430	158	183	0	0	0	0	67	146	13	39	430	576	171	222	False		
+rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	0	22	22	22	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	0	22	22	22	0	136315	147595	8341	9385	138707	161046	10696	12789	22718	23767	1593	1695	297740	332408	20630	23869	False		
+ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1286	1364	178	193	2220	2220	299	299	0	0	0	0	3506	3584	477	492	False		
+sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3628	4168	165	199	8399	14473	573	1147	2710	3000	151	175	14737	21641	889	1521	False		
+salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	0	2	2	3	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	0	3	3	3	0	73085	77081	2243	2319	90634	122835	3402	4726	13371	15818	513	586	177090	215734	6158	7631	False		
+salmon-kallisto-mtx-to-10x	_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	682	682	172	172	322	322	74	74	3	3	3	3	1007	1007	249	249	False		
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	463	463	119	119	1038	1038	87	87	410	410	24	24	1911	1911	230	230	False		
+sam2interval	sam2interval	Convert SAM to interval.								To update		SAM	sam2interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1155	1251	57	63	2264	18187	189	1748	525	590	10	17	3944	20028	256	1828	False		
+sam_bitwise_flag_filter	sam_bw_filter	Filter SAM on bitwise flag values								To update		SAM	sam_bitwise_flag_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter	1.0.1	python				1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	96	278	12	26	3554	76029	450	6346	229	345	16	29	3879	76652	478	6401	False		
+sambamba	sambamba_sample_or_filter	filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM								To update	http://artbio.fr	SAM	sambamba	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba	https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba	0.7.1+galaxy1	sambamba	1.0.1			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	684	684	17	17	684	684	17	17	False		
+sambamba	sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort	Sambamba: process your BAM data faster!								Up-to-date	https://github.com/biod/sambamba	SAM	sambamba	bgruening	https://github.com/biod/sambamba	https://github.com/bgruening/galaxytools/tree/master/tools/sambamba	1.0.1	sambamba	1.0.1			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	297	297	51	51	0	0	0	0	0	0	0	0	297	297	51	51	False		
+samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	Up-to-date	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.26	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3421	3859	340	382	883	883	109	109	1138	1138	15	15	5442	5880	464	506	False		
+samtools										To update	https://github.com/samtools/samtools	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools	1.20	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6485	6549	720	726	10127	10127	1518	1518	238	238	37	37	16850	16914	2275	2281	False		
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	52099	55110	4053	4497	73194	108684	6930	9936	14771	15714	1222	1419	140064	179508	12205	15852	False		
+sansa	sansa_annotate	Sansa is a tool for structural variant annotation.								To update	https://github.com/dellytools/sansa	Variant Analysis	sansa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa	0.2.1	sansa	0.2.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	138	138	36	36	0	0	0	0	0	0	0	0	138	138	36	36	False		
+sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	174	174	16	16	399	399	29	29	0	0	0	0	573	573	45	45	False		
+sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	140	140	5	5	253	253	6	6	0	0	0	0	393	393	11	11	False		
+sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sbml2sbol	sbml2sbol	Convert SBML to SBOL format								To update	https://github.com/neilswainston/SbmlToSbol	Synthetic Biology	sbml2sbol	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol	0.1.13	sbml2sbol				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	10	10	0	0	0	0	0	0	0	0	13	13	10	10	False		
+scaffold	scaffold, scaffold_export									To update			scaffold	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold	0.1.0	scaffold				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	477	520	13	16	0	0	0	0	0	0	0	0	477	520	13	16	False		
+scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			27	27	27	0	27	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	0	45501	45666	4832	4868	7304	7304	1846	1846	3106	3106	457	457	55911	56076	7135	7171	False		
+scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	63789	64034	2543	2547	29962	29962	1185	1185	18028	18028	379	379	111779	112024	4107	4111	False		
+scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			1	2	6	0	1	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	381	388	99	100	0	0	0	0	297	297	9	9	678	685	108	109	False		
+scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	1345	1371	350	351	0	0	0	0	903	903	29	29	2248	2274	379	380	False		
+scatterplot	scatterplot_rpy	Scatterplot of two numeric columns								To update		Graphics, Statistics	scatterplot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot	1.0.3	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1234	1752	179	261	680	9223	231	1927	0	49	0	18	1914	11024	410	2206	False		
+sccaf	run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out	SCCAF: Single Cell Clustering Assessment Framework.								To update	https://github.com/sccaf/sccaf	Transcriptomics	SCCAF	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf	0.0.9	sccaf	0.0.10			4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	110	110	19	19	0	0	0	0	0	0	0	0	110	110	19	19	False		
+sceasy	sceasy_convert	Convert scRNA data object between popular formats								To update		Transcriptomics	sceasy	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy	0.0.5	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1059	1059	222	222	426	426	71	71	1	1	1	1	1486	1486	294	294	False		
+sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1059	1059	222	222	426	426	71	71	1	1	1	1	1486	1486	294	294	False		
+schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	809	809	78	78	3	3	2	2	105	105	16	16	917	917	96	96	False		
+scikit-bio	scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1503	1955	283	402	0	0	0	0	1504	1956	284	403	False		
+scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	97	97	41	41	0	0	0	0	0	0	0	0	97	97	41	41	False		
+scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	901	901	90	90	0	0	0	0	0	0	0	0	901	901	90	90	False		
+scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	284	632	34	38	786	786	61	61	1	1	1	1	1071	1419	96	100	False		
+scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	25	5	5	0	0	0	0	0	0	0	0	25	25	5	5	False		
+scripting	singularity_scriptrunner	suite_scripting								To update	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	Text Manipulation	scripting tools	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+seacr	seacr	SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.								Up-to-date	https://github.com/FredHutch/SEACR	Epigenetics, ChIP-seq	seacr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr	1.3	seacr	1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5106	5106	116	116	6419	6419	241	241	0	0	0	0	11525	11525	357	357	False		
+sed	sed_stream_editor	Manipulate your data with the sed command line tool.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/sed	Text Manipulation	sed_wrapper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sed	https://github.com/bgruening/galaxytools/tree/master/tools/sed	0.0.1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	281	2284	10	53	0	0	0	0	0	0	0	0	281	2284	10	53	False		
+segalign	segalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/gsneha26/SegAlign	Next Gen Mappers	segalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	0.1.2.7	segalign-galaxy	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	252	252	47	47	0	0	0	0	252	252	47	47	False		
+segemehl	segemehl	segemehl - short read mapping with gaps								To update	http://www.bioinf.uni-leipzig.de/Software/segemehl/	Next Gen Mappers	segemehl	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	0.2.0.4	segemehl	0.3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1095	1306	98	113	0	0	0	0	0	0	0	0	1095	1306	98	113	False		
+segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	2	2	0	0	0	0	0	0	0	0	7	7	2	2	False		
+selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	305	463	43	50	0	0	0	0	0	0	0	0	305	463	43	50	False		
+selenzy_wrapper	selenzy_wrapper	Performs enzyme selection from a reaction query.								Up-to-date	https://github.com/brsynth/selenzy-wrapper	Synthetic Biology	selenzy_wrapper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper	0.3.0	selenzy_wrapper	0.3.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	931	931	93	93	0	0	0	0	0	0	0	0	931	931	93	93	False		
+seq2hla	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	342	342	40	40	0	0	0	0	0	0	0	0	342	342	40	40	False		
+seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1053	1186	137	195	680	680	206	206	0	0	0	0	1733	1866	343	401	False		
+seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30300	32553	732	799	21726	31891	619	621	2886	2886	144	144	54912	67330	1495	1564	False		
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4322	4714	180	205	0	0	0	0	0	0	0	0	4322	4714	180	205	False		
+seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2196	3529	260	289	2196	3529	260	289	False		
+seqcomplexity	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	70	70	19	19	109	109	47	47	0	0	0	0	179	179	66	66	False		
+seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	0	0	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3364	3364	247	247	0	0	0	0	244	244	33	33	3608	3608	280	280	False		
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2424	2424	102	102	0	0	0	0	0	0	0	0	2424	2424	102	102	False		
+seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4182	4182	42	42	0	0	0	0	0	0	0	0	4182	4182	42	42	False		
+seqtk	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	Data handling, Sequence file editing		15	15	15	0	15	15	15	0	0	0	0	0	0	0	0	0	0	14	0	14	0	0	14	0	0	0	15	0	0	0	0	0	0	14	14	14	14	72816	73514	2210	2300	102777	107831	2313	2669	154613	154613	682	682	330206	335958	5205	5651	False		
+seqtk_nml	seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seqwish	seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	271	271	2	2	0	0	0	0	0	0	0	0	271	271	2	2	False		
+seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	0	1	1	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	121	121	11	11	32	32	5	5	0	0	0	0	153	153	16	16	False		
+seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.4.0			14	14	14	0	14	14	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	0	2296	2328	673	676	141	141	39	39	0	0	0	0	2437	2469	712	715	False		
+sgwb	sgwb_astro_tool	SGWB								To update		Astronomy	sgwb_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb	0.0.1+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	2	2	0	0	0	0	0	0	0	0	5	5	2	2	False		
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	913	913	308	308	0	0	0	0	568	568	73	73	1481	1481	381	381	False		
+shift-longitudes	shyft_longitudes	Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/	Climate Analysis	shift_longitudes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	54	64	4	4	0	0	0	0	0	0	0	0	54	64	4	4	False		
+shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+short_reads_figure_score	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	145	163	25	30	196	3360	23	711	0	0	0	0	341	3523	48	741	False		
+short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	175	220	51	60	350	6657	85	1602	0	0	0	0	525	6877	136	1662	False		
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46125	47376	2273	2356	40577	40577	3971	3971	19960	21130	1085	1199	106662	109083	7329	7526	False		
+show_beginning	Show beginning1	Select lines from the beginning of a file.								To update		Text Manipulation	show_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	27232	36366	2184	2789	16648	84460	4191	18767	2785	3276	373	452	46665	124102	6748	22008	False		
+show_tail	Show tail1	Select lines from the end of a file.								To update		Text Manipulation	show_tail	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	1620	2660	378	589	10551	24579	682	1851	284	398	67	83	12455	27637	1127	2523	False		
+sicer	peakcalling_sicer	Statistical approach for the Identification of ChIP-Enriched Regions								Up-to-date	https://home.gwu.edu/~wpeng/Software.htm	ChIP-seq	sicer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer	1.1	SICER	1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	276	379	30	42	972	9053	146	1008	644	689	5	7	1892	10121	181	1057	False		
+sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	0	18184	18937	555	608	10514	10514	1063	1063	0	0	0	0	28698	29451	1618	1671	False		
+simtext	abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix	A text mining framework for interactive analysis and visualization of similarities among biomedical entities.								To update	https://github.com/dlal-group/simtext	Text Manipulation	simtext	iuc	https://github.com/galaxyproject/tools-iuc/tools/simtext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext	0.0.2	r-argparse	1.0.1			0	2	4	0	0	2	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	220	220	68	68	0	0	0	0	416	416	10	10	636	636	78	78	False		
+sina	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1369	1369	125	125	2398	2398	420	420	0	0	0	0	3767	3767	545	545	False		
+sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								Up-to-date	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.10.1	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	284	284	70	70	165	165	38	38	14	14	2	2	463	463	110	110	False		
+sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3457	3457	301	301	0	0	0	0	556	556	65	65	4013	4013	366	366	False		
+sixgill	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	312	312	71	71	0	0	0	0	0	0	0	0	312	312	71	71	False		
+sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	0	30	14	31	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	0	82169	116810	2402	2666	18101	18101	2375	2375	17549	17549	321	321	117819	152460	5098	5362	False		
+skyline2isocor	skyline2isocor	Converting skyline output to IsoCor input								Up-to-date	https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor	Metabolomics	skyline2isocor	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor	1.0.0	skyline2isocor	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	346	362	16	16	872	872	67	67	0	0	0	0	1218	1234	83	83	False		
+sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	141	141	26	26	0	0	0	0	0	0	0	0	141	141	26	26	False		
+slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	96	103	4	5	0	0	0	0	4	4	1	1	100	107	5	6	False		
+small_rna_clusters	small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+small_rna_maps	small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+small_rna_signatures	overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	158	158	8	8	0	0	0	0	0	0	0	0	158	158	8	8	False		
+smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smart_domains	smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smina	smina	smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization								To update	https://sourceforge.net/projects/smina/	Computational chemistry	smina	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina	1.0	smina	2017.11.9			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	499	499	16	16	44	44	10	10	0	0	0	0	543	543	26	26	False		
+smithsonian-volcanoes	smithsonian_volcanoes	Retrieve data from Volcanoes of the World (VOTW) Database								To update	https://volcano.si.edu/gvp_votw.cfm	Retrieve Data	smithsonian_volcanoes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	0.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	325	325	61	61	137	137	54	54	843	843	63	63	1305	1305	178	178	False		
+snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	1638	331	358	779	779	244	244	467	467	83	83	2745	2884	658	685	False		
+snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1817	1817	14	14	4	4	2	2	136	136	4	4	1957	1957	20	20	False		
+sniffles	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	Up-to-date	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	2.4	sniffles	2.4	Sequence analysis, Structural variation detection	Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1141	1141	134	134	606	606	156	156	2267	2267	80	80	4014	4014	370	370	False		
+snipit	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	Base position variability plotting	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	905	905	44	44	0	0	0	0	0	0	0	0	905	905	44	44	False		
+snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	0	121363	124773	3448	3602	92504	92504	3945	3945	48068	52034	2705	3073	261935	269311	10098	10620	False		
+snp-dists	snp_dists	Compute pairwise SNP distance matrix from a FASTA sequence alignment								Up-to-date	https://github.com/tseemann/snp-dists	Variant Analysis	snp_dists	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists	0.8.2	snp-dists	0.8.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6555	6555	807	807	5336	5336	171	171	1143	1143	182	182	13034	13034	1160	1160	False		
+snp-sites	snp_sites	Finds SNP sites from a multi-FASTA alignment file								Up-to-date	https://github.com/sanger-pathogens/snp-sites	Variant Analysis	snp_sites	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites	2.5.1	snp-sites	2.5.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6597	6597	663	663	1467	1467	256	256	1279	1279	114	114	9343	9343	1033	1033	False		
+snpeff	snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names	SnpEff is a genetic variant annotation and effect prediction toolbox								To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff		biopython	1.70			5	5	5	0	5	5	5	0	0	0	0	0	0	0	1	0	0	0	5	5	0	0	5	0	0	0	5	0	0	0	0	0	0	5	5	5	0	103826	108296	7181	7908	115727	178110	15871	22769	11817	13155	2148	2321	231370	299561	25200	32998	False		
+snpeff-covid19	snpeff_sars_cov_2	SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox	snpeff	snpeff		snpEff	Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).	SNP detection	DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs	To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff_sars_cov_2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19				SNP detection	DNA polymorphism, Nucleic acid sites, features and motifs	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	764895	764895	1276	1276	94572	94572	1636	1636	26990	26990	561	561	886457	886457	3473	3473	False		
+snpfreq	hgv_snpFreq	snpFreq significant SNPs in case-control data								To update		Variant Analysis, Statistics	snpfreq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	44	10	12	307	649	68	181	227	260	16	23	569	953	94	216	False		
+snpfreqplot	snpfreqplot	A plotting app to visualise the SNPs across a region								To update	https://github.com/BrownfieldPlantLab/SNPFreqPlot	Variant Analysis	snpfreqplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot	1.0	r-base				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	3683	3683	338	338	1401	1401	433	433	1029	1029	95	95	6113	6113	866	866	False		
+snpsift	snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck	snpEff SnpSift tools from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html	Variant Analysis	snpsift	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift		snpsift	5.2			8	8	8	0	8	8	8	0	0	0	0	0	0	0	8	0	0	0	0	8	0	0	8	0	0	0	8	0	0	0	0	0	0	8	8	8	0	5142904	5146618	3602	4283	382391	421190	7013	9678	104030	105024	960	1184	5629325	5672832	11575	15145	False		
+snpsift_dbnsfp	snpSift_dbnsfp	snpEff SnpSift dbnsfp tool from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html#dbNSFP	Variant Analysis	snpsift_dbnsfp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	52	55	23	24	421	421	75	75	0	0	0	0	473	476	98	99	False		
+snpsift_genesets	snpSift_geneSets	Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome								To update	http://snpeff.sourceforge.net/SnpSift.html#geneSets	Variant Analysis	snpsift_genesets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	509	554	107	128	474	474	190	190	0	0	0	0	983	1028	297	318	False		
+snv_matrix	snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+snvtocnv	sequenzaindex, snvtocnv	infer copy number variations from a vcf file with SNVs using R sequenza								To update	http://artbio.fr	Variant Analysis	snvtocnv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv	https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv	3.0.0+galaxy1	sequenza-utils	3.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+socru	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	659	659	42	42	296	296	92	92	0	0	0	0	955	955	134	134	False		
+sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19865	21034	1047	1126	3141	3141	328	328	3304	3304	189	189	26310	27479	1564	1643	False		
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	3	9	3	0	82716	87113	8209	8526	120471	120475	14787	14790	54067	61541	5817	6653	257254	269129	28813	29969	False		
+spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	450	491	91	100	4270	4270	288	288	0	0	0	0	4720	4761	379	388	False		
+spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spatyper	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spec2vec	spec2vec_similarity, spec2vec_training	Mass spectra similarity scoring using a trained Spec2Vec model.	spec2vec	spec2vec		Spec2Vec	Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	Up-to-date	https://github.com/iomega/spec2vec	Metabolomics	spec2vec	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	0.8.0	spec2vec	0.8.0	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+spectrast2spectrast_irt	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spectrast2tsv	gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+split_file_on_column	tp_split_on_column	Split a file on a specific column.								To update		Text Manipulation	split_file_on_column	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	0.6	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5995	6261	408	453	2150	2150	311	311	26	26	2	2	8171	8437	721	766	False		
+split_file_to_collection	split_file_to_collection	Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	Text Manipulation	split_file_to_collection	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	0.5.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	16415	16623	968	984	9133	9133	672	672	4140	4140	148	148	29688	29896	1788	1804	False		
+split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	44	51	2	3	0	0	0	0	0	0	0	0	44	51	2	3	False		
+split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	3	200	384	31	66	200	397	31	69	False		
+splitfasta	rbc_splitfasta	Split a multi-sequence fasta file into files containing single sequences								To update		Text Manipulation	splitfasta	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	0.4.0	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1772	1811	278	294	3012	3012	564	564	0	0	0	0	4784	4823	842	858	False		
+spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	789	840	130	134	0	0	0	0	0	0	0	0	789	840	130	134	False		
+spolpred	spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.1	giatools	0.3.1	Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	4	4	0	0	0	0	0	0	0	0	16	16	4	4	False		
+spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	23	23	0	0	0	0	0	0	0	0	1436	1436	23	23	False		
+spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	142	142	5	5	0	0	0	0	0	0	0	0	142	142	5	5	False		
+sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	80	80	1	1	0	0	0	0	80	80	1	1	False		
+sr_bowtie_dataset_annotation	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	0	3	3	3	0	364871	376580	16710	17342	583675	678448	53271	59638	48131	50455	5910	6181	996677	1105483	75891	83161	False		
+srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	0	4	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	239	239	34	34	44	44	13	13	0	0	0	0	283	283	47	47	False		
+srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41	False		
+srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41	False		
+sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	214	225	17	18	0	0	0	0	0	0	0	0	214	225	17	18	False		
+stacks	stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	Data handling	Mapping, Population genetics	0	13	13	0	0	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	13	0	6440	11998	465	593	0	0	0	0	4070	4070	76	76	10510	16068	541	669	False		
+stacks2	stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65			0	12	12	0	0	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	8437	8592	626	646	0	0	0	0	18016	18016	270	270	26453	26608	896	916	False		
+star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update	https://github.com/STAR-Fusion/STAR-Fusion	Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1312	1383	82	95	2198	3076	234	303	173	173	3	3	3683	4632	319	401	False		
+staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20778	20891	2030	2045	9520	9520	1424	1424	6753	6753	864	864	37051	37164	4318	4333	False		
+statistics	bg_statistical_hypothesis_testing	Tool for computing statistical tests.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	Statistics	bg_statistical_hypothesis_testing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	0.3	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	169	346	46	61	0	0	0	0	0	0	0	0	169	346	46	61	False		
+stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	328	328	38	38	0	0	0	0	0	0	0	0	328	328	38	38	False		
+straindesign	straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion	Toolbox to optimize biological model								To update	https://github.com/brsynth/straindesign	Systems Biology, Synthetic Biology	straindesign	iuc	https://github.com/brsynth/straindesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign	3.2.2	straindesign	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+strelka	strelka_germline, strelka_somatic	Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision.								Up-to-date	https://github.com/Illumina/strelka/	Variant Analysis	strelka	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka	2.9.10	strelka	2.9.10			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	669	669	112	112	1261	1261	417	417	0	0	0	0	1930	1930	529	529	False		
+stress_ng	stress_ng	stress test a computer system in various selectable ways								To update		Web Services	stress_ng	bgruening-util	https://github.com/ColinIanKing/stress-ng	https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng	0.12.04	stress-ng				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	62	3	3	0	0	0	0	0	0	0	0	62	62	3	3	False		
+stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+stringtie	stringtie, stringtie_merge	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	stringtie	stringtie		StringTie	Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.	Transcriptome assembly, RNA-Seq analysis	Transcriptomics, RNA-seq	Up-to-date	http://ccb.jhu.edu/software/stringtie/	Transcriptomics	stringtie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie	2.2.3	stringtie	2.2.3	Transcriptome assembly, RNA-Seq analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	178677	187728	4972	5347	320780	407379	10825	15171	26375	28921	1032	1167	525832	624028	16829	21685	False		
+structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2858	3001	118	123	0	0	0	0	0	0	0	0	2858	3001	118	123	False		
+structureharvester	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date	http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/	Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+substitution_rates	subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	121	3901	34	747	105	114	4	4	226	4015	38	751	False		
+substitutions	substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	93	901	13	84	0	0	0	0	93	901	13	84	False		
+subtract	gops_subtract_1	Subtract the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	566512	567199	410	470	49985	184650	1473	7631	20648	20897	155	188	637145	772746	2038	8289	False		
+subtract_query	subtract_query1	Subtract Whole Dataset from another dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract_query	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query	0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1178	1450	124	141	3169	40539	636	3435	799	950	26	38	5146	42939	786	3614	False		
+suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	249	249	32	32	16	16	10	10	102	102	16	16	367	367	58	58	False		
+suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	117	117	41	41	84	84	24	24	161	161	13	13	362	362	78	78	False		
+suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	217	217	47	47	42	42	20	20	96	96	12	12	355	355	79	79	False		
+suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	721	721	160	160	350	350	91	91	214	214	35	35	1285	1285	286	286	False		
+suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	125	125	30	30	13	13	9	9	83	83	8	8	221	221	47	47	False		
+suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	396	396	134	134	121	121	57	57	144	144	39	39	661	661	230	230	False		
+suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	22	0	21	21	22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	964	964	318	318	249	249	118	118	475	475	108	108	1688	1688	544	544	False		
+suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	8	8	8	8	13	13	11	11	1302	1302	19	19	1323	1323	38	38	False		
+suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	58	58	23	23	24	24	11	11	92	92	11	11	174	174	45	45	False		
+suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	863	863	220	220	237	237	98	98	181	181	41	41	1281	1281	359	359	False		
+suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	0	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	983	983	287	287	375	375	144	144	907	907	106	106	2265	2265	537	537	False		
+suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	46	46	13	13	9	9	5	5	0	0	0	0	55	55	18	18	False		
+suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	0	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	37	37	16	16	22	22	7	7	89	89	14	14	148	148	37	37	False		
+suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	615	615	143	143	246	246	75	75	115	115	27	27	976	976	245	245	False		
+suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	330	330	83	83	64	64	40	40	195	195	49	49	589	589	172	172	False		
+suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	4	4	4	4	5	5	5	5	1	1	1	1	10	10	10	10	False		
+suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	14	14	16	16	6	6	37	37	2	2	82	82	22	22	False		
+suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	0	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	10	10	3	3	14	14	10	10	5	5	5	5	29	29	18	18	False		
+suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	664	664	145	145	113	113	43	43	255	255	50	50	1032	1032	238	238	False		
+suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	84	84	52	52	25	25	16	16	9	9	5	5	118	118	73	73	False		
+suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14941	14941	383	383	25941	25941	255	255	2856	2856	112	112	43738	43738	750	750	False		
+suite_snvphyl		SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	5	5	0	0	0	0	0	0	0	0	26	26	5	5	False		
+swift	swiftlink	Parallel MCMC Linkage Analysis								Up-to-date	https://github.com/ajm/swiftlink	Variant Analysis	swiftlink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift	1.0	swiftlink	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+syndiva	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	30	30	2	2	0	0	0	0	0	0	0	0	30	30	2	2	False		
+t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	411	472	68	90	102	7952	13	1240	0	0	0	0	513	8424	81	1330	False		
+t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	927	959	65	78	130	7194	18	1143	0	0	0	0	1057	8153	83	1221	False		
+t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3783	9125	211	229	1	1	1	1	0	0	0	0	3784	9126	212	230	False		
+t_test_two_samples	t_test_two_samples	T Test for Two Samples								To update		Statistics	t_test_two_samples	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples	https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	141	215	20	31	520	1166	79	274	1025	1118	11	12	1686	2499	110	317	False		
+table_annovar	table_annovar	Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered								To update		Variant Analysis	table_annovar	devteam	Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar	https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar	0.2	annovar				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16526	64515	2803	7456	0	0	0	0	16526	64515	2803	7456	False		
+table_compute	table_compute	Perform general-purpose table operations								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	Text Manipulation	table_compute	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute	1.2.4	pandas				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	216072	216115	1811	1814	12326	12326	1558	1558	16136	16136	256	256	244534	244577	3625	3628	False		
+tables_arithmetic_operations	tables_arithmetic_operations	Arithmetic Operations on tables								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	tables_arithmetic_operations	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations	1.0.0	perl				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2188	2220	33	38	0	0	0	0	0	0	0	0	2188	2220	33	38	False		
+tabular_to_fasta	tab2fasta	Tabular-to-FASTA								To update		Convert Formats	tabular_to_fasta	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta	1.1.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	329032	333057	1489	1702	79033	215770	2441	8587	27876	33727	296	360	435941	582554	4226	10649	False		
+tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7011	8135	449	482	9473	28494	626	2183	850	1090	80	104	17334	37719	1155	2769	False		
+tag_pileup_frequency	tag_pileup_frequency	Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup	Statistics, SAM, Genomic Interval Operations	tag_pileup_frequency	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency	1.0.2	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	158	164	15	16	722	865	40	73	0	0	0	0	880	1029	55	89	False		
+tapscan	tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	19	6	6	0	0	0	0	0	0	0	0	19	19	6	6	False		
+tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	827	838	89	92	114	114	41	41	900	900	29	29	1841	1852	159	162	False		
+tasmanian_mismatch	tasmanian_mismatch	Analysis of positional mismatches								Up-to-date	https://github.com/nebiolabs/tasmanian-mismatch	Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	4	61	61	7	7	0	0	0	0	65	65	11	11	False		
+taxonkit	name2taxid, profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	taxonkit	taxonkit		TaxonKit	TaxonKit is a practical and efficient NCBI taxonomy toolkit.	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	Up-to-date	https://bioinf.shenwei.me/taxonkit/	Metagenomics	taxonkit	iuc	https://github.com/shenwei356/taxonkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit	0.17.0	taxonkit	0.17.0	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	36069	36922	5257	5431	25255	30822	5066	5826	7949	7949	1584	1584	69273	75693	11907	12841	False		
+taxpasta	taxpasta	standardise taxonomic profiles	taxpasta	taxpasta		taxpasta	TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	Up-to-date	https://taxpasta.readthedocs.io/en/latest/	Sequence Analysis	taxpasta	iuc	https://github.com/taxprofiler/taxpasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta	0.7.0	taxpasta	0.7.0	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	34	34	5	5	0	0	0	0	0	0	0	0	34	34	5	5	False		
+tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6372	6395	372	379	7339	7339	378	378	6966	6966	154	154	20677	20700	904	911	False		
+tb_variant_filter	tb_variant_filter	M. tuberculosis H37Rv VCF filter								Up-to-date	https://github.com/COMBAT-TB/tb_variant_filter	Variant Analysis	tb_variant_filter	iuc	https://github.com/COMBAT-TB/tb_variant_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter	0.4.0	tb_variant_filter	0.4.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22977	22977	461	461	3888	3888	274	274	3611	3611	80	80	30476	30476	815	815	False		
+tbl2gff3	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1941	1941	466	466	0	0	0	0	463	463	112	112	2404	2404	578	578	False		
+tbvcfreport	tbvcfreport	Generate HTML report from SnpEff M.tuberculosis VCF(s)								Up-to-date	https://github.com/COMBAT-TB/tbvcfreport	Variant Analysis	tbvcfreport	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport	1.0.1	tbvcfreport	1.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2955	2955	335	335	6090	6090	348	348	2347	2347	72	72	11392	11392	755	755	False		
+te_finder	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.21	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	20	20	0	0	0	0	0	0	0	0	203	203	20	20	False		
+telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+tetoolkit	tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1013	1013	74	74	0	0	0	0	70	70	4	4	1083	1083	78	78	False		
+tetyper	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	106	106	16	16	155	155	47	47	0	0	0	0	261	261	63	63	False		
+text_processing	tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq	High performance text processing tools using the GNU coreutils, sed, awk and friends.								To update	https://www.gnu.org/software/	Text Manipulation	text_processing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	9.3	coreutils	8.25			20	20	20	0	20	20	20	0	0	0	0	0	0	0	0	0	0	19	1	19	0	0	19	0	0	0	20	0	0	0	0	0	0	19	19	19	0	3898014	4015573	37698	42095	648268	915282	47636	69828	103365	105214	7778	7953	4649647	5036069	93112	119876	False		
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	51	51	0	0	0	0	0	0	0	0	547	547	51	51	False		
+tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	8	8	0	0	0	0	0	0	0	0	15	15	8	8	False		
+tn93	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								Up-to-date	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.14	tn93	1.0.14			4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1915	1915	42	42	1972	1972	225	225	0	0	0	0	3887	3887	267	267	False		
+tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	445	445	25	25	71	71	32	32	0	0	0	0	516	516	57	57	False		
+tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9.1	tooldistillator	0.9.1	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	9	9	6	6	5	5	0	0	0	0	71	71	14	14	False		
+tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	158	66524	28	7228	0	0	0	0	158	66525	28	7229	False		
+tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	15496	26623	1076	1664	83063	343017	8372	27829	5388	14057	508	1012	103947	383697	9956	30505	False		
+tophat_fusion_post	tophat_fusion_post	Wrapper for Tophat-Fusion post step								To update		Transcriptomics	tophat_fusion_post	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post	0.1	blast+				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	220	242	41	46	6	814	2	191	100	120	8	12	326	1176	51	249	False		
+topologyeditors	gromacs_modify_topology, gromacs_extract_topology	Set of python scripts and associated tool files that can be used to modify topology files.								To update	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	Molecular Dynamics, Computational chemistry	topologyeditors	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	0	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	57	57	10	10	20	20	8	8	0	0	0	0	77	77	18	18	False		
+tracegroomer	tracegroomer	TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.								Up-to-date	https://github.com/cbib/TraceGroomer	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer	0.1.4	tracegroomer	0.1.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	1	1	0	0	0	0	0	0	0	0	7	7	1	1	False		
+tracy	tracy_align, tracy_assemble, tracy_basecall, tracy_decompose									To update				iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy	0.6.1	tracy	0.7.8			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	3314	3314	124	124	0	0	0	0	0	0	0	0	3314	3314	124	124	False		
+transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5964	6418	944	970	5450	5450	1066	1066	2610	2796	317	344	14024	14664	2327	2380	False		
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	1039	1039	189	189	2672	3349	467	485	358	358	47	47	4069	4746	703	721	False		
+translate_bed	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	649	685	138	142	473	473	105	105	761	761	18	18	1883	1919	261	265	False		
+translate_bed_sequences	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	69	16	21	0	0	0	0	0	0	0	0	57	69	16	21	False		
+transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	250	254	31	31	174	174	45	45	0	0	0	0	424	428	76	76	False		
+tree_relabeler	tree_relabel	Relabels the tips of a newick formatted tree.								To update		Text Manipulation	tree_relabeler	nml	https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler	https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	229489	275008	5733	6500	228708	324716	11708	16638	22644	23869	1439	1527	480841	623593	18880	24665	False		
+trimmer	trimmer	Trim leading or trailing characters.								To update		Text Manipulation	trimmer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer	0.0.1					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	5304	7438	447	512	15698	108672	658	2946	266	822	53	81	21268	116932	1158	3539	False		
+trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	1	1	1	0	352353	383014	14547	15408	632385	839058	39323	49850	125340	139097	5268	5975	1110078	1361169	59138	71233	False		
+trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	To update	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.2	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	0	9	13	13	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	0	11	13	12	0	35698	39132	4376	4632	44509	44509	6714	6714	21883	23889	1924	2070	102090	107530	13014	13416	False		
+trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1968	2080	374	390	1825	1825	527	527	862	1060	161	195	4655	4965	1062	1112	False		
+tripal	analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync	Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal								To update	https://github.com/galaxy-genome-annotation/python-tripal	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal		python-tripal	3.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	4361	4601	741	807	0	0	0	0	2469	2469	190	190	6830	7070	931	997	False		
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	14681	14681	265	265	0	0	0	0	4488	4488	147	147	19169	19169	412	412	False		
+tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	7	7	0	0	0	0	0	0	0	0	17	17	7	7	False		
+tsne	tsne	T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation								To update	https://cran.r-project.org/web/packages/Rtsne/	Text Manipulation	tsne	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne	0.0.2	r-rtsne	0.13			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	379	31	37	281	281	64	64	0	0	0	0	536	660	95	101	False		
+twobittofa	ucsc-twobittofa	twoBitToFa is a tool to convert all or part of .2bit file to FASTA	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenpath/help/twoBit.html	Convert Formats	ucsc_twobittofa	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	469	ucsc-twobittofa	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	413	511	84	118	441	441	123	123	21	21	2	2	875	973	209	243	False		
+tximport	tximport	Wrapper for the Bioconductor package tximport	tximport	tximport		tximport	An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	Up-to-date	http://bioconductor.org/packages/tximport/	Transcriptomics	tximport	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport	1.30.0	bioconductor-tximport	1.30.0	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1802	1802	225	225	6963	6963	904	904	0	0	0	0	8765	8765	1129	1129	False		
+ucsc-cell-browser	ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets								To update	https://cells.ucsc.edu/	Transcriptomics	ucsc_cell_browser	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser	1.0.0+galaxy1	ucsc-cell-browser	1.2.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	965	975	178	181	0	0	0	0	0	0	0	0	965	975	178	181	False		
+ucsc_axtchain	ucsc_axtchain	Chain together genome alignments	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_axtchain	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain	469	ucsc-axtchain	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_axttomaf	ucsc_axtomaf	Convert dataset from axt to MAF format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_axttomaf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf	469	ucsc-axttomaf	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_blat	ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	Up-to-date	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	469	ucsc-blat	469	Sequence alignment	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainnet	ucsc_chainnet	Make alignment nets out of chains	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainnet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	469	ucsc-chainnet	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainprenet	ucsc_chainprenet	Remove chains that don't have a chance of being netted	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainprenet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet	469	ucsc-chainprenet	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainsort	ucsc_chainsort	Sort chains. By default sorts by score.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainsort	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort	469	ucsc-chainsort	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	373	463	134	151	2249	18611	638	4080	0	0	0	0	2622	19074	772	4231	False		
+ucsc_netfilter	ucsc_netfilter	Filter out parts of net	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netfilter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter	469	ucsc-netfilter	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_netsyntenic	ucsc_netsyntenic	Add synteny info to a net dataset	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netsyntenic	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic	469	ucsc-netsyntenic	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_nettoaxt	ucsc_nettoaxt	Convert net (and chain) to axt format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_nettoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt	469	ucsc-nettoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	0	3	5	5	0	55050	68123	1090	1223	9001	9001	906	906	12444	12444	187	187	76495	89568	2183	2316	False		
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	74120	77648	3798	3963	64946	90075	5451	7380	19516	20422	2010	2080	158582	188145	11259	13423	False		
+unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4900	5146	257	270	251	251	81	81	1069	1069	29	29	6220	6466	367	380	False		
+uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.6	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2117	2725	341	412	3111	5779	594	1011	806	806	50	50	6034	9310	985	1473	False		
+uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1488	1596	230	266	0	0	0	0	743	743	35	35	2231	2339	265	301	False		
+unzip	unzip	Unzip file								To update	https://github.com/bmcv	Convert Formats	unzip	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip	6.0	unzip				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6942	7024	1345	1356	1	1	1	1	2461	2461	266	266	9404	9486	1612	1623	False		
+upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1060	1060	5	5	0	0	0	0	0	0	0	0	1060	1060	5	5	False		
+valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	518	677	75	87	234	234	65	65	0	0	0	0	752	911	140	152	False		
+validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	112	38	38	0	0	0	0	0	0	0	0	112	112	38	38	False		
+vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5936	5936	147	147	523	523	15	15	0	0	0	0	6459	6459	162	162	False		
+vardict	vardict_java	VarDict - calls SNVs and indels for tumour-normal pairs								To update	https://github.com/AstraZeneca-NGS/VarDictJava	Variant Analysis	vardict_java	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict	1.8.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	381	381	37	37	0	0	0	0	0	0	0	0	381	381	37	37	False		
+variant_analyzer	mut2read, mut2sscs, read2mut	Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data								To update		Variant Analysis	variant_analyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer	2.0.0	matplotlib				3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	95	95	14	14	516	516	67	67	0	0	0	0	611	611	81	81	False		
+varscan	varscan_copynumber, varscan_mpileup, varscan_somatic	VarScan is a variant caller for high-throughput sequencing data								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/varscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan	2.4.3	varscan	2.4.6			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	10711	11502	1442	1560	16705	16705	3135	3135	1036	1036	100	100	28452	29243	4677	4795	False		
+varscan_vaf	varscan_vaf	Compute variant allele frequency in vcf files generated by varscan.								To update	http://artbio.fr	Variant Analysis	varscan_vaf	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf	https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+varscan_version_2	varscan	VarScan wrapper								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan_version_2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2	2.4.2	varscan	2.4.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5058	6139	606	699	17232	53268	2965	5686	2298	2656	424	482	24588	62063	3995	6867	False		
+varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	273	273	12	12	0	0	0	0	0	0	0	0	273	273	12	12	False		
+vcf2maf	vcf2maf	vcf2maf: Convert VCF into MAF								To update	https://github.com/mskcc/vcf2maf	Convert Formats	vcf2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf	1.6.21	vcf2maf	1.6.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1097	1097	46	46	0	0	0	0	65	65	5	5	1162	1162	51	51	False		
+vcf2pgsnp	vcf2pgSnp	VCF to pgSnp								To update		Variant Analysis	vcf2pgsnp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	191	221	57	65	1399	2700	209	584	0	0	0	0	1590	2921	266	649	False		
+vcf2snvalignment	vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vcf2tsv	vcf2tsv	Converts VCF files into tab-delimited format								To update	https://github.com/ekg/vcflib	Variant Analysis, Convert Formats	vcf2tsv	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	169090	169679	823	874	16304	42215	1141	2594	2485	2511	169	172	187879	214405	2133	3640	False		
+vcf_annotate	vcf_annotate	Annotate a VCF file (dbSNP, hapmap)								To update		Variant Analysis	vcf_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	1	0	1	263	340	31	54	263	342	31	56	False		
+vcf_extract	vcf_extract	Extract reads from a specified region								To update		Variant Analysis	vcf_extract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	513	569	6	9	513	569	6	9	False		
+vcf_filter	vcf_filter	Filter a VCF file								To update		Variant Analysis	vcf_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	400	455	129	140	0	0	0	0	238	606	19	56	638	1061	148	196	False		
+vcf_intersect	vcf_intersect	Generate the intersection of two VCF files								To update		Variant Analysis	vcf_intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	3	0	0	0	0	335	463	19	28	335	482	19	31	False		
+vcfaddinfo	vcfaddinfo	Adds info fields from the second dataset which are not present in the first dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfaddinfo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	882	888	30	32	6118	8261	36	114	175	184	6	6	7175	9333	72	152	False		
+vcfallelicprimitives	vcfallelicprimitives	Splits alleleic primitives (gaps or mismatches) into multiple VCF lines								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfallelicprimitives	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6879	17157	897	1219	7585	14509	1245	1925	1648	1681	225	229	16112	33347	2367	3373	False		
+vcfanno	vcfanno	Annotate VCF files	vcfanno	vcfanno		vcfanno	Fast, flexible annotation of genetic variants.	SNP annotation	Genetic variation, Data submission, annotation and curation	Up-to-date	https://github.com/brentp/vcfanno	Variant Analysis	vcfanno	iuc	https://github.com/galaxyproject/tools-iuc/vcfanno/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno	0.3.5	vcfanno	0.3.5	SNP annotation	Genetic variation, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1139	1139	174	174	0	0	0	0	0	0	0	0	1139	1139	174	174	False		
+vcfannotate	vcfannotate	Intersect VCF records with BED annotations								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotate	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2797	2850	157	181	3668	14532	652	1392	494	507	61	63	6959	17889	870	1636	False		
+vcfannotategenotypes	vcfannotategenotypes	Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotategenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	203	62	66	497	1828	155	387	184	197	11	11	870	2228	228	464	False		
+vcfbedintersect	vcfbedintersect	Intersect VCF and BED datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbedintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3017	4049	185	210	4709	20250	406	1147	507	527	40	42	8233	24826	631	1399	False		
+vcfbreakcreatemulti	vcfbreakcreatemulti	Break multiple alleles into multiple records, or combine overallpoing alleles into a single record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbreakcreatemulti	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	416	478	35	40	3969	10457	82	309	362	378	8	8	4747	11313	125	357	False		
+vcfcheck	vcfcheck	Verify that the reference allele matches the reference genome								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcheck	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	745	767	96	106	803	1895	222	627	241	256	16	17	1789	2918	334	750	False		
+vcfcombine	vcfcombine	Combine multiple VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcombine	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1422	2020	284	505	4951	19530	1021	2669	493	516	60	62	6866	22066	1365	3236	False		
+vcfcommonsamples	vcfcommonsamples	Output records belonging to samples commong between two datasets.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcommonsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	233	253	37	42	234	1839	79	287	199	214	11	12	666	2306	127	341	False		
+vcfdistance	vcfdistance	Calculate distance to the nearest variant.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfdistance	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	572	585	90	92	2063	2427	139	296	272	290	19	22	2907	3302	248	410	False		
+vcffilter	vcffilter2	Tool for filtering VCF files								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffilter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37489	47142	2113	2218	75128	162296	5730	10533	2626	2736	320	331	115243	212174	8163	13082	False		
+vcffixup	vcffixup	Count the allele frequencies across alleles present in each record in the VCF file.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffixup	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	926	957	155	173	2291	5323	313	985	251	265	28	31	3468	6545	496	1189	False		
+vcfflatten	vcfflatten2	Removes multi-allelic sites by picking the most common alternate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfflatten	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	172	183	21	25	351	879	67	201	312	342	15	16	835	1404	103	242	False		
+vcfgeno2haplo	vcfgeno2haplo	Convert genotype-based phased alleles into haplotype alleles								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgeno2haplo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	778	794	107	112	2414	3721	179	508	209	225	20	21	3401	4740	306	641	False		
+vcfgenotypes	vcfgenotypes	Convert numerical representation of genotypes to allelic.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	502	555	134	143	3428	6338	266	858	220	235	23	24	4150	7128	423	1025	False		
+vcfhethom	vcfhethom	Count the number of heterozygotes and alleles, compute het/hom ratio.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfhethom	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1964	1991	182	186	1937	3846	188	644	567	601	26	27	4468	6438	396	857	False		
+vcfleftalign	vcfleftalign	Left-align indels and complex variants in VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfleftalign	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	269	310	38	42	358	1071	89	287	179	213	12	14	806	1594	139	343	False		
+vcfprimers	vcfprimers	Extract flanking sequences for each VCF record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfprimers	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	590	711	28	33	403	831	75	200	190	214	10	12	1183	1756	113	245	False		
+vcfrandomsample	vcfrandomsample	Randomly sample sites from VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfrandomsample	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	161	168	13	15	153	350	27	75	184	192	6	6	498	710	46	96	False		
+vcfselectsamples	vcfselectsamples	Select samples from a VCF file								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfselectsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	830	900	69	88	1315	6257	237	959	344	363	20	21	2489	7520	326	1068	False		
+vcfsort	vcfsort	Sort VCF dataset by coordinate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfsort	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1868	1904	174	185	18378	24175	422	1279	537	674	70	73	20783	26753	666	1537	False		
+vcftools_annotate	vcftools_annotate	Annotate VCF using custom/user-defined annotations								To update	https://vcftools.github.io/	Variant Analysis	vcftools_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate	0.1	echo				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	155	192	81	90	1853	3943	581	1280	144	156	13	16	2152	4291	675	1386	False		
+vcftools_compare	vcftools_compare	Compare VCF files to get overlap and uniqueness statistics								To update	https://vcftools.github.io/	Variant Analysis	vcftools_compare	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	440	594	127	142	0	0	0	0	0	16	0	12	440	610	127	154	False		
+vcftools_consensus	vcftools_consensus	Apply VCF variants to a fasta file to create consensus sequence								To update	https://vcftools.github.io/	Variant Analysis	vcftools_consensus	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus	0.1.11	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vcftools_isec	vcftools_isec	Intersect multiple VCF datasets								To update	https://vcftools.github.io/	Variant Analysis	vcftools_isec	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec	0.1.1	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	379	537	104	118	0	1	0	1	39	496	28	48	418	1034	132	167	False		
+vcftools_merge	vcftools_merge	Merge multiple VCF datasets into a single dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge	0.1.11	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	817	1084	244	273	0	0	0	0	93	448	44	60	910	1532	288	333	False		
+vcftools_slice	vcftools_slice	Subset VCF dataset by genomic regions								To update	https://vcftools.github.io/	Variant Analysis	vcftools_slice	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice	0.1	echo				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	410	423	56	60	6261	8115	133	362	127	157	10	19	6798	8695	199	441	False		
+vcftools_subset	vcftools_subset	Select samples from a VCF dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_subset	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	134	142	46	49	0	0	0	0	120	142	12	19	254	284	58	68	False		
+vcfvcfintersect	vcfvcfintersect	Intersect two VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfvcfintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	976544	977015	703	748	64155	81830	981	2103	11044	11069	225	229	1051743	1069914	1909	3080	False		
+vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	2157	2287	198	209	3930	5591	446	744	0	0	0	0	6087	7878	644	953	False		
+velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	4	4	22	22	6	6	16	16	1	1	45	45	11	11	False		
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	25171	27943	3899	4270	51187	51187	7557	7557	28546	28619	3585	3613	104904	107749	15041	15440	False		
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4715	5343	888	965	9575	9576	2117	2117	3271	5524	1050	1397	17561	20443	4055	4479	False		
+venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4519	5476	667	730	9858	18420	986	2010	0	0	0	0	14377	23896	1653	2740	False		
+verify_map	verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	48	25	25	0	0	0	0	0	0	0	0	48	48	25	25	False		
+vg	vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.59.0			0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	478	478	17	17	0	0	0	0	0	0	0	0	478	478	17	17	False		
+vibrant	vibrant	Virus Identification By iteRative ANnoTation	VIBRANT	VIBRANT		VIBRANT	Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	Up-to-date	https://github.com/AnantharamanLab/VIBRANT	Metagenomics	vibrant	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant	1.2.1	vibrant	1.2.1	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vienna_rna	viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	0	3197	8107	344	415	0	0	0	0	0	0	0	0	3197	8107	344	415	False		
+vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	14412	14590	722	732	0	0	0	0	0	0	0	0	14412	14590	722	732	False		
+virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	94	94	16	16	0	0	0	0	0	0	0	0	94	94	16	16	False		
+virheat	virheat	generates a heatmap of allele frequencies from vcf files	virheat	virheat		virHEAT	VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.			Up-to-date	https://github.com/jonas-fuchs/virHEAT	Visualization, Variant Analysis	virheat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat	0.7.1	virheat	0.7.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	2	2	0	0	0	0	0	0	0	0	12	12	2	2	False		
+virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	574	574	76	76	0	0	0	0	0	0	0	0	574	574	76	76	False		
+virsorter	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	virsorter	virsorter		virsorter	Identify DNA and RNA virus sequences.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/jiarong/VirSorter2/	Metagenomics	virsorter	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter	2.2.4	virsorter	2.2.4	Taxonomic classification	Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+visceral_evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	1	1	0	0	0	0	0	0	0	0	20	25	1	1	False		
+vmd		vmd is a package for  visualizing and analyzing trajectories from molecular dynamics (MD) simulations								To update	https://www.ks.uiuc.edu/Research/vmd/	Computational chemistry	vmd	chemteam	https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	34917	36852	3670	3786	54931	54931	5597	5597	7183	7183	905	905	97031	98966	10172	10288	False		
+voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	43	43	3	3	0	0	0	0	0	0	0	0	43	43	3	3	False		
+vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.29.0	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	0	8	8	8	0	9694	10338	559	628	12282	53546	1031	2007	5334	5672	246	277	27310	69556	1836	2912	False		
+vsnp	vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+w4mclassfilter	w4mclassfilter	Filter W4M data by values or metadata								To update	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper	Metabolomics	w4mclassfilter	eschen42	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter	0.98.19	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2370	2836	9	10	0	0	0	0	1482	1509	4	4	3852	4345	13	14	False		
+w4mconcatenate	W4Mconcatenate	[W4M][Utils] concatenate two Metadata tables								To update	http://workflow4metabolomics.org	Metabolomics	w4mconcatenate	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate	1.0.0+galaxy0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+w4mcorcov	w4mcorcov	OPLS-DA Contrasts of Univariate Results								To update	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper	Metabolomics	w4mcorcov	eschen42	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov	0.98.18	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	238	375	10	10	0	0	0	0	10	10	2	2	248	385	12	12	False		
+w4mjoinpn	w4mjoinpn	Join positive- and negative-mode W4M datasets								To update	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper	Metabolomics	w4mjoinpn	eschen42	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn	0.98.2	coreutils	8.25			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	150	171	7	7	0	0	0	0	7	7	2	2	157	178	9	9	False		
+wade	wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+waveica	waveica	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.	waveica	waveica		WaveICA	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.	Standardisation and normalisation	Metabolomics	Up-to-date	https://github.com/RECETOX/WaveICA	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	0.2.0	r-recetox-waveica	0.2.0	Standardisation and normalisation	Metabolomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	39	6	6	4	4	3	3	0	0	0	0	43	43	9	9	False		
+weather_app	simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+weblogo3	rgweblogo3	Sequence Logo generator for fasta	weblogo	weblogo		WebLogo	Web-based application designed to make generate sequence logos.	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	To update		Graphics	weblogo3	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3	3.5.0	weblogo	3.7.9	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2720	2818	206	228	10299	30578	1354	3657	1226	1285	50	59	14245	34681	1610	3944	False		
+weightedaverage	wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	227	2307	17	75	0	0	0	0	227	2307	17	75	False		
+whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	96	96	13	13	0	0	0	0	0	0	0	0	96	96	13	13	False		
+wigtobigwig	ucsc_wigtobigwig	converts bedGraph (wig) files into binary bigwig	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenPath/help/bigWig.html	Convert Formats	ucsc_wigtobigwig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig	469	ucsc-wigtobigwig	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1601	1601	106	106	1108	1108	172	172	200	200	15	15	2909	2909	293	293	False		
+windowmasker	windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.16.0			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	537	537	19	19	12	12	7	7	297	297	2	2	846	846	28	28	False		
+windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	2	171	3961	34	328	0	0	0	0	171	3972	34	330	False		
+winnowmap	winnowmap	A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.								Up-to-date	https://github.com/marbl/Winnowmap	Next Gen Mappers	winnowmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap	2.03	winnowmap	2.03			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	279	279	46	46	12	12	4	4	0	0	0	0	291	291	50	50	False		
+woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	1	1	0	0	0	0	0	0	0	0	31	31	1	1	False		
+wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	38	2	3	0	0	0	0	0	0	0	0	32	38	2	3	False		
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1619	1715	337	376	0	0	0	0	0	0	0	0	1619	1715	337	376	False		
+xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	0	5	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	5995	5995	275	275	66	66	23	23	295	295	3	3	6356	6356	301	301	False		
+xcms	abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw		XCMS	XCMS		xcms	Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data.  The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling.	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Biological imaging, Data visualisation, Metabolomics	Up-to-date	https://github.com/sneumann/xcms	Metabolomics	xcms	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms	4.0.0	bioconductor-xcms	4.0.0	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Data visualisation, Metabolomics	9	11	12	0	9	11	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	10	9	0	31909	35790	1357	1384	7099	7099	413	413	5333	5357	330	330	44341	48246	2100	2127	False		
+xmlstarlet	xmlstarlet	Tool to convert a xml file from one metadata standard to another								To update		Convert Formats	xmlstarlet	ecology	https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet	https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet	1.6.1	xmlstarlet				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	59	59	17	17	0	0	0	0	0	0	0	0	59	59	17	17	False		
+xpath	xpath	XPath XML querying tool								To update	http://search.cpan.org/dist/XML-XPath/	Text Manipulation	xpath	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath	https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath		perl-xml-xpath	1.47			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	128	235	7	8	0	1	0	1	0	0	0	0	128	236	7	9	False		
+xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+xtb	xtb_molecular_optimization	Performs semiempirical molecular optimization.								To update	https://github.com/grimme-lab/xtb	Metabolomics	xtb_molecular_optimization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	6.6.1	xtb				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	143	143	4	4	0	0	0	0	0	0	0	0	143	143	4	4	False		
+xy_plot	XY_Plot_1	Plotting tool for multiple series and graph types								To update		Graphics, Statistics	xy_plot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot	1.0.2	r-base				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4490	6169	768	889	6120	15516	1921	3653	2033	2212	556	590	12643	23897	3245	5132	False		
+yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	618	618	176	176	336	336	62	62	588	588	25	25	1542	1542	263	263	False		
+zeiss_lmd_converter	ZeissLMDconverter	Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	2.0.4	shapely				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	1	1	0	0	0	0	0	0	0	0	4	4	1	1	False		
+zerone	zerone	ChIP-seq discretization and quality control								Up-to-date	https://github.com/nanakiksc/zerone	ChIP-seq	zerone	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone	https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone	1.0	zerone	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	83	96	9	12	0	0	0	0	0	0	0	0	83	96	9	12	False		
+zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	4	4	0	0	0	0	0	0	0	0	26	26	4	4	False		
diff --git a/communities/genome/resources/tools_filtered_by_ts_categories.tsv b/communities/genome/resources/tools_filtered_by_ts_categories.tsv
new file mode 100644
index 00000000..e8073b86
--- /dev/null
+++ b/communities/genome/resources/tools_filtered_by_ts_categories.tsv
@@ -0,0 +1,1470 @@
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+10x_bamtofastq	10x_bamtofastq	Converts 10x Genomics BAM to FASTQ								Up-to-date	https://github.com/10XGenomics/bamtofastq	Convert Formats	10x_bamtofastq	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	1.4.1	10x_bamtofastq	1.4.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	307	307	80	80	8	8	3	3	3	3	1	1	318	318	84	84	False		
+2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1434	6746	120	122	0	0	0	0	305	305	11	11	1739	7051	131	133	False		
+2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1156	13842	40	42	0	0	0	0	121	121	4	4	1277	13963	44	46	False		
+2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	591	6863	38	40	0	0	0	0	119	119	3	3	710	6982	41	43	False		
+2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	762	782	100	101	0	0	0	0	230	230	14	14	992	1012	114	115	False		
+2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	948	6261	98	100	0	0	0	0	153	153	13	13	1101	6414	111	113	False		
+AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	119	14	17	0	0	0	0	0	0	0	0	45	119	14	17	False		
+AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	189	3094	23	25	0	0	0	0	0	0	0	0	189	3094	23	25	False		
+CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25532	50045	45	57	0	0	0	0	0	0	0	0	25532	50045	45	57	False		
+CollectResults	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1119	2115	50	62	0	0	0	0	0	0	0	0	1119	2115	50	62	False		
+CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	108	1	3	0	0	0	0	0	0	0	0	37	108	1	3	False		
+EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	516	516	128	128	0	0	0	0	0	0	0	0	516	516	128	128	False		
+Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	352	352	36	36	0	0	0	0	0	0	0	0	352	352	36	36	False		
+Ensembl-REST	get_feature_info, get_genetree, get_sequences	A suite of Galaxy tools designed to work with Ensembl REST API.								To update	https://rest.ensembl.org	Data Source		earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	0.1.2	requests				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	474	2914	132	163	0	0	0	0	0	0	0	0	474	2914	132	163	False		
+GAFA	gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	47	6	6	0	0	0	0	0	0	0	0	40	47	6	6	False		
+GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	80	150	18	23	0	0	0	0	0	0	0	0	80	150	18	23	False		
+Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	53	53	18	18	0	0	0	0	0	0	0	0	53	53	18	18	False		
+LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25572	50177	45	57	0	0	0	0	0	0	0	0	25572	50177	45	57	False		
+NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	3210	62854	96	124	0	0	0	0	0	0	0	0	3210	62854	96	124	False		
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	1038	1038	146	146	0	0	0	0	849	849	38	38	1887	1887	184	184	False		
+Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	71	9	10	0	0	0	0	0	0	0	0	45	71	9	10	False		
+PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1202	2121	48	62	0	0	0	0	0	0	0	0	1202	2121	48	62	False		
+Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1116	1897	57	71	0	0	0	0	0	0	0	0	1116	1897	57	71	False		
+Structure_GSPAN	structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	991	3060	50	62	0	0	0	0	0	0	0	0	991	3060	50	62	False		
+ThermoRawFileParser	thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2467	2959	88	124	0	0	0	0	1097	1097	18	18	3564	4056	106	142	False		
+TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1003	1022	48	52	0	0	0	0	0	0	0	0	1003	1022	48	52	False		
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	43	43	20	20	0	0	0	0	0	0	0	0	43	43	20	20	False		
+ab1_fastq	ab1_fastq_converter	Tool to convert ab1 files into FASTQ files								To update		Convert Formats	ab1fastq	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq	1.20.0	bioconductor-sangerseqr	1.38.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	49465	49465	281	281	0	0	0	0	0	0	0	0	49465	49465	281	281	False		
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	619817	622353	4097	4130	320454	320454	2915	2915	496156	503743	2012	2227	1436427	1446550	9024	9272	False		
+abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1139	1139	109	109	0	0	0	0	0	0	0	0	1139	1139	109	109	False		
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5543	5543	1042	1042	1301	1305	413	414	2030	2030	299	299	8874	8878	1754	1755	False		
+adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	348	348	62	62	0	0	0	0	0	0	0	0	348	348	62	62	False		
+add_input_name_as_column	addName	Add input name as column on an existing tabular file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	Text Manipulation	add_input_name_as_column	mvdbeek	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	76834	86002	227	246	20174	20953	312	395	11	11	2	2	97019	106966	541	643	False		
+add_line_to_file	add_line_to_file	Adds a text line to the beginning or end of a file.								To update		Text Manipulation	add_line_to_file	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	0.1.0	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	15933	15933	378	378	1736	1736	214	214	380	380	28	28	18049	18049	620	620	False		
+add_value	addValue	Add a value as a new column.								To update		Text Manipulation	add_value	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value	https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value	1.0.1	perl				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	37860	374587	1293	1610	17588	293713	1243	6197	3873	4397	202	229	59321	672697	2738	8036	False		
+aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	200	200	77	77	83	83	39	39	1747	1747	44	44	2030	2030	160	160	False		
+agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	244	244	0	0	0	0	119	119	10	10	1555	1555	254	254	False		
+aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	262	36	36	0	0	0	0	0	0	0	0	262	262	36	36	False		
+align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	511	541	32	35	0	0	0	0	0	0	0	0	511	541	32	35	False		
+allegro	allegro	Linkage and haplotype analysis from deCODE	allegro	allegro		Allegro	It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	To update	http://www.decode.com/software/	Variant Analysis	allegro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro	@VER@.0	allegro	3	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ambertools	ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap	Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.								To update	http://ambermd.org/AmberTools.php	Molecular Dynamics, Computational chemistry	ambertools	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools	21.10	ambertools				7	2	7	0	7	2	7	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	5	0	41793	41881	510	511	1126	1126	159	159	1552	1552	85	85	44471	44559	754	755	False		
+amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	81	81	17	17	0	0	0	0	0	0	0	0	81	81	17	17	False		
+ampvis2	ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.9			Analysis, Visualisation	Biodiversity	0	0	19	0	0	0	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	1213	1213	155	155	0	0	0	0	0	0	0	0	1213	1213	155	155	False		
+amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5734	5734	334	334	1035	1035	106	106	0	0	0	0	6769	6769	440	440	False		
+ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	7	7	0	0	0	0	0	0	0	0	26	26	7	7	False		
+anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	41	2	2	0	0	0	0	0	0	0	0	36	41	2	2	False		
+anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	43047	43139	1826	1827	17240	17240	878	878	9309	9309	298	298	69596	69688	3002	3003	False		
+annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	29266	30655	2849	2973	59299	66180	5917	6355	5644	5644	1049	1049	94209	102479	9815	10377	False		
+antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	292	306	5	7	0	0	0	0	0	0	0	0	292	306	5	7	False		
+antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15949	16490	726	811	5113	5113	649	649	6043	6043	169	169	27105	27646	1544	1629	False		
+apoc	apoc	Large-scale structural comparison of protein pockets								To update	http://cssb.biology.gatech.edu/APoc	Computational chemistry	apoc	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc	1.0+galaxy1	apoc	1b16			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	4	4	4	1	1	1	1	0	0	0	0	5	5	5	5	False		
+apollo	create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism	Access an Apollo instance from Galaxy								To update	https://github.com/galaxy-genome-annotation/python-apollo	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo		apollo	4.2.13			0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	0	3600	3760	883	911	6	6	4	4	0	0	0	0	3606	3766	887	915	False		
+appendfdr	append_fdr									To update			appendfdr	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr	0.2.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	75	75	9	9	0	0	0	0	0	0	0	0	75	75	9	9	False		
+aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	59	74	10	12	0	0	0	0	0	0	0	0	59	74	10	12	False		
+argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3670	3670	71	71	3	3	2	2	234	234	10	10	3907	3907	83	83	False		
+art	art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/	Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	Conversion	Bioinformatics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	140	140	9	9	0	0	0	0	0	0	0	0	140	140	9	9	False		
+artbio_bam_cleaning	artbio_bam_cleaning	filter bam files before somatic-varscan or lumpy-smoove analysis								To update	http://artbio.fr	SAM, Variant Analysis	artbio_bam_cleaning	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	1.10+galaxy0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	9021	9021	238	238	0	0	0	0	0	0	0	0	9021	9021	238	238	False		
+askomics	askomics_integrate	Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/								To update	https://github.com/askomics/	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics		askocli	0.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+askor	askor_de	AskoR links EdgeR and AskOmics								To update	https://github.com/askomics/askoR	Transcriptomics	askor_de	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	0.2	bioconductor-limma	3.58.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+astral	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees								Up-to-date	https://github.com/smirarab/ASTRAL	Phylogenetics	astral	iuc	https://github.com/usegalaxy-be/galaxytools/tree/main/astral	https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral	5.7.8	astral-tree	5.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	151	151	5	5	151	151	5	5	False		
+astropytools	astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo	AstropyTools library contains Galaxy tools for elementary Astrophysical operations								To update	https://github.com/astropy/astropy	Astronomy	astropytools	volodymyrss	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	0.1.0+galaxy0	astropy				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	13	13	5	5	0	0	0	0	0	0	0	0	13	13	5	5	False		
+atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	232	279	62	72	0	0	0	0	0	0	0	0	232	279	62	72	False		
+augustus	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	12890	13988	1826	1988	14901	14901	2633	2633	6187	6187	511	511	33978	35076	4970	5132	False		
+augustus	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10109	11052	1378	1509	12573	12573	2206	2206	5274	5274	369	369	27956	28899	3953	4084	False		
+b2btools	b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.7	Protein disorder prediction, Protein secondary structure prediction		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	369	369	19	19	0	0	0	0	0	0	0	0	369	369	19	19	False		
+background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1	False		
+bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11117	11117	534	534	19	19	1	1	9601	9601	167	167	20737	20737	702	702	False		
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bam_to_scidx	bam_to_scidx	Contains a tool that converts a BAM file to an ScIdx file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx	Convert Formats	bam_to_scidx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	83	131	15	20	329	785	50	210	0	0	0	0	412	916	65	230	False		
+bamclipper	bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bamhash	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	158	181	40	44	0	0	0	0	0	0	0	0	158	181	40	44	False		
+bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	14693	15620	653	721	61872	101400	1656	5678	39	39	3	3	76604	117059	2312	6402	False		
+bamtools_filter	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115954	124795	2994	3180	95433	142254	6712	10660	5793	5793	497	497	217180	272842	10203	14337	False		
+bamtools_split	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	9073	9073	401	401	2746	2746	224	224	103	103	10	10	11922	11922	635	635	False		
+bamutil	bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	45	45	20	20	69	69	21	21	258	258	1	1	372	372	42	42	False		
+bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	55392	56095	4951	5035	47603	47603	4916	4916	18089	18089	3121	3121	121084	121787	12988	13072	False		
+barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	111	111	8	8	29	29	10	10	21	21	4	4	161	161	22	22	False		
+baric_archive	baric_archive_rennes, baric_archive_toulouse	A data source tool to fetch data from a BARIC Archive server.								To update	https://www.cesgo.org/catibaric/	Data Source		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	1.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+barrnap	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update	https://github.com/tseemann/barrnap	Sequence Analysis	barrnap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	Gene prediction	Genomics, Model organisms, Model organisms	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6041	6041	316	316	0	0	0	0	6723	7273	240	322	12764	13314	556	638	False		
+basecoverage	gops_basecoverage_1	Base Coverage of all intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	basecoverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	226	308	27	35	2615	45557	302	2284	482	522	32	36	3323	46387	361	2355	False		
+baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+basil	basil	Breakpoint detection, including large insertions								Up-to-date	https://github.com/seqan/anise_basil	Variant Analysis	basil	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil	1.2.0	anise_basil	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	306	311	82	83	467	467	99	99	0	0	0	0	773	778	181	182	False		
+batched_lastz	batched_lastz	Galaxy wrapper for the batching Lastz runs								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	batched_lastz	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	1.04.22	lastz	1.04.22			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	123	123	5	5	0	0	0	0	123	123	5	5	False		
+bax2bam	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	208	208	26	26	210	210	30	30	0	0	0	0	418	418	56	56	False		
+bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	90	90	28	28	0	0	0	0	0	0	0	0	90	90	28	28	False		
+bbgbigwig	bbgtobigwig	Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://www.encodeproject.org/software/bedgraphtobigwig/	Convert Formats	bbgbigwig	iuc	https://www.encodeproject.org/software/bedgraphtobigwig/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig	0.1	ucsc-bedgraphtobigwig	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	42	42	7	7	175	175	26	26	0	0	0	0	217	217	33	33	False		
+bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.09	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	4	0	0	11989	11989	768	768	4458	4458	652	652	2507	2507	80	80	18954	18954	1500	1500	False		
+bcftools	bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@	BCFtools toolkit wrappers	bcftools	bcftools		BCFtools	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.	Data handling, Variant calling	Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment	To update	https://samtools.github.io/bcftools/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools	1.15.1	bcftools	1.21	Data handling, Variant calling	DNA polymorphism, GWAS study, Genotyping experiment	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	7	0	2352	3092	234	265	0	0	0	0	0	0	0	0	2352	3092	234	265	False		
+beacon2	beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff	beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://github.com/EGA-archive/beacon2-ri-tools/tree/main	Variant Analysis	beacon2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2	2.0.0	beacon2-ri-tools	2.0.0	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	33	33	9	9	0	0	0	0	0	0	0	0	33	33	9	9	False		
+beacon2-import	beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence	Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants.	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://pypi.org/project/beacon2-import/	Variant Analysis	Beacon2_Import	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import	2.2.4	beacon2-import	2.2.4	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22	22	7	7	0	0	0	0	0	0	0	0	22	22	7	7	False		
+beagle	beagle	Beagle is a program for phasing and imputing missing genotypes.								To update	https://faculty.washington.edu/browning/beagle/beagle.html	Variant Analysis	beagle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle	5.2_21Apr21.304	beagle	5.4_22Jul22.46e			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	88	88	28	28	0	0	0	0	0	0	0	0	88	88	28	28	False		
+bed_to_protein_map	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	410	419	134	137	363	363	99	99	158	158	13	13	931	940	246	249	False		
+bedops	bedops-sort-bed	BEDOPS: high-performance genomic feature operations								Up-to-date	https://bedops.readthedocs.io/en/latest/	Genomic Interval Operations	bedops_sortbed	iuc	https://bedops.readthedocs.io/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops	2.4.41	bedops	2.4.41			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	93	93	36	36	181	181	62	62	0	0	0	0	274	274	98	98	False		
+bedtools	bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed	bedtools is a powerful toolset for genome arithmetic	bedtools	bedtools		BEDTools	BEDTools is an extensive suite of utilities for comparing genomic features in BED format.	Mapping	Genomics	Up-to-date	https://github.com/arq5x/bedtools2	Genomic Interval Operations, Text Manipulation	bedtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools	2.31.1	bedtools	2.31.1	Mapping	Genomics	37	37	37	0	37	37	37	0	0	0	0	0	0	0	0	0	0	37	6	37	0	0	37	0	0	0	37	0	0	0	0	0	0	37	37	37	0	916111	962278	13235	14525	407944	647621	25849	41751	84008	89233	2486	2832	1408063	1699132	41570	59108	False		
+bellerophon	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1611	1611	262	262	763	763	67	67	543	543	30	30	2917	2917	359	359	False		
+berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	617	617	63	63	617	617	63	63	False		
+best_regression_subsets	BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3	4	3	4	14	253	7	72	0	0	0	0	17	257	10	76	False		
+bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1635	1671	123	124	0	0	0	0	334	334	21	21	1969	2005	144	145	False		
+bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	2	0	0	0	0	0	0	0	0	3	3	2	2	False		
+bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	544	544	20	20	0	0	0	0	0	0	0	0	544	544	20	20	False		
+bigwig_outlier_bed	bigwig_outlier_bed	pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files	bigtools	bigtools		bigtools	Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.			To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	Sequence Analysis	bigwig_outlier_bed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed	0.2.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	218	218	5	5	0	0	0	0	0	0	0	0	218	218	5	5	False		
+bigwig_to_bedgraph	bigwig_to_bedgraph	Convert from bigWig to bedGraph format								To update		Convert Formats	bigwig_to_bedgraph	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	0.1.0	ucsc_tools				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5769	6802	567	650	0	0	0	0	0	3	0	1	5769	6805	567	651	False		
+bigwig_to_bedgraph	bigwig_to_bedgraph	Converts a bigWig file to bedGraph format								To update	http://artbio.fr	Convert Formats	bigwig_to_bedgraph	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	377+galaxy1	ucsc-bigwigtobedgraph	469			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5769	6802	567	650	0	0	0	0	0	3	0	1	5769	6805	567	651	False		
+bigwig_to_wig	bigwig_to_wig	Converts a bigWig file to Wiggle (WIG) format								To update	https://artbio.fr	Convert Formats	bigwig_to_wig	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	3+galaxy0	ucsc-bigwiginfo	469			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	401	1385	87	88	0	0	0	0	188	188	9	9	589	1573	96	97	False		
+binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	29	1	1	0	0	0	0	0	0	0	0	24	29	1	1	False		
+binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	126	126	42	42	0	0	0	0	0	0	0	0	126	126	42	42	False		
+bio3d	bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize	Bio3d is a program that can be used to analyse molecular dynamics trajectories.								To update	http://thegrantlab.org/bio3d/index.php	Computational chemistry	bio3d	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	2.4_1	r-bio3d	2.3_3			5	4	5	0	5	4	5	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	5	5	0	10600	10729	1150	1159	1042	1042	255	255	2756	2756	215	215	14398	14527	1620	1629	False		
+bioext	bioext_bam2msa, bioext_bealign	A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!								Up-to-date	https://pypi.python.org/pypi/biopython-extensions/	Next Gen Mappers		iuc	https://github.com/davebx/bioext-gx/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext	0.21.9	python-bioext	0.21.9			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	17413	17413	822	822	15349	15349	2020	2020	2	2	1	1	32764	32764	2843	2843	False		
+bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	61	61	4	4	0	0	0	0	0	0	0	0	61	61	4	4	False		
+biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+biohansel_bionumeric_converter	bionumeric_convert	Convert BioHansel output data to a Bionumerics friendly form								To update	https://github.com/phac-nml/galaxy_tools	Text Manipulation	biohansel_bionumeric_converter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter	0.2.0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	1	0	0	0	0	0	0	0	0	2	2	1	1	False		
+bioinformatics_cafe	fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1137	1137	97	97	1029	1029	71	71	0	0	0	0	2166	2166	168	168	False		
+biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12725	12725	297	297	2851	5049	450	638	2171	2371	214	239	17747	20145	961	1174	False		
+biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	25	11	11	0	0	0	0	0	0	0	0	25	25	11	11	False		
+biomoldyn	biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering	Tools for MD analysis								To update	https://github.com/moldyn/	Molecular Dynamics, Computational chemistry	biomoldyn	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn	1.5.2	scipy				4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	3	0	493	493	119	119	441	441	148	148	0	0	0	0	934	934	267	267	False		
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	151	151	143	143	43	43	596	596	22	22	1286	1286	216	216	False		
+bioperl	bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	Data handling, Service invocation	Genomics, Software engineering	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7738	7931	478	508	8301	8301	849	849	1369	1369	154	154	17408	17601	1481	1511	False		
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6243	6243	375	375	0	0	0	0	6243	6243	375	375	False		
+biotransformer	biotransformer	BioTransformer is a tool for prediction of small molecule metabolism in mammals.	biotransformer	biotransformer		BioTransformer	BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	Up-to-date	https://bitbucket.org/djoumbou/biotransformerjar/src/master/	Metabolomics	biotransformer	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	3.0.20230403	biotransformer	3.0.20230403	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	48	48	1	1	48	48	1	1	False		
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	3	1	1	0	0	0	0	0	0	0	0	3	3	1	1	False		
+bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	4	4	4	0	13715	14997	992	1099	0	0	0	0	197	197	22	22	13912	15194	1014	1121	False		
+blast	magicblast	Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome								Up-to-date	https://ncbi.github.io/magicblast/	Next Gen Mappers	magicblast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast	1.7.0	magicblast	1.7.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	738	738	151	151	0	0	0	0	2	2	1	1	740	740	152	152	False		
+blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1063	1237	257	300	0	0	0	0	0	0	0	0	1063	1237	257	300	False		
+blast_parser	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	417	438	99	104	0	0	0	0	0	0	0	0	417	438	99	104	False		
+blast_plus_remote_blastp	blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.16.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24916	27120	283	347	0	0	0	0	0	0	0	0	24916	27120	283	347	False		
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blastxml_to_gapped_gff3	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	585	585	102	102	172	172	63	63	135	135	16	16	892	892	181	181	False		
+blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	264392	265217	483	552	0	0	0	0	0	0	0	0	264392	265217	483	552	False		
+blat_coverage_report	generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blat_mapping	blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1527	1527	79	79	6	6	1	1	317	317	26	26	1850	1850	106	106	False		
+blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	768	3043	97	119	14	14	11	11	276	276	9	9	1058	3333	117	139	False		
+blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	811	1501	54	79	64	64	29	29	561	561	15	15	1436	2126	98	123	False		
+bowtie2	bowtie2	Bowtie2: Fast and sensitive read alignment	bowtie2	bowtie2		Bowtie 2	Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.	Read mapping	Mapping, Genomics, Mapping	To update	http://bowtie-bio.sourceforge.net/bowtie2	Next Gen Mappers	bowtie2	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2	2.5.3	bowtie2	2.5.4	Read mapping	Mapping, Genomics, Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	1	1	1	0	397893	427447	12133	13176	577209	903193	33086	52020	60105	67495	3779	4271	1035207	1398135	48998	69467	False		
+bowtie_wrappers	bowtie_wrapper	Galaxy wrappers for the Bowtie short read mapping tools.								To update	http://bowtie-bio.sourceforge.net/	Next Gen Mappers	bowtie_wrappers	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers	https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers	1.2.0	bowtie	1.3.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	24164	25149	1320	1480	17537	203397	1330	17491	15654	15992	291	351	57355	244538	2941	19322	False		
+bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	51378	51378	775	775	3298	3298	160	160	1660	1660	63	63	56336	56336	998	998	False		
+braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	165	165	48	48	0	0	0	0	0	0	0	0	165	165	48	48	False		
+braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1938	1938	294	294	0	0	0	0	412	412	71	71	2350	2350	365	365	False		
+breseq	breseq	Predicts mutations in microbial genomes	breseq	breseq		breseq	Runs Breseq software on a set of fastq files.	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	To update	https://github.com/barricklab/breseq	Variant Analysis	breseq	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq	0.35.5	breseq	0.39.0	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	2976	2976	98	98	0	0	0	0	884	884	70	70	3860	3860	168	168	False		
+brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template	brew3r.r	brew3r.r		BREW3R.r	This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.	Genome annotation	Transcriptomics, Genomics	To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2			Genome annotation	Transcriptomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6	6	2	2	0	0	0	0	7	7	3	3	False		
+bumbershoot	idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	1186	1356	21	32	0	0	0	0	0	0	0	0	1186	1356	21	32	False		
+bundle_collections	bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.58			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	1	1518	1526	73	76	1520	1528	74	77	False		
+busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	102717	103051	3877	3926	34251	34251	3506	3506	33192	34369	2439	2525	170160	171671	9822	9957	False		
+bwa	bwa_mem, bwa	Wrapper for bwa mem, aln, sampe, and samse	bwa	bwa		BWA	Fast, accurate, memory-efficient aligner for short and long sequencing reads	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	Up-to-date	http://bio-bwa.sourceforge.net/	Next Gen Mappers	bwa	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa	0.7.18	bwa	0.7.18	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	2	0	0	0	2	0	0	0	0	0	0	2	2	2	2	976935	1017671	13526	14401	474702	681286	32627	47624	79802	87191	4219	4954	1531439	1786148	50372	66979	False		
+bwa_mem2	bwa_mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.	bwa-mem2	bwa-mem2		Bwa-mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,  dataset and the running machine.	Sequence alignment	Mapping	Up-to-date	https://github.com/bwa-mem2/bwa-mem2	Next Gen Mappers	bwa_mem2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2	2.2.1	bwa-mem2	2.2.1	Sequence alignment	Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	56619	56619	2324	2324	36631	36631	2808	2808	18121	18121	713	713	111371	111371	5845	5845	False		
+bwameth	bwameth	Fast and accurate alignment of BS-seq reads								Up-to-date	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.7	bwameth	0.2.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7970	11724	643	826	5524	5524	611	611	1242	1242	114	114	14736	18490	1368	1551	False		
+c3s	c3s	Copernicus Climate Change Service (C3S)								To update	https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset	Climate Analysis	c3s	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	0.3.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	234	234	11	11	4	4	4	4	92	92	3	3	330	330	18	18	False		
+cactus	cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			Multiple sequence alignment, Genome alignment	Genomics, Sequence assembly, Mapping, Phylogenetics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	299	299	61	61	0	0	0	0	1339	1339	95	95	1638	1638	156	156	False		
+cads	cads	Copernicus Atmosphere Data Store (ADS)								To update	https://ads.atmosphere.copernicus.eu/#!/home	Climate Analysis	cads	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	52	52	1	1	0	0	0	0	0	0	0	0	52	52	1	1	False		
+calculate_contrast_threshold	calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+calculate_numeric_param	calculate_numeric_param	Calculate a numeric parameter value using integer and float values.								To update		Text Manipulation	calculate_numeric_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param	0.1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1393	1393	10	10	0	0	0	0	0	0	0	0	1393	1393	10	10	False		
+calisp	calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	False		
+camera	abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos									To update		Metabolomics	camera	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera	1.48.0	r-snow	0.4_1			1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	2	0	677	787	114	120	60	60	30	30	734	746	26	26	1471	1593	170	176	False		
+cami_amber	biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert	Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments								Up-to-date	https://github.com/CAMI-challenge/AMBER	Metagenomics	cami_amber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber	2.0.7	cami-amber	2.0.7			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	195	195	4	4	0	0	0	0	0	0	0	0	195	195	4	4	False		
+canonical_correlation_analysis	cca1	Canonical Correlation Analysis								To update		Statistics	canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis	1.0.0	R				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	66	75	16	18	141	505	31	147	0	0	0	0	207	580	47	165	False		
+canu	canu	Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).	canu	canu		CANU	De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.	De-novo assembly	Genomics	Up-to-date	https://github.com/marbl/canu		canu	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/canu	https://github.com/bgruening/galaxytools/tree/master/tools/canu	2.2	canu	2.2	De-novo assembly	Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13360	14618	1383	1444	0	0	0	0	3542	3542	385	385	16902	18160	1768	1829	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	9869	9869	158	158	0	0	0	0	6886	6886	146	146	16755	16755	304	304	False		
+cardinal	cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								Up-to-date	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	3.4.3	bioconductor-cardinal	3.4.3			0	9	11	0	0	9	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	0	9	11	9	0	41875	50702	663	713	12	12	1	1	7512	7512	231	231	49399	58226	895	945	False		
+cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3835	3835	597	597	1359	1359	467	467	646	646	98	98	5840	5840	1162	1162	False		
+categorize_elements_satisfying_criteria	categorize_elements_satisfying_criteria	Categorize Elements satisfying criteria.								To update		Statistics	categorize_elements_satisfying_criteria	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria	https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	41	4	5	0	0	0	0	168	186	12	14	205	227	16	19	False		
+ccat	peakcalling_ccat	Control-based ChIP-seq Analysis Tool								To update		ChIP-seq	ccat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat	0.0.2	ccat	3.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	175	28	39	0	0	0	0	0	0	0	0	88	175	28	39	False		
+cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5946	7379	407	628	0	0	0	0	5946	7379	407	628	False		
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10414	10414	510	510	2	2	1	1	2	2	1	1	10418	10418	512	512	False		
+cdo	cdo_info, cdo_operations	CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.								To update	https://code.mpimet.mpg.de/projects/cdo/	Climate Analysis		climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	2.0.0					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	218	218	17	17	0	0	0	0	0	0	0	0	218	218	17	17	False		
+cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	4	4	0	0	0	0	0	0	0	0	8	8	4	4	False		
+cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	4	4	0	0	0	0	0	0	0	0	14	14	4	4	False		
+cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	0	0	23	23	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	0	4773	4773	749	749	0	0	0	0	5688	5688	94	94	10461	10461	843	843	False		
+cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55	55	11	11	0	0	0	0	0	0	0	0	55	55	11	11	False		
+cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	225	225	32	32	271	271	61	61	0	0	0	0	496	496	93	93	False		
+cesm	cesm	Community Earth System Model (CESM)								Up-to-date	https://www.cesm.ucar.edu/	Climate Analysis	cesm	climate	https://github.com/ESCOMP/CESM	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm	2.1.3	cesm	2.1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	14	2	2	0	0	0	0	0	0	0	0	14	14	2	2	False		
+cfm	cfmid	Competitive Fragmentation Modeling (CFM)								Up-to-date	https://sourceforge.net/p/cfm-id/	Metabolomics	cfmid	computational-metabolomics	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	33	cfm	33			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+chado	analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree	Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado								To update	https://github.com/galaxy-genome-annotation/python-chado	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado		python-chado	2.3.9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	183	183	20	20	0	0	0	0	0	0	0	0	183	183	20	20	False		
+change_case	ChangeCase	Convert column case.								To update		Text Manipulation	change_case	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case	https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case	1.0.1	perl				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	0	1	1	1	1	10606	12531	2204	2547	9044	17167	1748	2394	923	938	240	245	20573	30636	4192	5186	False		
+charts	charts	Enables advanced visualization options in Galaxy Charts								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3383	4001	1576	1822	7870	13727	3823	6880	249	350	108	145	11502	18078	5507	8847	False		
+chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	62	12	12	0	0	0	0	0	0	0	0	62	62	12	12	False		
+checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	7500	7500	930	930	0	0	0	0	0	0	0	0	7500	7500	930	930	False		
+checkv	checkv_end_to_end	Assess quality of single-contig viral genomes	checkv	checkv		CheckV	CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	Up-to-date	https://bitbucket.org/berkeleylab/checkv/	Metagenomics	checkv	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv	1.0.3	checkv	1.0.3	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	207	207	1	1	0	0	0	0	0	0	0	0	207	207	1	1	False		
+cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+chewbbaca	chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema	BSR-Based Allele Calling Algorithm								To update	https://github.com/B-UMMI/chewBBACA/tree/master	Variant Analysis	chewbbaca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca		chewbbaca	3.3.10			0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	727	727	76	76	0	0	0	0	0	0	0	0	727	727	76	76	False		
+chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	16468	18344	956	991	33692	34453	2559	2625	2948	2948	104	104	53108	55745	3619	3720	False		
+chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	16542	16542	287	287	1061	1061	102	102	27	27	5	5	17630	17630	394	394	False		
+chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	6	6	0	0	0	0	14	14	6	6	False		
+chromeister	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2696	2696	398	398	0	0	0	0	1235	1235	186	186	3931	3931	584	584	False		
+chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+circexplorer	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	211	263	32	40	0	0	0	0	209	209	6	6	420	472	38	46	False		
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	524	524	32	32	0	0	0	0	0	0	0	0	524	524	32	32	False		
+circos	circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile	Build Circos Plots in Galaxy	galactic_circos	galactic_circos		Galactic Circos	Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.	Sequence visualisation		To update	http://circos.ca/	Graphics	circos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos	0.69.8	circos	0.69.9	Sequence visualisation		11	11	11	0	11	11	11	0	0	0	0	0	0	0	0	0	0	0	11	11	0	0	0	0	0	0	11	0	0	0	0	0	0	11	11	11	0	26265	26265	2483	2483	31332	31332	3535	3535	26359	26359	999	999	83956	83956	7017	7017	False		
+cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	21	4	4	9	9	5	5	18	18	1	1	48	48	10	10	False		
+clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3388	3388	187	187	1	1	1	1	1	1	1	1	3390	3390	189	189	False		
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+climate-stripes	climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	239	239	35	35	16	16	2	2	182	182	3	3	437	437	40	40	False		
+clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	548	548	18	18	0	0	0	0	548	548	18	18	False		
+clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	79867	80817	1675	1785	49493	87884	3703	7380	8797	9713	670	728	138157	178414	6048	9893	False		
+cluster	gops_cluster_1	Cluster the intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	cluster	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	513	813	18	35	2406	30579	156	1547	1353	1393	17	20	4272	32785	191	1602	False		
+clustering_from_distmat	clustering_from_distmat	Distance matrix-based hierarchical clustering using SciPy								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	Statistics	clustering_from_distmat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat	1.1.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	5	5	0	0	0	0	0	0	0	0	12	12	5	5	False		
+cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2609	2609	3	3	0	0	0	0	0	0	0	0	2609	2609	3	3	False		
+cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	90	112	11	14	0	0	0	0	0	0	0	0	90	112	11	14	False		
+cnv-phenopacket	cnv_phenopacket	cnv-phenopacket Converts TSV metadata file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv_phenopacket	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket	1.0.2	cnv-phenopacket				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	False		
+cnv-vcf2json	cnv_vcf2json	cnv-vcf2json Converts structural variants VCF file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv-vcf2json	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json	1.1.0	cnv-vcf2json				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5	False		
+cnvkit	cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target	detecting copy number variants and alterations genome-wide from high-throughput sequencing	cnvkit	cnvkit		CNVkit	CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.	Variant calling	DNA structural variation	Up-to-date	https://github.com/etal/cnvkit	Variant Analysis	cnvkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit	0.9.11	cnvkit	0.9.11	Variant calling		0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	618	618	177	177	0	0	0	0	0	0	0	0	618	618	177	177	False		
+codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	61197	61220	64	65	0	0	0	0	0	0	0	0	61197	61220	64	65	False		
+cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	316	355	25	29	0	0	0	0	0	0	0	0	316	355	25	29	False		
+cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2758	2758	22	22	20	20	10	10	0	0	0	0	2778	2778	32	32	False		
+colabfold	colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6771	6771	50	50	0	0	0	0	6771	6771	50	50	False		
+colibread	commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								Up-to-date	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14	commet	24.7.14			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	273	273	40	40	0	0	0	0	0	0	0	0	273	273	40	40	False		
+collapse_collection	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	39518	40471	3555	3629	22007	24841	3536	4045	3969	4101	814	835	65494	69413	7905	8509	False		
+collection_column_join	collection_column_join	Column Join on Collections								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	Text Manipulation	collection_column_join	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join	0.0.3	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	23979	25337	3827	4011	21671	25163	4645	5045	2939	3036	688	701	48589	53536	9160	9757	False		
+collection_element_identifiers	collection_element_identifiers	Extract element identifiers of a collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	Text Manipulation	collection_element_identifiers	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers	0.0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6905	7102	1620	1630	7761	7761	1897	1897	1157	1157	243	243	15823	16020	3760	3770	False		
+color_deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	16	2	3	0	0	0	0	0	0	0	0	15	16	2	3	False		
+colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	40	40	2	2	0	0	0	0	0	0	0	0	40	40	2	2	False		
+column_arrange_by_header	bg_column_arrange_by_header	Column arrange by header name								To update		Text Manipulation	column_arrange_by_header	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5356	5636	446	484	2026	2026	375	375	1400	1531	117	138	8782	9193	938	997	False		
+column_maker	Add_a_column1	Compute an expression on every row								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	Text Manipulation	column_maker	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker	2.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2940752	3907183	5422	6121	263254	737503	6095	13728	96478	97667	884	974	3300484	4742353	12401	20823	False		
+column_order_header_sort	column_order_header_sort	Sort Column Order by heading								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	Text Manipulation	column_order_header_sort	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort	0.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3735	3891	268	297	1923	1923	381	381	0	0	0	0	5658	5814	649	678	False		
+column_remove_by_header	column_remove_by_header	Remove columns by header								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	Text Manipulation	column_remove_by_header	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header	1.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8331	8917	613	662	5206	5206	716	716	1976	1976	27	27	15513	16099	1356	1405	False		
+combineJSON	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	530	530	65	65	8	8	6	6	0	0	0	0	538	538	71	71	False		
+combine_tabular_collection	combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	221	5	28	0	0	0	0	0	0	0	0	39	221	5	28	False		
+compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	332	28	32	0	0	0	0	0	0	0	0	306	332	28	32	False		
+compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	266	266	39	39	28	28	15	15	0	0	0	0	294	294	54	54	False		
+complement	gops_complement_1	Complement intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	complement	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	187	233	15	20	495	4810	165	836	405	451	7	7	1087	5494	187	863	False		
+compose_text_param	compose_text_param	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	compose_text_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param	0.1.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	0	0	0	45827	45831	689	691	7721	7721	303	303	1481	1481	121	121	55029	55033	1113	1115	False		
+compress_file	compress_file	Compress files.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	Text Manipulation	compress_file	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file	0.1.0	gzip				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6343	6343	290	290	3674	3674	286	286	11832	11832	59	59	21849	21849	635	635	False		
+compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	85	96	9	10	0	0	0	0	316	334	8	8	401	430	17	18	False		
+compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	55	65	2	2	0	0	0	0	317	335	5	5	372	400	7	7	False		
+compute_q_values	compute_q_values	Compute q-values based on multiple simultaneous tests p-values								To update		Statistics	compute_q_values	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values	1.0.1	R				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	35	0	3	0	0	0	0	0	0	0	0	0	35	0	3	False		
+concat	gops_concat_1	Concatenate two bed files								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	concat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat	1.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	575128	575441	694	783	43420	85345	629	3508	19330	19418	104	117	637878	680204	1427	4408	False		
+concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	76	82	11	12	0	0	0	0	0	0	0	0	76	82	11	12	False		
+concat_multi_datasets	cat_multi_datasets	Concatenate multiple datasets tail-to-head, including collection datasets.								To update	http://artbio.fr	Text Manipulation	concatenate_multiple_datasets	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	1.4.3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	4822	4824	613	614	1317	1317	204	204	3088	3795	252	289	9227	9936	1069	1107	False		
+concat_paired	concat_fastqs	Concatenate paired datasets								To update	https://github.com/phac-nml/concat	Text Manipulation	concat_paired	nml	https://github.com/phac-nml/concat	https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	2105	2105	155	155	0	0	0	0	0	0	0	0	2105	2105	155	155	False		
+condense_characters	Condense characters1	Condense consecutive characters.								To update		Text Manipulation	condense_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters	1.0.0					1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47	2173	28	368	195	205	8	8	242	2378	36	376	False		
+consensus_from_alignments	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1184	1184	154	154	0	0	0	0	0	0	0	0	1184	1184	154	154	False		
+consolidate_vcfs	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+convert_characters	Convert characters1	Convert delimiters to tab.								To update		Text Manipulation	convert_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters	1.0.1	python				1	1	1	0	1	1	1	0	1	1	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	23589	28986	1061	1200	23507	160693	2302	8699	5413	6446	251	329	52509	196125	3614	10228	False		
+convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cooler	cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify	cooler different tools to process Hi-C from mirnylab								To update	https://github.com/open2c/cooler	Epigenetics	cooler	lldelisle	https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler	0.9.3	htslib	1.21			4	0	5	0	4	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	170	170	26	26	195	195	39	39	0	0	0	0	365	365	65	65	False		
+coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16077	16547	11	11	0	0	0	0	0	0	0	0	16077	16547	11	11	False		
+coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+correlation	cor2	Correlation for numeric columns								To update		Statistics	correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation	1.0.0	rpy				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	398	876	106	134	412	5568	105	755	192	239	21	27	1002	6683	232	916	False		
+correlation_analysis	correlation_analysis	[Metabolomics][W4M] Metabolites Correlation Analysis								To update	http://workflow4metabolomics.org	Metabolomics	correlation_analysis	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis	1.0.1+galaxy0	r-batch	1.1_4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	280	307	110	124	712	1277	332	628	476	541	55	79	1468	2125	497	831	False		
+count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	314	326	73	75	0	0	0	0	129	129	6	6	443	455	79	81	False		
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage	gops_coverage_1	Coverage of a set of intervals on second set of intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	coverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1560	1725	43	58	4328	44209	193	2113	283	316	16	18	6171	46250	252	2189	False		
+coverage_report	CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1081	1081	151	151	0	0	0	0	0	0	0	0	1081	1081	151	151	False		
+cpat	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.								Up-to-date	https://github.com/liguowang/cpat	Transcriptomics	cpat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	3.0.5	cpat	3.0.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	204	204	47	47	165	165	40	40	125	125	7	7	494	494	94	94	False		
+cpm_tpm_rpk	cpm_tpm_rpk	Generate CPM,TPM or RPK from raw counts								To update	http://artbio.fr	Transcriptomics	cpm_tpm_rpk	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	0.6.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+crispr_studio	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	Visualisation	Sequence analysis, Genomics, Data visualisation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1052	1053	75	76	0	0	0	0	0	0	0	0	1052	1053	75	76	False		
+crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	276	390	61	76	131	131	42	42	0	0	0	0	407	521	103	118	False		
+crossmap	crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig	CrossMap converts genome coordinates or annotation files between genome assemblies								Up-to-date	http://crossmap.sourceforge.net/	Convert Formats, Genomic Interval Operations	crossmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap	0.7.0	crossmap	0.7.0			5	0	6	0	5	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	5	6	5	0	2182	2182	331	331	5251	5251	903	903	0	0	0	0	7433	7433	1234	1234	False		
+crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4066	4139	166	180	0	0	0	0	0	0	0	0	4066	4139	166	180	False		
+cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9942	9942	26	26	0	0	0	0	0	0	0	0	9942	9942	26	26	False		
+csvtk	csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq	Rapid data investigation and manipulation of csv/tsv files								To update	https://bioinf.shenwei.me/csvtk/	Text Manipulation	csvtk	nml	https://github.com/shenwei356/csvtk	https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk	0.20.0	csvtk	0.30.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	20	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cta	cta_astro_tool	Basic simulation of CTA telescope observations using gammapy package								To update		Astronomy	cta_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta	0.0.1+galaxy0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	196	211	41	48	1	447	1	161	0	0	0	0	197	658	42	209	False		
+cuffcompare	cuffcompare	Galaxy wrappers for the Cuffcompare tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffcompare	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1	1	0	768	1199	171	300	2205	24981	754	5750	251	493	46	98	3224	26673	971	6148	False		
+cuffdiff	cuffdiff	Galaxy wrappers for the Cuffdiff tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffdiff	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff	2.2.1	cufflinks	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	4176	6065	564	725	24284	117007	4952	20249	971	4231	193	616	29431	127303	5709	21590	False		
+cufflinks	cufflinks	Galaxy wrappers for the Cufflinks tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cufflinks	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	1	1	1	0	26122	33320	870	1213	70653	349091	6984	27076	3963	10315	440	836	100738	392726	8294	29125	False		
+cuffmerge	cuffmerge	Galaxy wrappers for the Cuffmerge tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffmerge	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1	1	0	2406	3448	351	637	20978	67769	3641	13764	1209	3057	227	573	24593	74274	4219	14974	False		
+cuffnorm	cuffnorm	The Cuffnorm tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffnorm	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	374	701	81	114	1032	13499	273	1166	262	322	53	70	1668	14522	407	1350	False		
+cuffquant	cuffquant	The Cuffquant tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffquant	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	408	732	54	71	1964	15883	267	1310	308	422	26	46	2680	17037	347	1427	False		
+cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1251	1803	98	166	3461	15159	486	2044	2425	3338	57	159	7137	20300	641	2369	False		
+cummerbund_to_tabular	cummerbund_to_cuffdiff	Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.								To update		Convert Formats, Next Gen Mappers	cummerbund_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular	1.0.1					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	888	1208	43	97	1334	2683	101	479	0	0	0	0	2222	3891	144	576	False		
+curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	12	2	2	0	0	0	0	0	0	0	0	12	12	2	2	False		
+custom_pro_db	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1729	1744	144	146	450	450	72	72	361	361	12	12	2540	2555	228	230	False		
+custom_pro_db_annotation_data_manager		CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cut_columns	Cut1	Select columns from a dataset.								To update		Text Manipulation	cut_columns	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns	1.0.2					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	0	1	1	1	1	1973168	2034965	11939	12833	352364	803522	12967	30199	128777	133584	2341	2572	2454309	2972071	27247	45604	False		
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	259754	272370	11716	12601	334550	362356	18618	20162	64377	65986	3507	3627	658681	700712	33841	36390	False		
+cutesv	cutesv	Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.	cuteSV	cuteSV		cuteSV	Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis	Split read mapping, Genotyping, Structural variation detection	DNA structural variation, Sequencing, Computer science	To update	https://github.com/tjiangHIT/cuteSV	Variant Analysis	cutesv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv	1.0.8	cutesv	2.1.1	Split read mapping, Genotyping, Structural variation detection	Sequencing, Computer science	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	260	260	43	43	0	0	0	0	119	119	8	8	379	379	51	51	False		
+cwpair2	cwpair2	Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.								To update		ChIP-seq	cwpair2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2	1.1.1	matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	173	280	41	83	0	0	0	0	173	280	41	83	False		
+dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	0	10	10	10	0	92240	92240	2716	2716	179176	179176	5317	5317	12478	12478	394	394	283894	283894	8427	8427	False		
+das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1323	1323	47	47	0	0	0	0	0	0	0	0	1323	1323	47	47	False		
+data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	441	451	83	87	3	3	2	2	0	0	0	0	444	454	85	89	False		
+data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	867	877	213	216	339	339	94	94	64	64	5	5	1270	1280	312	315	False		
+data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	967	967	308	308	0	0	0	0	0	0	0	0	967	967	308	308	False		
+data_manager_eggnog_mapper		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+data_manager_eggnog_mapper_abspath		download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+data_source_iris_tcga	data_source_iris_tcga	IRIS-TCGA Data source tool								To update		Data Source	data_source_iris_tcga	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga	https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+datamash	datamash_ops, datamash_reverse, datamash_transpose	GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.								To update	https://www.gnu.org/software/datamash/	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash	1.8	datamash	1.1.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	1	3	3	0	0	1	0	0	0	1	0	0	0	0	0	0	3	3	3	0	748586	760943	7066	7307	98089	112831	5306	6131	16235	16317	2161	2171	862910	890091	14533	15609	False		
+dbbuilder	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4813	5555	687	805	0	0	0	0	961	961	87	87	5774	6516	774	892	False		
+decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	121	121	28	28	0	0	0	0	0	0	0	0	121	121	28	28	False		
+decoupler	score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk	decoupler - Ensemble of methods to infer biological activities								To update	https://decoupler-py.readthedocs.io/en/latest/	Transcriptomics	suite_decoupler	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler	1.4.0+galaxy3	decoupler	1.5.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	54	6	6	0	0	0	0	0	0	0	0	54	54	6	6	False		
+decoyfasta		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	558	558	7	7	0	0	0	0	0	0	0	0	558	558	7	7	False		
+deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	37	37	0	0	0	0	0	0	0	0	65	65	37	37	False		
+deepvariant	deepvariant	DeepVariant is a deep learning-based variant caller								To update	https://github.com/google/deepvariant	Variant Analysis	deepvariant	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant	1.5.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2561	2561	325	325	2916	2916	460	460	0	0	0	0	5477	5477	785	785	False		
+deg_annotate	deg_annotate	Annotate DESeq2/DEXSeq output tables								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	Transcriptomics	deg_annotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate	1.1.0	bedtools	2.31.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22774	23146	4084	4155	33972	33972	5372	5372	4236	4236	846	846	60982	61354	10302	10373	False		
+delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	40	6	7	0	0	0	0	0	0	0	0	33	40	6	7	False		
+delly	delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge	Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.	delly2	delly2		Delly2	Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.	Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis	DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases	To update	https://github.com/dellytools/delly	Variant Analysis	delly	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly	https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly	0.9.1	delly	1.2.9	Indel detection, Structural variation detection, Genotyping	Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	6	0	0	0	0	0	0	6	6	0	0	1451	1451	288	288	0	0	0	0	0	0	0	0	1451	1451	288	288	False		
+deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	97434	109474	11355	12514	183905	246475	24951	31957	18551	20166	2647	2905	299890	376115	38953	47376	False		
+deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	43	48	8	8	0	0	0	0	0	0	0	0	43	48	8	8	False		
+dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	18	18	0	0	0	0	0	0	0	0	89	89	18	18	False		
+dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	14874	16927	533	837	18475	28854	1403	2568	3854	4271	141	163	37203	50052	2077	3568	False		
+dgidb_annotator	dgidb_annotate	Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)								To update		Systems Biology, Variant Analysis	dgidb_annotator	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator	0.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	69	26	30	0	304	0	133	0	0	0	0	59	373	26	163	False		
+dia_umpire	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	28	33	4	4	0	0	0	0	134	134	4	4	162	167	8	8	False		
+dialignr	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	40	2	2	0	0	0	0	0	0	0	0	40	40	2	2	False		
+diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	0	3	3	0	61376	61746	1847	1895	23164	28729	1140	1556	63034	63034	522	522	147574	153509	3509	3973	False		
+diann	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	72	72	14	14	0	0	0	0	171	171	14	14	243	243	28	28	False		
+diapysef	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	262	262	38	38	0	0	0	0	256	256	6	6	518	518	44	44	False		
+diff	diff	GNU diff tool that calculates the differences between two files.								To update	http://www.gnu.org/software/diffutils/	Text Manipulation	diff	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diff	https://github.com/bgruening/galaxytools/tree/master/tools/diff	3.7	diffutils				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	362	362	99	99	23	23	17	17	0	0	0	0	385	385	116	116	False		
+diffacto	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	11	7	7	0	0	0	0	0	0	0	0	11	11	7	7	False		
+diffbind	diffbind	Diffbind provides functions for  processing  ChIP-Seq  data.	diffbind	diffbind		DiffBind	Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.	Differential binding analysis	ChIP-seq	Up-to-date	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind	3.12.0	bioconductor-diffbind	3.12.0	Differential binding analysis	ChIP-seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7092	7663	606	652	14367	18624	1360	1916	1477	1640	69	84	22936	27927	2035	2652	False		
+diffbind		Diffbind provides functions for  processing  ChIP-Seq  data.								To update	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+digestdb	digestdb									To update			digestdb	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dimet	dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@	DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.								Up-to-date	https://github.com/cbib/DIMet	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet	0.2.4	dimet	0.2.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+directag_and_tagrecon										To update			directag_and_tagrecon	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	358	406	124	139	1361	1361	384	384	0	0	0	0	1719	1767	508	523	False		
+divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26	32	8	9	86	172	20	53	0	0	0	0	112	204	28	62	False		
+dnabot	dnabot	DNA assembly using BASIC on OpenTrons								To update	https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT	Synthetic Biology	dnabot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot	3.1.0	dnabot				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dnaweaver	dnaweaver	Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.								Up-to-date	https://github.com/Edinburgh-Genome-Foundry/DnaWeaver	Synthetic Biology	dnaweaver	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver	1.0.2	dnaweaver_synbiocad	1.0.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	921	1626	4	31	0	0	0	0	0	0	0	0	921	1626	4	31	False		
+dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	74	88	12	15	0	0	0	0	0	0	0	0	74	88	12	15	False		
+dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	7358	7358	88	88	0	0	0	0	0	0	0	0	7358	7358	88	88	False		
+draw_stacked_barplots	draw_stacked_barplots	Draw Stacked Bar Plots for different categories and different criteria								To update		Graphics, Statistics	draw_stacked_barplots	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots	https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots	1.0.0	R				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	216	47	52	0	0	0	0	183	213	22	31	372	429	69	83	False		
+drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	916	916	113	113	0	0	0	0	0	0	0	0	916	916	113	113	False		
+droplet-barcode-plot	_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1151	1151	184	184	356	356	77	77	3	3	1	1	1510	1510	262	262	False		
+dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1900	1901	412	413	609	609	131	131	0	0	0	0	2509	2510	543	544	False		
+dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4413	4442	430	431	4403	4403	255	255	1816	1816	33	33	10632	10661	718	719	False		
+dwt_cor_ava_perclass	compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Feature Occurrences								To update		Statistics	dwt_cor_ava_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	141	8	11	136	141	8	11	False		
+dwt_cor_avb_all	compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features								To update		Statistics	dwt_cor_avb_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	124	124	7	7	124	124	7	7	False		
+dwt_ivc_all	compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Second Moments for Feature Occurrences								To update		Statistics	dwt_ivc_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	121	123	5	7	121	123	5	7	False		
+dwt_var_perclass	compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom	Compute P-values and Max Variances for Feature Occurrences								To update		Statistics	dwt_var_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	131	132	7	8	131	132	7	8	False		
+dwt_var_perfeature	dwt_var1	Wavelet variance using Discrete Wavelet Transfoms								To update		Statistics	dwt_var_perfeature	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature	1.0.2	r-bitops				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	30	36	2	4	11	11	4	4	206	220	6	7	247	267	12	15	False		
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	28	28	2	2	0	0	0	0	0	0	0	0	28	28	2	2	False		
+ebi_tools	ebi_search_rest_results	Tools to query and download data from several EMBL-EBI databases								To update	http://www.ebi.ac.uk/services/all	Web Services, Data Source	ebi_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools	0.1.1	six				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	276	406	133	163	1421	1421	547	547	0	0	0	0	1697	1827	680	710	False		
+ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12996	12996	137	137	10	10	1	1	0	0	0	0	13006	13006	138	138	False		
+edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	19294	20905	2423	2618	48876	58723	6341	7527	8010	8705	846	892	76180	88333	9610	11037	False		
+edta	edta	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. 	edta	edta		The Extensive de novo TE Annotator (EDTA)	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	To update	https://github.com/oushujun/EDTA	Variant Analysis	edta	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta	https://github.com/bgruening/galaxytools/tree/master/tools/edta		edta	2.2.0	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4495	4495	111	111	0	0	0	0	0	0	0	0	4495	4495	111	111	False		
+effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	1	3	1	0	34432	34437	1149	1152	42	42	2	2	21027	21027	413	413	55501	55506	1564	1567	False		
+egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2809	3060	371	402	5179	5179	759	759	1931	1931	226	226	9919	10170	1356	1387	False		
+embl2fa	embl2fa	Converts EMBL flat format to fasta format								To update	http://artbio.fr	Text Manipulation	embl2fa	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	0	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	107	107	107	0	143762	148864	4481	5039	151989	296028	13224	31140	24955	27001	2397	2705	320706	471893	20102	38884	False		
+ena_upload	ena_upload	Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 								To update	https://github.com/usegalaxy-eu/ena-upload-cli	Data Export	ena_upload	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload	0.7.3	ena-upload-cli	0.7.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	366	366	41	41	0	0	0	0	1302	1302	14	14	1668	1668	55	55	False		
+enasearch	enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data	A Python library for interacting with ENA's API								To update	https://github.com/bebatut/enasearch	Data Source	enasearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch		enasearch	0.2.2			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	1989	2302	367	453	0	0	0	0	0	0	0	0	1989	2302	367	453	False		
+encyclopedia	encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30			2	4	7	0	2	4	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	738	738	98	98	1	1	1	1	42	42	4	4	781	781	103	103	False		
+ensembl_vep	ensembl_vep	Ensembl VEP: Annotate VCFs with variant effect predictions								Up-to-date	https://github.com/Ensembl/ensembl-vep	Variant Analysis	ensembl_vep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep	112.0	ensembl-vep	112.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3051	3051	171	171	0	0	0	0	0	0	0	0	3051	3051	171	171	False		
+eodie	eodie	Earth Observation Data Information Extractor								To update	https://eodie.readthedocs.io/	Climate Analysis	eodie	climate	https://gitlab.com/eetun-tiimi/EODIE	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie	1.0.2	eodie				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	45	45	4	4	0	0	0	0	0	0	0	0	45	45	4	4	False		
+epicseg	epicseg_segment	EpiCSeg is a tool for conducting chromatin segmentation.								To update	https://github.com/lamortenera/epicseg	Epigenetics	epicseg	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	@VERSION_STRING@	epicseg	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	160	252	17	21	0	0	0	0	0	0	0	0	160	252	17	21	False		
+episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	880	880	80	80	221	221	37	37	49	49	3	3	1150	1150	120	120	False		
+essential_climate_variables	cds_essential_variability	Get Copernicus Essential Climate Variables for assessing climate variability								To update	https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview	Climate Analysis, Data Source	cds_essential_variability	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	232	336	39	40	0	0	0	0	0	0	0	0	232	336	39	40	False		
+ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	820	966	89	106	0	0	0	0	0	0	0	0	820	966	89	106	False		
+evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+exomedepth	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	517	517	61	61	2995	2995	184	184	0	0	0	0	3512	3512	245	245	False		
+exonerate	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1030	1072	185	188	1058	1058	189	189	922	922	35	35	3010	3052	409	412	False		
+exparna	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5396	5938	580	607	628	628	168	168	519	519	107	107	6543	7085	855	882	False		
+export_to_cluster	export_to_cluster	Export datasets to cluster								To update	https://github.com/TGAC/earlham-galaxytools/	Data Export	export_to_cluster	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster	0.0.2	EXPORT_DIR_PREFIX				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+express	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	278	337	34	45	0	1184	0	117	2402	2844	23	60	2680	4365	57	222	False		
+extract_genomic_dna	Extract genomic DNA 1	Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.								To update		Genomic Interval Operations	extract_genomic_dna	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna	https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna	3.0.3+galaxy2	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	1	0	0	0	1	1	1	1	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	9409	12735	813	923	20180	259099	2072	11791	168	611	20	63	29757	272445	2905	12777	False		
+ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+falco	falco	A high throughput sequence QC analysis tool	falco	falco		Falco	A high-speed FastQC emulation for quality control of sequencing data.	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	Up-to-date	https://github.com/smithlabcode/falco/	Sequence Analysis	falco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco	https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco	1.2.4	falco	1.2.4	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4298	4298	34	34	0	0	0	0	0	0	0	0	4298	4298	34	34	False		
+fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	601	601	128	128	1165	1165	232	232	0	0	0	0	1766	1766	360	360	False		
+fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	469	ucsc-fasplit	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3278	3361	460	478	6144	6144	595	595	1139	1139	183	183	10561	10644	1238	1256	False		
+fasta2bed	fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5191	5367	104	130	5191	5367	104	130	False		
+fasta_compute_length	fasta_compute_length	Compute sequence length								To update	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.4	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	8547	9136	978	1129	17748	51150	1404	5670	4239	4404	162	190	30534	64690	2544	6989	False		
+fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39695	39742	242	255	13660	19007	600	1398	1521	1603	92	112	54876	60352	934	1765	False		
+fasta_extract	fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	10	10	1	1	0	0	0	0	1286	1827	144	181	1296	1837	145	182	False		
+fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	47494	51924	889	997	50663	101663	1488	3742	3919	5601	241	276	102076	159188	2618	5015	False		
+fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	1	5235	5486	237	288	4060	25609	480	2039	816	1093	73	89	10111	32188	790	2416	False		
+fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	30917	32191	1142	1257	36869	36869	1346	1346	5236	5236	230	230	73022	74296	2718	2833	False		
+fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	497	808	71	108	2249	5479	216	703	415	437	18	20	3161	6724	305	831	False		
+fasta_nucleotide_color_plot	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	164	179	42	47	758	905	128	170	0	0	0	0	922	1084	170	217	False		
+fasta_stats	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	43726	44512	3104	3259	19941	19941	3693	3693	16788	18589	2467	2650	80455	83042	9264	9602	False		
+fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	108876	113638	1572	1793	82527	192112	2209	8565	5711	7649	275	334	197114	313399	4056	10692	False		
+fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6685	6685	603	603	0	0	0	0	0	0	0	0	6685	6685	603	603	False		
+fastg2protlib	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	29	29	8	8	0	0	0	0	0	0	0	0	29	29	8	8	False		
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	136	11	11	0	0	0	0	0	0	0	0	136	136	11	11	False		
+fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	1	1126086	1127111	6847	6909	422259	422259	10722	10722	76462	76462	2242	2242	1624807	1625832	19811	19873	False		
+fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8604	8799	215	240	54200	75329	919	2957	1562	1680	76	85	64366	85808	1210	3282	False		
+fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15582	18350	690	771	40489	121585	2715	9239	4657	5793	214	287	60728	145728	3619	10297	False		
+fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	92594	102535	2576	2995	179461	897457	9437	44701	15434	25533	664	1073	287489	1025525	12677	48769	False		
+fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7560	7560	1266	1266	6539	6539	1581	1581	0	0	0	0	14099	14099	2847	2847	False		
+fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2488	3132	215	267	6241	14508	834	2121	4121	4592	131	158	12850	22232	1180	2546	False		
+fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	234	249	43	44	2648	8092	288	983	442	466	12	17	3324	8807	343	1044	False		
+fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5873	8936	532	657	14738	20229	1889	2366	2316	2711	225	261	22927	31876	2646	3284	False		
+fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18216	19573	2348	2492	23484	25936	3482	3851	6207	6551	1402	1442	47907	52060	7232	7785	False		
+fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15628	17130	536	679	24157	58368	1954	5716	1941	2266	172	214	41726	77764	2662	6609	False		
+fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3169	3521	459	535	19309	30747	1410	3441	807	1023	219	247	23285	35291	2088	4223	False		
+fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1271	1393	131	176	12763	58819	2073	8850	430	479	32	51	14464	60691	2236	9077	False		
+fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	335	352	44	47	1583	9696	269	2229	1131	1254	15	27	3049	11302	328	2303	False		
+fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	17279	18386	3826	4062	55268	136888	6055	12590	7685	9356	1854	2043	80232	164630	11735	18695	False		
+fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_stats	fastq_stats	FASTQ Summary Statistics by column								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3858	4595	680	815	15213	81513	3159	14109	3855	4163	184	256	22926	90271	4023	15180	False		
+fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	36069	37805	1151	1234	45213	99852	2691	6370	8457	13335	408	609	89739	150992	4250	8213	False		
+fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	12895	14110	269	297	13315	30673	612	1810	5125	5373	64	87	31335	50156	945	2194	False		
+fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10114	11383	582	665	23906	92351	1986	8818	1588	2607	108	212	35608	106341	2676	9695	False		
+fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								To update		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4881	6165	859	967	29458	99179	3455	11369	2171	2678	259	338	36510	108022	4573	12674	False		
+fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	1	0	1784056	1913280	41344	43940	2269843	3195869	90828	140008	410004	445555	14195	16026	4463903	5554704	146367	199974	False		
+fastqc_stats	FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5162	5162	2350	2350	10176	10176	4714	4714	2610	2610	991	991	17948	17948	8055	8055	False		
+fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	3	0	0	0	0	0	8	0	3	False		
+fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	208349	217568	3421	3732	131388	245005	5108	13227	18655	18655	679	679	358392	481228	9208	17638	False		
+fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	65542	65631	1049	1071	25992	25992	2147	2147	6733	7339	649	745	98267	98962	3845	3963	False		
+fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1769	2020	88	101	6948	24960	358	2424	623	998	32	50	9340	27978	478	2575	False		
+fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	16957	18124	225	260	37001	89126	919	2720	863	989	56	68	54821	108239	1200	3048	False		
+fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3140	3520	178	212	13975	117900	1198	6006	409	712	36	55	17524	122132	1412	6273	False		
+fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	64187	67981	326	349	87477	185555	781	3067	16563	17125	58	78	168227	270661	1165	3494	False		
+fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	174	272	61	92	4295	25068	1056	4180	1127	1171	70	89	5596	26511	1187	4361	False		
+fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2218	2344	168	206	20551	60032	3784	9866	2347	2460	234	256	25116	64836	4186	10328	False		
+fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2364	2526	180	214	6572	11745	303	1024	462	696	49	64	9398	14967	532	1302	False		
+fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10707	12597	356	415	21568	67304	574	1527	719	861	61	78	32994	80762	991	2020	False		
+fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	13584	14557	550	641	123676	206733	2034	8390	2819	4757	229	267	140079	226047	2813	9298	False		
+fates-emerald	ctsm_fates	EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model								To update	https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api	Climate Analysis	ctsm_fates	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	2.0	fates-emerald				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	264	264	69	69	34	34	11	11	103	103	1	1	401	401	81	81	False		
+fatovcf	fatovcf	Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_fatovcf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	448	ucsc-fatovcf	448		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	385	385	46	46	587	587	107	107	58	58	5	5	1030	1030	158	158	False		
+feature_alignment	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	18	18	1	1	0	0	0	0	0	0	0	0	18	18	1	1	False		
+featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22308	22388	16	19	350	13711	54	349	0	0	0	0	22658	36099	70	368	False		
+featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	740719	770524	11699	12547	643892	784396	23272	27598	66108	68867	2348	2463	1450719	1623787	37319	42608	False		
+feelnc	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	Annotation, Classification	Functional, regulatory and non-coding RNA	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1375	1500	95	99	797	797	116	116	59	59	3	3	2231	2356	214	218	False		
+feelnc2asko	feelnc2asko	Convert FeelNC GTF to GFF3								To update	https://github.com/tderrien/FEELnc	Convert Formats	feelnc2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+feht	feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	1	1	1	1	False		
+fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5618	5820	582	607	21673	21673	938	938	869	869	110	110	28160	28362	1630	1655	False		
+file_manipulation	bg_uniq	This tool returns all unique lines from a tab-separated file.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	Text Manipulation	unique	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	0.4	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	6690	8818	554	612	0	0	0	0	0	0	0	0	6690	8818	554	612	False		
+filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	26717	29932	1026	1072	42990	42990	1176	1176	9619	9619	230	230	79326	82541	2432	2478	False		
+filter_compounds	filter_orgmet_anorg	Tool for filtering organometallics/anorganic compounds from a list of compounds.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	filter_compounds	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	3.1.1	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_density	filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_stats	filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_transcripts_via_tracking	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23	24	9	10	62	635	26	241	2	2	2	2	87	661	37	253	False		
+filter_vcf	filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	53310	53944	1499	1575	25043	25043	726	726	10824	10824	593	593	89177	89811	2818	2894	False		
+find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	62	70	10	12	3	1787	1	204	0	0	0	0	65	1857	11	216	False		
+find_repeats	findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+find_subsequences	bg_find_subsequences									To update			find_subsequences	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences	0.3	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	554	784	69	79	2820	3047	323	361	20	20	1	1	3394	3851	393	441	False		
+fisher_test	fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	1985	1985	41	41	0	0	0	0	0	0	0	0	1985	1985	41	41	False		
+flanking_features	flanking_features_1	Fetch closest non-overlapping feature for every interval								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	flanking_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features	4.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	589	731	51	63	2445	32847	304	2549	1214	1294	15	22	4248	34872	370	2634	False		
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22017	22304	239	255	9399	14886	462	709	4	4	1	1	31420	37194	702	965	False		
+flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	661	715	52	54	0	0	0	0	167	167	15	15	828	882	67	69	False		
+flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	2	2	0	0	0	0	0	0	0	0	9	9	2	2	False		
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32514	32675	3379	3422	19434	19434	2537	2537	9843	9843	1624	1624	61791	61952	7540	7583	False		
+footprint	footprint	Find transcription factor footprints								To update	https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/	Epigenetics	footprint	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	1.0.0	footprint	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	57	5	5	0	0	0	0	0	0	0	0	57	57	5	5	False		
+format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	189	203	57	60	0	0	0	0	0	0	0	0	189	203	57	60	False		
+format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5940	6474	558	608	0	0	0	0	0	0	0	0	5940	6474	558	608	False		
+fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1257	1450	150	162	0	0	0	0	1052	1052	45	45	2309	2502	195	207	False		
+fragpipe	fragpipe	Data analysis for mass spectrometry-based proteomics.								Up-to-date	https://fragpipe.nesvilab.org/	Proteomics	fragpipe	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	20.0	fragpipe	20.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	64	64	9	9	0	0	0	0	0	0	0	0	64	64	9	9	False		
+free_energy		Free energy tools of BRIDGE.								To update		Molecular Dynamics, Computational chemistry	freeenergy	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+freebayes	freebayes, bamleftalign	Galaxy Freebayes Bayesian genetic variant detector tool	freebayes	freebayes		FreeBayes	Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	To update	https://github.com/ekg/freebayes	Variant Analysis	freebayes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes	1.3.6	freebayes	1.3.8	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	149715	171093	8158	8794	144708	256315	15996	25107	19156	21936	2251	2571	313579	449344	26405	36472	False		
+freec	control_freec	Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.	freec	freec		FREEC	A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.	Copy number estimation, Variant calling, Genome alignment	DNA structural variation, Oncology, Human genetics, Data mining	To update	http://boevalab.inf.ethz.ch/FREEC/	Variant Analysis	control_freec	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec	11.6	gawk		Copy number estimation, Variant calling, Genome alignment	Oncology, Human genetics, Data mining	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	748	748	91	91	0	0	0	0	12	12	1	1	760	760	92	92	False		
+freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	21757	21757	101	101	217	217	21	21	0	0	0	0	21974	21974	122	122	False		
+frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fromHicupToJuicebox	fromHicupToJuicebox	Convert the output of hicup (as sam or bam) to the input of juicebox.								To update		Epigenetics	from_hicup_to_juicebox	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fromgtfTobed12	fromgtfTobed12	Convert GTF files to BED12 format								To update	https://pythonhosted.org/gffutils/contents.html	Convert Formats	fromgtftobed12	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	0.11.1+galaxy1	gffutils	0.13			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fsd	fsd, fsd_beforevsafter, fsd_regions, td	Tool that plots a histogram of sizes of read families								To update		Graphics	duplex_family_size_distribution	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd	1.0.2	matplotlib				4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	578	578	34	34	0	0	0	0	578	578	34	34	False		
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	8648	8648	1408	1408	32	32	6	6	6406	6406	597	597	15086	15086	2011	2011	False		
+garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	11	11	0	0	0	0	0	0	0	0	27	27	11	11	False		
+gatk4	filtermutectcalls, mergemutectstats, mutect2	Find somatic variations								To update	http://artbio.fr	Variant Analysis	gatk4	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gatk4	gatk4_mutect2	A Galaxy wrapper for Mutect2 from GATK								To update	https://software.broadinstitute.org/gatk/gatk4	Variant Analysis	gatk4_mutect2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3463	3463	452	452	9040	9040	1639	1639	0	0	0	0	12503	12503	2091	2091	False		
+gblocks	gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	466	466	62	62	466	466	62	62	False		
+gc_derivatization	gc_derivatization	In silico derivatization for GC.								Up-to-date	https://github.com/RECETOX/gc-meox-tms	Metabolomics	gc_derivatization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	1.0.1	gc-meox-tms	1.0.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gcms2isocor	gcms2isocor	Conversion from GCMS PostRun Analysis to Isocor								To update		Metabolomics	gcms2isocor	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gcms2isocor	gcms2isocor	Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs								To update	https://github.com/p2m2/p2m2tools	Metabolomics	gcms2isocor	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor	0.2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	1409	1498	39	42	0	0	0	0	0	0	0	0	1409	1498	39	42	False		
+gdcwebapp	data_source_gdcwebapp	GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format								To update	http://bioinf.iasi.cnr.it/gdcwebapp/	Data Source, Convert Formats	gdcwebapp	iuc	https://github.com/fabio-cumbo/GDCWebApp4Galaxy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp	1.0.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gecko	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	723	723	235	235	0	0	0	0	786	786	95	95	1509	1509	330	330	False		
+gemini	gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	Sequence analysis, Genetic variation analysis	Sequence analysis	1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	4967	5475	1863	1992	992	1118	279	370	3756	3811	423	425	9715	10404	2565	2787	False		
+genebed_maf_to_fasta	GeneBed_Maf_Fasta2	Stitch gene blocks given a set of coding exon intervals								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	Genomic Interval Operations	genebed_maf_to_fasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta	1.0.1+galaxy0					1	1	1	0	1	1	1	0	0	1	0	0	0	1	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	1	0	4	4	2	2	221	2905	23	279	0	0	0	0	225	2909	25	281	False		
+genehunter_modscore	genehunter_modscore	Maximised LOD score pedigree analysis utility								To update	https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1	Variant Analysis	genehunter_modscore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore	3.0.0	ghm	3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+geneiobio	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	101	101	25	25	0	0	0	0	59	59	6	6	160	160	31	31	False		
+genenotebook	genenotebook_build	Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io								Up-to-date	https://genenotebook.github.io	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	0.4.16	genoboo	0.4.16			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+generate_pc_lda_matrix	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115	124	29	30	518	1029	102	261	184	198	14	17	817	1351	145	308	False		
+genetrack	genetrack	"Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand."								To update		ChIP-seq	genetrack	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack		numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	445	660	104	197	0	0	0	0	445	660	104	197	False		
+genform	genform	genform: generation of molecular formulas by high-resolution MS and MS/MS data								To update	https://sourceforge.net/projects/genform/	Metabolomics	genform	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform		genform	r8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	68	68	4	4	0	0	0	0	0	0	0	0	68	68	4	4	False		
+genomad	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	genomad	genomad		geNomad	geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.	Sequence annotation, Taxonomic classification	Sequence analysis	To update	https://github.com/apcamargo/genomad/	Metagenomics	genomad	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad	1.8.0	genomad	1.8.1	Sequence annotation, Taxonomic classification	Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+genomescope	genomescope	Analyze unassembled short reads								Up-to-date	https://github.com/tbenavi1/genomescope2.0	Statistics	genomescope	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope	2.0.1	genomescope2	2.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3181	3181	665	665	2112	2112	435	435	1622	1622	148	148	6915	6915	1248	1248	False		
+genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	47	47	13	13	0	0	0	0	0	0	0	0	47	47	13	13	False		
+genrich	genrich	Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).								To update	https://github.com/jsh58/Genrich	ChIP-seq	genrich	iuc	https://github.com/jsh58/Genrich	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich	0.5+galaxy2	genrich	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3534	3577	402	405	2840	2840	419	419	571	571	31	31	6945	6988	852	855	False		
+getTn5ExtendedCoverage	getTn5ExtendedCoverage	Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension								To update		Epigenetics	gettn5extendedcoverage	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+get_flanks	get_flanks1	Get flanks returns flanking region/s for every gene								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	get_flanks	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3768	325011	1462	2044	9350	242043	2201	6583	787	1070	119	146	13905	568124	3782	8773	False		
+get_hrun	get_hrun	Annotate indel variants with homopolymer context								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	Variant Analysis	get_hrun	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun	0.5.9.2	pyfaidx	0.8.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5	False		
+get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	746	746	136	136	0	0	0	0	1504	1504	244	244	2250	2250	380	380	False		
+get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+getindelrates_3way	indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	290	20	86	0	0	0	0	70	290	20	86	False		
+getindels_2way	getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	74	237	24	61	0	0	0	0	74	237	24	61	False		
+getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1542	1542	159	159	0	0	0	0	587	587	64	64	2129	2129	223	223	False		
+gfa_to_fa	gfa_to_fa	gfa_to_fa - Converting GFA format to Fasta format								To update	http://gfa-spec.github.io/GFA-spec/	Convert Formats	gfa_to_fa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa	0.1.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9664	9775	763	765	5623	5623	493	493	1000	1000	135	135	16287	16398	1391	1393	False		
+gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	To update	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.7	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11748	11748	767	767	6560	6560	397	397	2556	2556	106	106	20864	20864	1270	1270	False		
+gff3_rebase	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	806	812	68	68	197	197	37	37	132	132	12	12	1135	1141	117	117	False		
+gffcompare	gffcompare	Galaxy wrappers for Geo Pertea's GffCompare package.	gffcompare	gffcompare		gffcompare	Program for comparing, annotating, merging and tracking transcripts in GFF files.	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	https://github.com/gpertea/gffcompare/	Transcriptomics	gffcompare	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare	0.12.6	gffcompare	0.12.6	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3560	3980	916	999	5281	8000	1713	2521	1468	1642	208	225	10309	13622	2837	3745	False		
+gffcompare_to_bed	gffcompare_to_bed	Filter and convert a gffCompare GTF to BED								To update	https://github.com/gpertea/gffcompare/	Convert Formats	gffcompare_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	0.2.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1375	2230	329	347	1071	1071	362	362	492	492	64	64	2938	3793	755	773	False		
+gffread	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12828	13716	1740	1829	15217	23818	2588	3486	4423	4423	732	732	32468	41957	5060	6047	False		
+ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	0	5	5	5	0	24606	25662	3463	3630	26805	26808	5143	5144	8174	8237	1259	1279	59585	60707	9865	10053	False		
+ggupset	emc-ggupset	Create Upset Plots with ggupset								To update	https://github.com/const-ae/ggupset	Graphics	ggupset	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset	1.0	r-ggupset				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	490	682	74	109	127	14058	20	1798	0	0	0	0	617	14740	94	1907	False		
+glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	0	4343	4343	407	407	0	0	0	0	0	0	0	0	4343	4343	407	407	False		
+glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	11	6	6	85	984	29	230	10	11	7	8	106	1006	42	244	False		
+gnali	gnali	A tool to find nonessential, loss-of-function gene variants								Up-to-date	https://github.com/phac-nml/gnali/	Variant Analysis	gnali	nml	https://github.com/phac-nml/gnali/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali	1.1.0	gnali	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	5800	6212	826	871	7756	7756	1048	1048	1149	1149	215	215	14705	15117	2089	2134	False		
+goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	20207	21960	2807	3139	24488	26198	3066	3321	4155	4155	545	545	48850	52313	6418	7005	False		
+gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	72	5	7	0	0	0	0	0	0	0	0	34	72	5	7	False		
+gprofiler	gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense	functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more								To update	https://biit.cs.ut.ee/gprofiler	Statistics, Web Services	gprofiler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler	@TOOL_VERSION@+galaxy11	r-gprofiler2				5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	4001	4001	614	614	7882	7882	1238	1238	0	0	0	0	11883	11883	1852	1852	False		
+graph_converter	graph_converter	Convert between different graph formats								To update		Convert Formats	graph_converter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+graphclust	graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	1	0	0	0	0	0	0	0	0	0	6	0	1	False		
+graphembed	graphembed	Compute a 2D embedding of a data matrix given supervised class information								Up-to-date	https://github.com/fabriziocosta/GraphEmbed	Statistics, Graphics	graphembed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed	2.4	graph_embed	2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	78	78	6	6	120	120	43	43	0	0	0	0	198	198	49	49	False		
+graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1725	2708	97	99	2	2	2	2	0	0	0	0	1727	2710	99	101	False		
+graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	9816	10927	1285	1350	1273	1273	368	368	1104	1104	242	242	12193	13304	1895	1960	False		
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	7012	7344	323	338	0	0	0	0	0	0	0	0	7012	7344	323	338	False		
+graphprot	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy2	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	463	484	18	19	0	0	0	0	0	0	0	0	463	484	18	19	False		
+gromacs	gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj	GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.								To update	https://github.com/gromacs	Molecular Dynamics, Computational chemistry	gromacs	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	2022	gromacs	2021.3			14	8	15	0	14	8	15	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	15	9	0	184067	184203	3441	3451	9382	9382	1438	1438	10325	10325	648	648	203774	203910	5527	5537	False		
+gsc_center_scale	center_scale	Center or scale (standardize) data								To update	http://artbio.fr	Statistics	gsc_center_scale	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_filter_cells	filter_cells	Filter single cell RNAseq data on libray depth and number of detected genes								To update	http://artbio.fr	Transcriptomics	gsc_filter_cells	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_filter_genes	filter_genes	Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_filter_genes	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_gene_expression_correlations	single_cell_gene_expression_correlations	Compute single-cell paire-wise gene expressions correlations								To update	http://artbio.fr	Transcriptomics	gsc_gene_expression_correlations	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_mannwhitney_de	mannwhitney_de	Perform a mann-whitney differential testing between two sets of gene expression data								To update	http://artbio.fr	Transcriptomics	gsc_mannwhitney_de	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	4.1.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_scran_normalize	scran_normalize	Normalize raw counts using scran								To update	http://artbio.fr	Transcriptomics	gsc_scran_normalize	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	1.28.1+galaxy0	bioconductor-scran	1.30.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	24	24	3	3	2	2	10	10	2	2	102	102	28	28	False		
+gsc_signature_score	signature_score	Compute signature scores from single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_signature_score	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	2.3.9+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gstf_preparation	gstf_preparation	GeneSeqToFamily preparation converts data for the workflow								To update	https://github.com/TGAC/earlham-galaxytools/	Convert Formats	gstf_preparation	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	0.4.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	377	400	17	17	0	0	0	0	0	0	0	0	377	400	17	17	False		
+gtdb_to_taxdump	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	gtdb_to_taxdump	gtdb_to_taxdump		gtdb_to_taxdump	Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.	Data handling, Mapping, Generation	Computational biology	Up-to-date	https://github.com/nick-youngblut/gtdb_to_taxdump	Metagenomics	gtdb_to_taxdump	iuc	https://github.com/nick-youngblut/gtdb_to_taxdump	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	0.1.9	Data handling, Mapping, Generation	Computational biology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	Up-to-date	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.4.0	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	476	476	87	87	0	0	0	0	588	588	74	74	1064	1064	161	161	False		
+gtf-2-gene-list	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1982	1983	323	324	1040	1040	343	343	205	205	38	38	3227	3228	704	705	False		
+gtfToBed12	gtftobed12	Convert GTF files to BED12 format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README	Convert Formats	gtftobed12	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12	357	ucsc-gtftogenepred	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	8329	9363	3336	3828	8009	8009	3130	3130	1577	1577	344	344	17915	18949	6810	7302	False		
+gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3690	3811	326	336	3323	3323	235	235	1895	2429	234	258	8908	9563	795	829	False		
+guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	1	1	7	7	1	1	False		
+gvcftools	gvcftools_extract_variants	gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf.								To update	https://github.com/sequencing/gvcftools	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools	0.1	gvcftools	0.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gwastools	gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	Deposition, Analysis, Annotation	GWAS study	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	7303	7303	222	222	20	20	2	2	0	0	0	0	7323	7323	224	224	False		
+hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	349	359	32	33	364	364	53	53	0	0	0	0	713	723	85	86	False		
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	103	103	4	4	103	103	4	4	False		
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	502	502	66	66	0	0	0	0	0	0	0	0	502	502	66	66	False		
+happy	som.py	A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.	hap.py	hap.py		hap.py	This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	To update	https://github.com/Illumina/hap.py	Variant Analysis	happy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy	0.3.14	hap.py	0.3.15	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hardklor	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	98	111	5	8	0	0	0	0	0	0	0	0	98	111	5	8	False		
+hclust2	hclust2	Plots heatmaps								To update	https://bitbucket.org/nsegata/hclust2/	Data Visualization	hclust2	rnateam	https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2	https://github.com/bgruening/galaxytools/tree/master/tools/hclust2	0.99	hclust2	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hcluster_sg	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	243	263	54	57	0	0	0	0	0	0	0	0	243	263	54	57	False		
+hcluster_sg_parser	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	266	293	22	25	0	0	0	0	0	0	0	0	266	293	22	25	False		
+heatmap2	ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	0	46700	50808	4645	5114	64214	70429	5799	6830	7783	7912	704	724	118697	129149	11148	12668	False		
+heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	bionet, heinz		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	1281	1434	367	442	1559	1559	636	636	678	678	52	52	3518	3671	1055	1130	False		
+helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	267	267	39	39	0	0	0	0	80	80	7	7	347	347	46	46	False		
+hess	hess_astro_tool	Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope								To update		Astronomy	hess_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess	0.0.2+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+hgv_fundo	hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	145	1794	33	397	0	0	0	0	145	1794	33	397	False		
+hgv_hilbertvis	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	119	265	16	60	0	0	0	0	119	265	16	60	False		
+hgvsparser	hgvsparser	Parsing and building variant descriptor strings compliant with the HGVS standard								To update	https://github.com/VariantEffect/hgvsParseR/tree/master	Variant Analysis	hgvsparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6346	6346	2	2	0	0	0	0	0	0	0	0	6346	6346	2	2	False		
+hicexplorer	hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								Up-to-date	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.5	hicexplorer	3.7.5			38	38	38	0	38	38	38	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	33	36	33	0	44449	68602	3236	4177	46	46	21	21	1328	1328	67	67	45823	69976	3324	4265	False		
+hicstuff	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices								To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hictk	hictk	Convert cooler to juicebox_hic								Up-to-date	https://github.com/paulsengroup/hictk	Convert Formats, Epigenetics	hictk	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	1.0.0	hictk	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	9	9	0	0	0	0	0	0	0	0	17	17	9	9	False		
+hicup	hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater	The HiCUP-Pipeline from the Bioinformatics Babraham Institute.								To update	https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html	Epigenetics	hicup	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	0.9.2					7	0	7	0	7	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	6	0	901	1020	160	184	440	440	111	111	0	0	0	0	1341	1460	271	295	False		
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1819	1819	539	539	1334	1334	389	389	2472	2472	137	137	5625	5625	1065	1065	False		
+hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	156	156	20	20	0	0	0	0	220	220	11	11	376	376	31	31	False		
+high_dim_heatmap	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	2	2	0	0	0	0	0	0	0	0	18	18	2	2	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	0	12	0	0	0	0	0	0	0	0	0	228	0	12	False		
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	337151	353499	10046	10719	699868	896164	26656	34018	87016	94859	5302	5695	1124035	1344522	42004	50432	False		
+histogram	histogram_rpy	Histogram of a numeric column								To update		Graphics, Statistics	histogram	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram	https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram	1.0.4	rpy2	2.7.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3748	4661	866	1002	5993	48272	1507	7101	549	746	152	253	10290	53679	2525	8356	False		
+hivclustering	hivclustering	Infers transmission networks from pairwise distances inferred by tn93								To update	https://pypi.org/project/hivclustering/	Next Gen Mappers	hivclustering	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering	1.3.1	python-hivclustering	1.8.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	0	0	12	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	12	0	35919	36952	1283	1321	0	0	0	0	3023	3023	180	180	38942	39975	1463	1501	False		
+homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+homer	homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	Sequence motif discovery		0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	5	0	0	8531	8531	633	633	0	0	0	0	0	0	0	0	8531	8531	633	633	False		
+htseq-clip	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	98	98	19	19	0	0	0	0	0	0	0	0	98	98	19	19	False		
+htseq_count	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	Nucleic acid sequence analysis	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	144907	168824	3703	4366	213407	346792	10798	16485	27209	33124	2613	2854	385523	548740	17114	23705	False		
+humann	humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.9	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	10	10	0	6	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	26659	26659	2067	2067	865	865	174	174	3238	3238	351	351	30762	30762	2592	2592	False		
+hybpiper	hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.3.0	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1571	1571	3	3	0	0	0	0	144	144	4	4	1715	1715	7	7	False		
+hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	0	17	2	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	12	17	12	0	11429	11429	428	428	7751	7751	676	676	715	715	58	58	19895	19895	1162	1162	False		
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	473	473	93	93	0	0	0	0	0	0	0	0	473	473	93	93	False		
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	1200	1220	187	195	1588	1588	267	267	0	0	0	0	2788	2808	454	462	False		
+idconvert	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	241	276	24	33	0	0	0	0	0	0	0	0	241	276	24	33	False		
+idr	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2953	3027	109	114	1710	1710	199	199	0	0	0	0	4663	4737	308	313	False		
+idr_download	idr_download_by_ids	Image Data Resource downloading tool								To update	https://idr.openmicroscopy.org	Data Source	idr_download_by_ids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download	0.45	omero-py	5.11.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	404	404	37	37	0	0	0	0	24	24	1	1	428	428	38	38	False		
+iedb_api	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1539	1539	35	35	0	0	0	0	0	0	0	0	1539	1539	35	35	False		
+illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	273	659	101	102	0	0	0	0	153	153	15	15	426	812	116	117	False		
+image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	2	2	0	0	0	0	0	0	0	0	58	58	2	2	False		
+image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	5	5	0	0	0	0	0	0	0	0	16	16	5	5	False		
+imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21409	21849	10	12	0	0	0	0	0	0	0	0	21409	21849	10	12	False		
+imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20240614			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	1731	1731	109	109	0	0	0	0	0	0	0	0	1731	1731	109	109	False		
+improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	22	1	1	44	292	3	21	0	0	0	0	62	314	4	22	False		
+infercnv	infercnv	Infer Copy Number Variation from Single-Cell RNA-Seq Data								Up-to-date	https://github.com/broadinstitute/infercnv	Transcriptomics, Variant Analysis	infercnv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv	1.20.0	bioconductor-infercnv	1.20.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	2	2	0	0	0	0	0	0	0	0	10	10	2	2	False		
+infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	59700	112582	223	282	0	0	0	0	1157	1221	34	35	60857	113803	257	317	False		
+influx_data_manager	influx_data_manager	Handling influx_si data inputs in Galaxy workflows								To update	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/	Metabolomics	influx_si_data_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager	1.0.2	influx-si-data-manager	1.0.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+influx_si	influx_si	metabolic flux estimation based on [in]stationary labeling								To update	https://github.com/sgsokol/influx	Metabolomics	influx_si	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si	7.0.1	influx_si	7.0.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+inforna		INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	157	157	14	14	0	0	0	0	0	0	0	0	157	157	14	14	False		
+instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	102	102	16	16	0	0	0	0	0	0	0	0	102	102	16	16	False		
+intarna	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.1	intarna	3.4.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3071	7652	41	47	0	0	0	0	0	0	0	0	3071	7652	41	47	False		
+integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55149	55149	161	161	0	0	0	0	6085	6085	73	73	61234	61234	234	234	False		
+intermine_galaxy_exchange	galaxy_intermine_exchange	InterMine Exporter								To update	https://github.com/intermine	Convert Formats	intermine_galaxy_exchange	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange	0.0.1	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	46	6	12	72	87	13	15	108	108	1	1	217	241	20	28	False		
+interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	70	7	7	0	0	0	0	0	0	0	0	70	70	7	7	False		
+interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34689	55189	1634	1713	65	65	15	15	10897	10897	607	607	45651	66151	2256	2335	False		
+intersect	gops_intersect_1	Intersect the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	20472	349984	2351	3007	45587	778988	4359	14116	6087	7417	484	561	72146	1136389	7194	17684	False		
+interval2maf	Interval2Maf1	Extract MAF blocks given a set of intervals	bx-python	bx-python		bx-python	Tools for manipulating biological data, particularly multiple sequence alignments.		Sequence analysis	To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	interval2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf	1.0.1+galaxy1	bx-python	0.13.0		Sequence analysis	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	32	107	7	10	758	19538	87	1246	16	24	2	2	806	19669	96	1258	False		
+intervene	intervene_pairwise, intervene_upset	Create pairwise and upset plots	intervene	intervene		Intervene	Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.	Sequence comparison, Sequence visualisation	Computational biology	Up-to-date	https://intervene.readthedocs.io	Statistics	intervene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene	0.6.5	intervene	0.6.5	Sequence comparison, Sequence visualisation	Computational biology	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1557	1607	278	292	4458	4458	458	458	0	0	0	0	6015	6065	736	750	False		
+ipo	ipo4retgroup, ipo4xcmsSet	[W4M][LC-MS] IPO								To update	https://github.com/rietho/IPO	Metabolomics	ipo	lecorguille	https://github.com/rietho/IPO	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo	1.10.0	bioconductor-ipo	1.28.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	28279	28481	1623	1646	24662	24662	2093	2093	9780	10086	979	992	62721	63229	4695	4731	False		
+irissv	irissv	Refine insertion sequences								To update	https://github.com/mkirsche/Iris	Variant Analysis	irissv	iuc	https://github.com/galaxyproject/tools-iuc/tools/irissv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv	1.0.5	samtools	1.21			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	29	29	8	8	0	0	0	0	0	0	0	0	29	29	8	8	False		
+isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	59386	59386	151	151	56	56	1	1	4741	4741	59	59	64183	64183	211	211	False		
+isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1301	1301	59	59	1331	1331	60	60	507	507	9	9	3139	3139	128	128	False		
+isolib	isolib	Create an isotopic pattern library for given compounds and adducts.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	isolib	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	1.0.1+galaxy0	bioconductor-metabocoreutils	1.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+isoplot	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	4	3	3	0	0	0	0	0	0	0	0	4	4	3	3	False		
+itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1426	1426	71	71	0	0	0	0	0	0	0	0	1426	1426	71	71	False		
+ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	0	5	5	5	0	1252220	1252220	2366	2366	126027	126027	2496	2496	41901	41901	993	993	1420148	1420148	5855	5855	False		
+iwtomics	iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot	Interval-Wise Testing for Omics Data	iwtomics	iwtomics		IWTomics	"Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset."	Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison	Statistics and probability	To update	https://bioconductor.org/packages/release/bioc/html/IWTomics.html	Statistics	iwtomics	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics	1.0.0	bioconductor-iwtomics	1.26.0	Differential gene expression analysis, Peak calling, Genome annotation, Comparison	Statistics and probability	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	675	690	27	28	159	251	29	49	383	383	12	12	1217	1324	68	89	False		
+jasminesv	jasminesv	Merge structural variants across samples								To update	https://github.com/mkirsche/Jasmine/	Variant Analysis	jasminesv	iuc	https://github.com/galaxyproject/tools-iuc/jasminesv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv	1.0.11	jasminesv	1.1.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32	32	9	9	53	53	19	19	0	0	0	0	85	85	28	28	False		
+jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	21153	22174	5514	5779	17428	17428	6458	6458	15673	17267	3248	3786	54254	56869	15220	16023	False		
+jbrowse	jbrowse_to_container	A tool allowing to export a JBrowse dataset into a JBrowse docker container								To update	https://jbrowse.org	Web Services	jbrowse_to_container	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse		python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse_2	jbrowse_2		JBrowse 2	Modular genome browser with views of synteny and structural variation.	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.15.4	jbrowse2	2.15.4	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1312	1312	219	219	116	116	58	58	37	37	6	6	1465	1465	283	283	False		
+jcvi_gff_stats	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.16			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2747	2926	596	637	2311	2311	741	741	1145	1145	469	469	6203	6382	1806	1847	False		
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1825	1825	237	237	0	0	0	0	971	971	56	56	2796	2796	293	293	False		
+join	gops_join_1	Join the intervals of two datasets side-by-side								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	join	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	15624	330820	1864	2438	52317	513688	10198	39421	1329	1645	213	289	69270	846153	12275	42148	False		
+join_files_by_id	join_files_by_id	This tool will join datasets according to a column with identifier								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	Text Manipulation	join_files_by_id	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id	1.0	r-data.table	1.11.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+join_files_on_column_fuzzy	join_files_on_column_fuzzy	Join two files on a common column, allowing a certain difference.								To update		Text Manipulation	join_files_on_column_fuzzy	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	1.0.1	python				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1980	2697	345	410	0	0	0	0	1081	1081	44	44	3061	3778	389	454	False		
+jq	jq	JQ is a lightweight and flexible command-line JSON processor								To update	https://stedolan.github.io/jq/	Text Manipulation	jq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq	1.0	jq	1.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	660	2374	61	63	336	336	82	82	281	281	11	11	1277	2991	154	156	False		
+jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	30	30	2	2	0	0	0	0	0	0	0	0	30	30	2	2	False		
+justdiff	justdiff	Unix diff								To update	http://artbio.fr	Text Manipulation	justdiff	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	3.10+galaxy0	diffutils				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+justgzip	justgzip	Compress fastq sequence files								To update	http://artbio.fr	Convert Formats	justgzip	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	2.8+galaxy0	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+jvarkit	jvarkit_wgscoverageplotter	Jvarkit : Java utilities for Bioinformatics								Up-to-date	https://lindenb.github.io/jvarkit/	SAM	jvarkit	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit	20201223	jvarkit-wgscoverageplotter	20201223			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7179	7179	509	509	11138	11138	1145	1145	0	0	0	0	18317	18317	1654	1654	False		
+kallisto	kallisto_pseudo, kallisto_quant	kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.	kallisto	kallisto		kallisto	A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.	Gene expression profiling	Transcriptomics, RNA-seq, Gene expression	To update	https://pachterlab.github.io/kallisto/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto	0.48.0	kallisto	0.51.1	Gene expression profiling	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	28398	29031	932	965	73705	80087	2603	3025	5333	5567	218	230	107436	114685	3753	4220	False		
+kaptive	kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kat_sect	kat_@EXECUTABLE@	SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.								To update			kat_sect	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	379	379	53	53	8259	8259	271	271	0	0	0	0	8638	8638	324	324	False		
+kegalign	kegalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	kegalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	0.1.2.7	kegalign-full	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	5	5	1	1	False		
+kernel_canonical_correlation_analysis	kcca1	Kernel Canonical Correlation Analysis								To update		Statistics	kernel_canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis	1.0.0	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	62	70	4	4	207	334	27	71	0	0	0	0	269	404	31	75	False		
+kernel_principal_component_analysis	kpca1	Kernel Principal Component Analysis								To update		Statistics	kernel_principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis	1.0.0	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	144	157	26	30	268	707	83	248	0	0	0	0	412	864	109	278	False		
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	8	8	8	0	1995	2091	174	193	1430	1430	389	389	1580	1580	56	56	5005	5101	619	638	False		
+king	king	Kinship-based INference for Gwas								Up-to-date	http://people.virginia.edu/~wc9c/KING/	Variant Analysis	king	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/king	2.2.7	king	2.2.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	8	4	4	0	0	0	0	0	0	0	0	8	8	4	4	False		
+kinwalker		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.1.0	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	503	503	58	58	0	0	0	0	0	0	0	0	503	503	58	58	False		
+kma	kma_map	Map with KMA								To update	https://bitbucket.org/genomicepidemiology/kma	Next Gen Mappers	kma	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma	1.4.14	kma	1.4.15			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+kmd_hmdb_data_plot	kmd_hmdb_data_plot	retrieves data from KMD HMDB API and produce plot and csv file								To update	https://github.com/workflow4metabolomics/tools-metabolomics	Metabolomics	kmd_hmdb_data_plot	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1342	1342	63	63	0	0	0	0	0	0	0	0	1342	1342	63	63	False		
+kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	5	5	5	0	48136	48164	2754	2760	59952	130398	5869	8654	29008	31148	1936	2200	137096	209710	10559	13614	False		
+kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	271367	271786	6384	6409	101752	101752	4662	4662	53562	53562	1663	1663	426681	427100	12709	12734	False		
+kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23008	23014	1060	1061	16194	24490	1719	2168	14898	14898	436	436	54100	62402	3215	3665	False		
+kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3185	3185	495	495	0	0	0	0	385	385	48	48	3570	3570	543	543	False		
+kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3981	3986	769	771	4087	5610	991	1284	88	88	41	41	8156	9684	1801	2096	False		
+krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	48516	48516	2373	2373	8787	8787	943	943	4369	4369	393	393	61672	61672	3709	3709	False		
+krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	38	2	2	0	0	0	0	0	0	0	0	34	38	2	2	False		
+labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	887	927	13	15	4	4	3	3	0	0	0	0	891	931	16	18	False		
+last	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1584	Sequence alignment	Comparative genomics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	329	329	94	94	0	0	0	0	0	0	0	0	329	329	94	94	False		
+lastz	lastz_wrapper_2, lastz_d_wrapper	Galaxy wrappers for the Lastz and Lastz_d	lastz	lastz		LASTZ	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.	Sequence alignment, Read mapping	Genomics	Up-to-date	https://github.com/lastz/lastz	Next Gen Mappers	lastz	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz	1.04.22	lastz	1.04.22	Sequence alignment, Read mapping	Genomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	77409	84356	447	475	156658	193590	870	3511	38579	38780	173	203	272646	316726	1490	4189	False		
+lastz_paired_reads	lastz_paired_reads_wrapper	Galaxy wrapper for the Lastz alignment tool on paired reads								To update		Next Gen Mappers	lastz_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads	1.1.1	lastz	1.04.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	9	3	4	0	0	0	0	8	10	5	5	15	19	8	9	False		
+lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	89	137	4	20	118	6136	15	1112	0	0	0	0	207	6273	19	1132	False		
+lcrgenie	lcrgenie	Ligase Chain Reaction Genie								To update	https://github.com/neilswainston/LCRGenie	Synthetic Biology	lcrgenie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie	1.0.2	lcr_genie				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lda_analysis	lda_analy1	Perform Linear Discriminant Analysis								To update		Graphics, Statistics	lda_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis	1.0.1	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	147	159	46	48	793	1538	101	314	0	4	0	3	940	1701	147	365	False		
+legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	92	92	8	8	0	0	0	0	0	0	0	0	92	92	8	8	False		
+length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	4349	4466	666	698	2093	2286	928	998	201	201	77	77	6643	6953	1671	1773	False		
+lfq_protein_quant	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	78	116	12	19	0	0	0	0	0	0	0	0	78	116	12	19	False		
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	171	27	30	0	0	0	0	0	0	0	0	149	171	27	30	False		
+limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23442	24466	2379	2475	45734	49342	4565	5032	9327	9517	835	842	78503	83325	7779	8349	False		
+lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	39	4	4	0	0	0	0	0	0	0	0	39	39	4	4	False		
+linear_regression	LinearRegression1	Perform Linear Regression								To update		Statistics	linear_regression	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression	https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression	1.0.1	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	146	1103	31	271	0	0	0	0	146	1103	31	271	False		
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	512	512	126	126	0	0	0	0	480	480	65	65	992	992	191	191	False		
+locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								Up-to-date	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	2.0.1	locarna	2.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	314	350	36	46	0	0	0	0	0	0	0	0	314	350	36	46	False		
+lofreq	lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi	LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.								Up-to-date	https://csb5.github.io/lofreq/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq	2.1.5	lofreq	2.1.5			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	0	0	0	4	0	0	0	0	0	0	5	5	5	0	4176367	4176367	4301	4301	509615	509615	8213	8213	106342	106342	1815	1815	4792324	4792324	14329	14329	False		
+logistic_regression_vif	LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	64	173	12	48	0	0	0	0	64	173	12	48	False		
+logol	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+longorf	longORF	obtain longest ORF in six-frame translations								To update		Sequence Analysis	longorf	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf	0.3.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	822	822	14	14	0	0	0	0	0	0	0	0	822	822	14	14	False		
+lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1219	1219	182	182	0	0	0	0	37	37	4	4	1256	1256	186	186	False		
+ltq_iquant_cli										To update			ltq_iquant_cli	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lumpy_smoove	lumpy_smoove, vcf2hrdetect	Galaxy wrapper of the lumpy-using smoove workflow								To update	http://artbio.fr	Variant Analysis	lumpy_smoove	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	0.2.8+galaxy1	svtyper	0.7.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lumpy_sv	lumpy_prep, lumpy_sv	LUMPY - a general probabilistic framework for structural variant discovery								Up-to-date	http://layerlab.org/software/	Variant Analysis	lumpy_sv	iuc	https://github.com/arq5x/lumpy-sv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv	0.3.1	lumpy-sv	0.3.1			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	1534	1534	199	199	0	0	0	0	0	0	0	0	1534	1534	199	199	False		
+lumpy_sv	lumpy	Find structural variations								To update	http://artbio.fr	Variant Analysis	lumpy_sv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv	1.3	lumpy-sv	0.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	44	44	11	11	0	0	0	0	0	0	0	0	44	44	11	11	False		
+maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2835	2835	59	59	0	0	0	0	0	0	0	0	2835	2835	59	59	False		
+macs2	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	0	0	9	0	0	0	0	0	0	9	9	9	0	87810	96069	4980	5629	153500	227569	12946	18825	10988	12301	692	807	252298	335939	18618	25261	False		
+maf_cpg_filter	cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	85	356	6	28	0	0	0	0	85	356	6	28	False		
+maf_stats	maf_stats1	MAF Coverage statistics								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	maf_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats	1.0.2+galaxy0					1	1	1	0	1	1	1	0	0	1	0	0	0	1	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	1	0	15	21	7	9	227	2470	52	464	1	1	1	1	243	2492	60	474	False		
+mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	0	2	2	2	0	172433	174456	1865	1951	108640	122790	4266	5521	20027	20027	1172	1172	301100	317273	7303	8644	False		
+maftoaxt	maftoaxt	Convert dataset from MAF to axt format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_maftoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	469	ucsc-maftoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mageck	mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test	Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	mageck	mageck		MAGeCK	Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	Genetic variation analysis	Genetics, Genetic variation, Genomics	To update	https://sourceforge.net/projects/mageck/	Genome editing		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck	0.5.9.2	mageck	0.5.9.5	Genetic variation analysis	Genetics, Genetic variation, Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	11761	12093	873	889	5762	5762	473	473	5610	5610	343	343	23133	23465	1689	1705	False		
+mahotas_features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	44	6	6	0	0	0	0	0	0	0	0	39	44	6	6	False		
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6417	6861	1315	1366	7235	7235	1858	1858	4112	4112	902	902	17764	18208	4075	4126	False		
+maldiquant	maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base				0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1452	3822	61	68	0	0	0	0	1065	1065	39	39	2517	4887	100	107	False		
+malt	malt_run	Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.								To update	https://github.com/husonlab/malt	Next Gen Mappers	malt_run	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt	0.5.3	malt	0.62			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	24	9	9	0	0	0	0	0	0	0	0	24	24	9	9	False		
+manta	manta	Structural variant and indel caller for mapped sequencing data								To update	http://artbio.fr	Variant Analysis	manta	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/manta	https://github.com/ARTbio/tools-artbio/tree/main/tools/manta	1.6	manta	1.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	218	218	34	34	0	0	0	0	0	0	0	0	218	218	34	34	False		
+map_param_value	map_param_value	Map a parameter value to another value								To update		Text Manipulation	map_param_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3780	3780	67	67	1012	1012	57	57	105	105	3	3	4897	4897	127	127	False		
+map_peptides_to_bed	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	38	44	6	7	0	0	0	0	0	0	0	0	38	44	6	7	False		
+mapping_quality_stats	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mapping_to_ucsc	mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7871	7871	32	32	0	0	0	0	0	0	0	0	7871	7871	32	32	False		
+marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	51	51	4	4	0	0	0	0	0	0	0	0	51	51	4	4	False		
+mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	10119	10119	61	61	19	19	9	9	647	647	7	7	10785	10785	77	77	False		
+mashmap	mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	894	894	12	12	81	81	5	5	0	0	0	0	975	975	17	17	False		
+masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	471	582	35	40	589	589	80	80	0	0	0	0	1060	1171	115	120	False		
+matchms	matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting	Searching, filtering and converting mass spectral libraries.	matchms	matchms		Matchms	Tool to import, process, clean, and compare mass spectrometry data.	Spectral library search, Format validation, Filtering	Metabolomics	Up-to-date	https://github.com/matchms/matchms	Metabolomics	matchms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	0.27.0	matchms	0.27.0	Spectral library search, Format validation, Filtering	Metabolomics	2	14	14	0	2	14	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	1620	1620	70	70	27	27	8	8	1685	1685	12	12	3332	3332	90	90	False		
+mauve_contig_mover	mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mavedb	mavedb_importer	data source for MaveDB								To update		Data Source	mavedb_importer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb	0.9					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	2	2	0	0	0	0	0	0	0	0	8	8	2	2	False		
+maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	1	0	2798	2798	314	314	2452	2452	508	508	914	914	89	89	6164	6164	911	911	False		
+maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6863	7021	1251	1264	2798	2798	543	543	3189	3189	352	352	12850	13008	2146	2159	False		
+mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	35	13	13	0	0	0	0	0	0	0	0	35	35	13	13	False		
+mdanalysis	mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf	MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations								To update	https://github.com/MDAnalysis/mdanalysis	Computational chemistry	mdanalysis	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis	1.0.0	mdanalysis				10	5	10	0	10	5	10	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	3209	3268	318	326	182	182	51	51	397	397	39	39	3788	3847	408	416	False		
+mdfileconverter	md_converter	A tool for interconverting between different MD structure and trajectory file formats.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter	1.9.7	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26720	26762	251	253	784	784	54	54	977	977	53	53	28481	28523	358	360	False		
+mdslicer	md_slicer	A tool for slicing trajectory files using MDTraj.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer	1.9.9	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	174	174	19	19	6	6	4	4	441	441	7	7	621	621	30	30	False		
+mdtraj	traj_selections_and_merge	MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories								To update	https://github.com/mdtraj/mdtraj	Computational chemistry	mdtraj	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj	1.9.7	mdtraj				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	36	8	8	63	63	4	4	0	0	0	0	99	99	12	12	False		
+mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	73	86	5	5	0	0	0	0	0	0	0	0	73	86	5	5	False		
+mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	3	3	0	0	0	0	0	0	0	0	20	25	3	3	False		
+measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	0	3	3	3	0	117975	117975	1693	1693	55063	55063	796	796	9325	9325	639	639	182363	182363	3128	3128	False		
+medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	9	9	0	0	0	0	0	0	0	0	27	27	9	9	False		
+megablast_xml_parser	megablast_xml_parser	Parse blast XML output								To update		Next Gen Mappers, Convert Formats	megablast_xml_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	743	816	103	141	292	2868	82	459	0	0	0	0	1035	3684	185	600	False		
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	12692	13292	1349	1400	16645	16645	2140	2140	6214	6214	431	431	35551	36151	3920	3971	False		
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	513	557	152	155	74	74	35	35	10	10	4	4	597	641	191	194	False		
+megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	4130	4130	447	447	0	0	0	0	0	0	0	0	4130	4130	447	447	False		
+meme	meme_dreme, meme_fimo, meme_meme, meme_psp_gen	The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.	meme_meme	meme_fimo, meme_meme		meme_meme	An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	To update	http://meme-suite.org/	ChIP-seq	meme	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme	5.5.6	meme	5.5.7	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	3	0	4	0	3	0	4	0	0	0	0	0	0	0	0	0	0	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	4	4	0	20990	22979	762	892	10975	25929	1551	3249	0	0	0	0	31965	48908	2313	4141	False		
+meme_chip	meme_chip	Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.								To update	http://meme-suite.org/	ChIP-seq	meme_chip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip	4.11.2	graphicsmagick	1.3.26			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6413	7000	705	743	7260	7260	1171	1171	0	0	0	0	13673	14260	1876	1914	False		
+meneco	meneco	Meneco computes minimal completions to your draft network with reactions from a repair network								Up-to-date	http://bioasp.github.io/meneco/	Systems Biology	meneco	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	1.5.2	meneco	1.5.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+merge	gops_merge_1	Merge the overlapping intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	565922	566630	418	441	45844	107523	671	4353	19828	19994	100	137	631594	694147	1189	4931	False		
+merge_cols	mergeCols1	Merge columns together.								To update		Text Manipulation	merge_cols	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols	https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols	1.0.3	python				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	20905	31051	1906	2128	21780	132833	885	3172	1524	1925	122	152	44209	165809	2913	5452	False		
+mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	25	2	3	0	0	0	0	0	0	0	0	18	25	2	3	False		
+merlin	merlin	Pedigree Analysis package	merlin	merlin		Merlin	Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation	Haplotype mapping, Genetic mapping	GWAS study, Mapping	Up-to-date	http://csg.sph.umich.edu/abecasis/Merlin/	Variant Analysis	merlin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin	1.1.2	merlin	1.1.2	Haplotype mapping	GWAS study, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3150	3150	477	477	730	730	196	196	1183	1183	151	151	5063	5063	824	824	False		
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+meta_proteome_analyzer	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	126	126	20	20	0	0	0	0	0	0	0	0	126	126	20	20	False		
+metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	0	2	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	6135	6135	382	382	881	881	151	151	1094	1094	104	104	8110	8110	637	637	False		
+metabuli	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	metabuli	metabuli		metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid	Taxonomic classification	Taxonomy	To update	https://github.com/steineggerlab/Metabuli	Sequence Analysis, Metagenomics	metabuli	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli	1.0.5	metabuli	1.0.8	Taxonomic classification	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	7.bba0d80	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	312	312	40	40	0	0	0	0	0	0	0	0	312	312	40	40	False		
+metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	980	980	323	323	0	0	0	0	0	0	0	0	980	980	323	323	False		
+metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	556	756	17	21	310	514	35	55	0	0	0	0	866	1270	52	76	False		
+metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4471	4471	29	29	0	0	0	0	0	0	0	0	4471	4471	29	29	False		
+metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	0	1	2	4	0	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	16629	16648	1183	1187	3983	3983	572	572	4747	4747	278	278	25359	25378	2033	2037	False		
+metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	2730	2831	260	262	0	0	0	0	1540	1540	71	71	4270	4371	331	333	False		
+metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	142	142	32	32	0	0	0	0	379	379	47	47	521	521	79	79	False		
+metfrag	metfrag	[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity)								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag	2.4.5+galaxy3	metfrag	2.4.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	192	192	20	20	0	0	0	0	0	0	0	0	192	192	20	20	False		
+metfrag-vis	metfrag_vis	[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis	2.4.5+galaxy0	metfrag	2.4.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	50	14	14	0	0	0	0	0	0	0	0	50	50	14	14	False		
+methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	632	5461	155	453	0	0	0	0	0	0	0	0	632	5461	155	453	False		
+methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	14907	18971	638	894	2677	2677	230	230	2313	2313	83	83	19897	23961	951	1207	False		
+methylkit	methylkit	A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.								To update	http://bioconductor.org/packages/release/bioc/html/methylKit.html	Epigenetics	methylkit	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	0.99.2	bioconductor-methylkit	1.28.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3209	4572	312	442	479	479	79	79	315	315	51	51	4003	5366	442	572	False		
+mfassignr	mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot	The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements	mfassignr	mfassignr		MFAssignR	Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements.	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	Up-to-date	https://github.com/RECETOX/MFAssignR	Metabolomics	MFAssignR	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	1.1.1	r-mfassignr	1.1.1	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	8	8	0	0	0	0	0	0	0	0	10	10	8	8	False		
+mg_toolkit	mg_toolkit_bulk_download, mg_toolkit_original_metadata	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	mg-toolkit	mg-toolkit		mg-toolkit	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	Data retrieval	Metagenomics	Up-to-date	https://github.com/EBI-Metagenomics/emg-toolkit	Metagenomics	mg_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	0.10.4	mg-toolkit	0.10.4	Data retrieval	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+mgf_formatter	mgf_formatter									Up-to-date			mgf_formatter	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter	1.0.0	mgf-formatter	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	573	573	3	3	0	0	0	0	0	0	0	0	573	573	3	3	False		
+miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+microsatbed	microsatbed	Select microsatellites for a bed file								To update	https://github.com/lmdu/pytrf	Sequence Analysis	microsatbed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed	1.3.3	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	228	4	4	18	18	1	1	0	0	0	0	246	246	5	5	False		
+microsatellite_birthdeath	microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+microsats_alignment_level	microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	135	973	50	140	0	0	0	0	135	973	50	140	False		
+microsats_mutability	microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	34	312	22	87	0	0	0	0	34	312	22	87	False		
+migmap	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	Sequence analysis, Read mapping	Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1082	1229	25	33	1153	1376	70	89	0	0	0	0	2235	2605	95	122	False		
+minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1213	1309	115	124	0	0	0	0	0	0	0	0	1213	1309	115	124	False		
+mine	maximal_information_based_nonparametric_exploration	Maximal Information-based Nonparametric Exploration								To update		Variant Analysis	mine	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine	0.0.1	MINE				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	11	8	8	17	63	6	19	0	0	0	0	26	74	14	27	False		
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7116	7116	256	256	0	0	0	0	278	278	60	60	7394	7394	316	316	False		
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13357	13479	554	562	8416	8416	448	448	898	898	85	85	22671	22793	1087	1095	False		
+minimap2	minimap2	A fast pairwise aligner for genomic and spliced nucleotide sequences	minimap2	minimap2		Minimap2	Pairwise aligner for genomic and spliced nucleotide sequences	Pairwise sequence alignment	Mapping	Up-to-date	https://github.com/lh3/minimap2	Next Gen Mappers	minimap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2	2.28	minimap2	2.28	Pairwise sequence alignment	Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	346530	349075	4323	4419	108535	108535	4075	4075	22331	22331	1166	1166	477396	479941	9564	9660	False		
+minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	229	229	32	32	0	0	0	0	0	0	0	0	229	229	32	32	False		
+miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1244	1244	86	86	24	24	15	15	0	0	0	0	1268	1268	101	101	False		
+miranda	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6408	6514	94	99	0	0	0	0	0	0	0	0	6408	6514	94	99	False		
+miranda2asko	miranda2asko	Converts miRanda output into AskOmics format								To update		Convert Formats	miranda2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	0.2	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1458	1458	36	36	1458	1458	36	36	False		
+mirmachine	mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	False		
+mirnature	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	18	18	9	9	0	0	0	0	0	0	0	0	18	18	9	9	False		
+misc	target_screen, use_theoretical_mz_annotations									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	1.0.0	pandas				0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	2	2	0	0	0	0	0	0	0	0	6	6	2	2	False		
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1117	1117	116	116	0	0	0	0	295	295	25	25	1412	1412	141	141	False		
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1020	1020	176	176	414	414	73	73	277	277	20	20	1711	1711	269	269	False		
+mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	0	191295	191295	1111	1111	42265	42265	320	320	10904	10904	83	83	244464	244464	1514	1514	False		
+mixmodel4repeated_measures	mixmodel4repeated_measures	[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model								To update	http://workflow4metabolomics.org	Metabolomics	mixmodel4repeated_measures	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures	3.1.0	r-lme4				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	13300	13471	1480	1501	6532	6532	1167	1167	10334	11841	1083	1300	30166	31844	3730	3968	False		
+moFF	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	331	762	20	34	0	0	0	0	137	137	4	4	468	899	24	38	False		
+moabs	moabs	MOABS for differential methylation analysis on Bisulfite sequencing data.								To update	https://github.com/sunnyisgalaxy/moabs	Epigenetics	moabs	iuc	https://github.com/sunnyisgalaxy/moabs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs	1.3.4.6	moabs	1.3.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	339	339	56	56	0	0	0	0	0	0	0	0	339	339	56	56	False		
+mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	119024	119024	628	628	42	42	2	2	36310	36310	191	191	155376	155376	821	821	False		
+molecule2gspan	bg_mol2gspan	converter								To update	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	Convert Formats	molecule_to_gspan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	0.2	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3610	3610	559	559	1728	1728	434	434	0	0	0	0	5338	5338	993	993	False		
+morpheus	morpheus	Morpheus MS Search Application	morpheus	morpheus		Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.	Peptide database search	Proteomics	To update	https://cwenger.github.io/Morpheus	Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	288	morpheus	290	Peptide database search	Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	105	153	12	19	0	0	0	0	833	833	93	93	938	986	105	112	False		
+morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mosdepth	mosdepth	fast and flexible BAM/CRAM depth calculation								Up-to-date	https://github.com/brentp/mosdepth	SAM	mosdepth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth	0.3.8	mosdepth	0.3.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1278	1278	87	87	168	168	24	24	102	102	5	5	1548	1548	116	116	False		
+mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	0	129	129	129	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	126	129	129	0	297546	326056	37506	41763	565218	682083	72163	89926	167400	182490	26963	28404	1030164	1190629	136632	160093	False		
+motus	mereg_mOTUs_tables, motus_profiler	Tool for profiling the abundance of microbial taxa.	mOTUs	mOTUs		Metagenomic operational taxonomic units (mOTUs)	Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/motu-tool/mOTUs	Metagenomics	motus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs	https://github.com/bgruening/galaxytools/tree/master/tools/motus	3.1.0	motus	3.1.0	Taxonomic classification	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	76	9	9	0	0	0	0	0	0	0	0	71	76	9	9	False		
+mqppep	mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	13	13	3	3	0	0	0	0	0	0	0	0	13	13	3	3	False		
+mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ms2deepscore	ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training	Mass spectra similarity scoring using a trained ms2deepscore model.	ms2deepscore	ms2deepscore		MS2DeepScore	MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	To update	https://github.com/matchms/ms2deepscore	Metabolomics	ms2deepscore	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	2.0.0	ms2deepscore	2.1.0	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ms2snoop	ms2snoop	[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.								To update	http://workflow4metabolomics.org	Metabolomics	ms2snoop	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop	2.2.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+msPurity	mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								Up-to-date	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity	1.28.0	bioconductor-mspurity	1.28.0			0	0	10	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	848	848	91	91	0	0	0	0	0	0	0	0	848	848	91	91	False		
+msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	864	929	91	101	1100	1100	175	175	0	0	0	0	1964	2029	266	276	False		
+msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20749	22184	455	469	1239	1239	71	71	2666	2666	53	53	24654	26089	579	593	False		
+msgfplus	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	473	529	33	43	0	0	0	0	0	0	0	0	473	529	33	43	False		
+msmetaenhancer	msmetaenhancer		msmetaenhancer	msmetaenhancer		MSMetaEnhancer	Tool for mass spectra metadata annotation.	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/MSMetaEnhancer	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	0.4.0	msmetaenhancer	0.4.0	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	10	10	0	0	0	0	48	48	1	1	251	251	11	11	False		
+msms_extractor	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	110	110	11	11	0	0	0	0	0	0	0	0	110	110	11	11	False		
+msp_merge	msp_merge									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	0.1.0	matchms	0.27.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+msp_split	msp_split	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								To update	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		tomnl	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split	0.0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+msstats	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2353	2353	559	559	1122	1122	211	211	1091	1091	35	35	4566	4566	805	805	False		
+msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	795	795	104	104	0	0	0	0	461	461	12	12	1256	1256	116	116	False		
+mt2mq	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	275	275	38	38	0	0	0	0	0	0	0	0	275	275	38	38	False		
+multigps	multigps	Analyzes collections of multi-condition ChIP-seq data.								To update	http://mahonylab.org/software/multigps/	ChIP-seq	multigps	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps	0.74.0	fonts-conda-ecosystem				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	485	871	159	298	0	0	0	0	485	871	159	298	False		
+multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	106	106	25	25	0	0	0	0	0	0	0	0	106	106	25	25	False		
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	182221	192389	19343	20494	163961	182413	26449	29758	40663	41855	5974	6157	386845	416657	51766	56409	False		
+multispecies_orthologous_microsats	multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mummer	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	883	921	199	211	730	730	199	199	136	202	34	49	1749	1853	432	459	False		
+mummer4	mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1			6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	6	3	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	21587	22119	1940	2033	29284	29284	3626	3626	8194	8194	545	545	59065	59597	6111	6204	False		
+music_deconvolution	music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)								Up-to-date	https://github.com/xuranw/MuSiC	Transcriptomics	music	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/	https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution	0.1.1	music-deconvolution	0.1.1			5	5	4	0	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	2801	2801	289	289	364	364	80	80	1357	1357	21	21	4522	4522	390	390	False		
+mutate_snp_codon	mutate_snp_codon_1	Mutate Codons with SNPs								To update		Variant Analysis	mutate_snp_codon	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	44	49	5	5	81	417	23	118	0	0	0	0	125	466	28	123	False		
+mutational_patterns	mutational_patterns	Mutational patterns and signatures in base substitution catalogs								Up-to-date	http://artbio.fr	Variant Analysis	mutational_patterns	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	3.12.0	bioconductor-mutationalpatterns	3.12.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	854	860	110	111	79	79	15	15	274	274	13	13	1207	1213	138	139	False		
+mzmine	mzmine_batch	mass-spectrometry data processing, with the main focus on LC-MS data	mzmine	mzmine		MZmine	Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	Up-to-date	http://mzmine.github.io/	Metabolomics	mzmine_batch	iuc	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine	3.9.0	mzmine	3.9.0	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5	False		
+mzml_validator	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mzxmlshaper	mzxmlshaper	Convert mzML, mzXML or netCDF files to mzML or mzXML								To update	https://rdrr.io/bioc/mzR/	Metabolomics	mzxmlshaper	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper	1.0.0+galaxy0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+naltorfs	bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2			3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	204	204	75	75	0	0	0	0	204	204	75	75	False		
+nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	839	839	12	12	0	0	0	0	269	269	5	5	1108	1108	17	17	False		
+nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	99052	100009	5671	5755	40386	40386	3371	3371	17919	17919	2188	2188	157357	158314	11230	11314	False		
+nanopolish	nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants	Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.								Up-to-date	https://github.com/jts/nanopolish		nanopolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	0.14.0	nanopolish	0.14.0			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	9284	9694	215	229	0	0	0	0	2358	2358	49	49	11642	12052	264	278	False		
+nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1091	1091	44	44	0	0	0	0	0	0	0	0	1091	1091	44	44	False		
+nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	40	1	1	0	0	0	0	0	0	0	0	36	40	1	1	False		
+ncbi_acc_download	ncbi_acc_download	Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API								Up-to-date	https://github.com/kblin/ncbi-acc-download	Data Source	ncbi_acc_download	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download	0.2.8	ncbi-acc-download	0.2.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6873	6873	1664	1664	17651	17651	4513	4513	6228	6228	972	972	30752	30752	7149	7149	False		
+ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	15	16	16	15	0	391141	443752	9760	10546	306361	350178	11767	13684	227235	244814	3192	3617	924737	1038744	24719	27847	False		
+ncbi_datasets	datasets_download_gene, datasets_download_genome	NCBI datasets downloads biological sequence data across all domains of life from NCBI.	ncbi_datasets	ncbi_datasets		NCBI Datasets	NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.	Data handling, Sequence database search, Data retrieval	Biological databases	To update	https://github.com/ncbi/datasets	Data Source	ncbi_datasets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets	16.20.0	ncbi-datasets-cli		Data handling, Sequence database search, Data retrieval	Biological databases	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	1	2	2	0	4417	4417	1024	1024	6940	6940	2275	2275	1	1	1	1	11358	11358	3300	3300	False		
+ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	6	6	0	0	0	0	15	15	6	6	False		
+ncbi_entrez_direct	ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch	NCBI Entrez Direct allow fetching data from NCBI Databases								Up-to-date	http://www.ncbi.nlm.nih.gov/books/NBK179288/	Data Source	ncbi_entrez_direct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct	22.4	entrez-direct	22.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	2	0	0	0	0	0	3	0	2	False		
+ncbi_entrez_eutils	ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary	NCBI Entrez E-Utilties allow fetching data from NCBI Databases								To update	https://www.ncbi.nlm.nih.gov/books/NBK25501/	Data Source	ncbi_entrez_eutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils	1.70	python				0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	4	0	0	0	2	0	0	0	0	0	0	0	7	7	0	2794	3191	533	664	0	0	0	0	0	0	0	0	2794	3191	533	664	False		
+ncbi_fcs_adaptor	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	842	842	93	93	0	0	0	0	842	842	93	93	False		
+ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	125	125	26	26	2489	2489	139	139	0	0	0	0	2614	2614	165	165	False		
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	790	790	160	160	0	0	0	0	0	0	0	0	790	790	160	160	False		
+netboxr	netboxr	netboxr enables automated discovery of biological process modules by network analysis								To update		Systems Biology	netboxr	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/netboxr	1.6.0	bioconductor-netboxr	1.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	12	6	6	0	0	0	0	0	0	0	0	12	12	6	6	False		
+newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33637	34195	1113	1172	16257	16257	1816	1816	7582	7582	899	899	57476	58034	3828	3887	False		
+nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	0	2	0	0	4411	4411	396	396	9708	9708	279	279	2099	2099	212	212	16218	16218	887	887	False		
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	391	391	158	158	0	0	0	0	0	0	0	0	391	391	158	158	False		
+ngmlr	ngmlr	CoNvex Gap-cost alignMents for Long Reads	ngmlr	ngmlr		NGMLR	An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping, DNA structural variation	Up-to-date	https://github.com/philres/ngmlr	Next Gen Mappers	ngmlr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr	0.2.7	ngmlr	0.2.7	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1403	1403	49	49	0	0	0	0	0	0	0	0	1403	1403	49	49	False		
+ngsutils	ngsutils_bam_filter	NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.	ngsutils	ngsutils		NGSUtils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets	Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering	Genomics, Transcriptomics	To update	https://github.com/ngsutils/ngsutils	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils		ngsutils	0.5.9	Read pre-processing, Variant calling, Formatting, Sequence contamination filtering	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	24611	29662	633	716	15523	21395	740	1128	7751	8972	125	145	47885	60029	1498	1989	False		
+nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+nmr_annotation	NmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation								To update	http://workflow4metabolomics.org	Metabolomics	nmr_annotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_annotation	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation	3.0.0	r-batch	1.1_4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	49	49	5	5	0	0	0	0	0	0	0	0	49	49	5	5	False		
+nmr_annotation2d	2DNmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra								To update	http://workflow4metabolomics.org	Metabolomics	2dnmrannotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d	2.0.0	r-batch	1.1_4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+nmr_preprocessing	NMR_Preprocessing, NMR_Read	[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction								To update	http://workflow4metabolomics.org	Metabolomics	nmr_preprocessing	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_preprocessing	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing		r-batch	1.1_4			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	142	142	8	8	0	0	0	0	335	341	9	9	477	483	17	17	False		
+nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	107	143	13	15	148	148	20	20	0	0	0	0	255	291	33	35	False		
+normalization	normalization	[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data								To update	http://workflow4metabolomics.org	Metabolomics	normalization	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/normalization	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization	1.0.7	r-batch	1.1_4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	152	162	39	40	0	0	0	0	233	236	12	12	385	398	51	52	False		
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	7780	7780	337	337	1	1	1	1	2323	2323	99	99	10104	10104	437	437	False		
+nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	118	863	19	26	0	0	0	0	0	0	0	0	118	863	19	26	False		
+nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+numeric_clustering	numeric_clustering	Clustering tool for numberic values								To update	http://scikit-learn.org/stable/index.html	Statistics	numeric_clustering	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	0.9	anaconda				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	391	486	5	11	0	0	0	0	0	0	0	0	391	486	5	11	False		
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	352	352	42	42	8	8	6	6	0	0	0	0	360	360	48	48	False		
+obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	37598	37598	1277	1277	0	0	0	0	3862	3862	280	280	41460	41460	1557	1557	False		
+ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	54	6	6	0	0	0	0	0	0	0	0	54	54	6	6	False		
+ococo	ococo	Variant detection of SNVs								To update	https://github.com/karel-brinda/ococo	Variant Analysis	ococo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo	0.1.2.6	ococo	0.1.2.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1850	1963	79	93	1370	1370	194	194	0	0	0	0	3220	3333	273	287	False		
+odgi	odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	26	26	6	6	0	0	0	0	0	0	0	0	26	26	6	6	False		
+ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	98	6	6	0	0	0	0	0	0	0	0	98	98	6	6	False		
+ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	57	57	4	4	0	0	0	0	0	0	0	0	57	57	4	4	False		
+omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	158	158	12	12	0	0	0	0	0	0	0	0	158	158	12	12	False		
+omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	3051	3051	87	87	0	0	0	0	0	0	0	0	3051	3051	87	87	False		
+onto_toolkit	onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def	ONTO-Toolkit is a collection of tools for managing ontologies.								Up-to-date	http://search.cpan.org/~easr/ONTO-PERL-1.45/	Ontology Manipulation	onto_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit	1.45	perl-onto-perl	1.45			0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	0	582	663	68	69	0	0	0	0	0	0	0	0	582	663	68	69	False		
+openlabcds2csv	openlabcds2csv	"Creates a summary of several ""Internal Standard Report"" OpenLabCDS results."								To update		Metabolomics	openlabcds2csv	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+openmm	pdbfixer	OpenMM is a toolkit for molecular simulation using high performance GPU code.								To update	https://github.com/openmm	Molecular Dynamics, Computational chemistry	openmm	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	1.8.1	pdbfixer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	491	491	52	52	0	0	0	0	0	0	0	0	491	491	52	52	False		
+openms	AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	3.1	openms	3.2.0			8	34	144	0	8	34	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	141	124	0	32169	108654	3316	4889	50	50	15	15	940	940	245	245	33159	109644	3576	5149	False		
+openms	AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.2.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	135	134	0	31121	108907	3369	5029	50	50	15	15	933	933	242	242	32104	109890	3626	5286	False		
+optdoe	optdoe	Optimal Design Of Experiment								To update	https://github.com/pablocarb/doebase	Synthetic Biology	optdoe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe	v2.0.2	doebase				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+optitype	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	500	500	45	45	0	0	0	0	0	0	0	0	500	500	45	45	False		
+orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	897	897	99	99	1792	1792	239	239	0	0	0	0	2689	2689	338	338	False		
+orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	To update	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	3.0.1b1	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2018	2018	419	419	0	0	0	0	438	438	58	58	2456	2456	477	477	False		
+overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	149	149	31	31	0	0	0	0	18	18	1	1	167	167	32	32	False		
+packaged_annotation_loader	packaged_annotation_loader	Tool to make cached genome annotation data available as a list of datasets collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	Data Source	packaged_annotation_loader	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+packmol	packmol	PACKMOL is a package for creating starting structures for Molecular Dynamics simulations								To update	http://m3g.iqm.unicamp.br/packmol/home.shtml	Molecular Dynamics, Computational chemistry	packmol	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol	18.169.1	packmol				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	282	295	32	33	420	420	8	8	0	0	0	0	702	715	40	41	False		
+pacu	pacu_map, pacu_snp	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.	pacu	pacu		PACU	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).	Clustering	Phylogenetics, Sequence analysis	Up-to-date	https://github.com/BioinformaticsPlatformWIV-ISP/PACU	Sequence Analysis, Phylogenetics	pacu	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu	0.0.5	pacu_snp	0.0.5	Clustering	Phylogenetics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pairtools	pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0			5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	196	196	16	16	19	19	14	14	0	0	0	0	215	215	30	30	False		
+pandas_rolling_window	pandas_rolling_window	Rolling window calculations								To update	https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html	Statistics	pandas_rolling_window	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	0.1	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	261	275	12	12	63	63	22	22	0	0	0	0	324	338	34	34	False		
+pangolin	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	0	0	7457	7457	508	508	8518	8518	377	377	2760	2760	259	259	18735	18735	1144	1144	False		
+pangolin	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	Tree-based sequence alignment, Variant classification	Virology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	0	0	7457	7457	508	508	8518	8518	377	377	2760	2760	259	259	18735	18735	1144	1144	False		
+paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	322	349	24	29	0	0	0	0	0	0	0	0	322	349	24	29	False		
+parse_mito_blast	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	65	65	288	288	62	62	110	110	20	20	601	601	147	147	False		
+partialr_square	partialRsq	Compute partial R square								To update		Statistics	partialr_square	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square	https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	55	142	8	42	0	0	0	0	55	142	8	42	False		
+pathifier	pathifier	pathifier								Up-to-date	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	1.40.0	bioconductor-pathifier	1.40.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	245	245	10	10	0	0	0	0	0	0	0	0	245	245	10	10	False		
+pathview	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6204	6211	1261	1261	6667	6667	1143	1143	1160	1160	189	189	14031	14038	2593	2593	False		
+pathwaymatcher	reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	174	244	65	76	0	0	0	0	0	0	0	0	174	244	65	76	False		
+patrist	patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pbgcpp	pbgcpp	Compute genomic consensus and call variants using PacBio reads mapped to a reference	genomicconsensus	genomicconsensus		GenomicConsensus	The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.	Variant calling	Mapping	Up-to-date	https://github.com/PacificBiosciences/gcpp	Variant Analysis	pbgcpp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp	2.0.2	pbgcpp	2.0.2	Variant calling	Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pbmm2	pbmm2	A minimap2 SMRT wrapper for PacBio data.	pbmm2	pbmm2		pbmm2	pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.	Pairwise sequence alignment, Sorting	Mapping	Up-to-date	https://github.com/PacificBiosciences/pbmm2	Next Gen Mappers	pbmm2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2	1.14.99	pbmm2	1.14.99	Pairwise sequence alignment, Sorting	Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	70	17	17	0	0	0	0	0	0	0	0	70	70	17	17	False		
+pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	22	22	109	109	19	19	0	0	0	0	167	167	41	41	False		
+pe_histogram	pe_histogram	Contains a tool that produces an insert size histogram for a paired-end BAM file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram	Graphics	pe_histogram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram	1.0.2	openjdk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	5505	5505	510	510	7932	8582	811	909	736	736	119	119	14173	14823	1440	1538	False		
+peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2807	3337	178	196	0	0	0	0	0	0	0	0	2807	3337	178	196	False		
+peakzilla	peakzilla	Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.								To update	https://github.com/steinmann/peakzilla	ChIP-seq	peakzilla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla	1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	9	9	0	0	0	0	0	0	0	0	18	18	9	9	False		
+pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	6269	6866	260	292	5530	20068	467	1664	5647	8471	198	300	17446	35405	925	2256	False		
+pearson_correlation	Pearson_and_apos_Correlation1	Pearson and apos Correlation between any two numeric columns								To update		Statistics	pearson_correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	2	0	2	False		
+pep_pointer	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	506	511	54	55	21	21	12	12	163	163	8	8	690	695	74	75	False		
+pepquery	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7047	7047	76	76	0	0	0	0	0	0	0	0	7047	7047	76	76	False		
+pepquery2	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2			0	1	3	0	0	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1222	1222	28	28	0	0	0	0	0	0	0	0	1222	1222	28	28	False		
+peptide_genomic_coordinate	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	472	472	56	56	16	16	10	10	149	149	5	5	637	637	71	71	False		
+peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.11			4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	2	0	11986	17898	1046	1153	1314	1314	389	389	3034	3034	118	118	16334	22246	1553	1660	False		
+peptimapper	peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pepxml_to_xls		Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+percolator	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.7.1			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	338	378	15	16	0	0	0	0	1059	1059	13	13	1397	1437	28	29	False		
+perf	stats_perf_tool	suitable for boolean classification problems								To update	http://osmot.cs.cornell.edu/kddcup/software.html		stats_perf_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/perf	https://github.com/bgruening/galaxytools/tree/master/tools/perf	5.11.0	perf				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	42	1	2	0	0	0	0	0	0	0	0	36	42	1	2	False		
+pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	773	773	60	60	495	495	72	72	246	246	17	17	1514	1514	149	149	False		
+pg_tools	pg_dump, pg_import, pg_query	tool suite for dealing with Postgresql databases from Galaxy's history								To update	https://www.postgresql.org	Data Export, Data Source	pgtools	bgruening	https://github.com/bgruening/galaxytools/tools/pgtools	https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools		postgresql				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pgsnp2gd_snp	pgSnp2gd_snp	Convert from pgSnp to gd_snp								To update		Variant Analysis	pgsnp2gd_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pharmcat	pharmcat	Pharmacogenomics Clinical Annotation Tool								To update	https://pharmcat.org/	Variant Analysis	pharmcat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat						1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	109	109	29	29	250	250	84	84	0	0	0	0	359	359	113	113	False		
+pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
+                pharokka
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	5462	5462	334	334	0	0	0	0	309	309	52	52	5771	5771	386	386	False		
+phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	0	0	1	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	1199	1199	193	193	0	0	0	0	6	6	1	1	1205	1205	194	194	False		
+phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1975	2034	246	258	0	0	0	0	553	564	140	144	2528	2598	386	402	False		
+physiofit	physiofit	PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit	workflow4metabolomics	https://github.com/MetaSys-LISBP/PhysioFit	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit	3.4.0	physiofit	3.4.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+physiofit_manager	physiofit_data_manager	Handling of physiofit input files								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager	1.0.1	physiofit_data_manager	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pi_db_tools	calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+picard	picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile	Picard SAM/BAM manipulation tools.	picard_samtofastq	picard_samtofastq, picard_replacesamheader, picard_fastqtosam, picard_reordersam		picard_samtofastq	Create a FASTQ file.	Formatting	Sequencing	To update	http://broadinstitute.github.io/picard/	SAM	picard	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard	3.1.1	picard	3.2.0	Formatting	Sequencing	31	31	31	0	31	31	31	0	0	0	0	0	0	0	0	0	0	31	4	31	0	0	31	0	0	0	31	0	0	0	0	0	0	31	31	31	0	386934	399039	11024	11956	366646	589980	32000	57111	56622	62258	2845	3398	810202	1051277	45869	72465	False		
+pick_value	pick_value	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	pick_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1607	1607	41	41	490	490	53	53	127	127	4	4	2224	2224	98	98	False		
+picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	867	1128	144	165	0	0	0	0	2106	2106	121	121	2973	3234	265	286	False		
+picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	2532	2532	382	382	1	1	1	1	1311	1311	83	83	3844	3844	466	466	False		
+pileup_interval	pileup_interval	Pileup-to-Interval condenses pileup format into ranges of bases								To update		SAM	pileup_interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval	1.0.3	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	613	640	48	54	1381	7804	201	1552	756	815	22	30	2750	9259	271	1636	False		
+pileup_parser	pileup_parser	Filter pileup on coverage and SNPs								To update	https://github.com/galaxyproject/tools-devteam/	SAM	pileup_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser	1.0.2	perl				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3639	3774	414	461	9754	52522	1247	4531	1893	2433	191	318	15286	58729	1852	5310	False		
+pilon	pilon	pilon is a tool for assembly improvement and variant analysis in bacteria	pilon	pilon		pilon	Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.	Sequence assembly, Analysis, Read alignment	Assembly	To update	https://github.com/broadinstitute/pilon/wiki	Variant Analysis	pilon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon	1.20.1	pilon	1.24	Sequence assembly, Analysis	Assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9045	9458	1115	1144	7989	7989	1070	1070	3945	4137	726	741	20979	21584	2911	2955	False		
+pindel	pindel	Pindel detects genome-wide structural variation.								Up-to-date	http://artbio.fr	Variant Analysis	pindel	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel	https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel	0.2.5b9	pindel	0.2.5b9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pipelign	pipelign	Multipe sequence alignment								Up-to-date	https://github.com/asmmhossain/pipelign/	Next Gen Mappers	pipelign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign	0.2	pipelign	0.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1245	1245	231	231	9046	9046	630	630	0	0	0	0	10291	10291	861	861	False		
+pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	238	283	42	45	0	0	0	0	0	0	0	0	238	283	42	45	False		
+piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1408	2068	94	119	0	0	0	0	0	0	0	0	1408	2068	94	119	False		
+pizzly	pizzly	Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.								To update	https://github.com/pmelsted/pizzly/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly	0.37.3.1	pizzly	0.37.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	201	210	23	24	998	998	76	76	0	0	0	0	1199	1208	99	100	False		
+plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37086	37272	711	734	6346	6346	583	583	3065	3065	61	61	46497	46683	1355	1378	False		
+plasmid_profiler	plasmid_profiler	Explores plasmid content in WGS data								To update			plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler	0.1.6	r				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plasmid_profiler_suite		Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14652	14652	251	251	0	0	0	0	101	101	18	18	14753	14753	269	269	False		
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plink	plink	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	plink	plink		PLINK	Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	Genetic variation analysis	GWAS study	Up-to-date	https://www.cog-genomics.org/plink	Genome-Wide Association Study	plink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink	1.90b6.21	plink	1.90b6.21	Genetic variation analysis	GWAS study	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	851	851	127	127	249	249	43	43	0	0	0	0	1100	1100	170	170	False		
+plot_from_lda	plot_for_lda_output1	"Draw ROC plot on ""Perform LDA"" output"								To update		Graphics, Statistics	plot_from_lda	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda	https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda	1.0.1	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	65	77	19	25	153	886	38	343	142	155	8	10	360	1118	65	378	False		
+plotheatmap	plotheatmap	This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output.								To update		Computational chemistry	plotheatmap	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	1.0	bioconductor-preprocesscore	1.64.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.4	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1342	1472	184	197	902	902	156	156	630	630	24	24	2874	3004	364	377	False		
+plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	408	664	91	122	627	627	118	118	605	605	26	26	1640	1896	235	266	False		
+plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	764	879	213	237	304	304	95	95	193	193	26	26	1261	1376	334	358	False		
+pmd_fdr	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pneumocat	pneumocat	Pneumococcal Capsular Typing of illumina fastq reads								Up-to-date	https://github.com/phe-bioinformatics/PneumoCaT	Variant Analysis	pneumocat	nml	https://github.com/phe-bioinformatics/PneumoCaT	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat	1.2.1	pneumocat	1.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	33	33	2	2	0	0	0	0	0	0	0	0	33	33	2	2	False		
+points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	4	4	0	0	0	0	0	0	0	0	29	29	4	4	False		
+poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	112	120	16	16	4	562	1	140	320	347	7	8	436	1029	24	164	False		
+polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	731	731	86	86	0	0	0	0	42	42	4	4	773	773	90	90	False		
+porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	262015	262852	2627	2711	83623	83623	1918	1918	52558	52558	1037	1037	398196	399033	5582	5666	False		
+poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	13	0	19942	20587	1055	1245	33619	40808	2183	2594	9261	9261	365	365	62822	70656	3603	4204	False		
+positions2snv_alignment	positions2snv_alignment	Generate alignment of SNVs from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+positions2snv_invariant_alignment	positions2snv_invariant_alignment	Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_invariant_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+presto	presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	63244	65177	1392	1599	0	0	0	0	63244	65177	1392	1599	False		
+pretext	pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6			3	2	3	0	3	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	3463	3463	538	538	1853	1853	256	256	1097	1097	70	70	6413	6413	864	864	False		
+principal_component_analysis	pca1	Principal Component Analysis								To update		Statistics	principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis	1.0.2	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9788	10032	207	244	3072	8054	607	1488	0	0	0	0	12860	18086	814	1732	False		
+prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10152	10626	253	281	10581	10581	1240	1240	0	0	0	0	20733	21207	1493	1521	False		
+probecoverage	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1902	1902	167	167	0	0	0	0	0	0	0	0	1902	1902	167	167	False		
+progressivemauve	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update	http://darlinglab.org/mauve/user-guide/progressivemauve.html	Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2064	2173	678	695	2900	2900	1034	1034	0	0	0	0	4964	5073	1712	1729	False		
+projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	86	4	6	0	0	0	0	0	0	0	0	40	86	4	6	False		
+projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20858	21444	14	18	0	0	0	0	0	0	0	0	20858	21444	14	18	False		
+prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	464359	476554	7475	7721	313285	331256	11243	12384	131211	141875	4358	4947	908855	949685	23076	25052	False		
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+prot-scriber	prot_scriber	Protein annotation of short human readable descriptions								Up-to-date	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.6	prot-scriber	0.1.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	10	7	7	0	0	0	0	0	0	0	0	10	10	7	7	False		
+protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	129	155	15	21	0	0	0	0	0	0	0	0	129	155	15	21	False		
+protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	11743	12752	1137	1278	2	2	1	1	0	0	0	0	11745	12754	1138	1279	False		
+protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	465	638	81	100	0	0	0	0	0	0	0	0	465	638	81	100	False		
+proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3962	3962	501	501	0	0	0	0	0	0	0	0	3962	3962	501	501	False		
+proteinpilot	convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml									To update			proteinpilot	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+proteomiqon_joinquantpepionswithproteins	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	366	366	4	4	0	0	0	0	0	0	0	0	366	366	4	4	False		
+proteomiqon_labeledproteinquantification	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	8	8	0	0	0	0	0	0	0	0	16	16	8	8	False		
+proteomiqon_labelfreeproteinquantification	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	6	4	4	0	0	0	0	0	0	0	0	6	6	4	4	False		
+proteomiqon_mzmltomzlite	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	721	721	8	8	0	0	0	0	0	0	0	0	721	721	8	8	False		
+proteomiqon_peptidedb	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	96	96	12	12	0	0	0	0	0	0	0	0	96	96	12	12	False		
+proteomiqon_peptidespectrummatching	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	686	686	5	5	0	0	0	0	0	0	0	0	686	686	5	5	False		
+proteomiqon_proteininference	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	6	6	0	0	0	0	0	0	0	0	89	89	6	6	False		
+proteomiqon_psmbasedquantification	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	604	604	4	4	0	0	0	0	0	0	0	0	604	604	4	4	False		
+proteomiqon_psmstatistics	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	694	694	6	6	0	0	0	0	0	0	0	0	694	694	6	6	False		
+proteore_venn_diagram	proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	1	1	0	0	0	0	0	0	0	0	15	15	1	1	False		
+protxml_to_xls	protxml_to_xls									To update			protxml_to_xls	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pseudogenome	pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+psiclass	psiclass	PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.	psiclass	psiclass		PsiCLASS	Reference-based transcriptome assembler for single or multiple RNA-seq samples	Transcriptome assembly	Sequence assembly	Up-to-date	https://github.com/splicebox/PsiCLASS	Transcriptomics	psiclass	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass	https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass	1.0.3	psiclass	1.0.3	Transcriptome assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	24	5	5	0	0	0	0	0	0	0	0	24	24	5	5	False		
+psm2sam	PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+psm_eval	psm_eval									To update			psm_eval	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval	0.1.0	binaries_for_psm_eval				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+psm_validation	psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	20	20	4	4	0	0	0	0	0	0	0	0	20	20	4	4	False		
+psy-maps	psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.3.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	333	502	62	62	0	0	0	0	0	0	0	0	333	502	62	62	False		
+pureclip	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1319	1507	81	92	0	0	0	0	0	0	0	0	1319	1507	81	92	False		
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17782	17782	287	287	853	853	65	65	2224	2224	65	65	20859	20859	417	417	False		
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22742	22742	557	557	2159	2159	716	716	776	776	448	448	25677	25677	1721	1721	False		
+pyega3	pyega3	EGA python client uses the EGA REST API to download authorized datasets and files.								To update	https://github.com/EGA-archive/ega-download-client	Data Source	ega_download_client	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3	5.0.2	pyega3	5.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2716	2716	104	104	134	134	43	43	40	40	1	1	2890	2890	148	148	False		
+pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12858	13232	986	996	8092	8092	943	943	3238	3238	124	124	24188	24562	2053	2063	False		
+pyprophet	pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5			0	5	6	0	0	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	6	6	0	2626	2626	150	150	0	0	0	0	609	609	9	9	3235	3235	159	159	False		
+pyscenic	pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/								To update		Transcriptomics, RNA, Sequence Analysis	suite_pyscenic	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic	0.12.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pysradb	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.2	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	163	163	35	35	0	0	0	0	0	0	0	0	163	163	35	35	False		
+pyteomics	mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.4	Protein identification	Proteomics, Proteomics experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	92	92	4	4	0	0	0	0	0	0	0	0	92	92	4	4	False		
+pyvo_integration	astronomical_archives	Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy								To update		Data Source	astronomicalarchivestool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration	0.10.0	astropy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	53	6	6	0	0	0	0	0	0	0	0	53	53	6	6	False		
+qcxms	qcxms_getres, qcxms_neutral_run, qcxms_production_run	QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).								To update	https://github.com/grimme-lab/QCxMS	Computational chemistry, Molecular Dynamics	QCxMS	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	5.2.1					0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11246	11246	13	13	0	0	0	0	0	0	0	0	11246	11246	13	13	False		
+qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2092	2342	209	238	0	0	0	0	2	2	1	1	2094	2344	210	239	False		
+qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	0	0	0	32	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	31825	34677	3375	3785	1	1	1	1	14	14	4	4	31840	34692	3380	3790	False		
+qiime_extract_viz	qiime_extract_viz	Extract vizualization from QIIME artifacts								To update	http://www.qiime.org	Metagenomics	qiime_extract_viz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz	0.1.0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	8	8	0	0	0	0	0	0	0	0	17	17	8	8	False		
+qq_tools	qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	0	4	4	4	0	684820	684820	3239	3239	90503	90503	3881	3881	29018	29018	826	826	804341	804341	7946	7946	False		
+quality_filter	qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.13.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	724	35	62	0	0	0	0	98	724	35	62	False		
+quantp	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	197	241	17	22	0	0	0	0	0	0	0	0	197	241	17	22	False		
+quantwiz_iq	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	32	3	3	0	0	0	0	0	0	0	0	32	32	3	3	False		
+quasitools	aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0			0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13483	13483	434	434	13483	13483	434	434	False		
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	67737	69738	7787	7971	51925	56602	9692	10646	32003	34145	3890	4127	151665	160485	21369	22744	False		
+query	query	Execute an SQL statement on a set of tables								To update		Text Manipulation	query	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/query	https://github.com/RECETOX/galaxytools/tree/master/tools/query	0.2	click				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+query_impc	query_impc	Contains a tool to query the IMPC database.								To update	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	Convert Formats, Web Services	query_impc	iuc	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc	0.9.0	requests				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	2	0	0	0	0	0	0	0	0	3	3	2	2	False		
+query_tabular	filter_tabular, query_tabular, sqlite_to_tabular	Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular	3.3.1	python				3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	3	2	0	0	0	0	0	0	1	0	0	0	0	0	0	3	3	3	0	130124	135361	1265	1305	11135	11135	922	922	5939	5939	153	153	147198	152435	2340	2380	False		
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	172	172	9	9	0	0	0	0	0	0	0	0	172	172	9	9	False		
+rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3077	4581	395	518	2856	2856	1093	1093	1977	1977	19	19	7910	9414	1507	1630	False		
+racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	27113	27315	839	850	9089	9089	475	475	5452	5452	171	171	41654	41856	1485	1496	False		
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4844	4844	480	480	0	0	0	0	7	7	3	3	4851	4851	483	483	False		
+ramclustr	ramclustr, ramclustr_define_experiment		ramclustr	ramclustr		RAMClustR	A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	To update	https://rdrr.io/cran/RAMClustR/	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	1.3.0	r-ramclustr	1.3.1	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	58	58	22	22	29	29	14	14	344	344	4	4	431	431	40	40	False		
+rapidnj	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2		Phylogeny	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	339	339	30	30	1737	1737	256	256	6	6	1	1	2082	2082	287	287	False		
+rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	42	42	9	9	0	0	0	0	0	0	0	0	42	42	9	9	False		
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9477	9477	438	438	0	0	0	0	10585	10585	182	182	20062	20062	620	620	False		
+rawtools	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	166	179	32	33	0	0	0	0	414	414	13	13	580	593	45	46	False		
+raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10905	10905	966	966	5100	5114	587	587	4955	6094	765	892	20960	22113	2318	2445	False		
+rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	1.0		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	90	90	6	6	0	0	0	0	0	0	0	0	90	90	6	6	False		
+rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	860	1257	88	98	0	0	0	0	0	0	0	0	860	1257	88	98	False		
+rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	655	655	57	57	0	0	0	0	0	0	0	0	655	655	57	57	False		
+rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	49	191	5	46	0	0	0	0	49	191	5	46	False		
+rcx-tk	rcx-tk	Tools to process metadata or alkane files.								To update	https://github.com/RECETOX/rcx-tk	Metabolomics	rcx_tk	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk	0.1.0+galaxy0	rcx-tk	0.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rdock	rdock	Docking ligands to proteins and nucleic acids								To update	http://rdock.sourceforge.net/	Computational chemistry	rdock	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock	1.0	rDock	2013.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3710	3710	80	80	7	7	6	6	0	0	0	0	3717	3717	86	86	False		
+reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.15.0	recentrifuge	1.15.0	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	472	472	92	92	32	32	13	13	6	6	4	4	510	510	109	109	False		
+recetox_aplcms	recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise	Peak detection tool for HRMS profile data.	recetox-aplcms	recetox-aplcms		recetox-aplcms	recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	Up-to-date	https://github.com/RECETOX/recetox-aplcms	Metabolomics	recetox-aplcms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	0.13.3	r-recetox-aplcms	0.13.3	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	862	862	12	12	0	0	0	0	48	48	1	1	910	910	13	13	False		
+recetox_msfinder	recetox_msfinder		recetox-msfinder	recetox-msfinder		recetox-msfinder	This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.	Annotation	Metabolomics	To update	https://github.com/RECETOX/recetox-msfinder	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	v3.5.2			Annotation	Metabolomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47	47	4	4	0	0	0	0	0	0	0	0	47	47	4	4	False		
+recetox_xmsannotator	recetox_xmsannotator_advanced		recetox-xmsannotator	recetox-xmsannotator		recetox-xMSannotator	Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		Up-to-date	https://github.com/RECETOX/recetox-xMSannotator	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator	0.10.0	r-recetox-xmsannotator	0.10.0	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	93	93	2	2	93	93	2	2	False		
+red	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	859	859	203	203	305	305	142	142	227	227	58	58	1391	1391	403	403	False		
+refseq_masher	refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	428	428	35	35	141	141	42	42	0	0	0	0	569	569	77	77	False		
+regex_find_replace	regex1, regexColumn1	Use python regular expressions to find and replace text								To update		Text Manipulation	regex_find_replace	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	1.0.3	python				2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	78648	78834	1144	1156	18063	18063	870	870	4455	6051	194	289	101166	102948	2208	2315	False		
+regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	438	542	128	157	0	0	0	0	0	0	0	0	438	542	128	157	False		
+rem_complex	rem_complex	Removes molecular coordination complexes.								To update	https://github.com/RECETOX/galaxytools	Metabolomics	rem_complex	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	2	2	0	0	0	0	0	0	0	0	18	18	2	2	False		
+remove_beginning	Remove beginning1	Remove lines from the beginning of a file.								To update		Text Manipulation	remove_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	148572	169964	3525	3682	36694	113826	3910	8163	9713	10577	1475	1598	194979	294367	8910	13443	False		
+remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	44	6	7	0	0	0	0	0	0	0	0	39	44	6	7	False		
+rename_annotated_feature	rename_annotated_feature	Update column names in an abundance table using a annotation table with spectral matching results								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	rename_annotated_feature	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1	False		
+repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.0.9_p2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5998	5998	810	810	7618	7618	803	803	3135	3135	292	292	16751	16751	1905	1905	False		
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	95	38	38	0	0	0	0	0	0	0	0	95	95	38	38	False		
+repeatmasker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.0.9_p2	Genome annotation	Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5998	5998	810	810	7618	7618	803	803	3135	3135	292	292	16751	16751	1905	1905	False		
+repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7963	7963	413	413	1485	1485	220	220	8402	8402	168	168	17850	17850	801	801	False		
+repenrich	edger-repenrich, repenrich	Repeat element profiling								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	Transcriptomics	repenrich	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	2.31.1					0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1725	1790	56	57	1725	1790	56	57	False		
+repenrich2	edger-repenrich2, repenrich2	Repeat element profiling using bowtie2 aligner								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	Transcriptomics	repenrich2	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	2.31.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+replaceColumn	replace_column_with_key_value_file	A tool to replace all column entries of a file given by values of a key-value file.								To update		Text Manipulation	replace_column_by_key_value_file	bgruening	https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn	https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn	0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	577184	577312	463	492	43900	44233	283	373	2190	2190	112	112	623274	623735	858	977	False		
+replace_chromosome_names	replace_chromosome_names	Replace chromosome names								To update		Text Manipulation	replace_chromosome_names	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names	0.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	514	573	69	83	0	0	0	0	0	0	0	0	514	573	69	83	False		
+repmatch_gff3	repmatch_gff3	Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.								To update		ChIP-seq	repmatch_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3		matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	415	721	128	219	0	0	0	0	415	721	128	219	False		
+reshape2	cast, melt	Flexibly restructure and aggregate data using just the two functions melt and dcast								To update	https://cran.r-project.org/web/packages/reshape2/index.html	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2	1.4.2	r-reshape2				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	3543	3619	108	111	536	536	157	157	0	0	0	0	4079	4155	265	268	False		
+resize_coordinate_window	resize_coordinate_window	Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.								To update		Genomic Interval Operations	resize_coordinate_window	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window	https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window	1.0.2	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	75	86	8	9	138	216	30	57	0	0	0	0	213	302	38	66	False		
+rest_tool	pubchem_rest_tool	This tool fetches data from pubchem via the PubChem REST API.								To update	https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html	Data Source	pubchem_rest_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+retip	retip_apply, retip_descriptors, retip_filter_rt, retip_train		retip	retip		Retip	Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.	Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	To update	https://github.com/PaoloBnn/Retip	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	0.5.4			Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+retrieve_ensembl_bed	retrieve_ensembl_bed	Retrieve cDNA features from Ensembl REST API in BED format								To update	http://rest.ensembl.org/	Data Source	retrieve_ensembl_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+revertR2orientationInBam	revertR2orientationInBam	Revert the mapped orientation of R2 mates in a bam.								To update		SAM	revertr2orientationinbam	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	0.0.2	samtools	1.21			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	40	11	11	520	520	31	31	0	0	0	0	560	560	42	42	False		
+revoluzer	revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	Structural variation detection	Molecular evolution, Phylogeny	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2444	2444	52	52	0	0	0	0	0	0	0	0	2444	2444	52	52	False		
+rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	7	7	0	0	0	0	0	0	0	0	15	15	7	7	False		
+rgcca	rgcca	multi-block analysis								To update	https://github.com/rgcca-factory/RGCCA	Statistics	rgcca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca	3.0.2	rgccacmd	3.0.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	44	44	6	6	77	77	35	35	0	0	0	0	121	121	41	41	False		
+rgrnastar	rna_star, rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	star	star		STAR	Ultrafast universal RNA-seq data aligner	Sequence alignment	RNA-Seq, Transcriptomics	To update	https://github.com/alexdobin/STAR	Next Gen Mappers, Transcriptomics	rgrnastar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar	2.7.11a	star	2.7.11b	Sequence alignment	RNA-Seq, Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	2	0	0	0	2	0	0	0	0	0	1	2	2	2	0	438078	473957	10142	10900	325474	403925	15284	18791	49662	53138	1359	1449	813214	931020	26785	31140	False		
+riassigner	riassigner, riassigner_from_comment		riassigner	riassigner		RIAssigner	RIAssigner is a python tool for retention index (RI) computation for GC-MS data.	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/RIAssigner	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	0.4.1	riassigner	0.4.1	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	46	46	19	19	15	15	4	4	1	1	1	1	62	62	24	24	False		
+ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	661	681	78	78	0	0	0	0	0	0	0	0	661	681	78	78	False		
+ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	171	171	20	20	0	0	0	0	0	0	0	0	171	171	20	20	False		
+rmap	rmap_wrapper	RMAP for Solexa Short Reads Alignment								To update		Next Gen Mappers	rmap	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rmapq	rmapq_wrapper	RMAPQ for Solexa Short Reads Alignment with Quality Scores								To update		Next Gen Mappers	rmapq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rmassbank	rmassbank	RMassBank is an R package for processing tandem MS files and building of MassBank records.								To update	https://github.com/MassBank/RMassBank	Metabolomics	rmassbank	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	3.0.0	python				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	48	48	1	1	48	48	1	1	False		
+rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	137	173	40	49	0	0	0	0	0	0	0	0	137	173	40	49	False		
+rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	90	196	9	11	0	0	0	0	0	0	0	0	90	196	9	11	False		
+rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	878	1363	29	35	0	0	0	0	0	0	0	0	878	1363	29	35	False		
+rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1024	1077	18	21	0	0	0	0	0	0	0	0	1024	1077	18	21	False		
+rnaformer	infer_rnaformer	RNAformer: RNA secondary structure prediction								To update	https://github.com/automl/RNAformer	RNA	rnaformer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	1.0.0	rnaformer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	6	6	0	0	0	0	0	0	0	0	26	26	6	6	False		
+rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	33	10	14	0	0	0	0	0	0	0	0	23	33	10	14	False		
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1522	1522	254	254	372	372	75	75	5	5	1	1	1899	1899	330	330	False		
+rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	65	89	14	18	0	0	0	0	0	0	0	0	65	89	14	18	False		
+rnaz	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	1156	43309	93	121	0	0	0	0	0	0	0	0	1156	43309	93	121	False		
+roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15196	15685	1459	1501	12188	12188	1768	1768	4881	5539	518	555	32265	33412	3745	3824	False		
+rp2biosensor	rp2biosensor	Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output								To update	https://github.com/brsynth/rp2biosensor	Synthetic Biology	rp2biosensor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor	3.2.1	rp2biosensor				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rp2paths	rp2paths	Enumerate and seperate the different pathways generated by RetroPath2.0								To update	https://github.com/brsynth/rp2paths	Synthetic Biology	rp2paths	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths	1.5.1	rp2paths				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rpbasicdesign	rpbasicdesign	Extracting enzyme IDs from rpSBML files								To update	https://github.com/brsynth/rpbasicdesign	Synthetic Biology	rpbasicdesign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign	1.2.2	rpbasicdesign				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rpfba	rpfba	Perform FBA for the RetroPath2.0 heterologous pathways								To update	https://github.com/brsynth/rptools/releases	Synthetic Biology	rpfba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba	5.12.3	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rptools	rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz	Suite of tools that work on rpSBML format								To update	https://github.com/brsynth/rptools	Synthetic Biology	rptools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools	5.13.1	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rrparser	rrparser	Reaction Rules Parser								To update	https://github.com/brsynth/RRParser	Synthetic Biology	rrparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser	2.5.2	rrparser				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rsat_filter_snps	rsat_filter_snps	Filter SNPs in RSAT Matrix Scan output								To update	https://github.com/TGAC/earlham-galaxytools/	ChIP-seq, Systems Biology	rsat_filter_snps	earlham	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	1	1	0	363	430	158	183	0	0	0	0	67	146	13	39	430	576	171	222	False		
+rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	0	22	22	22	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	0	22	22	22	0	136315	147595	8341	9385	138707	161046	10696	12789	22718	23767	1593	1695	297740	332408	20630	23869	False		
+ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1286	1364	178	193	2220	2220	299	299	0	0	0	0	3506	3584	477	492	False		
+sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3628	4168	165	199	8399	14473	573	1147	2710	3000	151	175	14737	21641	889	1521	False		
+salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	0	2	2	3	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	0	3	3	3	0	73085	77081	2243	2319	90634	122835	3402	4726	13371	15818	513	586	177090	215734	6158	7631	False		
+salmon-kallisto-mtx-to-10x	_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	682	682	172	172	322	322	74	74	3	3	3	3	1007	1007	249	249	False		
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	463	463	119	119	1038	1038	87	87	410	410	24	24	1911	1911	230	230	False		
+sam2interval	sam2interval	Convert SAM to interval.								To update		SAM	sam2interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1155	1251	57	63	2264	18187	189	1748	525	590	10	17	3944	20028	256	1828	False		
+sam_bitwise_flag_filter	sam_bw_filter	Filter SAM on bitwise flag values								To update		SAM	sam_bitwise_flag_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter	1.0.1	python				1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	96	278	12	26	3554	76029	450	6346	229	345	16	29	3879	76652	478	6401	False		
+sambamba	sambamba_sample_or_filter	filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM								To update	http://artbio.fr	SAM	sambamba	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba	https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba	0.7.1+galaxy1	sambamba	1.0.1			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	684	684	17	17	684	684	17	17	False		
+sambamba	sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort	Sambamba: process your BAM data faster!								Up-to-date	https://github.com/biod/sambamba	SAM	sambamba	bgruening	https://github.com/biod/sambamba	https://github.com/bgruening/galaxytools/tree/master/tools/sambamba	1.0.1	sambamba	1.0.1			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	297	297	51	51	0	0	0	0	0	0	0	0	297	297	51	51	False		
+samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	Up-to-date	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.26	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3421	3859	340	382	883	883	109	109	1138	1138	15	15	5442	5880	464	506	False		
+samtools										To update	https://github.com/samtools/samtools	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools	1.20	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6485	6549	720	726	10127	10127	1518	1518	238	238	37	37	16850	16914	2275	2281	False		
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	52099	55110	4053	4497	73194	108684	6930	9936	14771	15714	1222	1419	140064	179508	12205	15852	False		
+sansa	sansa_annotate	Sansa is a tool for structural variant annotation.								To update	https://github.com/dellytools/sansa	Variant Analysis	sansa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa	0.2.1	sansa	0.2.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	138	138	36	36	0	0	0	0	0	0	0	0	138	138	36	36	False		
+sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	174	174	16	16	399	399	29	29	0	0	0	0	573	573	45	45	False		
+sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	140	140	5	5	253	253	6	6	0	0	0	0	393	393	11	11	False		
+sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sbml2sbol	sbml2sbol	Convert SBML to SBOL format								To update	https://github.com/neilswainston/SbmlToSbol	Synthetic Biology	sbml2sbol	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol	0.1.13	sbml2sbol				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	10	10	0	0	0	0	0	0	0	0	13	13	10	10	False		
+scaffold	scaffold, scaffold_export									To update			scaffold	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold	0.1.0	scaffold				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	477	520	13	16	0	0	0	0	0	0	0	0	477	520	13	16	False		
+scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			27	27	27	0	27	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	0	45501	45666	4832	4868	7304	7304	1846	1846	3106	3106	457	457	55911	56076	7135	7171	False		
+scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	63789	64034	2543	2547	29962	29962	1185	1185	18028	18028	379	379	111779	112024	4107	4111	False		
+scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			1	2	6	0	1	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	381	388	99	100	0	0	0	0	297	297	9	9	678	685	108	109	False		
+scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	1345	1371	350	351	0	0	0	0	903	903	29	29	2248	2274	379	380	False		
+scatterplot	scatterplot_rpy	Scatterplot of two numeric columns								To update		Graphics, Statistics	scatterplot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot	1.0.3	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1234	1752	179	261	680	9223	231	1927	0	49	0	18	1914	11024	410	2206	False		
+sccaf	run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out	SCCAF: Single Cell Clustering Assessment Framework.								To update	https://github.com/sccaf/sccaf	Transcriptomics	SCCAF	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf	0.0.9	sccaf	0.0.10			4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	110	110	19	19	0	0	0	0	0	0	0	0	110	110	19	19	False		
+sceasy	sceasy_convert	Convert scRNA data object between popular formats								To update		Transcriptomics	sceasy	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy	0.0.5	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1059	1059	222	222	426	426	71	71	1	1	1	1	1486	1486	294	294	False		
+sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1059	1059	222	222	426	426	71	71	1	1	1	1	1486	1486	294	294	False		
+schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	809	809	78	78	3	3	2	2	105	105	16	16	917	917	96	96	False		
+scikit-bio	scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1503	1955	283	402	0	0	0	0	1504	1956	284	403	False		
+scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	97	97	41	41	0	0	0	0	0	0	0	0	97	97	41	41	False		
+scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	901	901	90	90	0	0	0	0	0	0	0	0	901	901	90	90	False		
+scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	284	632	34	38	786	786	61	61	1	1	1	1	1071	1419	96	100	False		
+scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	25	5	5	0	0	0	0	0	0	0	0	25	25	5	5	False		
+scripting	singularity_scriptrunner	suite_scripting								To update	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	Text Manipulation	scripting tools	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+seacr	seacr	SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.								Up-to-date	https://github.com/FredHutch/SEACR	Epigenetics, ChIP-seq	seacr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr	1.3	seacr	1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5106	5106	116	116	6419	6419	241	241	0	0	0	0	11525	11525	357	357	False		
+sed	sed_stream_editor	Manipulate your data with the sed command line tool.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/sed	Text Manipulation	sed_wrapper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sed	https://github.com/bgruening/galaxytools/tree/master/tools/sed	0.0.1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	281	2284	10	53	0	0	0	0	0	0	0	0	281	2284	10	53	False		
+segalign	segalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/gsneha26/SegAlign	Next Gen Mappers	segalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	0.1.2.7	segalign-galaxy	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	252	252	47	47	0	0	0	0	252	252	47	47	False		
+segemehl	segemehl	segemehl - short read mapping with gaps								To update	http://www.bioinf.uni-leipzig.de/Software/segemehl/	Next Gen Mappers	segemehl	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	0.2.0.4	segemehl	0.3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1095	1306	98	113	0	0	0	0	0	0	0	0	1095	1306	98	113	False		
+segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	2	2	0	0	0	0	0	0	0	0	7	7	2	2	False		
+selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	305	463	43	50	0	0	0	0	0	0	0	0	305	463	43	50	False		
+selenzy_wrapper	selenzy_wrapper	Performs enzyme selection from a reaction query.								Up-to-date	https://github.com/brsynth/selenzy-wrapper	Synthetic Biology	selenzy_wrapper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper	0.3.0	selenzy_wrapper	0.3.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	931	931	93	93	0	0	0	0	0	0	0	0	931	931	93	93	False		
+seq2hla	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	342	342	40	40	0	0	0	0	0	0	0	0	342	342	40	40	False		
+seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1053	1186	137	195	680	680	206	206	0	0	0	0	1733	1866	343	401	False		
+seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30300	32553	732	799	21726	31891	619	621	2886	2886	144	144	54912	67330	1495	1564	False		
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4322	4714	180	205	0	0	0	0	0	0	0	0	4322	4714	180	205	False		
+seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2196	3529	260	289	2196	3529	260	289	False		
+seqcomplexity	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	70	70	19	19	109	109	47	47	0	0	0	0	179	179	66	66	False		
+seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	0	0	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3364	3364	247	247	0	0	0	0	244	244	33	33	3608	3608	280	280	False		
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2424	2424	102	102	0	0	0	0	0	0	0	0	2424	2424	102	102	False		
+seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4182	4182	42	42	0	0	0	0	0	0	0	0	4182	4182	42	42	False		
+seqtk	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	Data handling, Sequence file editing		15	15	15	0	15	15	15	0	0	0	0	0	0	0	0	0	0	14	0	14	0	0	14	0	0	0	15	0	0	0	0	0	0	14	14	14	14	72816	73514	2210	2300	102777	107831	2313	2669	154613	154613	682	682	330206	335958	5205	5651	False		
+seqtk_nml	seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seqwish	seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	271	271	2	2	0	0	0	0	0	0	0	0	271	271	2	2	False		
+seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	0	1	1	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	121	121	11	11	32	32	5	5	0	0	0	0	153	153	16	16	False		
+seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.4.0			14	14	14	0	14	14	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	0	2296	2328	673	676	141	141	39	39	0	0	0	0	2437	2469	712	715	False		
+sgwb	sgwb_astro_tool	SGWB								To update		Astronomy	sgwb_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb	0.0.1+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	2	2	0	0	0	0	0	0	0	0	5	5	2	2	False		
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	913	913	308	308	0	0	0	0	568	568	73	73	1481	1481	381	381	False		
+shift-longitudes	shyft_longitudes	Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/	Climate Analysis	shift_longitudes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	54	64	4	4	0	0	0	0	0	0	0	0	54	64	4	4	False		
+shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+short_reads_figure_score	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	145	163	25	30	196	3360	23	711	0	0	0	0	341	3523	48	741	False		
+short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	175	220	51	60	350	6657	85	1602	0	0	0	0	525	6877	136	1662	False		
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46125	47376	2273	2356	40577	40577	3971	3971	19960	21130	1085	1199	106662	109083	7329	7526	False		
+show_beginning	Show beginning1	Select lines from the beginning of a file.								To update		Text Manipulation	show_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	27232	36366	2184	2789	16648	84460	4191	18767	2785	3276	373	452	46665	124102	6748	22008	False		
+show_tail	Show tail1	Select lines from the end of a file.								To update		Text Manipulation	show_tail	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	1620	2660	378	589	10551	24579	682	1851	284	398	67	83	12455	27637	1127	2523	False		
+sicer	peakcalling_sicer	Statistical approach for the Identification of ChIP-Enriched Regions								Up-to-date	https://home.gwu.edu/~wpeng/Software.htm	ChIP-seq	sicer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer	1.1	SICER	1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	276	379	30	42	972	9053	146	1008	644	689	5	7	1892	10121	181	1057	False		
+sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	0	18184	18937	555	608	10514	10514	1063	1063	0	0	0	0	28698	29451	1618	1671	False		
+simtext	abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix	A text mining framework for interactive analysis and visualization of similarities among biomedical entities.								To update	https://github.com/dlal-group/simtext	Text Manipulation	simtext	iuc	https://github.com/galaxyproject/tools-iuc/tools/simtext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext	0.0.2	r-argparse	1.0.1			0	2	4	0	0	2	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	220	220	68	68	0	0	0	0	416	416	10	10	636	636	78	78	False		
+sina	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1369	1369	125	125	2398	2398	420	420	0	0	0	0	3767	3767	545	545	False		
+sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								Up-to-date	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.10.1	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	284	284	70	70	165	165	38	38	14	14	2	2	463	463	110	110	False		
+sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3457	3457	301	301	0	0	0	0	556	556	65	65	4013	4013	366	366	False		
+sixgill	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	312	312	71	71	0	0	0	0	0	0	0	0	312	312	71	71	False		
+sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	0	30	14	31	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	0	82169	116810	2402	2666	18101	18101	2375	2375	17549	17549	321	321	117819	152460	5098	5362	False		
+skyline2isocor	skyline2isocor	Converting skyline output to IsoCor input								Up-to-date	https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor	Metabolomics	skyline2isocor	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor	1.0.0	skyline2isocor	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	346	362	16	16	872	872	67	67	0	0	0	0	1218	1234	83	83	False		
+sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	141	141	26	26	0	0	0	0	0	0	0	0	141	141	26	26	False		
+slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	96	103	4	5	0	0	0	0	4	4	1	1	100	107	5	6	False		
+small_rna_clusters	small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+small_rna_maps	small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+small_rna_signatures	overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	158	158	8	8	0	0	0	0	0	0	0	0	158	158	8	8	False		
+smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smart_domains	smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smina	smina	smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization								To update	https://sourceforge.net/projects/smina/	Computational chemistry	smina	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina	1.0	smina	2017.11.9			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	499	499	16	16	44	44	10	10	0	0	0	0	543	543	26	26	False		
+smithsonian-volcanoes	smithsonian_volcanoes	Retrieve data from Volcanoes of the World (VOTW) Database								To update	https://volcano.si.edu/gvp_votw.cfm	Retrieve Data	smithsonian_volcanoes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	0.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	325	325	61	61	137	137	54	54	843	843	63	63	1305	1305	178	178	False		
+snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	1638	331	358	779	779	244	244	467	467	83	83	2745	2884	658	685	False		
+snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1817	1817	14	14	4	4	2	2	136	136	4	4	1957	1957	20	20	False		
+sniffles	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	Up-to-date	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	2.4	sniffles	2.4	Sequence analysis, Structural variation detection	Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1141	1141	134	134	606	606	156	156	2267	2267	80	80	4014	4014	370	370	False		
+snipit	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	Base position variability plotting	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	905	905	44	44	0	0	0	0	0	0	0	0	905	905	44	44	False		
+snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	0	121363	124773	3448	3602	92504	92504	3945	3945	48068	52034	2705	3073	261935	269311	10098	10620	False		
+snp-dists	snp_dists	Compute pairwise SNP distance matrix from a FASTA sequence alignment								Up-to-date	https://github.com/tseemann/snp-dists	Variant Analysis	snp_dists	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists	0.8.2	snp-dists	0.8.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6555	6555	807	807	5336	5336	171	171	1143	1143	182	182	13034	13034	1160	1160	False		
+snp-sites	snp_sites	Finds SNP sites from a multi-FASTA alignment file								Up-to-date	https://github.com/sanger-pathogens/snp-sites	Variant Analysis	snp_sites	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites	2.5.1	snp-sites	2.5.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6597	6597	663	663	1467	1467	256	256	1279	1279	114	114	9343	9343	1033	1033	False		
+snpeff	snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names	SnpEff is a genetic variant annotation and effect prediction toolbox								To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff		biopython	1.70			5	5	5	0	5	5	5	0	0	0	0	0	0	0	1	0	0	0	5	5	0	0	5	0	0	0	5	0	0	0	0	0	0	5	5	5	0	103826	108296	7181	7908	115727	178110	15871	22769	11817	13155	2148	2321	231370	299561	25200	32998	False		
+snpeff-covid19	snpeff_sars_cov_2	SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox	snpeff	snpeff		snpEff	Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).	SNP detection	DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs	To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff_sars_cov_2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19				SNP detection	DNA polymorphism, Nucleic acid sites, features and motifs	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	764895	764895	1276	1276	94572	94572	1636	1636	26990	26990	561	561	886457	886457	3473	3473	False		
+snpfreq	hgv_snpFreq	snpFreq significant SNPs in case-control data								To update		Variant Analysis, Statistics	snpfreq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	44	10	12	307	649	68	181	227	260	16	23	569	953	94	216	False		
+snpfreqplot	snpfreqplot	A plotting app to visualise the SNPs across a region								To update	https://github.com/BrownfieldPlantLab/SNPFreqPlot	Variant Analysis	snpfreqplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot	1.0	r-base				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	3683	3683	338	338	1401	1401	433	433	1029	1029	95	95	6113	6113	866	866	False		
+snpsift	snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck	snpEff SnpSift tools from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html	Variant Analysis	snpsift	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift		snpsift	5.2			8	8	8	0	8	8	8	0	0	0	0	0	0	0	8	0	0	0	0	8	0	0	8	0	0	0	8	0	0	0	0	0	0	8	8	8	0	5142904	5146618	3602	4283	382391	421190	7013	9678	104030	105024	960	1184	5629325	5672832	11575	15145	False		
+snpsift_dbnsfp	snpSift_dbnsfp	snpEff SnpSift dbnsfp tool from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html#dbNSFP	Variant Analysis	snpsift_dbnsfp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	52	55	23	24	421	421	75	75	0	0	0	0	473	476	98	99	False		
+snpsift_genesets	snpSift_geneSets	Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome								To update	http://snpeff.sourceforge.net/SnpSift.html#geneSets	Variant Analysis	snpsift_genesets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	509	554	107	128	474	474	190	190	0	0	0	0	983	1028	297	318	False		
+snv_matrix	snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+snvtocnv	sequenzaindex, snvtocnv	infer copy number variations from a vcf file with SNVs using R sequenza								To update	http://artbio.fr	Variant Analysis	snvtocnv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv	https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv	3.0.0+galaxy1	sequenza-utils	3.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+socru	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	659	659	42	42	296	296	92	92	0	0	0	0	955	955	134	134	False		
+sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19865	21034	1047	1126	3141	3141	328	328	3304	3304	189	189	26310	27479	1564	1643	False		
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	3	9	3	0	82716	87113	8209	8526	120471	120475	14787	14790	54067	61541	5817	6653	257254	269129	28813	29969	False		
+spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	450	491	91	100	4270	4270	288	288	0	0	0	0	4720	4761	379	388	False		
+spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spatyper	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spec2vec	spec2vec_similarity, spec2vec_training	Mass spectra similarity scoring using a trained Spec2Vec model.	spec2vec	spec2vec		Spec2Vec	Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	Up-to-date	https://github.com/iomega/spec2vec	Metabolomics	spec2vec	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	0.8.0	spec2vec	0.8.0	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+spectrast2spectrast_irt	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spectrast2tsv	gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+split_file_on_column	tp_split_on_column	Split a file on a specific column.								To update		Text Manipulation	split_file_on_column	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	0.6	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5995	6261	408	453	2150	2150	311	311	26	26	2	2	8171	8437	721	766	False		
+split_file_to_collection	split_file_to_collection	Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	Text Manipulation	split_file_to_collection	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	0.5.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	16415	16623	968	984	9133	9133	672	672	4140	4140	148	148	29688	29896	1788	1804	False		
+split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	44	51	2	3	0	0	0	0	0	0	0	0	44	51	2	3	False		
+split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	3	200	384	31	66	200	397	31	69	False		
+splitfasta	rbc_splitfasta	Split a multi-sequence fasta file into files containing single sequences								To update		Text Manipulation	splitfasta	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	0.4.0	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1772	1811	278	294	3012	3012	564	564	0	0	0	0	4784	4823	842	858	False		
+spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	789	840	130	134	0	0	0	0	0	0	0	0	789	840	130	134	False		
+spolpred	spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.1	giatools	0.3.1	Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	4	4	0	0	0	0	0	0	0	0	16	16	4	4	False		
+spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	23	23	0	0	0	0	0	0	0	0	1436	1436	23	23	False		
+spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	142	142	5	5	0	0	0	0	0	0	0	0	142	142	5	5	False		
+sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	80	80	1	1	0	0	0	0	80	80	1	1	False		
+sr_bowtie_dataset_annotation	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	0	3	3	3	0	364871	376580	16710	17342	583675	678448	53271	59638	48131	50455	5910	6181	996677	1105483	75891	83161	False		
+srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	0	4	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	239	239	34	34	44	44	13	13	0	0	0	0	283	283	47	47	False		
+srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41	False		
+srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41	False		
+sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	214	225	17	18	0	0	0	0	0	0	0	0	214	225	17	18	False		
+stacks	stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	Data handling	Mapping, Population genetics	0	13	13	0	0	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	13	0	6440	11998	465	593	0	0	0	0	4070	4070	76	76	10510	16068	541	669	False		
+stacks2	stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65			0	12	12	0	0	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	8437	8592	626	646	0	0	0	0	18016	18016	270	270	26453	26608	896	916	False		
+star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update	https://github.com/STAR-Fusion/STAR-Fusion	Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1312	1383	82	95	2198	3076	234	303	173	173	3	3	3683	4632	319	401	False		
+staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20778	20891	2030	2045	9520	9520	1424	1424	6753	6753	864	864	37051	37164	4318	4333	False		
+statistics	bg_statistical_hypothesis_testing	Tool for computing statistical tests.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	Statistics	bg_statistical_hypothesis_testing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	0.3	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	169	346	46	61	0	0	0	0	0	0	0	0	169	346	46	61	False		
+stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	328	328	38	38	0	0	0	0	0	0	0	0	328	328	38	38	False		
+straindesign	straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion	Toolbox to optimize biological model								To update	https://github.com/brsynth/straindesign	Systems Biology, Synthetic Biology	straindesign	iuc	https://github.com/brsynth/straindesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign	3.2.2	straindesign	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+strelka	strelka_germline, strelka_somatic	Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision.								Up-to-date	https://github.com/Illumina/strelka/	Variant Analysis	strelka	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka	2.9.10	strelka	2.9.10			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	669	669	112	112	1261	1261	417	417	0	0	0	0	1930	1930	529	529	False		
+stress_ng	stress_ng	stress test a computer system in various selectable ways								To update		Web Services	stress_ng	bgruening-util	https://github.com/ColinIanKing/stress-ng	https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng	0.12.04	stress-ng				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	62	3	3	0	0	0	0	0	0	0	0	62	62	3	3	False		
+stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+stringtie	stringtie, stringtie_merge	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	stringtie	stringtie		StringTie	Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.	Transcriptome assembly, RNA-Seq analysis	Transcriptomics, RNA-seq	Up-to-date	http://ccb.jhu.edu/software/stringtie/	Transcriptomics	stringtie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie	2.2.3	stringtie	2.2.3	Transcriptome assembly, RNA-Seq analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	178677	187728	4972	5347	320780	407379	10825	15171	26375	28921	1032	1167	525832	624028	16829	21685	False		
+structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2858	3001	118	123	0	0	0	0	0	0	0	0	2858	3001	118	123	False		
+structureharvester	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date	http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/	Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+substitution_rates	subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	121	3901	34	747	105	114	4	4	226	4015	38	751	False		
+substitutions	substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	93	901	13	84	0	0	0	0	93	901	13	84	False		
+subtract	gops_subtract_1	Subtract the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	566512	567199	410	470	49985	184650	1473	7631	20648	20897	155	188	637145	772746	2038	8289	False		
+subtract_query	subtract_query1	Subtract Whole Dataset from another dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract_query	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query	0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1178	1450	124	141	3169	40539	636	3435	799	950	26	38	5146	42939	786	3614	False		
+suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	249	249	32	32	16	16	10	10	102	102	16	16	367	367	58	58	False		
+suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	117	117	41	41	84	84	24	24	161	161	13	13	362	362	78	78	False		
+suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	217	217	47	47	42	42	20	20	96	96	12	12	355	355	79	79	False		
+suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	721	721	160	160	350	350	91	91	214	214	35	35	1285	1285	286	286	False		
+suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	125	125	30	30	13	13	9	9	83	83	8	8	221	221	47	47	False		
+suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	396	396	134	134	121	121	57	57	144	144	39	39	661	661	230	230	False		
+suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	22	0	21	21	22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	964	964	318	318	249	249	118	118	475	475	108	108	1688	1688	544	544	False		
+suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	8	8	8	8	13	13	11	11	1302	1302	19	19	1323	1323	38	38	False		
+suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	58	58	23	23	24	24	11	11	92	92	11	11	174	174	45	45	False		
+suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	863	863	220	220	237	237	98	98	181	181	41	41	1281	1281	359	359	False		
+suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	0	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	983	983	287	287	375	375	144	144	907	907	106	106	2265	2265	537	537	False		
+suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	46	46	13	13	9	9	5	5	0	0	0	0	55	55	18	18	False		
+suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	0	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	37	37	16	16	22	22	7	7	89	89	14	14	148	148	37	37	False		
+suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	615	615	143	143	246	246	75	75	115	115	27	27	976	976	245	245	False		
+suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	330	330	83	83	64	64	40	40	195	195	49	49	589	589	172	172	False		
+suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	4	4	4	4	5	5	5	5	1	1	1	1	10	10	10	10	False		
+suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	14	14	16	16	6	6	37	37	2	2	82	82	22	22	False		
+suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	0	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	10	10	3	3	14	14	10	10	5	5	5	5	29	29	18	18	False		
+suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	664	664	145	145	113	113	43	43	255	255	50	50	1032	1032	238	238	False		
+suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	84	84	52	52	25	25	16	16	9	9	5	5	118	118	73	73	False		
+suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14941	14941	383	383	25941	25941	255	255	2856	2856	112	112	43738	43738	750	750	False		
+suite_snvphyl		SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	5	5	0	0	0	0	0	0	0	0	26	26	5	5	False		
+swift	swiftlink	Parallel MCMC Linkage Analysis								Up-to-date	https://github.com/ajm/swiftlink	Variant Analysis	swiftlink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift	1.0	swiftlink	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+syndiva	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	30	30	2	2	0	0	0	0	0	0	0	0	30	30	2	2	False		
+t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	411	472	68	90	102	7952	13	1240	0	0	0	0	513	8424	81	1330	False		
+t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	927	959	65	78	130	7194	18	1143	0	0	0	0	1057	8153	83	1221	False		
+t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3783	9125	211	229	1	1	1	1	0	0	0	0	3784	9126	212	230	False		
+t_test_two_samples	t_test_two_samples	T Test for Two Samples								To update		Statistics	t_test_two_samples	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples	https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	141	215	20	31	520	1166	79	274	1025	1118	11	12	1686	2499	110	317	False		
+table_annovar	table_annovar	Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered								To update		Variant Analysis	table_annovar	devteam	Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar	https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar	0.2	annovar				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16526	64515	2803	7456	0	0	0	0	16526	64515	2803	7456	False		
+table_compute	table_compute	Perform general-purpose table operations								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	Text Manipulation	table_compute	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute	1.2.4	pandas				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	216072	216115	1811	1814	12326	12326	1558	1558	16136	16136	256	256	244534	244577	3625	3628	False		
+tables_arithmetic_operations	tables_arithmetic_operations	Arithmetic Operations on tables								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	tables_arithmetic_operations	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations	1.0.0	perl				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2188	2220	33	38	0	0	0	0	0	0	0	0	2188	2220	33	38	False		
+tabular_to_fasta	tab2fasta	Tabular-to-FASTA								To update		Convert Formats	tabular_to_fasta	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta	1.1.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	329032	333057	1489	1702	79033	215770	2441	8587	27876	33727	296	360	435941	582554	4226	10649	False		
+tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7011	8135	449	482	9473	28494	626	2183	850	1090	80	104	17334	37719	1155	2769	False		
+tag_pileup_frequency	tag_pileup_frequency	Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup	Statistics, SAM, Genomic Interval Operations	tag_pileup_frequency	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency	1.0.2	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	158	164	15	16	722	865	40	73	0	0	0	0	880	1029	55	89	False		
+tapscan	tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	19	6	6	0	0	0	0	0	0	0	0	19	19	6	6	False		
+tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	827	838	89	92	114	114	41	41	900	900	29	29	1841	1852	159	162	False		
+tasmanian_mismatch	tasmanian_mismatch	Analysis of positional mismatches								Up-to-date	https://github.com/nebiolabs/tasmanian-mismatch	Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	4	61	61	7	7	0	0	0	0	65	65	11	11	False		
+taxonkit	name2taxid, profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	taxonkit	taxonkit		TaxonKit	TaxonKit is a practical and efficient NCBI taxonomy toolkit.	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	Up-to-date	https://bioinf.shenwei.me/taxonkit/	Metagenomics	taxonkit	iuc	https://github.com/shenwei356/taxonkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit	0.17.0	taxonkit	0.17.0	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	36069	36922	5257	5431	25255	30822	5066	5826	7949	7949	1584	1584	69273	75693	11907	12841	False		
+taxpasta	taxpasta	standardise taxonomic profiles	taxpasta	taxpasta		taxpasta	TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	Up-to-date	https://taxpasta.readthedocs.io/en/latest/	Sequence Analysis	taxpasta	iuc	https://github.com/taxprofiler/taxpasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta	0.7.0	taxpasta	0.7.0	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	34	34	5	5	0	0	0	0	0	0	0	0	34	34	5	5	False		
+tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6372	6395	372	379	7339	7339	378	378	6966	6966	154	154	20677	20700	904	911	False		
+tb_variant_filter	tb_variant_filter	M. tuberculosis H37Rv VCF filter								Up-to-date	https://github.com/COMBAT-TB/tb_variant_filter	Variant Analysis	tb_variant_filter	iuc	https://github.com/COMBAT-TB/tb_variant_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter	0.4.0	tb_variant_filter	0.4.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22977	22977	461	461	3888	3888	274	274	3611	3611	80	80	30476	30476	815	815	False		
+tbl2gff3	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1941	1941	466	466	0	0	0	0	463	463	112	112	2404	2404	578	578	False		
+tbvcfreport	tbvcfreport	Generate HTML report from SnpEff M.tuberculosis VCF(s)								Up-to-date	https://github.com/COMBAT-TB/tbvcfreport	Variant Analysis	tbvcfreport	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport	1.0.1	tbvcfreport	1.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2955	2955	335	335	6090	6090	348	348	2347	2347	72	72	11392	11392	755	755	False		
+te_finder	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.21	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	20	20	0	0	0	0	0	0	0	0	203	203	20	20	False		
+telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+tetoolkit	tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1013	1013	74	74	0	0	0	0	70	70	4	4	1083	1083	78	78	False		
+tetyper	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	106	106	16	16	155	155	47	47	0	0	0	0	261	261	63	63	False		
+text_processing	tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq	High performance text processing tools using the GNU coreutils, sed, awk and friends.								To update	https://www.gnu.org/software/	Text Manipulation	text_processing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	9.3	coreutils	8.25			20	20	20	0	20	20	20	0	0	0	0	0	0	0	0	0	0	19	1	19	0	0	19	0	0	0	20	0	0	0	0	0	0	19	19	19	0	3898014	4015573	37698	42095	648268	915282	47636	69828	103365	105214	7778	7953	4649647	5036069	93112	119876	False		
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	51	51	0	0	0	0	0	0	0	0	547	547	51	51	False		
+tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	8	8	0	0	0	0	0	0	0	0	15	15	8	8	False		
+tn93	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								Up-to-date	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.14	tn93	1.0.14			4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1915	1915	42	42	1972	1972	225	225	0	0	0	0	3887	3887	267	267	False		
+tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	445	445	25	25	71	71	32	32	0	0	0	0	516	516	57	57	False		
+tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9.1	tooldistillator	0.9.1	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	9	9	6	6	5	5	0	0	0	0	71	71	14	14	False		
+tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	158	66524	28	7228	0	0	0	0	158	66525	28	7229	False		
+tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	15496	26623	1076	1664	83063	343017	8372	27829	5388	14057	508	1012	103947	383697	9956	30505	False		
+tophat_fusion_post	tophat_fusion_post	Wrapper for Tophat-Fusion post step								To update		Transcriptomics	tophat_fusion_post	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post	0.1	blast+				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	220	242	41	46	6	814	2	191	100	120	8	12	326	1176	51	249	False		
+topologyeditors	gromacs_modify_topology, gromacs_extract_topology	Set of python scripts and associated tool files that can be used to modify topology files.								To update	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	Molecular Dynamics, Computational chemistry	topologyeditors	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	0	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	57	57	10	10	20	20	8	8	0	0	0	0	77	77	18	18	False		
+tracegroomer	tracegroomer	TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.								Up-to-date	https://github.com/cbib/TraceGroomer	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer	0.1.4	tracegroomer	0.1.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	1	1	0	0	0	0	0	0	0	0	7	7	1	1	False		
+tracy	tracy_align, tracy_assemble, tracy_basecall, tracy_decompose									To update				iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy	0.6.1	tracy	0.7.8			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	3314	3314	124	124	0	0	0	0	0	0	0	0	3314	3314	124	124	False		
+transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5964	6418	944	970	5450	5450	1066	1066	2610	2796	317	344	14024	14664	2327	2380	False		
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	1039	1039	189	189	2672	3349	467	485	358	358	47	47	4069	4746	703	721	False		
+translate_bed	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	649	685	138	142	473	473	105	105	761	761	18	18	1883	1919	261	265	False		
+translate_bed_sequences	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	69	16	21	0	0	0	0	0	0	0	0	57	69	16	21	False		
+transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	250	254	31	31	174	174	45	45	0	0	0	0	424	428	76	76	False		
+tree_relabeler	tree_relabel	Relabels the tips of a newick formatted tree.								To update		Text Manipulation	tree_relabeler	nml	https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler	https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	229489	275008	5733	6500	228708	324716	11708	16638	22644	23869	1439	1527	480841	623593	18880	24665	False		
+trimmer	trimmer	Trim leading or trailing characters.								To update		Text Manipulation	trimmer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer	0.0.1					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	5304	7438	447	512	15698	108672	658	2946	266	822	53	81	21268	116932	1158	3539	False		
+trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	1	1	1	0	352353	383014	14547	15408	632385	839058	39323	49850	125340	139097	5268	5975	1110078	1361169	59138	71233	False		
+trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	To update	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.2	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	0	9	13	13	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	0	11	13	12	0	35698	39132	4376	4632	44509	44509	6714	6714	21883	23889	1924	2070	102090	107530	13014	13416	False		
+trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1968	2080	374	390	1825	1825	527	527	862	1060	161	195	4655	4965	1062	1112	False		
+tripal	analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync	Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal								To update	https://github.com/galaxy-genome-annotation/python-tripal	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal		python-tripal	3.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	4361	4601	741	807	0	0	0	0	2469	2469	190	190	6830	7070	931	997	False		
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	14681	14681	265	265	0	0	0	0	4488	4488	147	147	19169	19169	412	412	False		
+tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	7	7	0	0	0	0	0	0	0	0	17	17	7	7	False		
+tsne	tsne	T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation								To update	https://cran.r-project.org/web/packages/Rtsne/	Text Manipulation	tsne	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne	0.0.2	r-rtsne	0.13			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	379	31	37	281	281	64	64	0	0	0	0	536	660	95	101	False		
+twobittofa	ucsc-twobittofa	twoBitToFa is a tool to convert all or part of .2bit file to FASTA	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenpath/help/twoBit.html	Convert Formats	ucsc_twobittofa	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	469	ucsc-twobittofa	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	413	511	84	118	441	441	123	123	21	21	2	2	875	973	209	243	False		
+tximport	tximport	Wrapper for the Bioconductor package tximport	tximport	tximport		tximport	An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	Up-to-date	http://bioconductor.org/packages/tximport/	Transcriptomics	tximport	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport	1.30.0	bioconductor-tximport	1.30.0	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1802	1802	225	225	6963	6963	904	904	0	0	0	0	8765	8765	1129	1129	False		
+ucsc-cell-browser	ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets								To update	https://cells.ucsc.edu/	Transcriptomics	ucsc_cell_browser	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser	1.0.0+galaxy1	ucsc-cell-browser	1.2.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	965	975	178	181	0	0	0	0	0	0	0	0	965	975	178	181	False		
+ucsc_axtchain	ucsc_axtchain	Chain together genome alignments	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_axtchain	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain	469	ucsc-axtchain	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_axttomaf	ucsc_axtomaf	Convert dataset from axt to MAF format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_axttomaf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf	469	ucsc-axttomaf	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_blat	ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	Up-to-date	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	469	ucsc-blat	469	Sequence alignment	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainnet	ucsc_chainnet	Make alignment nets out of chains	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainnet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	469	ucsc-chainnet	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainprenet	ucsc_chainprenet	Remove chains that don't have a chance of being netted	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainprenet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet	469	ucsc-chainprenet	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainsort	ucsc_chainsort	Sort chains. By default sorts by score.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainsort	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort	469	ucsc-chainsort	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	373	463	134	151	2249	18611	638	4080	0	0	0	0	2622	19074	772	4231	False		
+ucsc_netfilter	ucsc_netfilter	Filter out parts of net	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netfilter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter	469	ucsc-netfilter	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_netsyntenic	ucsc_netsyntenic	Add synteny info to a net dataset	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netsyntenic	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic	469	ucsc-netsyntenic	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_nettoaxt	ucsc_nettoaxt	Convert net (and chain) to axt format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_nettoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt	469	ucsc-nettoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	0	3	5	5	0	55050	68123	1090	1223	9001	9001	906	906	12444	12444	187	187	76495	89568	2183	2316	False		
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	74120	77648	3798	3963	64946	90075	5451	7380	19516	20422	2010	2080	158582	188145	11259	13423	False		
+unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4900	5146	257	270	251	251	81	81	1069	1069	29	29	6220	6466	367	380	False		
+uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.6	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2117	2725	341	412	3111	5779	594	1011	806	806	50	50	6034	9310	985	1473	False		
+uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1488	1596	230	266	0	0	0	0	743	743	35	35	2231	2339	265	301	False		
+unzip	unzip	Unzip file								To update	https://github.com/bmcv	Convert Formats	unzip	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip	6.0	unzip				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6942	7024	1345	1356	1	1	1	1	2461	2461	266	266	9404	9486	1612	1623	False		
+upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1060	1060	5	5	0	0	0	0	0	0	0	0	1060	1060	5	5	False		
+valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	518	677	75	87	234	234	65	65	0	0	0	0	752	911	140	152	False		
+validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	112	38	38	0	0	0	0	0	0	0	0	112	112	38	38	False		
+vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5936	5936	147	147	523	523	15	15	0	0	0	0	6459	6459	162	162	False		
+vardict	vardict_java	VarDict - calls SNVs and indels for tumour-normal pairs								To update	https://github.com/AstraZeneca-NGS/VarDictJava	Variant Analysis	vardict_java	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict	1.8.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	381	381	37	37	0	0	0	0	0	0	0	0	381	381	37	37	False		
+variant_analyzer	mut2read, mut2sscs, read2mut	Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data								To update		Variant Analysis	variant_analyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer	2.0.0	matplotlib				3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	95	95	14	14	516	516	67	67	0	0	0	0	611	611	81	81	False		
+varscan	varscan_copynumber, varscan_mpileup, varscan_somatic	VarScan is a variant caller for high-throughput sequencing data								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/varscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan	2.4.3	varscan	2.4.6			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	10711	11502	1442	1560	16705	16705	3135	3135	1036	1036	100	100	28452	29243	4677	4795	False		
+varscan_vaf	varscan_vaf	Compute variant allele frequency in vcf files generated by varscan.								To update	http://artbio.fr	Variant Analysis	varscan_vaf	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf	https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+varscan_version_2	varscan	VarScan wrapper								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan_version_2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2	2.4.2	varscan	2.4.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5058	6139	606	699	17232	53268	2965	5686	2298	2656	424	482	24588	62063	3995	6867	False		
+varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	273	273	12	12	0	0	0	0	0	0	0	0	273	273	12	12	False		
+vcf2maf	vcf2maf	vcf2maf: Convert VCF into MAF								To update	https://github.com/mskcc/vcf2maf	Convert Formats	vcf2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf	1.6.21	vcf2maf	1.6.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1097	1097	46	46	0	0	0	0	65	65	5	5	1162	1162	51	51	False		
+vcf2pgsnp	vcf2pgSnp	VCF to pgSnp								To update		Variant Analysis	vcf2pgsnp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	191	221	57	65	1399	2700	209	584	0	0	0	0	1590	2921	266	649	False		
+vcf2snvalignment	vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vcf2tsv	vcf2tsv	Converts VCF files into tab-delimited format								To update	https://github.com/ekg/vcflib	Variant Analysis, Convert Formats	vcf2tsv	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	169090	169679	823	874	16304	42215	1141	2594	2485	2511	169	172	187879	214405	2133	3640	False		
+vcf_annotate	vcf_annotate	Annotate a VCF file (dbSNP, hapmap)								To update		Variant Analysis	vcf_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	1	0	1	263	340	31	54	263	342	31	56	False		
+vcf_extract	vcf_extract	Extract reads from a specified region								To update		Variant Analysis	vcf_extract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	513	569	6	9	513	569	6	9	False		
+vcf_filter	vcf_filter	Filter a VCF file								To update		Variant Analysis	vcf_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	400	455	129	140	0	0	0	0	238	606	19	56	638	1061	148	196	False		
+vcf_intersect	vcf_intersect	Generate the intersection of two VCF files								To update		Variant Analysis	vcf_intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	3	0	0	0	0	335	463	19	28	335	482	19	31	False		
+vcfaddinfo	vcfaddinfo	Adds info fields from the second dataset which are not present in the first dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfaddinfo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	882	888	30	32	6118	8261	36	114	175	184	6	6	7175	9333	72	152	False		
+vcfallelicprimitives	vcfallelicprimitives	Splits alleleic primitives (gaps or mismatches) into multiple VCF lines								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfallelicprimitives	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6879	17157	897	1219	7585	14509	1245	1925	1648	1681	225	229	16112	33347	2367	3373	False		
+vcfanno	vcfanno	Annotate VCF files	vcfanno	vcfanno		vcfanno	Fast, flexible annotation of genetic variants.	SNP annotation	Genetic variation, Data submission, annotation and curation	Up-to-date	https://github.com/brentp/vcfanno	Variant Analysis	vcfanno	iuc	https://github.com/galaxyproject/tools-iuc/vcfanno/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno	0.3.5	vcfanno	0.3.5	SNP annotation	Genetic variation, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1139	1139	174	174	0	0	0	0	0	0	0	0	1139	1139	174	174	False		
+vcfannotate	vcfannotate	Intersect VCF records with BED annotations								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotate	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2797	2850	157	181	3668	14532	652	1392	494	507	61	63	6959	17889	870	1636	False		
+vcfannotategenotypes	vcfannotategenotypes	Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotategenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	203	62	66	497	1828	155	387	184	197	11	11	870	2228	228	464	False		
+vcfbedintersect	vcfbedintersect	Intersect VCF and BED datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbedintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3017	4049	185	210	4709	20250	406	1147	507	527	40	42	8233	24826	631	1399	False		
+vcfbreakcreatemulti	vcfbreakcreatemulti	Break multiple alleles into multiple records, or combine overallpoing alleles into a single record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbreakcreatemulti	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	416	478	35	40	3969	10457	82	309	362	378	8	8	4747	11313	125	357	False		
+vcfcheck	vcfcheck	Verify that the reference allele matches the reference genome								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcheck	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	745	767	96	106	803	1895	222	627	241	256	16	17	1789	2918	334	750	False		
+vcfcombine	vcfcombine	Combine multiple VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcombine	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1422	2020	284	505	4951	19530	1021	2669	493	516	60	62	6866	22066	1365	3236	False		
+vcfcommonsamples	vcfcommonsamples	Output records belonging to samples commong between two datasets.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcommonsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	233	253	37	42	234	1839	79	287	199	214	11	12	666	2306	127	341	False		
+vcfdistance	vcfdistance	Calculate distance to the nearest variant.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfdistance	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	572	585	90	92	2063	2427	139	296	272	290	19	22	2907	3302	248	410	False		
+vcffilter	vcffilter2	Tool for filtering VCF files								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffilter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37489	47142	2113	2218	75128	162296	5730	10533	2626	2736	320	331	115243	212174	8163	13082	False		
+vcffixup	vcffixup	Count the allele frequencies across alleles present in each record in the VCF file.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffixup	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	926	957	155	173	2291	5323	313	985	251	265	28	31	3468	6545	496	1189	False		
+vcfflatten	vcfflatten2	Removes multi-allelic sites by picking the most common alternate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfflatten	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	172	183	21	25	351	879	67	201	312	342	15	16	835	1404	103	242	False		
+vcfgeno2haplo	vcfgeno2haplo	Convert genotype-based phased alleles into haplotype alleles								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgeno2haplo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	778	794	107	112	2414	3721	179	508	209	225	20	21	3401	4740	306	641	False		
+vcfgenotypes	vcfgenotypes	Convert numerical representation of genotypes to allelic.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	502	555	134	143	3428	6338	266	858	220	235	23	24	4150	7128	423	1025	False		
+vcfhethom	vcfhethom	Count the number of heterozygotes and alleles, compute het/hom ratio.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfhethom	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1964	1991	182	186	1937	3846	188	644	567	601	26	27	4468	6438	396	857	False		
+vcfleftalign	vcfleftalign	Left-align indels and complex variants in VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfleftalign	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	269	310	38	42	358	1071	89	287	179	213	12	14	806	1594	139	343	False		
+vcfprimers	vcfprimers	Extract flanking sequences for each VCF record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfprimers	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	590	711	28	33	403	831	75	200	190	214	10	12	1183	1756	113	245	False		
+vcfrandomsample	vcfrandomsample	Randomly sample sites from VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfrandomsample	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	161	168	13	15	153	350	27	75	184	192	6	6	498	710	46	96	False		
+vcfselectsamples	vcfselectsamples	Select samples from a VCF file								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfselectsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	830	900	69	88	1315	6257	237	959	344	363	20	21	2489	7520	326	1068	False		
+vcfsort	vcfsort	Sort VCF dataset by coordinate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfsort	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1868	1904	174	185	18378	24175	422	1279	537	674	70	73	20783	26753	666	1537	False		
+vcftools_annotate	vcftools_annotate	Annotate VCF using custom/user-defined annotations								To update	https://vcftools.github.io/	Variant Analysis	vcftools_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate	0.1	echo				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	155	192	81	90	1853	3943	581	1280	144	156	13	16	2152	4291	675	1386	False		
+vcftools_compare	vcftools_compare	Compare VCF files to get overlap and uniqueness statistics								To update	https://vcftools.github.io/	Variant Analysis	vcftools_compare	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	440	594	127	142	0	0	0	0	0	16	0	12	440	610	127	154	False		
+vcftools_consensus	vcftools_consensus	Apply VCF variants to a fasta file to create consensus sequence								To update	https://vcftools.github.io/	Variant Analysis	vcftools_consensus	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus	0.1.11	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vcftools_isec	vcftools_isec	Intersect multiple VCF datasets								To update	https://vcftools.github.io/	Variant Analysis	vcftools_isec	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec	0.1.1	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	379	537	104	118	0	1	0	1	39	496	28	48	418	1034	132	167	False		
+vcftools_merge	vcftools_merge	Merge multiple VCF datasets into a single dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge	0.1.11	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	817	1084	244	273	0	0	0	0	93	448	44	60	910	1532	288	333	False		
+vcftools_slice	vcftools_slice	Subset VCF dataset by genomic regions								To update	https://vcftools.github.io/	Variant Analysis	vcftools_slice	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice	0.1	echo				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	410	423	56	60	6261	8115	133	362	127	157	10	19	6798	8695	199	441	False		
+vcftools_subset	vcftools_subset	Select samples from a VCF dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_subset	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	134	142	46	49	0	0	0	0	120	142	12	19	254	284	58	68	False		
+vcfvcfintersect	vcfvcfintersect	Intersect two VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfvcfintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	976544	977015	703	748	64155	81830	981	2103	11044	11069	225	229	1051743	1069914	1909	3080	False		
+vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	2157	2287	198	209	3930	5591	446	744	0	0	0	0	6087	7878	644	953	False		
+velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	4	4	22	22	6	6	16	16	1	1	45	45	11	11	False		
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	25171	27943	3899	4270	51187	51187	7557	7557	28546	28619	3585	3613	104904	107749	15041	15440	False		
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4715	5343	888	965	9575	9576	2117	2117	3271	5524	1050	1397	17561	20443	4055	4479	False		
+venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4519	5476	667	730	9858	18420	986	2010	0	0	0	0	14377	23896	1653	2740	False		
+verify_map	verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	48	25	25	0	0	0	0	0	0	0	0	48	48	25	25	False		
+vg	vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.59.0			0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	478	478	17	17	0	0	0	0	0	0	0	0	478	478	17	17	False		
+vibrant	vibrant	Virus Identification By iteRative ANnoTation	VIBRANT	VIBRANT		VIBRANT	Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	Up-to-date	https://github.com/AnantharamanLab/VIBRANT	Metagenomics	vibrant	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant	1.2.1	vibrant	1.2.1	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vienna_rna	viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	0	3197	8107	344	415	0	0	0	0	0	0	0	0	3197	8107	344	415	False		
+vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	14412	14590	722	732	0	0	0	0	0	0	0	0	14412	14590	722	732	False		
+virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	94	94	16	16	0	0	0	0	0	0	0	0	94	94	16	16	False		
+virheat	virheat	generates a heatmap of allele frequencies from vcf files	virheat	virheat		virHEAT	VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.			Up-to-date	https://github.com/jonas-fuchs/virHEAT	Visualization, Variant Analysis	virheat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat	0.7.1	virheat	0.7.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	2	2	0	0	0	0	0	0	0	0	12	12	2	2	False		
+virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	574	574	76	76	0	0	0	0	0	0	0	0	574	574	76	76	False		
+virsorter	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	virsorter	virsorter		virsorter	Identify DNA and RNA virus sequences.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/jiarong/VirSorter2/	Metagenomics	virsorter	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter	2.2.4	virsorter	2.2.4	Taxonomic classification	Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+visceral_evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	1	1	0	0	0	0	0	0	0	0	20	25	1	1	False		
+vmd		vmd is a package for  visualizing and analyzing trajectories from molecular dynamics (MD) simulations								To update	https://www.ks.uiuc.edu/Research/vmd/	Computational chemistry	vmd	chemteam	https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	34917	36852	3670	3786	54931	54931	5597	5597	7183	7183	905	905	97031	98966	10172	10288	False		
+voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	43	43	3	3	0	0	0	0	0	0	0	0	43	43	3	3	False		
+vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.29.0	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	0	8	8	8	0	9694	10338	559	628	12282	53546	1031	2007	5334	5672	246	277	27310	69556	1836	2912	False		
+vsnp	vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+w4mclassfilter	w4mclassfilter	Filter W4M data by values or metadata								To update	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper	Metabolomics	w4mclassfilter	eschen42	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter	0.98.19	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2370	2836	9	10	0	0	0	0	1482	1509	4	4	3852	4345	13	14	False		
+w4mconcatenate	W4Mconcatenate	[W4M][Utils] concatenate two Metadata tables								To update	http://workflow4metabolomics.org	Metabolomics	w4mconcatenate	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate	1.0.0+galaxy0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+w4mcorcov	w4mcorcov	OPLS-DA Contrasts of Univariate Results								To update	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper	Metabolomics	w4mcorcov	eschen42	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov	0.98.18	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	238	375	10	10	0	0	0	0	10	10	2	2	248	385	12	12	False		
+w4mjoinpn	w4mjoinpn	Join positive- and negative-mode W4M datasets								To update	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper	Metabolomics	w4mjoinpn	eschen42	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn	0.98.2	coreutils	8.25			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	150	171	7	7	0	0	0	0	7	7	2	2	157	178	9	9	False		
+wade	wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+waveica	waveica	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.	waveica	waveica		WaveICA	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.	Standardisation and normalisation	Metabolomics	Up-to-date	https://github.com/RECETOX/WaveICA	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	0.2.0	r-recetox-waveica	0.2.0	Standardisation and normalisation	Metabolomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	39	6	6	4	4	3	3	0	0	0	0	43	43	9	9	False		
+weather_app	simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+weblogo3	rgweblogo3	Sequence Logo generator for fasta	weblogo	weblogo		WebLogo	Web-based application designed to make generate sequence logos.	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	To update		Graphics	weblogo3	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3	3.5.0	weblogo	3.7.9	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2720	2818	206	228	10299	30578	1354	3657	1226	1285	50	59	14245	34681	1610	3944	False		
+weightedaverage	wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	227	2307	17	75	0	0	0	0	227	2307	17	75	False		
+whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	96	96	13	13	0	0	0	0	0	0	0	0	96	96	13	13	False		
+wigtobigwig	ucsc_wigtobigwig	converts bedGraph (wig) files into binary bigwig	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenPath/help/bigWig.html	Convert Formats	ucsc_wigtobigwig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig	469	ucsc-wigtobigwig	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1601	1601	106	106	1108	1108	172	172	200	200	15	15	2909	2909	293	293	False		
+windowmasker	windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.16.0			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	537	537	19	19	12	12	7	7	297	297	2	2	846	846	28	28	False		
+windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	2	171	3961	34	328	0	0	0	0	171	3972	34	330	False		
+winnowmap	winnowmap	A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.								Up-to-date	https://github.com/marbl/Winnowmap	Next Gen Mappers	winnowmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap	2.03	winnowmap	2.03			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	279	279	46	46	12	12	4	4	0	0	0	0	291	291	50	50	False		
+woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	1	1	0	0	0	0	0	0	0	0	31	31	1	1	False		
+wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	38	2	3	0	0	0	0	0	0	0	0	32	38	2	3	False		
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1619	1715	337	376	0	0	0	0	0	0	0	0	1619	1715	337	376	False		
+xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	0	5	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	5995	5995	275	275	66	66	23	23	295	295	3	3	6356	6356	301	301	False		
+xcms	abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw		XCMS	XCMS		xcms	Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data.  The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling.	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Biological imaging, Data visualisation, Metabolomics	Up-to-date	https://github.com/sneumann/xcms	Metabolomics	xcms	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms	4.0.0	bioconductor-xcms	4.0.0	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Data visualisation, Metabolomics	9	11	12	0	9	11	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	10	9	0	31909	35790	1357	1384	7099	7099	413	413	5333	5357	330	330	44341	48246	2100	2127	False		
+xmlstarlet	xmlstarlet	Tool to convert a xml file from one metadata standard to another								To update		Convert Formats	xmlstarlet	ecology	https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet	https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet	1.6.1	xmlstarlet				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	59	59	17	17	0	0	0	0	0	0	0	0	59	59	17	17	False		
+xpath	xpath	XPath XML querying tool								To update	http://search.cpan.org/dist/XML-XPath/	Text Manipulation	xpath	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath	https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath		perl-xml-xpath	1.47			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	128	235	7	8	0	1	0	1	0	0	0	0	128	236	7	9	False		
+xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+xtb	xtb_molecular_optimization	Performs semiempirical molecular optimization.								To update	https://github.com/grimme-lab/xtb	Metabolomics	xtb_molecular_optimization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	6.6.1	xtb				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	143	143	4	4	0	0	0	0	0	0	0	0	143	143	4	4	False		
+xy_plot	XY_Plot_1	Plotting tool for multiple series and graph types								To update		Graphics, Statistics	xy_plot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot	1.0.2	r-base				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4490	6169	768	889	6120	15516	1921	3653	2033	2212	556	590	12643	23897	3245	5132	False		
+yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	618	618	176	176	336	336	62	62	588	588	25	25	1542	1542	263	263	False		
+zeiss_lmd_converter	ZeissLMDconverter	Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	2.0.4	shapely				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	1	1	0	0	0	0	0	0	0	0	4	4	1	1	False		
+zerone	zerone	ChIP-seq discretization and quality control								Up-to-date	https://github.com/nanakiksc/zerone	ChIP-seq	zerone	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone	https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone	1.0	zerone	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	83	96	9	12	0	0	0	0	0	0	0	0	83	96	9	12	False		
+zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	4	4	0	0	0	0	0	0	0	0	26	26	4	4	False		
diff --git a/communities/genome/resources/tools_wordcloud.png b/communities/genome/resources/tools_wordcloud.png
new file mode 100644
index 00000000..764a31ab
Binary files /dev/null and b/communities/genome/resources/tools_wordcloud.png differ
diff --git a/communities/imaging/resources/tools.html b/communities/imaging/resources/tools.html
index 22558511..49d54f8a 100644
--- a/communities/imaging/resources/tools.html
+++ b/communities/imaging/resources/tools.html
@@ -95,7 +95,6 @@
       <th>Tools available on CoralSNP</th>
       <th>Tools available on CropGalaxy</th>
       <th>Tools available on Dintor</th>
-      <th>Tools available on FreeBioinfo</th>
       <th>Tools available on GASLINI</th>
       <th>Tools available on Galaxy@AuBi</th>
       <th>Tools available on Galaxy@Pasteur</th>
@@ -112,12 +111,27 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
+      <th>Tools available on PhagePromotor</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
       <th>Tools available on Viral Variant Visualizer (VVV)</th>
-      <th>No. of tool users (2022-2023) (usegalaxy.eu)</th>
-      <th>Total tool usage (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.eu)</th>
+      <th>No. of tool users (all time) (usegalaxy.eu)</th>
+      <th>Tool usage (5 years) (usegalaxy.eu)</th>
+      <th>Tool usage (all time) (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org)</th>
+      <th>No. of tool users (all time) (usegalaxy.org)</th>
+      <th>Tool usage (5 years) (usegalaxy.org)</th>
+      <th>Tool usage (all time) (usegalaxy.org)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org.au)</th>
+      <th>No. of tool users (all time) (usegalaxy.org.au)</th>
+      <th>Tool usage (5 years) (usegalaxy.org.au)</th>
+      <th>Tool usage (all time) (usegalaxy.org.au)</th>
+      <th>No. of tool users (5 years) - all main servers</th>
+      <th>No. of tool users (all time) - all main servers</th>
+      <th>Tool usage (5 years) - all main servers</th>
+      <th>Tool usage (all time) - all main servers</th>
       <th>Deprecated</th>
     </tr>
   </thead>
@@ -149,11 +163,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
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       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -183,8 +197,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>39</td>
-      <td>6541</td>
+      <td>1434</td>
+      <td>6746</td>
+      <td>120</td>
+      <td>122</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>305</td>
+      <td>305</td>
+      <td>11</td>
+      <td>11</td>
+      <td>1739</td>
+      <td>7051</td>
+      <td>131</td>
+      <td>133</td>
       <td></td>
     </tr>
     <tr>
@@ -248,8 +276,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>19</td>
-      <td>13760</td>
+      <td>1156</td>
+      <td>13842</td>
+      <td>40</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1277</td>
+      <td>13963</td>
+      <td>44</td>
+      <td>46</td>
       <td></td>
     </tr>
     <tr>
@@ -313,8 +355,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>18</td>
-      <td>6834</td>
+      <td>591</td>
+      <td>6863</td>
+      <td>38</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>119</td>
+      <td>3</td>
+      <td>3</td>
+      <td>710</td>
+      <td>6982</td>
+      <td>41</td>
+      <td>43</td>
       <td></td>
     </tr>
     <tr>
@@ -344,11 +400,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
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       <td>1</td>
       <td>1</td>
-      <td>1</td>
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       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -378,8 +434,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>39</td>
-      <td>656</td>
+      <td>762</td>
+      <td>782</td>
+      <td>100</td>
+      <td>101</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>230</td>
+      <td>230</td>
+      <td>14</td>
+      <td>14</td>
+      <td>992</td>
+      <td>1012</td>
+      <td>114</td>
+      <td>115</td>
       <td></td>
     </tr>
     <tr>
@@ -409,9 +479,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -439,77 +508,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>35</td>
-      <td>6156</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>3d_tensor_feature_dimension_reduction</td>
-      <td>ip_3d_tensor_feature_dimension_reduction</td>
-      <td>Dimensionality reduction for features (channels) of 3D tensor data using UMAP</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>To update</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis</td>
-      <td>Imaging</td>
-      <td>3d_tensor_feature_dimension_reduction</td>
-      <td>imgteam</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction</td>
-      <td>0.0.1</td>
-      <td>numpy</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
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-      <td>0</td>
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-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>948</td>
+      <td>6261</td>
+      <td>98</td>
+      <td>100</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>153</td>
+      <td>153</td>
+      <td>13</td>
+      <td>13</td>
+      <td>1101</td>
+      <td>6414</td>
+      <td>111</td>
+      <td>113</td>
       <td></td>
     </tr>
     <tr>
@@ -573,8 +592,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>36</td>
+      <td>41</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
       <td>0</td>
-      <td>40</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>36</td>
+      <td>41</td>
+      <td>2</td>
+      <td>2</td>
       <td></td>
     </tr>
     <tr>
@@ -638,8 +671,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>5</td>
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+      <td>0</td>
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       <td>0</td>
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+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -669,9 +716,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -699,12 +745,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>38</td>
-      <td>1523</td>
+      <td>1635</td>
+      <td>1671</td>
+      <td>123</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>334</td>
+      <td>334</td>
+      <td>21</td>
+      <td>21</td>
+      <td>1969</td>
+      <td>2005</td>
+      <td>144</td>
+      <td>145</td>
       <td></td>
     </tr>
     <tr>
@@ -768,7 +829,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
       <td>2</td>
       <td></td>
     </tr>
@@ -833,8 +908,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>34</td>
-      <td>1273</td>
+      <td>401</td>
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+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>188</td>
+      <td>188</td>
+      <td>9</td>
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+      <td>589</td>
+      <td>1573</td>
+      <td>96</td>
+      <td>97</td>
       <td></td>
     </tr>
     <tr>
@@ -898,8 +987,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>24</td>
+      <td>29</td>
+      <td>1</td>
+      <td>1</td>
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       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
       <td>29</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -929,10 +1032,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
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@@ -964,7 +1066,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
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+      <td>61</td>
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       <td></td>
     </tr>
     <tr>
@@ -1028,8 +1145,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>2</td>
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       <td>0</td>
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       <td></td>
     </tr>
     <tr>
@@ -1093,8 +1224,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
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       <td>0</td>
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       <td></td>
     </tr>
     <tr>
@@ -1124,11 +1269,11 @@
       <td>0</td>
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-      <td>19</td>
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       <td>0</td>
@@ -1158,8 +1303,22 @@
       <td>23</td>
       <td>19</td>
       <td>0</td>
-      <td>178</td>
-      <td>4614</td>
+      <td>4773</td>
+      <td>4773</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5688</td>
+      <td>5688</td>
+      <td>94</td>
+      <td>94</td>
+      <td>10461</td>
+      <td>10461</td>
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       <td></td>
     </tr>
     <tr>
@@ -1189,10 +1348,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1220,16 +1378,31 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
-      <td>43</td>
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+      <td>55</td>
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+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>55</td>
+      <td>11</td>
+      <td>11</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>color-deconvolution</td>
+      <td>color_deconvolution</td>
       <td>ip_color_deconvolution</td>
       <td>Color-deconvolution methods</td>
       <td>galaxy_image_analysis</td>
@@ -1245,7 +1418,7 @@
       <td>color_deconvolution</td>
       <td>imgteam</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution</td>
       <td>0.8-2</td>
       <td>scikit-image</td>
       <td></td>
@@ -1288,8 +1461,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>15</td>
+      <td>16</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
       <td>16</td>
+      <td>2</td>
+      <td>3</td>
       <td></td>
     </tr>
     <tr>
@@ -1353,8 +1540,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
       <td></td>
     </tr>
     <tr>
@@ -1418,11 +1619,25 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3</td>
-      <td>78</td>
-      <td></td>
-    </tr>
-    <tr>
+      <td>76</td>
+      <td>82</td>
+      <td>11</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>76</td>
+      <td>82</td>
+      <td>11</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
       <td></td>
       <td>coordinates_of_roi</td>
       <td>ip_coordinates_of_roi</td>
@@ -1483,8 +1698,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>8</td>
-      <td>16546</td>
+      <td>16077</td>
+      <td>16547</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16077</td>
+      <td>16547</td>
+      <td>11</td>
+      <td>11</td>
       <td></td>
     </tr>
     <tr>
@@ -1514,11 +1743,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -1548,8 +1777,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>25</td>
-      <td>272</td>
+      <td>314</td>
+      <td>326</td>
+      <td>73</td>
+      <td>75</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>129</td>
+      <td>129</td>
+      <td>6</td>
+      <td>6</td>
+      <td>443</td>
+      <td>455</td>
+      <td>79</td>
+      <td>81</td>
       <td></td>
     </tr>
     <tr>
@@ -1613,8 +1856,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
       <td></td>
     </tr>
     <tr>
@@ -1678,8 +1935,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
-      <td>46</td>
+      <td>43</td>
+      <td>48</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>48</td>
+      <td>8</td>
+      <td>8</td>
       <td></td>
     </tr>
     <tr>
@@ -1743,8 +2014,22 @@
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>43</td>
-      <td>2605</td>
+      <td>1725</td>
+      <td>2708</td>
+      <td>97</td>
+      <td>99</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1727</td>
+      <td>2710</td>
+      <td>99</td>
+      <td>101</td>
       <td></td>
     </tr>
     <tr>
@@ -1810,6 +2095,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1839,11 +2138,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -1873,8 +2172,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>41</td>
-      <td>621</td>
+      <td>273</td>
+      <td>659</td>
+      <td>101</td>
+      <td>102</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>153</td>
+      <td>153</td>
+      <td>15</td>
+      <td>15</td>
+      <td>426</td>
+      <td>812</td>
+      <td>116</td>
+      <td>117</td>
       <td></td>
     </tr>
     <tr>
@@ -1938,8 +2251,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>2</td>
+      <td>2</td>
       <td></td>
     </tr>
     <tr>
@@ -2003,8 +2330,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>12</td>
+      <td>16</td>
+      <td>16</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>5</td>
+      <td>5</td>
       <td></td>
     </tr>
     <tr>
@@ -2068,8 +2409,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>7</td>
-      <td>21825</td>
+      <td>21409</td>
+      <td>21849</td>
+      <td>10</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21409</td>
+      <td>21849</td>
+      <td>10</td>
+      <td>12</td>
       <td></td>
     </tr>
     <tr>
@@ -2133,8 +2488,22 @@
       <td>27</td>
       <td>27</td>
       <td>0</td>
-      <td>26</td>
-      <td>1537</td>
+      <td>1731</td>
+      <td>1731</td>
+      <td>109</td>
+      <td>109</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1731</td>
+      <td>1731</td>
+      <td>109</td>
+      <td>109</td>
       <td></td>
     </tr>
     <tr>
@@ -2200,6 +2569,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2265,6 +2648,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2328,8 +2725,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>34</td>
+      <td>38</td>
+      <td>2</td>
+      <td>2</td>
       <td>0</td>
-      <td>36</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>38</td>
+      <td>2</td>
+      <td>2</td>
       <td></td>
     </tr>
     <tr>
@@ -2393,13 +2804,27 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>9</td>
-      <td>857</td>
+      <td>887</td>
+      <td>927</td>
+      <td>13</td>
+      <td>15</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>891</td>
+      <td>931</td>
+      <td>16</td>
+      <td>18</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>mahotas-features</td>
+      <td>mahotas_features</td>
       <td>ip_mahotas_features</td>
       <td>Compute image features using mahotas.</td>
       <td></td>
@@ -2415,7 +2840,7 @@
       <td>mahotas_features</td>
       <td>imgteam</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features</td>
       <td>0.7-2</td>
       <td>mahotas</td>
       <td></td>
@@ -2458,8 +2883,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>39</td>
+      <td>44</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
       <td>0</td>
-      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>44</td>
+      <td>6</td>
+      <td>6</td>
       <td></td>
     </tr>
     <tr>
@@ -2525,6 +2964,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2588,8 +3041,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>18</td>
+      <td>25</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
       <td>25</td>
+      <td>2</td>
+      <td>3</td>
       <td></td>
     </tr>
     <tr>
@@ -2655,6 +3122,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2720,6 +3201,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2785,6 +3280,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2850,6 +3359,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2915,6 +3438,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -2980,6 +3517,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
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       <td></td>
     </tr>
     <tr>
@@ -3045,6 +3596,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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       <td></td>
     </tr>
     <tr>
@@ -3110,6 +3675,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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       <td></td>
     </tr>
     <tr>
@@ -3139,11 +3718,11 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3173,8 +3752,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>21</td>
-      <td>60</td>
+      <td>149</td>
+      <td>149</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td>167</td>
+      <td>167</td>
+      <td>32</td>
+      <td>32</td>
       <td></td>
     </tr>
     <tr>
@@ -3238,8 +3831,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>36</td>
+      <td>42</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>36</td>
       <td>42</td>
+      <td>1</td>
+      <td>2</td>
       <td></td>
     </tr>
     <tr>
@@ -3305,71 +3912,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td></td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>points2binaryimage</td>
-      <td>ip_points_to_binaryimage</td>
-      <td>Points to Binary Image</td>
-      <td>galaxy_image_analysis</td>
-      <td>galaxy_image_analysis</td>
-      <td></td>
-      <td>Galaxy Image Analysis</td>
-      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
-      <td>Image analysis</td>
-      <td>Imaging, Bioinformatics</td>
-      <td>To update</td>
-      <td>https://github.com/bmcv</td>
-      <td>Imaging</td>
-      <td>points2binaryimage</td>
-      <td>imgteam</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage</td>
-      <td>0.3</td>
-      <td>scikit-image</td>
-      <td></td>
-      <td>Image analysis</td>
-      <td>Imaging, Bioinformatics</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
-      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>2</td>
-      <td>41</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -3433,8 +3989,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
       <td>0</td>
-      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>2</td>
+      <td>2</td>
       <td></td>
     </tr>
     <tr>
@@ -3498,8 +4068,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
       <td>29</td>
+      <td>29</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>4</td>
+      <td>4</td>
       <td></td>
     </tr>
     <tr>
@@ -3563,8 +4147,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
-      <td>85</td>
+      <td>40</td>
+      <td>86</td>
+      <td>4</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>86</td>
+      <td>4</td>
+      <td>6</td>
       <td></td>
     </tr>
     <tr>
@@ -3628,8 +4226,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>9</td>
-      <td>21343</td>
+      <td>20858</td>
+      <td>21444</td>
+      <td>14</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20858</td>
+      <td>21444</td>
+      <td>14</td>
+      <td>18</td>
       <td></td>
     </tr>
     <tr>
@@ -3693,8 +4305,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
-      <td>59</td>
+      <td>172</td>
+      <td>172</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>172</td>
+      <td>172</td>
+      <td>9</td>
+      <td>9</td>
       <td></td>
     </tr>
     <tr>
@@ -3758,8 +4384,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -3823,7 +4463,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>7</td>
       <td>7</td>
       <td></td>
     </tr>
@@ -3888,8 +4542,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>9</td>
-      <td>512</td>
+      <td>477</td>
+      <td>520</td>
+      <td>13</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>477</td>
+      <td>520</td>
+      <td>13</td>
+      <td>16</td>
       <td></td>
     </tr>
     <tr>
@@ -3953,8 +4621,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>2</td>
       <td>2</td>
-      <td>3</td>
       <td></td>
     </tr>
     <tr>
@@ -4018,8 +4700,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>96</td>
+      <td>103</td>
+      <td>4</td>
+      <td>5</td>
       <td>0</td>
-      <td>102</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>100</td>
+      <td>107</td>
+      <td>5</td>
+      <td>6</td>
       <td></td>
     </tr>
     <tr>
@@ -4083,8 +4779,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>44</td>
+      <td>51</td>
+      <td>2</td>
+      <td>3</td>
       <td>0</td>
-      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>44</td>
+      <td>51</td>
+      <td>2</td>
+      <td>3</td>
       <td></td>
     </tr>
     <tr>
@@ -4148,8 +4858,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
       <td>16</td>
+      <td>16</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>4</td>
+      <td>4</td>
       <td></td>
     </tr>
     <tr>
@@ -4213,8 +4937,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>67</td>
+      <td>142</td>
+      <td>142</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>142</td>
+      <td>142</td>
+      <td>5</td>
+      <td>5</td>
       <td></td>
     </tr>
     <tr>
@@ -4278,8 +5016,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>16</td>
+      <td>26</td>
+      <td>26</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>5</td>
+      <td>5</td>
       <td></td>
     </tr>
     <tr>
@@ -4345,11 +5097,25 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
       <td></td>
-      <td>visceral-evaluatesegmentation</td>
+      <td>visceral_evaluatesegmentation</td>
       <td>ip_visceral_evaluatesegmentation</td>
       <td>Visceral Project - Evaluate Segmentation Tool</td>
       <td></td>
@@ -4365,7 +5131,7 @@
       <td>visceral_evaluatesegmentation</td>
       <td>imgteam</td>
       <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation</td>
-      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation</td>
       <td>0.5-2</td>
       <td>visceral-evaluatesegmentation</td>
       <td>2015.07.03</td>
@@ -4408,8 +5174,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>20</td>
+      <td>25</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
       <td>25</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -4473,8 +5253,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>3</td>
+      <td>3</td>
       <td></td>
     </tr>
     <tr>
@@ -4538,8 +5332,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>1</td>
+      <td>1</td>
       <td></td>
     </tr>
     <tr>
@@ -4603,8 +5411,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
+      <td>32</td>
+      <td>38</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>32</td>
       <td>38</td>
+      <td>2</td>
+      <td>3</td>
       <td></td>
     </tr>
   </tbody>
diff --git a/communities/imaging/resources/tools.tsv b/communities/imaging/resources/tools.tsv
index 9fd99532..b115acb5 100644
--- a/communities/imaging/resources/tools.tsv
+++ b/communities/imaging/resources/tools.tsv
@@ -1,70 +1,68 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	6541	False		
-2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	13760	False		
-2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	6834	False		
-2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	656	False		
-2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	6156	False		
-3d_tensor_feature_dimension_reduction	ip_3d_tensor_feature_dimension_reduction	Dimensionality reduction for features (channels) of 3D tensor data using UMAP								To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	3d_tensor_feature_dimension_reduction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction	0.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40	False		
-background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	38	1523	False		
-bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	False		
-binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	1273	False		
-binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	29	False		
-bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	False		
-bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	0	178	4614	False		
-cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	43	False		
-color-deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	16	False		
-colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	78	False		
-coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	16546	False		
-count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	25	272	False		
-curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	12	False		
-detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	46	False		
-graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	43	2605	False		
-hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	41	621	False		
-image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	12	False		
-imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	21825	False		
-imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20240614			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	26	1537	False		
-incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	36	False		
-landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	857	False		
-mahotas-features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	37	False		
-measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25	False		
-morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	60	False		
-permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42	False		
-plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-points2binaryimage	ip_points_to_binaryimage	Points to Binary Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2binaryimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage	0.3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	41	False		
-points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	31	False		
-points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	29	False		
-projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	85	False		
-projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	21343	False		
-qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	59	False		
-repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	False		
-scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	512	False		
-segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	3	False		
-slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	102	False		
-split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42	False		
-spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.1	giatools	0.3.1	Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	16	False		
-spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	67	False		
-superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	16	False		
-upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-visceral-evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25	False		
-voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	38	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1434	6746	120	122	0	0	0	0	305	305	11	11	1739	7051	131	133	False		
+2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1156	13842	40	42	0	0	0	0	121	121	4	4	1277	13963	44	46	False		
+2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	591	6863	38	40	0	0	0	0	119	119	3	3	710	6982	41	43	False		
+2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	762	782	100	101	0	0	0	0	230	230	14	14	992	1012	114	115	False		
+2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	948	6261	98	100	0	0	0	0	153	153	13	13	1101	6414	111	113	False		
+anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	41	2	2	0	0	0	0	0	0	0	0	36	41	2	2	False		
+background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1	False		
+bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1635	1671	123	124	0	0	0	0	334	334	21	21	1969	2005	144	145	False		
+bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	2	0	0	0	0	0	0	0	0	3	3	2	2	False		
+binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	401	1385	87	88	0	0	0	0	188	188	9	9	589	1573	96	97	False		
+binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	29	1	1	0	0	0	0	0	0	0	0	24	29	1	1	False		
+bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	61	61	4	4	0	0	0	0	0	0	0	0	61	61	4	4	False		
+bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	1	0	0	0	0	0	0	0	0	2	2	1	1	False		
+cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	4	4	0	0	0	0	0	0	0	0	14	14	4	4	False		
+cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	0	0	23	23	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	0	4773	4773	749	749	0	0	0	0	5688	5688	94	94	10461	10461	843	843	False		
+cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55	55	11	11	0	0	0	0	0	0	0	0	55	55	11	11	False		
+color_deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	16	2	3	0	0	0	0	0	0	0	0	15	16	2	3	False		
+colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	40	40	2	2	0	0	0	0	0	0	0	0	40	40	2	2	False		
+concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	76	82	11	12	0	0	0	0	0	0	0	0	76	82	11	12	False		
+coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16077	16547	11	11	0	0	0	0	0	0	0	0	16077	16547	11	11	False		
+count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	314	326	73	75	0	0	0	0	129	129	6	6	443	455	79	81	False		
+curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	12	2	2	0	0	0	0	0	0	0	0	12	12	2	2	False		
+detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	43	48	8	8	0	0	0	0	0	0	0	0	43	48	8	8	False		
+graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1725	2708	97	99	2	2	2	2	0	0	0	0	1727	2710	99	101	False		
+hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	273	659	101	102	0	0	0	0	153	153	15	15	426	812	116	117	False		
+image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	2	2	0	0	0	0	0	0	0	0	58	58	2	2	False		
+image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	5	5	0	0	0	0	0	0	0	0	16	16	5	5	False		
+imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21409	21849	10	12	0	0	0	0	0	0	0	0	21409	21849	10	12	False		
+imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20240614			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	1731	1731	109	109	0	0	0	0	0	0	0	0	1731	1731	109	109	False		
+incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	38	2	2	0	0	0	0	0	0	0	0	34	38	2	2	False		
+landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	887	927	13	15	4	4	3	3	0	0	0	0	891	931	16	18	False		
+mahotas_features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	44	6	6	0	0	0	0	0	0	0	0	39	44	6	6	False		
+measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	25	2	3	0	0	0	0	0	0	0	0	18	25	2	3	False		
+morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	149	149	31	31	0	0	0	0	18	18	1	1	167	167	32	32	False		
+permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	42	1	2	0	0	0	0	0	0	0	0	36	42	1	2	False		
+plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	33	33	2	2	0	0	0	0	0	0	0	0	33	33	2	2	False		
+points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	4	4	0	0	0	0	0	0	0	0	29	29	4	4	False		
+projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	86	4	6	0	0	0	0	0	0	0	0	40	86	4	6	False		
+projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20858	21444	14	18	0	0	0	0	0	0	0	0	20858	21444	14	18	False		
+qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	172	172	9	9	0	0	0	0	0	0	0	0	172	172	9	9	False		
+repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1	False		
+rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	7	7	0	0	0	0	0	0	0	0	15	15	7	7	False		
+scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	477	520	13	16	0	0	0	0	0	0	0	0	477	520	13	16	False		
+segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	2	2	0	0	0	0	0	0	0	0	7	7	2	2	False		
+slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	96	103	4	5	0	0	0	0	4	4	1	1	100	107	5	6	False		
+split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	44	51	2	3	0	0	0	0	0	0	0	0	44	51	2	3	False		
+spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.1	giatools	0.3.1	Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	4	4	0	0	0	0	0	0	0	0	16	16	4	4	False		
+spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	142	142	5	5	0	0	0	0	0	0	0	0	142	142	5	5	False		
+superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	5	5	0	0	0	0	0	0	0	0	26	26	5	5	False		
+upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+visceral_evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	1	1	0	0	0	0	0	0	0	0	20	25	1	1	False		
+voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	43	43	3	3	0	0	0	0	0	0	0	0	43	43	3	3	False		
+woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	1	1	0	0	0	0	0	0	0	0	31	31	1	1	False		
+wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	38	2	3	0	0	0	0	0	0	0	0	32	38	2	3	False		
diff --git a/communities/imaging/resources/tools_filtered_by_ts_categories.tsv b/communities/imaging/resources/tools_filtered_by_ts_categories.tsv
index 9fd99532..b115acb5 100644
--- a/communities/imaging/resources/tools_filtered_by_ts_categories.tsv
+++ b/communities/imaging/resources/tools_filtered_by_ts_categories.tsv
@@ -1,70 +1,68 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	6541	False		
-2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	13760	False		
-2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	6834	False		
-2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39	656	False		
-2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	6156	False		
-3d_tensor_feature_dimension_reduction	ip_3d_tensor_feature_dimension_reduction	Dimensionality reduction for features (channels) of 3D tensor data using UMAP								To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	3d_tensor_feature_dimension_reduction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction	0.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40	False		
-background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	38	1523	False		
-bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	False		
-binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34	1273	False		
-binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	29	False		
-bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	False		
-bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	0	178	4614	False		
-cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	43	False		
-color-deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	16	False		
-colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	78	False		
-coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	16546	False		
-count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	25	272	False		
-curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	12	False		
-detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	46	False		
-graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	43	2605	False		
-hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	41	621	False		
-image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	12	False		
-imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	21825	False		
-imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20240614			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	26	1537	False		
-incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	36	False		
-landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	857	False		
-mahotas-features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	37	False		
-measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25	False		
-morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	60	False		
-permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42	False		
-plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-points2binaryimage	ip_points_to_binaryimage	Points to Binary Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2binaryimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage	0.3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	41	False		
-points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	31	False		
-points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	29	False		
-projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	85	False		
-projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	21343	False		
-qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	59	False		
-repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	False		
-scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	512	False		
-segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	3	False		
-slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	102	False		
-split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	42	False		
-spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.1	giatools	0.3.1	Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	16	False		
-spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	67	False		
-superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	16	False		
-upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-visceral-evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	25	False		
-voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	38	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1434	6746	120	122	0	0	0	0	305	305	11	11	1739	7051	131	133	False		
+2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1156	13842	40	42	0	0	0	0	121	121	4	4	1277	13963	44	46	False		
+2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	591	6863	38	40	0	0	0	0	119	119	3	3	710	6982	41	43	False		
+2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	762	782	100	101	0	0	0	0	230	230	14	14	992	1012	114	115	False		
+2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	948	6261	98	100	0	0	0	0	153	153	13	13	1101	6414	111	113	False		
+anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	41	2	2	0	0	0	0	0	0	0	0	36	41	2	2	False		
+background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1	False		
+bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1635	1671	123	124	0	0	0	0	334	334	21	21	1969	2005	144	145	False		
+bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	2	0	0	0	0	0	0	0	0	3	3	2	2	False		
+binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	401	1385	87	88	0	0	0	0	188	188	9	9	589	1573	96	97	False		
+binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	29	1	1	0	0	0	0	0	0	0	0	24	29	1	1	False		
+bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	61	61	4	4	0	0	0	0	0	0	0	0	61	61	4	4	False		
+bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	1	0	0	0	0	0	0	0	0	2	2	1	1	False		
+cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	4	4	0	0	0	0	0	0	0	0	14	14	4	4	False		
+cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	0	0	23	23	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	0	4773	4773	749	749	0	0	0	0	5688	5688	94	94	10461	10461	843	843	False		
+cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55	55	11	11	0	0	0	0	0	0	0	0	55	55	11	11	False		
+color_deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	16	2	3	0	0	0	0	0	0	0	0	15	16	2	3	False		
+colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	40	40	2	2	0	0	0	0	0	0	0	0	40	40	2	2	False		
+concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	76	82	11	12	0	0	0	0	0	0	0	0	76	82	11	12	False		
+coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16077	16547	11	11	0	0	0	0	0	0	0	0	16077	16547	11	11	False		
+count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	314	326	73	75	0	0	0	0	129	129	6	6	443	455	79	81	False		
+curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	12	2	2	0	0	0	0	0	0	0	0	12	12	2	2	False		
+detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	43	48	8	8	0	0	0	0	0	0	0	0	43	48	8	8	False		
+graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1725	2708	97	99	2	2	2	2	0	0	0	0	1727	2710	99	101	False		
+hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	273	659	101	102	0	0	0	0	153	153	15	15	426	812	116	117	False		
+image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	2	2	0	0	0	0	0	0	0	0	58	58	2	2	False		
+image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	5	5	0	0	0	0	0	0	0	0	16	16	5	5	False		
+imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21409	21849	10	12	0	0	0	0	0	0	0	0	21409	21849	10	12	False		
+imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20240614			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	1731	1731	109	109	0	0	0	0	0	0	0	0	1731	1731	109	109	False		
+incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	38	2	2	0	0	0	0	0	0	0	0	34	38	2	2	False		
+landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	887	927	13	15	4	4	3	3	0	0	0	0	891	931	16	18	False		
+mahotas_features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	44	6	6	0	0	0	0	0	0	0	0	39	44	6	6	False		
+measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	25	2	3	0	0	0	0	0	0	0	0	18	25	2	3	False		
+morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	149	149	31	31	0	0	0	0	18	18	1	1	167	167	32	32	False		
+permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	42	1	2	0	0	0	0	0	0	0	0	36	42	1	2	False		
+plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	33	33	2	2	0	0	0	0	0	0	0	0	33	33	2	2	False		
+points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	4	4	0	0	0	0	0	0	0	0	29	29	4	4	False		
+projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	86	4	6	0	0	0	0	0	0	0	0	40	86	4	6	False		
+projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20858	21444	14	18	0	0	0	0	0	0	0	0	20858	21444	14	18	False		
+qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	172	172	9	9	0	0	0	0	0	0	0	0	172	172	9	9	False		
+repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1	False		
+rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	7	7	0	0	0	0	0	0	0	0	15	15	7	7	False		
+scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	477	520	13	16	0	0	0	0	0	0	0	0	477	520	13	16	False		
+segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	2	2	0	0	0	0	0	0	0	0	7	7	2	2	False		
+slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	96	103	4	5	0	0	0	0	4	4	1	1	100	107	5	6	False		
+split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	44	51	2	3	0	0	0	0	0	0	0	0	44	51	2	3	False		
+spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.1	giatools	0.3.1	Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	4	4	0	0	0	0	0	0	0	0	16	16	4	4	False		
+spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	142	142	5	5	0	0	0	0	0	0	0	0	142	142	5	5	False		
+superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	5	5	0	0	0	0	0	0	0	0	26	26	5	5	False		
+upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+visceral_evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	1	1	0	0	0	0	0	0	0	0	20	25	1	1	False		
+voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	43	43	3	3	0	0	0	0	0	0	0	0	43	43	3	3	False		
+woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	1	1	0	0	0	0	0	0	0	0	31	31	1	1	False		
+wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	38	2	3	0	0	0	0	0	0	0	0	32	38	2	3	False		
diff --git a/communities/imaging/resources/tools_wordcloud.png b/communities/imaging/resources/tools_wordcloud.png
index f1b1d5ef..794ff983 100644
Binary files a/communities/imaging/resources/tools_wordcloud.png and b/communities/imaging/resources/tools_wordcloud.png differ
diff --git a/communities/machine-learning/resources/tools.html b/communities/machine-learning/resources/tools.html
index f8ba0823..99243e99 100644
--- a/communities/machine-learning/resources/tools.html
+++ b/communities/machine-learning/resources/tools.html
@@ -95,7 +95,6 @@
       <th>Tools available on CoralSNP</th>
       <th>Tools available on CropGalaxy</th>
       <th>Tools available on Dintor</th>
-      <th>Tools available on FreeBioinfo</th>
       <th>Tools available on GASLINI</th>
       <th>Tools available on Galaxy@AuBi</th>
       <th>Tools available on Galaxy@Pasteur</th>
@@ -112,12 +111,27 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
+      <th>Tools available on PhagePromotor</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
       <th>Tools available on Viral Variant Visualizer (VVV)</th>
-      <th>No. of tool users (2022-2023) (usegalaxy.eu)</th>
-      <th>Total tool usage (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.eu)</th>
+      <th>No. of tool users (all time) (usegalaxy.eu)</th>
+      <th>Tool usage (5 years) (usegalaxy.eu)</th>
+      <th>Tool usage (all time) (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org)</th>
+      <th>No. of tool users (all time) (usegalaxy.org)</th>
+      <th>Tool usage (5 years) (usegalaxy.org)</th>
+      <th>Tool usage (all time) (usegalaxy.org)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org.au)</th>
+      <th>No. of tool users (all time) (usegalaxy.org.au)</th>
+      <th>Tool usage (5 years) (usegalaxy.org.au)</th>
+      <th>Tool usage (all time) (usegalaxy.org.au)</th>
+      <th>No. of tool users (5 years) - all main servers</th>
+      <th>No. of tool users (all time) - all main servers</th>
+      <th>Tool usage (5 years) - all main servers</th>
+      <th>Tool usage (all time) - all main servers</th>
       <th>Deprecated</th>
     </tr>
   </thead>
@@ -183,8 +197,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>25</td>
+      <td>25</td>
+      <td>11</td>
+      <td>11</td>
       <td>0</td>
-      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25</td>
+      <td>25</td>
+      <td>11</td>
+      <td>11</td>
       <td></td>
     </tr>
     <tr>
@@ -248,8 +276,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>62</td>
+      <td>62</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>62</td>
+      <td>62</td>
+      <td>12</td>
+      <td>12</td>
       <td></td>
     </tr>
     <tr>
@@ -315,6 +357,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>6</td>
+      <td>6</td>
       <td></td>
     </tr>
     <tr>
@@ -378,8 +434,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>15</td>
-      <td>99</td>
+      <td>121</td>
+      <td>121</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>28</td>
+      <td>28</td>
       <td></td>
     </tr>
     <tr>
@@ -443,8 +513,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>3</td>
-      <td>501</td>
+      <td>558</td>
+      <td>558</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>558</td>
+      <td>558</td>
+      <td>7</td>
+      <td>7</td>
       <td></td>
     </tr>
     <tr>
@@ -508,8 +592,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>2</td>
+      <td>2</td>
       <td></td>
     </tr>
     <tr>
@@ -539,11 +637,11 @@
       <td>30</td>
       <td>14</td>
       <td>31</td>
-      <td>16</td>
+      <td>0</td>
       <td>30</td>
       <td>14</td>
       <td>31</td>
-      <td>16</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -573,8 +671,22 @@
       <td>31</td>
       <td>27</td>
       <td>0</td>
-      <td>958</td>
-      <td>113932</td>
+      <td>82169</td>
+      <td>116810</td>
+      <td>2402</td>
+      <td>2666</td>
+      <td>18101</td>
+      <td>18101</td>
+      <td>2375</td>
+      <td>2375</td>
+      <td>17549</td>
+      <td>17549</td>
+      <td>321</td>
+      <td>321</td>
+      <td>117819</td>
+      <td>152460</td>
+      <td>5098</td>
+      <td>5362</td>
       <td></td>
     </tr>
     <tr>
@@ -638,8 +750,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>15</td>
       <td>445</td>
+      <td>445</td>
+      <td>25</td>
+      <td>25</td>
+      <td>71</td>
+      <td>71</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>516</td>
+      <td>516</td>
+      <td>57</td>
+      <td>57</td>
       <td></td>
     </tr>
     <tr>
@@ -703,8 +829,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>40</td>
-      <td>234</td>
+      <td>574</td>
+      <td>574</td>
+      <td>76</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>574</td>
+      <td>574</td>
+      <td>76</td>
+      <td>76</td>
       <td></td>
     </tr>
     <tr>
@@ -768,8 +908,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>96</td>
+      <td>96</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>96</td>
+      <td>96</td>
+      <td>13</td>
+      <td>13</td>
       <td></td>
     </tr>
   </tbody>
diff --git a/communities/machine-learning/resources/tools.tsv b/communities/machine-learning/resources/tools.tsv
index a9ba70a9..ca626d5e 100644
--- a/communities/machine-learning/resources/tools.tsv
+++ b/communities/machine-learning/resources/tools.tsv
@@ -1,12 +1,12 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	False		
-chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	99	False		
-deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	501	False		
-flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	30	True	False	False
-sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	16	30	14	31	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	0	958	113932	False		
-tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	445	False		
-virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	234	False		
-whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	25	11	11	0	0	0	0	0	0	0	0	25	25	11	11	False		
+chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	62	12	12	0	0	0	0	0	0	0	0	62	62	12	12	False		
+chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	6	6	0	0	0	0	14	14	6	6	False		
+decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	121	121	28	28	0	0	0	0	0	0	0	0	121	121	28	28	False		
+deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	558	558	7	7	0	0	0	0	0	0	0	0	558	558	7	7	False		
+flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	2	2	0	0	0	0	0	0	0	0	9	9	2	2	False		
+jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	30	30	2	2	0	0	0	0	0	0	0	0	30	30	2	2	True	False	False
+sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	0	30	14	31	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	0	82169	116810	2402	2666	18101	18101	2375	2375	17549	17549	321	321	117819	152460	5098	5362	False		
+tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	445	445	25	25	71	71	32	32	0	0	0	0	516	516	57	57	False		
+virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	574	574	76	76	0	0	0	0	0	0	0	0	574	574	76	76	False		
+whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	96	96	13	13	0	0	0	0	0	0	0	0	96	96	13	13	False		
diff --git a/communities/machine-learning/resources/tools_filtered_by_ts_categories.tsv b/communities/machine-learning/resources/tools_filtered_by_ts_categories.tsv
index a9ba70a9..ca626d5e 100644
--- a/communities/machine-learning/resources/tools_filtered_by_ts_categories.tsv
+++ b/communities/machine-learning/resources/tools_filtered_by_ts_categories.tsv
@@ -1,12 +1,12 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	False		
-chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	99	False		
-deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	501	False		
-flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	30	True	False	False
-sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	16	30	14	31	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	0	958	113932	False		
-tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	445	False		
-virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	234	False		
-whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	25	11	11	0	0	0	0	0	0	0	0	25	25	11	11	False		
+chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	62	12	12	0	0	0	0	0	0	0	0	62	62	12	12	False		
+chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	6	6	0	0	0	0	14	14	6	6	False		
+decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	121	121	28	28	0	0	0	0	0	0	0	0	121	121	28	28	False		
+deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	558	558	7	7	0	0	0	0	0	0	0	0	558	558	7	7	False		
+flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	2	2	0	0	0	0	0	0	0	0	9	9	2	2	False		
+jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	30	30	2	2	0	0	0	0	0	0	0	0	30	30	2	2	True	False	False
+sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	0	30	14	31	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	0	82169	116810	2402	2666	18101	18101	2375	2375	17549	17549	321	321	117819	152460	5098	5362	False		
+tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	445	445	25	25	71	71	32	32	0	0	0	0	516	516	57	57	False		
+virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	574	574	76	76	0	0	0	0	0	0	0	0	574	574	76	76	False		
+whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	96	96	13	13	0	0	0	0	0	0	0	0	96	96	13	13	False		
diff --git a/communities/machine-learning/resources/tools_wordcloud.png b/communities/machine-learning/resources/tools_wordcloud.png
index d6347257..1298cfe4 100644
Binary files a/communities/machine-learning/resources/tools_wordcloud.png and b/communities/machine-learning/resources/tools_wordcloud.png differ
diff --git a/communities/microgalaxy/resources/tools.html b/communities/microgalaxy/resources/tools.html
index 46ed2739..0594b041 100644
--- a/communities/microgalaxy/resources/tools.html
+++ b/communities/microgalaxy/resources/tools.html
@@ -95,7 +95,6 @@
       <th>Tools available on CoralSNP</th>
       <th>Tools available on CropGalaxy</th>
       <th>Tools available on Dintor</th>
-      <th>Tools available on FreeBioinfo</th>
       <th>Tools available on GASLINI</th>
       <th>Tools available on Galaxy@AuBi</th>
       <th>Tools available on Galaxy@Pasteur</th>
@@ -112,12 +111,27 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
+      <th>Tools available on PhagePromotor</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
       <th>Tools available on Viral Variant Visualizer (VVV)</th>
-      <th>No. of tool users (2022-2023) (usegalaxy.eu)</th>
-      <th>Total tool usage (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.eu)</th>
+      <th>No. of tool users (all time) (usegalaxy.eu)</th>
+      <th>Tool usage (5 years) (usegalaxy.eu)</th>
+      <th>Tool usage (all time) (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org)</th>
+      <th>No. of tool users (all time) (usegalaxy.org)</th>
+      <th>Tool usage (5 years) (usegalaxy.org)</th>
+      <th>Tool usage (all time) (usegalaxy.org)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org.au)</th>
+      <th>No. of tool users (all time) (usegalaxy.org.au)</th>
+      <th>Tool usage (5 years) (usegalaxy.org.au)</th>
+      <th>Tool usage (all time) (usegalaxy.org.au)</th>
+      <th>No. of tool users (5 years) - all main servers</th>
+      <th>No. of tool users (all time) - all main servers</th>
+      <th>Tool usage (5 years) - all main servers</th>
+      <th>Tool usage (all time) - all main servers</th>
       <th>Deprecated</th>
     </tr>
   </thead>
@@ -149,11 +163,11 @@
       <td>0</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>0</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -183,8 +197,22 @@
       <td>5</td>
       <td>4</td>
       <td>0</td>
-      <td>73</td>
-      <td>1004</td>
+      <td>1038</td>
+      <td>1038</td>
+      <td>146</td>
+      <td>146</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>849</td>
+      <td>849</td>
+      <td>38</td>
+      <td>38</td>
+      <td>1887</td>
+      <td>1887</td>
+      <td>184</td>
+      <td>184</td>
       <td>False</td>
     </tr>
     <tr>
@@ -230,7 +258,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -245,11 +272,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>23</td>
-      <td>984</td>
+      <td>1003</td>
+      <td>1022</td>
+      <td>48</td>
+      <td>52</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1003</td>
+      <td>1022</td>
+      <td>48</td>
+      <td>52</td>
       <td>False</td>
     </tr>
     <tr>
@@ -279,11 +321,10 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -315,6 +356,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -344,8 +400,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -374,12 +429,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>1764</td>
-      <td>496717</td>
+      <td>619817</td>
+      <td>622353</td>
+      <td>4097</td>
+      <td>4130</td>
+      <td>320454</td>
+      <td>320454</td>
+      <td>2915</td>
+      <td>2915</td>
+      <td>496156</td>
+      <td>503743</td>
+      <td>2012</td>
+      <td>2227</td>
+      <td>1436427</td>
+      <td>1446550</td>
+      <td>9024</td>
+      <td>9272</td>
       <td>False</td>
     </tr>
     <tr>
@@ -443,8 +513,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>109</td>
+      <td>109</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>109</td>
+      <td>109</td>
       <td>False</td>
     </tr>
     <tr>
@@ -474,9 +558,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -504,12 +587,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>391</td>
-      <td>4278</td>
+      <td>5543</td>
+      <td>5543</td>
+      <td>1042</td>
+      <td>1042</td>
+      <td>1301</td>
+      <td>1305</td>
+      <td>413</td>
+      <td>414</td>
+      <td>2030</td>
+      <td>2030</td>
+      <td>299</td>
+      <td>299</td>
+      <td>8874</td>
+      <td>8878</td>
+      <td>1754</td>
+      <td>1755</td>
       <td>False</td>
     </tr>
     <tr>
@@ -573,8 +671,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>13</td>
-      <td>129</td>
+      <td>262</td>
+      <td>262</td>
+      <td>36</td>
+      <td>36</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>262</td>
+      <td>262</td>
+      <td>36</td>
+      <td>36</td>
       <td>False</td>
     </tr>
     <tr>
@@ -638,8 +750,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>12</td>
-      <td>53</td>
+      <td>81</td>
+      <td>81</td>
+      <td>17</td>
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+      <td>0</td>
+      <td>81</td>
+      <td>81</td>
+      <td>17</td>
+      <td>17</td>
       <td>False</td>
     </tr>
     <tr>
@@ -669,10 +795,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -704,7 +829,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>591</td>
+      <td>5734</td>
+      <td>5734</td>
+      <td>334</td>
+      <td>334</td>
+      <td>1035</td>
+      <td>1035</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>6769</td>
+      <td>6769</td>
+      <td>440</td>
+      <td>440</td>
       <td>False</td>
     </tr>
     <tr>
@@ -768,7 +908,21 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
+      <td>26</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>7</td>
       <td>7</td>
       <td>False</td>
     </tr>
@@ -812,7 +966,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -830,11 +983,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>279</td>
-      <td>14596</td>
+      <td>15949</td>
+      <td>16490</td>
+      <td>726</td>
+      <td>811</td>
+      <td>5113</td>
+      <td>5113</td>
+      <td>649</td>
+      <td>649</td>
+      <td>6043</td>
+      <td>6043</td>
+      <td>169</td>
+      <td>169</td>
+      <td>27105</td>
+      <td>27646</td>
+      <td>1544</td>
+      <td>1629</td>
       <td>False</td>
     </tr>
     <tr>
@@ -880,7 +1048,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -894,12 +1061,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>2</td>
       <td>1</td>
       <td>0</td>
-      <td>123</td>
-      <td>8175</td>
+      <td>9021</td>
+      <td>9021</td>
+      <td>238</td>
+      <td>238</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9021</td>
+      <td>9021</td>
+      <td>238</td>
+      <td>238</td>
       <td>False</td>
     </tr>
     <tr>
@@ -945,7 +1127,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -965,6 +1146,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -994,8 +1190,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -1025,11 +1220,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>151</td>
-      <td>2982</td>
+      <td>11117</td>
+      <td>11117</td>
+      <td>534</td>
+      <td>534</td>
+      <td>19</td>
+      <td>19</td>
+      <td>1</td>
+      <td>1</td>
+      <td>9601</td>
+      <td>9601</td>
+      <td>167</td>
+      <td>167</td>
+      <td>20737</td>
+      <td>20737</td>
+      <td>702</td>
+      <td>702</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1059,8 +1269,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -1089,12 +1298,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>208</td>
-      <td>14021</td>
+      <td>14693</td>
+      <td>15620</td>
+      <td>653</td>
+      <td>721</td>
+      <td>61872</td>
+      <td>101400</td>
+      <td>1656</td>
+      <td>5678</td>
+      <td>39</td>
+      <td>39</td>
+      <td>3</td>
+      <td>3</td>
+      <td>76604</td>
+      <td>117059</td>
+      <td>2312</td>
+      <td>6402</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1124,8 +1348,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -1154,12 +1377,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>2016</td>
-      <td>44390</td>
+      <td>55392</td>
+      <td>56095</td>
+      <td>4951</td>
+      <td>5035</td>
+      <td>47603</td>
+      <td>47603</td>
+      <td>4916</td>
+      <td>4916</td>
+      <td>18089</td>
+      <td>18089</td>
+      <td>3121</td>
+      <td>3121</td>
+      <td>121084</td>
+      <td>121787</td>
+      <td>12988</td>
+      <td>13072</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1223,8 +1461,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>8</td>
-      <td>64</td>
+      <td>90</td>
+      <td>90</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>90</td>
+      <td>90</td>
+      <td>28</td>
+      <td>28</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1270,7 +1522,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -1285,11 +1536,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>420</td>
-      <td>6381</td>
+      <td>11989</td>
+      <td>11989</td>
+      <td>768</td>
+      <td>768</td>
+      <td>4458</td>
+      <td>4458</td>
+      <td>652</td>
+      <td>652</td>
+      <td>2507</td>
+      <td>2507</td>
+      <td>80</td>
+      <td>80</td>
+      <td>18954</td>
+      <td>18954</td>
+      <td>1500</td>
+      <td>1500</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1353,8 +1619,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>544</td>
+      <td>544</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>544</td>
+      <td>544</td>
+      <td>20</td>
+      <td>20</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1400,7 +1680,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1415,11 +1694,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>21</td>
-      <td>81</td>
+      <td>126</td>
+      <td>126</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>126</td>
+      <td>126</td>
+      <td>42</td>
+      <td>42</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1485,6 +1779,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1529,7 +1837,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1544,12 +1851,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>98</td>
-      <td>3906</td>
+      <td>12725</td>
+      <td>12725</td>
+      <td>297</td>
+      <td>297</td>
+      <td>2851</td>
+      <td>5049</td>
+      <td>450</td>
+      <td>638</td>
+      <td>2171</td>
+      <td>2371</td>
+      <td>214</td>
+      <td>239</td>
+      <td>17747</td>
+      <td>20145</td>
+      <td>961</td>
+      <td>1174</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1615,6 +1937,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6243</td>
+      <td>6243</td>
+      <td>375</td>
+      <td>375</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6243</td>
+      <td>6243</td>
+      <td>375</td>
+      <td>375</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1678,8 +2014,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>101</td>
-      <td>1232</td>
+      <td>1063</td>
+      <td>1237</td>
+      <td>257</td>
+      <td>300</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1063</td>
+      <td>1237</td>
+      <td>257</td>
+      <td>300</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1725,7 +2075,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1740,13 +2089,28 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>121</td>
-      <td>22499</td>
-      <td>False</td>
-    </tr>
+      <td>24916</td>
+      <td>27120</td>
+      <td>283</td>
+      <td>347</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24916</td>
+      <td>27120</td>
+      <td>283</td>
+      <td>347</td>
+      <td>False</td>
+    </tr>
     <tr>
       <td></td>
       <td>blastxml_to_top_descr</td>
@@ -1789,7 +2153,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -1805,11 +2168,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>159</td>
-      <td>264558</td>
+      <td>264392</td>
+      <td>265217</td>
+      <td>483</td>
+      <td>552</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>264392</td>
+      <td>265217</td>
+      <td>483</td>
+      <td>552</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1839,8 +2217,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -1870,11 +2247,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>326</td>
-      <td>18351</td>
+      <td>51378</td>
+      <td>51378</td>
+      <td>775</td>
+      <td>775</td>
+      <td>3298</td>
+      <td>3298</td>
+      <td>160</td>
+      <td>160</td>
+      <td>1660</td>
+      <td>1660</td>
+      <td>63</td>
+      <td>63</td>
+      <td>56336</td>
+      <td>56336</td>
+      <td>998</td>
+      <td>998</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1904,8 +2296,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -1934,12 +2325,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1804</td>
-      <td>86180</td>
+      <td>102717</td>
+      <td>103051</td>
+      <td>3877</td>
+      <td>3926</td>
+      <td>34251</td>
+      <td>34251</td>
+      <td>3506</td>
+      <td>3506</td>
+      <td>33192</td>
+      <td>34369</td>
+      <td>2439</td>
+      <td>2525</td>
+      <td>170160</td>
+      <td>171671</td>
+      <td>9822</td>
+      <td>9957</td>
       <td>False</td>
     </tr>
     <tr>
@@ -1985,7 +2391,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -1999,12 +2404,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>268</td>
-      <td>2878</td>
+      <td>3835</td>
+      <td>3835</td>
+      <td>597</td>
+      <td>597</td>
+      <td>1359</td>
+      <td>1359</td>
+      <td>467</td>
+      <td>467</td>
+      <td>646</td>
+      <td>646</td>
+      <td>98</td>
+      <td>98</td>
+      <td>5840</td>
+      <td>5840</td>
+      <td>1162</td>
+      <td>1162</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2050,7 +2470,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2070,6 +2489,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5946</td>
+      <td>7379</td>
+      <td>407</td>
+      <td>628</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5946</td>
+      <td>7379</td>
+      <td>407</td>
+      <td>628</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2099,10 +2533,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2130,11 +2563,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>280</td>
-      <td>4474</td>
+      <td>10414</td>
+      <td>10414</td>
+      <td>510</td>
+      <td>510</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>10418</td>
+      <td>10418</td>
+      <td>512</td>
+      <td>512</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2198,8 +2646,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
-      <td>98</td>
+      <td>225</td>
+      <td>225</td>
+      <td>32</td>
+      <td>32</td>
+      <td>271</td>
+      <td>271</td>
+      <td>61</td>
+      <td>61</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>496</td>
+      <td>496</td>
+      <td>93</td>
+      <td>93</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2229,9 +2691,8 @@
       <td>0</td>
       <td>10</td>
       <td>10</td>
-      <td>10</td>
       <td>0</td>
-      <td>10</td>
+      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
@@ -2260,11 +2721,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>10</td>
       <td>0</td>
       <td>0</td>
-      <td>390</td>
-      <td>5165</td>
+      <td>7500</td>
+      <td>7500</td>
+      <td>930</td>
+      <td>930</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7500</td>
+      <td>7500</td>
+      <td>930</td>
+      <td>930</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2310,7 +2786,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -2325,11 +2800,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>68</td>
-      <td>1856</td>
+      <td>3388</td>
+      <td>3388</td>
+      <td>187</td>
+      <td>187</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>3390</td>
+      <td>3390</td>
+      <td>189</td>
+      <td>189</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2395,6 +2885,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>548</td>
+      <td>548</td>
+      <td>18</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>548</td>
+      <td>548</td>
+      <td>18</td>
+      <td>18</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2424,8 +2928,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2454,12 +2957,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>651</td>
-      <td>46793</td>
+      <td>79867</td>
+      <td>80817</td>
+      <td>1675</td>
+      <td>1785</td>
+      <td>49493</td>
+      <td>87884</td>
+      <td>3703</td>
+      <td>7380</td>
+      <td>8797</td>
+      <td>9713</td>
+      <td>670</td>
+      <td>728</td>
+      <td>138157</td>
+      <td>178414</td>
+      <td>6048</td>
+      <td>9893</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2523,8 +3041,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>102</td>
+      <td>2609</td>
+      <td>2609</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2609</td>
+      <td>2609</td>
+      <td>3</td>
+      <td>3</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2588,8 +3120,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>29</td>
-      <td>60901</td>
+      <td>61197</td>
+      <td>61220</td>
+      <td>64</td>
+      <td>65</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>61197</td>
+      <td>61220</td>
+      <td>64</td>
+      <td>65</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2653,8 +3199,22 @@
       <td>3</td>
       <td>0</td>
       <td>0</td>
+      <td>2758</td>
+      <td>2758</td>
+      <td>22</td>
+      <td>22</td>
       <td>20</td>
-      <td>2757</td>
+      <td>20</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2778</td>
+      <td>2778</td>
+      <td>32</td>
+      <td>32</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2720,6 +3280,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2783,8 +3357,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
-      <td>147</td>
+      <td>530</td>
+      <td>530</td>
+      <td>65</td>
+      <td>65</td>
+      <td>8</td>
+      <td>8</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>538</td>
+      <td>538</td>
+      <td>71</td>
+      <td>71</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2848,8 +3436,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>10</td>
+      <td>306</td>
+      <td>332</td>
+      <td>28</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>306</td>
       <td>332</td>
+      <td>28</td>
+      <td>32</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2879,8 +3481,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -2914,7 +3515,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>266</td>
+      <td>266</td>
+      <td>39</td>
+      <td>39</td>
+      <td>28</td>
+      <td>28</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>294</td>
+      <td>294</td>
+      <td>54</td>
+      <td>54</td>
       <td>False</td>
     </tr>
     <tr>
@@ -2944,10 +3560,9 @@
       <td>0</td>
       <td>0</td>
       <td>5</td>
-      <td>5</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
@@ -2975,11 +3590,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
-      <td>92</td>
-      <td>786</td>
+      <td>2105</td>
+      <td>2105</td>
+      <td>155</td>
+      <td>155</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2105</td>
+      <td>2105</td>
+      <td>155</td>
+      <td>155</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3009,10 +3639,9 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -3040,11 +3669,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>72</td>
-      <td>529</td>
+      <td>1081</td>
+      <td>1081</td>
+      <td>151</td>
+      <td>151</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1081</td>
+      <td>1081</td>
+      <td>151</td>
+      <td>151</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3108,8 +3752,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>16</td>
-      <td>8518</td>
+      <td>9942</td>
+      <td>9942</td>
+      <td>26</td>
+      <td>26</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9942</td>
+      <td>9942</td>
+      <td>26</td>
+      <td>26</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3139,8 +3797,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3172,9 +3829,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>5090</td>
-      <td>232004</td>
+      <td>259754</td>
+      <td>272370</td>
+      <td>11716</td>
+      <td>12601</td>
+      <td>334550</td>
+      <td>362356</td>
+      <td>18618</td>
+      <td>20162</td>
+      <td>64377</td>
+      <td>65986</td>
+      <td>3507</td>
+      <td>3627</td>
+      <td>658681</td>
+      <td>700712</td>
+      <td>33841</td>
+      <td>36390</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3204,8 +3876,7 @@
       <td>10</td>
       <td>10</td>
       <td>10</td>
-      <td>10</td>
-      <td>10</td>
+      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>10</td>
@@ -3234,12 +3905,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
-      <td>1263</td>
-      <td>66609</td>
+      <td>92240</td>
+      <td>92240</td>
+      <td>2716</td>
+      <td>2716</td>
+      <td>179176</td>
+      <td>179176</td>
+      <td>5317</td>
+      <td>5317</td>
+      <td>12478</td>
+      <td>12478</td>
+      <td>394</td>
+      <td>394</td>
+      <td>283894</td>
+      <td>283894</td>
+      <td>8427</td>
+      <td>8427</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3269,11 +3955,11 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -3303,8 +3989,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>24</td>
-      <td>706</td>
+      <td>1323</td>
+      <td>1323</td>
+      <td>47</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1323</td>
+      <td>1323</td>
+      <td>47</td>
+      <td>47</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3334,8 +4034,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -3367,9 +4066,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>4990</td>
-      <td>95752</td>
+      <td>97434</td>
+      <td>109474</td>
+      <td>11355</td>
+      <td>12514</td>
+      <td>183905</td>
+      <td>246475</td>
+      <td>24951</td>
+      <td>31957</td>
+      <td>18551</td>
+      <td>20166</td>
+      <td>2647</td>
+      <td>2905</td>
+      <td>299890</td>
+      <td>376115</td>
+      <td>38953</td>
+      <td>47376</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3399,8 +4113,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -3430,11 +4143,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>963</td>
-      <td>49711</td>
+      <td>61376</td>
+      <td>61746</td>
+      <td>1847</td>
+      <td>1895</td>
+      <td>23164</td>
+      <td>28729</td>
+      <td>1140</td>
+      <td>1556</td>
+      <td>63034</td>
+      <td>63034</td>
+      <td>522</td>
+      <td>522</td>
+      <td>147574</td>
+      <td>153509</td>
+      <td>3509</td>
+      <td>3973</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3480,7 +4208,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3494,12 +4221,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>42</td>
-      <td>369</td>
+      <td>358</td>
+      <td>406</td>
+      <td>124</td>
+      <td>139</td>
+      <td>1361</td>
+      <td>1361</td>
+      <td>384</td>
+      <td>384</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1719</td>
+      <td>1767</td>
+      <td>508</td>
+      <td>523</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3563,8 +4305,22 @@
       <td>5</td>
       <td>0</td>
       <td>0</td>
-      <td>39</td>
-      <td>6886</td>
+      <td>7358</td>
+      <td>7358</td>
+      <td>88</td>
+      <td>88</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7358</td>
+      <td>7358</td>
+      <td>88</td>
+      <td>88</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3594,10 +4350,9 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -3624,12 +4379,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>46</td>
-      <td>646</td>
+      <td>916</td>
+      <td>916</td>
+      <td>113</td>
+      <td>113</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>916</td>
+      <td>916</td>
+      <td>113</td>
+      <td>113</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3675,7 +4445,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -3690,11 +4459,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>53</td>
-      <td>9907</td>
+      <td>12996</td>
+      <td>12996</td>
+      <td>137</td>
+      <td>137</td>
+      <td>10</td>
+      <td>10</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13006</td>
+      <td>13006</td>
+      <td>138</td>
+      <td>138</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3760,6 +4544,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3789,8 +4587,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -3819,12 +4616,27 @@
       <td>0</td>
       <td>0</td>
       <td>3</td>
+      <td>0</td>
       <td>1</td>
       <td>3</td>
       <td>1</td>
       <td>0</td>
-      <td>510</td>
-      <td>30565</td>
+      <td>34432</td>
+      <td>34437</td>
+      <td>1149</td>
+      <td>1152</td>
+      <td>42</td>
+      <td>42</td>
+      <td>2</td>
+      <td>2</td>
+      <td>21027</td>
+      <td>21027</td>
+      <td>413</td>
+      <td>413</td>
+      <td>55501</td>
+      <td>55506</td>
+      <td>1564</td>
+      <td>1567</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3854,8 +4666,7 @@
       <td>107</td>
       <td>107</td>
       <td>107</td>
-      <td>107</td>
-      <td>107</td>
+      <td>0</td>
       <td>107</td>
       <td>107</td>
       <td>107</td>
@@ -3884,12 +4695,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>107</td>
       <td>107</td>
       <td>107</td>
       <td>0</td>
-      <td>1816</td>
-      <td>89530</td>
+      <td>143762</td>
+      <td>148864</td>
+      <td>4481</td>
+      <td>5039</td>
+      <td>151989</td>
+      <td>296028</td>
+      <td>13224</td>
+      <td>31140</td>
+      <td>24955</td>
+      <td>27001</td>
+      <td>2397</td>
+      <td>2705</td>
+      <td>320706</td>
+      <td>471893</td>
+      <td>20102</td>
+      <td>38884</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3919,10 +4745,9 @@
       <td>0</td>
       <td>0</td>
       <td>7</td>
-      <td>7</td>
       <td>0</td>
       <td>0</td>
-      <td>7</td>
+      <td>0</td>
       <td>7</td>
       <td>0</td>
       <td>0</td>
@@ -3950,11 +4775,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>7</td>
       <td>7</td>
       <td>0</td>
-      <td>45</td>
-      <td>899</td>
+      <td>820</td>
+      <td>966</td>
+      <td>89</td>
+      <td>106</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>820</td>
+      <td>966</td>
+      <td>89</td>
+      <td>106</td>
       <td>False</td>
     </tr>
     <tr>
@@ -3984,8 +4824,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4014,12 +4853,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>200</td>
-      <td>5265</td>
+      <td>5396</td>
+      <td>5938</td>
+      <td>580</td>
+      <td>607</td>
+      <td>628</td>
+      <td>628</td>
+      <td>168</td>
+      <td>168</td>
+      <td>519</td>
+      <td>519</td>
+      <td>107</td>
+      <td>107</td>
+      <td>6543</td>
+      <td>7085</td>
+      <td>855</td>
+      <td>882</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4072,7 +4926,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4085,6 +4938,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4130,7 +4998,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4144,12 +5011,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>52</td>
-      <td>459</td>
+      <td>601</td>
+      <td>601</td>
+      <td>128</td>
+      <td>128</td>
+      <td>1165</td>
+      <td>1165</td>
+      <td>232</td>
+      <td>232</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1766</td>
+      <td>1766</td>
+      <td>360</td>
+      <td>360</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4179,10 +5061,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4209,12 +5090,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>250</td>
-      <td>3498</td>
+      <td>6685</td>
+      <td>6685</td>
+      <td>603</td>
+      <td>603</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6685</td>
+      <td>6685</td>
+      <td>603</td>
+      <td>603</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4278,8 +5174,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>136</td>
+      <td>136</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>136</td>
+      <td>136</td>
+      <td>11</td>
+      <td>11</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4309,8 +5219,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4339,12 +5248,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>2803</td>
-      <td>1055760</td>
+      <td>1126086</td>
+      <td>1127111</td>
+      <td>6847</td>
+      <td>6909</td>
+      <td>422259</td>
+      <td>422259</td>
+      <td>10722</td>
+      <td>10722</td>
+      <td>76462</td>
+      <td>76462</td>
+      <td>2242</td>
+      <td>2242</td>
+      <td>1624807</td>
+      <td>1625832</td>
+      <td>19811</td>
+      <td>19873</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4374,8 +5298,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4404,12 +5327,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1266</td>
-      <td>4333</td>
+      <td>5162</td>
+      <td>5162</td>
+      <td>2350</td>
+      <td>2350</td>
+      <td>10176</td>
+      <td>10176</td>
+      <td>4714</td>
+      <td>4714</td>
+      <td>2610</td>
+      <td>2610</td>
+      <td>991</td>
+      <td>991</td>
+      <td>17948</td>
+      <td>17948</td>
+      <td>8055</td>
+      <td>8055</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4439,8 +5377,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4469,12 +5406,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>379</td>
-      <td>55434</td>
+      <td>65542</td>
+      <td>65631</td>
+      <td>1049</td>
+      <td>1071</td>
+      <td>25992</td>
+      <td>25992</td>
+      <td>2147</td>
+      <td>2147</td>
+      <td>6733</td>
+      <td>7339</td>
+      <td>649</td>
+      <td>745</td>
+      <td>98267</td>
+      <td>98962</td>
+      <td>3845</td>
+      <td>3963</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4504,8 +5456,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4537,9 +5488,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>4679</td>
-      <td>696399</td>
+      <td>740719</td>
+      <td>770524</td>
+      <td>11699</td>
+      <td>12547</td>
+      <td>643892</td>
+      <td>784396</td>
+      <td>23272</td>
+      <td>27598</td>
+      <td>66108</td>
+      <td>68867</td>
+      <td>2348</td>
+      <td>2463</td>
+      <td>1450719</td>
+      <td>1623787</td>
+      <td>37319</td>
+      <td>42608</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4585,7 +5551,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4605,6 +5570,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4634,8 +5614,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4664,12 +5643,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>617</td>
-      <td>30483</td>
+      <td>53310</td>
+      <td>53944</td>
+      <td>1499</td>
+      <td>1575</td>
+      <td>25043</td>
+      <td>25043</td>
+      <td>726</td>
+      <td>726</td>
+      <td>10824</td>
+      <td>10824</td>
+      <td>593</td>
+      <td>593</td>
+      <td>89177</td>
+      <td>89811</td>
+      <td>2818</td>
+      <td>2894</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4733,8 +5727,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>17</td>
-      <td>645</td>
+      <td>661</td>
+      <td>715</td>
+      <td>52</td>
+      <td>54</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>167</td>
+      <td>167</td>
+      <td>15</td>
+      <td>15</td>
+      <td>828</td>
+      <td>882</td>
+      <td>67</td>
+      <td>69</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4764,8 +5772,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -4794,12 +5801,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1499</td>
-      <td>20904</td>
+      <td>32514</td>
+      <td>32675</td>
+      <td>3379</td>
+      <td>3422</td>
+      <td>19434</td>
+      <td>19434</td>
+      <td>2537</td>
+      <td>2537</td>
+      <td>9843</td>
+      <td>9843</td>
+      <td>1624</td>
+      <td>1624</td>
+      <td>61791</td>
+      <td>61952</td>
+      <td>7540</td>
+      <td>7583</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4845,7 +5867,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -4859,12 +5880,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>166</td>
-      <td>5588</td>
+      <td>5940</td>
+      <td>6474</td>
+      <td>558</td>
+      <td>608</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5940</td>
+      <td>6474</td>
+      <td>558</td>
+      <td>608</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4894,9 +5930,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -4924,12 +5959,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>68</td>
-      <td>1102</td>
+      <td>1257</td>
+      <td>1450</td>
+      <td>150</td>
+      <td>162</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1052</td>
+      <td>1052</td>
+      <td>45</td>
+      <td>45</td>
+      <td>2309</td>
+      <td>2502</td>
+      <td>195</td>
+      <td>207</td>
       <td>False</td>
     </tr>
     <tr>
@@ -4975,7 +6025,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
@@ -4990,11 +6039,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>55</td>
-      <td>20021</td>
+      <td>21757</td>
+      <td>21757</td>
+      <td>101</td>
+      <td>101</td>
+      <td>217</td>
+      <td>217</td>
+      <td>21</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21974</td>
+      <td>21974</td>
+      <td>122</td>
+      <td>122</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5024,11 +6088,10 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>28</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>28</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5060,6 +6123,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5089,11 +6167,11 @@
       <td>3</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>3</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -5123,8 +6201,22 @@
       <td>5</td>
       <td>0</td>
       <td>0</td>
-      <td>900</td>
-      <td>5906</td>
+      <td>8648</td>
+      <td>8648</td>
+      <td>1408</td>
+      <td>1408</td>
+      <td>32</td>
+      <td>32</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6406</td>
+      <td>6406</td>
+      <td>597</td>
+      <td>597</td>
+      <td>15086</td>
+      <td>15086</td>
+      <td>2011</td>
+      <td>2011</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5170,7 +6262,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5190,6 +6281,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5219,8 +6325,7 @@
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
@@ -5249,12 +6354,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>1388</td>
-      <td>22148</td>
+      <td>24606</td>
+      <td>25662</td>
+      <td>3463</td>
+      <td>3630</td>
+      <td>26805</td>
+      <td>26808</td>
+      <td>5143</td>
+      <td>5144</td>
+      <td>8174</td>
+      <td>8237</td>
+      <td>1259</td>
+      <td>1279</td>
+      <td>59585</td>
+      <td>60707</td>
+      <td>9865</td>
+      <td>10053</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5299,7 +6419,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5314,12 +6433,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>27</td>
-      <td>660</td>
+      <td>490</td>
+      <td>682</td>
+      <td>74</td>
+      <td>109</td>
+      <td>127</td>
+      <td>14058</td>
+      <td>20</td>
+      <td>1798</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>617</td>
+      <td>14740</td>
+      <td>94</td>
+      <td>1907</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5383,8 +6517,22 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>187</td>
-      <td>3965</td>
+      <td>4343</td>
+      <td>4343</td>
+      <td>407</td>
+      <td>407</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4343</td>
+      <td>4343</td>
+      <td>407</td>
+      <td>407</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5450,6 +6598,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5479,8 +6641,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -5509,12 +6670,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>408</td>
-      <td>5484</td>
+      <td>5800</td>
+      <td>6212</td>
+      <td>826</td>
+      <td>871</td>
+      <td>7756</td>
+      <td>7756</td>
+      <td>1048</td>
+      <td>1048</td>
+      <td>1149</td>
+      <td>1149</td>
+      <td>215</td>
+      <td>215</td>
+      <td>14705</td>
+      <td>15117</td>
+      <td>2089</td>
+      <td>2134</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5544,8 +6720,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -5574,12 +6749,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1210</td>
-      <td>19167</td>
+      <td>20207</td>
+      <td>21960</td>
+      <td>2807</td>
+      <td>3139</td>
+      <td>24488</td>
+      <td>26198</td>
+      <td>3066</td>
+      <td>3321</td>
+      <td>4155</td>
+      <td>4155</td>
+      <td>545</td>
+      <td>545</td>
+      <td>48850</td>
+      <td>52313</td>
+      <td>6418</td>
+      <td>7005</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5609,8 +6799,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -5639,12 +6828,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>432</td>
-      <td>9277</td>
+      <td>9816</td>
+      <td>10927</td>
+      <td>1285</td>
+      <td>1350</td>
+      <td>1273</td>
+      <td>1273</td>
+      <td>368</td>
+      <td>368</td>
+      <td>1104</td>
+      <td>1104</td>
+      <td>242</td>
+      <td>242</td>
+      <td>12193</td>
+      <td>13304</td>
+      <td>1895</td>
+      <td>1960</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5690,7 +6894,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -5704,12 +6907,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>136</td>
-      <td>6651</td>
+      <td>7012</td>
+      <td>7344</td>
+      <td>323</td>
+      <td>338</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7012</td>
+      <td>7344</td>
+      <td>323</td>
+      <td>338</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5739,9 +6957,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -5774,7 +6991,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>476</td>
+      <td>476</td>
+      <td>87</td>
+      <td>87</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>588</td>
+      <td>588</td>
+      <td>74</td>
+      <td>74</td>
+      <td>1064</td>
+      <td>1064</td>
+      <td>161</td>
+      <td>161</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5820,7 +7052,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -5834,12 +7065,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>145</td>
-      <td>3340</td>
+      <td>3690</td>
+      <td>3811</td>
+      <td>326</td>
+      <td>336</td>
+      <td>3323</td>
+      <td>3323</td>
+      <td>235</td>
+      <td>235</td>
+      <td>1895</td>
+      <td>2429</td>
+      <td>234</td>
+      <td>258</td>
+      <td>8908</td>
+      <td>9563</td>
+      <td>795</td>
+      <td>829</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5869,10 +7115,9 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -5900,11 +7145,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>117</td>
-      <td>4459</td>
+      <td>7303</td>
+      <td>7303</td>
+      <td>222</td>
+      <td>222</td>
+      <td>20</td>
+      <td>20</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7323</td>
+      <td>7323</td>
+      <td>224</td>
+      <td>224</td>
       <td>False</td>
     </tr>
     <tr>
@@ -5968,8 +7228,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>18</td>
-      <td>339</td>
+      <td>349</td>
+      <td>359</td>
+      <td>32</td>
+      <td>33</td>
+      <td>364</td>
+      <td>364</td>
+      <td>53</td>
+      <td>53</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>713</td>
+      <td>723</td>
+      <td>85</td>
+      <td>86</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6033,8 +7307,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>12</td>
-      <td>137</td>
+      <td>156</td>
+      <td>156</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>220</td>
+      <td>220</td>
+      <td>11</td>
+      <td>11</td>
+      <td>376</td>
+      <td>376</td>
+      <td>31</td>
+      <td>31</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6083,7 +7371,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6100,6 +7387,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6129,9 +7431,8 @@
       <td>0</td>
       <td>12</td>
       <td>12</td>
-      <td>12</td>
       <td>0</td>
-      <td>12</td>
+      <td>0</td>
       <td>12</td>
       <td>12</td>
       <td>0</td>
@@ -6159,12 +7460,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>12</td>
       <td>12</td>
       <td>12</td>
       <td>0</td>
-      <td>439</td>
-      <td>33702</td>
+      <td>35919</td>
+      <td>36952</td>
+      <td>1283</td>
+      <td>1321</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3023</td>
+      <td>3023</td>
+      <td>180</td>
+      <td>180</td>
+      <td>38942</td>
+      <td>39975</td>
+      <td>1463</td>
+      <td>1501</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6194,11 +7510,10 @@
       <td>6</td>
       <td>10</td>
       <td>10</td>
-      <td>10</td>
+      <td>0</td>
       <td>6</td>
       <td>10</td>
       <td>10</td>
-      <td>10</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6224,12 +7539,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
-      <td>1037</td>
-      <td>19490</td>
+      <td>26659</td>
+      <td>26659</td>
+      <td>2067</td>
+      <td>2067</td>
+      <td>865</td>
+      <td>865</td>
+      <td>174</td>
+      <td>174</td>
+      <td>3238</td>
+      <td>3238</td>
+      <td>351</td>
+      <td>351</td>
+      <td>30762</td>
+      <td>30762</td>
+      <td>2592</td>
+      <td>2592</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6259,11 +7589,10 @@
       <td>17</td>
       <td>2</td>
       <td>17</td>
-      <td>2</td>
+      <td>0</td>
       <td>17</td>
       <td>2</td>
       <td>17</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -6289,12 +7618,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>12</td>
       <td>17</td>
       <td>12</td>
       <td>0</td>
-      <td>161</td>
-      <td>10370</td>
+      <td>11429</td>
+      <td>11429</td>
+      <td>428</td>
+      <td>428</td>
+      <td>7751</td>
+      <td>7751</td>
+      <td>676</td>
+      <td>676</td>
+      <td>715</td>
+      <td>715</td>
+      <td>58</td>
+      <td>58</td>
+      <td>19895</td>
+      <td>19895</td>
+      <td>1162</td>
+      <td>1162</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6358,8 +7702,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>39</td>
-      <td>354</td>
+      <td>473</td>
+      <td>473</td>
+      <td>93</td>
+      <td>93</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>473</td>
+      <td>93</td>
+      <td>93</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6405,7 +7763,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -6425,6 +7782,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6454,10 +7826,9 @@
       <td>3</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
       <td>0</td>
       <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -6484,12 +7855,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>69</td>
-      <td>1127</td>
+      <td>1200</td>
+      <td>1220</td>
+      <td>187</td>
+      <td>195</td>
+      <td>1588</td>
+      <td>1588</td>
+      <td>267</td>
+      <td>267</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2788</td>
+      <td>2808</td>
+      <td>454</td>
+      <td>462</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6553,8 +7939,22 @@
       <td>6</td>
       <td>6</td>
       <td>0</td>
-      <td>67</td>
-      <td>100294</td>
+      <td>59700</td>
+      <td>112582</td>
+      <td>223</td>
+      <td>282</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1157</td>
+      <td>1221</td>
+      <td>34</td>
+      <td>35</td>
+      <td>60857</td>
+      <td>113803</td>
+      <td>257</td>
+      <td>317</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6618,20 +8018,34 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
-      <td>94</td>
-      <td>False</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>integron_finder</td>
-      <td>integron_finder</td>
-      <td>"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"</td>
-      <td>integron_finder</td>
-      <td>integron_finder</td>
-      <td></td>
-      <td>Integron Finder</td>
-      <td>A tool to detect Integron in DNA sequences.</td>
+      <td>102</td>
+      <td>102</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>102</td>
+      <td>102</td>
+      <td>16</td>
+      <td>16</td>
+      <td>False</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>integron_finder</td>
+      <td>integron_finder</td>
+      <td>"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"</td>
+      <td>integron_finder</td>
+      <td>integron_finder</td>
+      <td></td>
+      <td>Integron Finder</td>
+      <td>A tool to detect Integron in DNA sequences.</td>
       <td>Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation</td>
       <td>Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis</td>
       <td>Up-to-date</td>
@@ -6649,8 +8063,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -6680,11 +8093,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>58</td>
-      <td>52965</td>
+      <td>55149</td>
+      <td>55149</td>
+      <td>161</td>
+      <td>161</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6085</td>
+      <td>6085</td>
+      <td>73</td>
+      <td>73</td>
+      <td>61234</td>
+      <td>61234</td>
+      <td>234</td>
+      <td>234</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6714,8 +8142,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -6744,12 +8171,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>677</td>
-      <td>35243</td>
+      <td>34689</td>
+      <td>55189</td>
+      <td>1634</td>
+      <td>1713</td>
+      <td>65</td>
+      <td>65</td>
+      <td>15</td>
+      <td>15</td>
+      <td>10897</td>
+      <td>10897</td>
+      <td>607</td>
+      <td>607</td>
+      <td>45651</td>
+      <td>66151</td>
+      <td>2256</td>
+      <td>2335</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6815,6 +8257,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6858,7 +8314,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -6874,12 +8329,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>681</td>
-      <td>21598</td>
+      <td>28279</td>
+      <td>28481</td>
+      <td>1623</td>
+      <td>1646</td>
+      <td>24662</td>
+      <td>24662</td>
+      <td>2093</td>
+      <td>2093</td>
+      <td>9780</td>
+      <td>10086</td>
+      <td>979</td>
+      <td>992</td>
+      <td>62721</td>
+      <td>63229</td>
+      <td>4695</td>
+      <td>4731</td>
       <td>False</td>
     </tr>
     <tr>
@@ -6909,8 +8379,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -6940,11 +8409,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>50</td>
-      <td>57581</td>
+      <td>59386</td>
+      <td>59386</td>
+      <td>151</td>
+      <td>151</td>
+      <td>56</td>
+      <td>56</td>
+      <td>1</td>
+      <td>1</td>
+      <td>4741</td>
+      <td>4741</td>
+      <td>59</td>
+      <td>59</td>
+      <td>64183</td>
+      <td>64183</td>
+      <td>211</td>
+      <td>211</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7008,8 +8492,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>38</td>
-      <td>868</td>
+      <td>1426</td>
+      <td>1426</td>
+      <td>71</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1426</td>
+      <td>1426</td>
+      <td>71</td>
+      <td>71</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7039,8 +8537,7 @@
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
@@ -7069,12 +8566,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>1171</td>
-      <td>1224275</td>
+      <td>1252220</td>
+      <td>1252220</td>
+      <td>2366</td>
+      <td>2366</td>
+      <td>126027</td>
+      <td>126027</td>
+      <td>2496</td>
+      <td>2496</td>
+      <td>41901</td>
+      <td>41901</td>
+      <td>993</td>
+      <td>993</td>
+      <td>1420148</td>
+      <td>1420148</td>
+      <td>5855</td>
+      <td>5855</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7104,8 +8616,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -7134,12 +8645,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>2346</td>
-      <td>18229</td>
+      <td>21153</td>
+      <td>22174</td>
+      <td>5514</td>
+      <td>5779</td>
+      <td>17428</td>
+      <td>17428</td>
+      <td>6458</td>
+      <td>6458</td>
+      <td>15673</td>
+      <td>17267</td>
+      <td>3248</td>
+      <td>3786</td>
+      <td>54254</td>
+      <td>56869</td>
+      <td>15220</td>
+      <td>16023</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7169,9 +8695,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7200,11 +8725,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>91</td>
-      <td>1138</td>
+      <td>1825</td>
+      <td>1825</td>
+      <td>237</td>
+      <td>237</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>971</td>
+      <td>971</td>
+      <td>56</td>
+      <td>56</td>
+      <td>2796</td>
+      <td>2796</td>
+      <td>293</td>
+      <td>293</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7270,6 +8810,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7333,8 +8887,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>19</td>
-      <td>363</td>
+      <td>379</td>
+      <td>379</td>
+      <td>53</td>
+      <td>53</td>
+      <td>8259</td>
+      <td>8259</td>
+      <td>271</td>
+      <td>271</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8638</td>
+      <td>8638</td>
+      <td>324</td>
+      <td>324</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7379,7 +8947,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7394,12 +8961,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
-      <td>63</td>
-      <td>2022</td>
+      <td>1995</td>
+      <td>2091</td>
+      <td>174</td>
+      <td>193</td>
+      <td>1430</td>
+      <td>1430</td>
+      <td>389</td>
+      <td>389</td>
+      <td>1580</td>
+      <td>1580</td>
+      <td>56</td>
+      <td>56</td>
+      <td>5005</td>
+      <td>5101</td>
+      <td>619</td>
+      <td>638</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7423,7 +9005,7 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate</td>
       <td>2.3.2</td>
       <td>kleborate</td>
-      <td>3.0.9</td>
+      <td>3.1.0</td>
       <td>Multilocus sequence typing, Genome assembly, Virulence prediction</td>
       <td>Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing</td>
       <td>0</td>
@@ -7445,7 +9027,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7460,11 +9041,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>38</td>
-      <td>319</td>
+      <td>503</td>
+      <td>503</td>
+      <td>58</td>
+      <td>58</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>503</td>
+      <td>503</td>
+      <td>58</td>
+      <td>58</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7494,10 +9090,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7524,12 +9119,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>33</td>
-      <td>594</td>
+      <td>1342</td>
+      <td>1342</td>
+      <td>63</td>
+      <td>63</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1342</td>
+      <td>1342</td>
+      <td>63</td>
+      <td>63</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7559,8 +9169,7 @@
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
@@ -7572,7 +9181,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>0</td>
@@ -7589,12 +9198,27 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>1209</td>
-      <td>33778</td>
+      <td>48136</td>
+      <td>48164</td>
+      <td>2754</td>
+      <td>2760</td>
+      <td>59952</td>
+      <td>130398</td>
+      <td>5869</td>
+      <td>8654</td>
+      <td>29008</td>
+      <td>31148</td>
+      <td>1936</td>
+      <td>2200</td>
+      <td>137096</td>
+      <td>209710</td>
+      <td>10559</td>
+      <td>13614</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7624,8 +9248,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -7654,12 +9277,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2367</td>
-      <td>185308</td>
+      <td>271367</td>
+      <td>271786</td>
+      <td>6384</td>
+      <td>6409</td>
+      <td>101752</td>
+      <td>101752</td>
+      <td>4662</td>
+      <td>4662</td>
+      <td>53562</td>
+      <td>53562</td>
+      <td>1663</td>
+      <td>1663</td>
+      <td>426681</td>
+      <td>427100</td>
+      <td>12709</td>
+      <td>12734</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7703,7 +9341,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -7719,12 +9356,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>481</td>
-      <td>14683</td>
+      <td>23008</td>
+      <td>23014</td>
+      <td>1060</td>
+      <td>1061</td>
+      <td>16194</td>
+      <td>24490</td>
+      <td>1719</td>
+      <td>2168</td>
+      <td>14898</td>
+      <td>14898</td>
+      <td>436</td>
+      <td>436</td>
+      <td>54100</td>
+      <td>62402</td>
+      <td>3215</td>
+      <td>3665</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7754,9 +9406,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -7785,11 +9436,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>182</td>
-      <td>1444</td>
+      <td>3185</td>
+      <td>3185</td>
+      <td>495</td>
+      <td>495</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>385</td>
+      <td>385</td>
+      <td>48</td>
+      <td>48</td>
+      <td>3570</td>
+      <td>3570</td>
+      <td>543</td>
+      <td>543</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7853,8 +9519,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>354</td>
-      <td>2527</td>
+      <td>3981</td>
+      <td>3986</td>
+      <td>769</td>
+      <td>771</td>
+      <td>4087</td>
+      <td>5610</td>
+      <td>991</td>
+      <td>1284</td>
+      <td>88</td>
+      <td>88</td>
+      <td>41</td>
+      <td>41</td>
+      <td>8156</td>
+      <td>9684</td>
+      <td>1801</td>
+      <td>2096</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7884,8 +9564,7 @@
       <td>6</td>
       <td>6</td>
       <td>6</td>
-      <td>6</td>
-      <td>6</td>
+      <td>0</td>
       <td>6</td>
       <td>6</td>
       <td>6</td>
@@ -7915,11 +9594,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
-      <td>703</td>
-      <td>16525</td>
+      <td>48516</td>
+      <td>48516</td>
+      <td>2373</td>
+      <td>2373</td>
+      <td>8787</td>
+      <td>8787</td>
+      <td>943</td>
+      <td>943</td>
+      <td>4369</td>
+      <td>4369</td>
+      <td>393</td>
+      <td>393</td>
+      <td>61672</td>
+      <td>61672</td>
+      <td>3709</td>
+      <td>3709</td>
       <td>False</td>
     </tr>
     <tr>
@@ -7965,7 +9659,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -7985,6 +9678,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8048,8 +9756,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
+      <td>89</td>
       <td>137</td>
+      <td>4</td>
+      <td>20</td>
+      <td>118</td>
+      <td>6136</td>
+      <td>15</td>
+      <td>1112</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>207</td>
+      <td>6273</td>
+      <td>19</td>
+      <td>1132</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8113,8 +9835,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>7</td>
-      <td>55</td>
+      <td>92</td>
+      <td>92</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>92</td>
+      <td>92</td>
+      <td>8</td>
+      <td>8</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8178,16 +9914,30 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>9</td>
-      <td>152</td>
-      <td>False</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>limma_voom</td>
-      <td>limma_voom</td>
-      <td>Perform RNA-Seq differential expression analysis using limma voom pipeline</td>
-      <td>limma</td>
+      <td>149</td>
+      <td>171</td>
+      <td>27</td>
+      <td>30</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>149</td>
+      <td>171</td>
+      <td>27</td>
+      <td>30</td>
+      <td>False</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>limma_voom</td>
+      <td>limma_voom</td>
+      <td>Perform RNA-Seq differential expression analysis using limma voom pipeline</td>
+      <td>limma</td>
       <td>limma</td>
       <td></td>
       <td>limma</td>
@@ -8209,11 +9959,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -8243,8 +9993,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1012</td>
-      <td>20344</td>
+      <td>23442</td>
+      <td>24466</td>
+      <td>2379</td>
+      <td>2475</td>
+      <td>45734</td>
+      <td>49342</td>
+      <td>4565</td>
+      <td>5032</td>
+      <td>9327</td>
+      <td>9517</td>
+      <td>835</td>
+      <td>842</td>
+      <td>78503</td>
+      <td>83325</td>
+      <td>7779</td>
+      <td>8349</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8308,8 +10072,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>37</td>
+      <td>39</td>
+      <td>39</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>39</td>
+      <td>4</td>
+      <td>4</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8373,8 +10151,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>9</td>
-      <td>647</td>
+      <td>822</td>
+      <td>822</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>822</td>
+      <td>822</td>
+      <td>14</td>
+      <td>14</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8438,8 +10230,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>114</td>
-      <td>936</td>
+      <td>1219</td>
+      <td>1219</td>
+      <td>182</td>
+      <td>182</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>37</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1256</td>
+      <td>1256</td>
+      <td>186</td>
+      <td>186</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8503,8 +10309,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>44</td>
+      <td>44</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
       <td>0</td>
-      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>44</td>
+      <td>44</td>
+      <td>11</td>
+      <td>11</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8568,8 +10388,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>29</td>
-      <td>188</td>
+      <td>2835</td>
+      <td>2835</td>
+      <td>59</td>
+      <td>59</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2835</td>
+      <td>2835</td>
+      <td>59</td>
+      <td>59</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8599,8 +10433,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -8629,12 +10462,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>817</td>
-      <td>143045</td>
+      <td>172433</td>
+      <td>174456</td>
+      <td>1865</td>
+      <td>1951</td>
+      <td>108640</td>
+      <td>122790</td>
+      <td>4266</td>
+      <td>5521</td>
+      <td>20027</td>
+      <td>20027</td>
+      <td>1172</td>
+      <td>1172</td>
+      <td>301100</td>
+      <td>317273</td>
+      <td>7303</td>
+      <td>8644</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8700,6 +10548,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8729,8 +10591,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -8759,12 +10620,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>554</td>
-      <td>5591</td>
+      <td>6417</td>
+      <td>6861</td>
+      <td>1315</td>
+      <td>1366</td>
+      <td>7235</td>
+      <td>7235</td>
+      <td>1858</td>
+      <td>1858</td>
+      <td>4112</td>
+      <td>4112</td>
+      <td>902</td>
+      <td>902</td>
+      <td>17764</td>
+      <td>18208</td>
+      <td>4075</td>
+      <td>4126</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8810,7 +10686,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -8825,11 +10700,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>167</td>
+      <td>7871</td>
+      <td>7871</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7871</td>
+      <td>7871</td>
+      <td>32</td>
+      <td>32</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8859,8 +10749,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -8889,12 +10778,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>27</td>
-      <td>9763</td>
+      <td>10119</td>
+      <td>10119</td>
+      <td>61</td>
+      <td>61</td>
+      <td>19</td>
+      <td>19</td>
+      <td>9</td>
+      <td>9</td>
+      <td>647</td>
+      <td>647</td>
+      <td>7</td>
+      <td>7</td>
+      <td>10785</td>
+      <td>10785</td>
+      <td>77</td>
+      <td>77</td>
       <td>False</td>
     </tr>
     <tr>
@@ -8924,8 +10828,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -8954,12 +10857,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>118</td>
-      <td>2059</td>
+      <td>2798</td>
+      <td>2798</td>
+      <td>314</td>
+      <td>314</td>
+      <td>2452</td>
+      <td>2452</td>
+      <td>508</td>
+      <td>508</td>
+      <td>914</td>
+      <td>914</td>
+      <td>89</td>
+      <td>89</td>
+      <td>6164</td>
+      <td>6164</td>
+      <td>911</td>
+      <td>911</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9004,7 +10922,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -9019,12 +10936,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>415</td>
-      <td>6078</td>
+      <td>6863</td>
+      <td>7021</td>
+      <td>1251</td>
+      <td>1264</td>
+      <td>2798</td>
+      <td>2798</td>
+      <td>543</td>
+      <td>543</td>
+      <td>3189</td>
+      <td>3189</td>
+      <td>352</td>
+      <td>352</td>
+      <td>12850</td>
+      <td>13008</td>
+      <td>2146</td>
+      <td>2159</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9088,8 +11020,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>10</td>
-      <td>29</td>
+      <td>35</td>
+      <td>35</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>35</td>
+      <td>35</td>
+      <td>13</td>
+      <td>13</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9119,8 +11065,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -9149,12 +11094,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>768</td>
-      <td>99863</td>
+      <td>117975</td>
+      <td>117975</td>
+      <td>1693</td>
+      <td>1693</td>
+      <td>55063</td>
+      <td>55063</td>
+      <td>796</td>
+      <td>796</td>
+      <td>9325</td>
+      <td>9325</td>
+      <td>639</td>
+      <td>639</td>
+      <td>182363</td>
+      <td>182363</td>
+      <td>3128</td>
+      <td>3128</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9184,8 +11144,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -9214,12 +11173,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>548</td>
-      <td>9530</td>
+      <td>12692</td>
+      <td>13292</td>
+      <td>1349</td>
+      <td>1400</td>
+      <td>16645</td>
+      <td>16645</td>
+      <td>2140</td>
+      <td>2140</td>
+      <td>6214</td>
+      <td>6214</td>
+      <td>431</td>
+      <td>431</td>
+      <td>35551</td>
+      <td>36151</td>
+      <td>3920</td>
+      <td>3971</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9249,8 +11223,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -9280,11 +11253,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>54</td>
-      <td>475</td>
+      <td>513</td>
+      <td>557</td>
+      <td>152</td>
+      <td>155</td>
+      <td>74</td>
+      <td>74</td>
+      <td>35</td>
+      <td>35</td>
+      <td>10</td>
+      <td>10</td>
+      <td>4</td>
+      <td>4</td>
+      <td>597</td>
+      <td>641</td>
+      <td>191</td>
+      <td>194</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9348,8 +11336,22 @@
       <td>7</td>
       <td>0</td>
       <td>0</td>
-      <td>261</td>
-      <td>3610</td>
+      <td>4130</td>
+      <td>4130</td>
+      <td>447</td>
+      <td>447</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4130</td>
+      <td>4130</td>
+      <td>447</td>
+      <td>447</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9415,6 +11417,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9444,11 +11460,11 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -9478,8 +11494,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>244</td>
-      <td>2483</td>
+      <td>3150</td>
+      <td>3150</td>
+      <td>477</td>
+      <td>477</td>
+      <td>730</td>
+      <td>730</td>
+      <td>196</td>
+      <td>196</td>
+      <td>1183</td>
+      <td>1183</td>
+      <td>151</td>
+      <td>151</td>
+      <td>5063</td>
+      <td>5063</td>
+      <td>824</td>
+      <td>824</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9545,6 +11575,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9574,11 +11618,10 @@
       <td>2</td>
       <td>1</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>1</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -9605,11 +11648,26 @@
       <td>0</td>
       <td>1</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>192</td>
-      <td>4329</td>
+      <td>6135</td>
+      <td>6135</td>
+      <td>382</td>
+      <td>382</td>
+      <td>881</td>
+      <td>881</td>
+      <td>151</td>
+      <td>151</td>
+      <td>1094</td>
+      <td>1094</td>
+      <td>104</td>
+      <td>104</td>
+      <td>8110</td>
+      <td>8110</td>
+      <td>637</td>
+      <td>637</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9631,7 +11689,7 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk</td>
-      <td>5.34c21f2</td>
+      <td>7.bba0d80</td>
       <td>metaeuk</td>
       <td>6.a5d39d9</td>
       <td>Homology-based gene prediction</td>
@@ -9673,17 +11731,31 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>16</td>
-      <td>184</td>
-      <td>False</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>metagene_annotator</td>
-      <td>metagene_annotator</td>
-      <td>MetaGeneAnnotator gene-finding program for prokaryote and phage</td>
-      <td>metageneannotator</td>
-      <td>metageneannotator</td>
+      <td>312</td>
+      <td>312</td>
+      <td>40</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>312</td>
+      <td>312</td>
+      <td>40</td>
+      <td>40</td>
+      <td>False</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metagene_annotator</td>
+      <td>metagene_annotator</td>
+      <td>MetaGeneAnnotator gene-finding program for prokaryote and phage</td>
+      <td>metageneannotator</td>
+      <td>metageneannotator</td>
       <td></td>
       <td>MetaGeneAnnotator</td>
       <td>Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.</td>
@@ -9718,7 +11790,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -9735,11 +11806,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>115</td>
-      <td>636</td>
+      <td>980</td>
+      <td>980</td>
+      <td>323</td>
+      <td>323</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>980</td>
+      <td>980</td>
+      <td>323</td>
+      <td>323</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9769,10 +11855,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -9799,12 +11884,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>6</td>
-      <td>753</td>
+      <td>556</td>
+      <td>756</td>
+      <td>17</td>
+      <td>21</td>
+      <td>310</td>
+      <td>514</td>
+      <td>35</td>
+      <td>55</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>866</td>
+      <td>1270</td>
+      <td>52</td>
+      <td>76</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9868,8 +11968,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>15</td>
-      <td>4181</td>
+      <td>4471</td>
+      <td>4471</td>
+      <td>29</td>
+      <td>29</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4471</td>
+      <td>4471</td>
+      <td>29</td>
+      <td>29</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9899,11 +12013,10 @@
       <td>1</td>
       <td>2</td>
       <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>1</td>
       <td>2</td>
       <td>4</td>
-      <td>4</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -9930,11 +12043,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
-      <td>499</td>
-      <td>11069</td>
+      <td>16629</td>
+      <td>16648</td>
+      <td>1183</td>
+      <td>1187</td>
+      <td>3983</td>
+      <td>3983</td>
+      <td>572</td>
+      <td>572</td>
+      <td>4747</td>
+      <td>4747</td>
+      <td>278</td>
+      <td>278</td>
+      <td>25359</td>
+      <td>25378</td>
+      <td>2033</td>
+      <td>2037</td>
       <td>False</td>
     </tr>
     <tr>
@@ -9998,8 +12126,22 @@
       <td>6</td>
       <td>6</td>
       <td>0</td>
-      <td>104</td>
-      <td>2522</td>
+      <td>2730</td>
+      <td>2831</td>
+      <td>260</td>
+      <td>262</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1540</td>
+      <td>1540</td>
+      <td>71</td>
+      <td>71</td>
+      <td>4270</td>
+      <td>4371</td>
+      <td>331</td>
+      <td>333</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10063,8 +12205,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>142</td>
+      <td>142</td>
+      <td>32</td>
+      <td>32</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>379</td>
+      <td>379</td>
+      <td>47</td>
+      <td>47</td>
+      <td>521</td>
+      <td>521</td>
+      <td>79</td>
+      <td>79</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10110,7 +12266,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10124,12 +12279,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>109</td>
-      <td>2206</td>
+      <td>7116</td>
+      <td>7116</td>
+      <td>256</td>
+      <td>256</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>278</td>
+      <td>278</td>
+      <td>60</td>
+      <td>60</td>
+      <td>7394</td>
+      <td>7394</td>
+      <td>316</td>
+      <td>316</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10159,8 +12329,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -10189,12 +12358,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>178</td>
-      <td>11938</td>
+      <td>13357</td>
+      <td>13479</td>
+      <td>554</td>
+      <td>562</td>
+      <td>8416</td>
+      <td>8416</td>
+      <td>448</td>
+      <td>448</td>
+      <td>898</td>
+      <td>898</td>
+      <td>85</td>
+      <td>85</td>
+      <td>22671</td>
+      <td>22793</td>
+      <td>1087</td>
+      <td>1095</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10240,7 +12424,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10255,11 +12438,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>21</td>
-      <td>185</td>
+      <td>229</td>
+      <td>229</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>229</td>
+      <td>229</td>
+      <td>32</td>
+      <td>32</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10289,10 +12487,9 @@
       <td>2</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -10320,11 +12517,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>30</td>
-      <td>842</td>
+      <td>1244</td>
+      <td>1244</td>
+      <td>86</td>
+      <td>86</td>
+      <td>24</td>
+      <td>24</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1268</td>
+      <td>1268</td>
+      <td>101</td>
+      <td>101</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10370,7 +12582,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10384,12 +12595,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>1</td>
       <td>0</td>
-      <td>236</td>
-      <td>100920</td>
+      <td>191295</td>
+      <td>191295</td>
+      <td>1111</td>
+      <td>1111</td>
+      <td>42265</td>
+      <td>42265</td>
+      <td>320</td>
+      <td>320</td>
+      <td>10904</td>
+      <td>10904</td>
+      <td>83</td>
+      <td>83</td>
+      <td>244464</td>
+      <td>244464</td>
+      <td>1514</td>
+      <td>1514</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10419,8 +12645,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -10449,12 +12674,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>635</td>
-      <td>9304</td>
+      <td>13300</td>
+      <td>13471</td>
+      <td>1480</td>
+      <td>1501</td>
+      <td>6532</td>
+      <td>6532</td>
+      <td>1167</td>
+      <td>1167</td>
+      <td>10334</td>
+      <td>11841</td>
+      <td>1083</td>
+      <td>1300</td>
+      <td>30166</td>
+      <td>31844</td>
+      <td>3730</td>
+      <td>3968</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10484,9 +12724,8 @@
       <td>0</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
@@ -10515,11 +12754,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>322</td>
-      <td>89021</td>
+      <td>119024</td>
+      <td>119024</td>
+      <td>628</td>
+      <td>628</td>
+      <td>42</td>
+      <td>42</td>
+      <td>2</td>
+      <td>2</td>
+      <td>36310</td>
+      <td>36310</td>
+      <td>191</td>
+      <td>191</td>
+      <td>155376</td>
+      <td>155376</td>
+      <td>821</td>
+      <td>821</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10549,8 +12803,7 @@
       <td>129</td>
       <td>129</td>
       <td>129</td>
-      <td>129</td>
-      <td>129</td>
+      <td>0</td>
       <td>129</td>
       <td>129</td>
       <td>129</td>
@@ -10579,12 +12832,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>126</td>
       <td>129</td>
       <td>129</td>
       <td>0</td>
-      <td>14353</td>
-      <td>302916</td>
+      <td>297546</td>
+      <td>326056</td>
+      <td>37506</td>
+      <td>41763</td>
+      <td>565218</td>
+      <td>682083</td>
+      <td>72163</td>
+      <td>89926</td>
+      <td>167400</td>
+      <td>182490</td>
+      <td>26963</td>
+      <td>28404</td>
+      <td>1030164</td>
+      <td>1190629</td>
+      <td>136632</td>
+      <td>160093</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10629,7 +12897,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -10644,12 +12911,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10679,11 +12961,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -10713,8 +12995,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>189</td>
-      <td>19958</td>
+      <td>20749</td>
+      <td>22184</td>
+      <td>455</td>
+      <td>469</td>
+      <td>1239</td>
+      <td>1239</td>
+      <td>71</td>
+      <td>71</td>
+      <td>2666</td>
+      <td>2666</td>
+      <td>53</td>
+      <td>53</td>
+      <td>24654</td>
+      <td>26089</td>
+      <td>579</td>
+      <td>593</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10778,8 +13074,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>71</td>
-      <td>726</td>
+      <td>795</td>
+      <td>795</td>
+      <td>104</td>
+      <td>104</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>461</td>
+      <td>461</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1256</td>
+      <td>1256</td>
+      <td>116</td>
+      <td>116</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10843,8 +13153,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>53</td>
+      <td>106</td>
+      <td>106</td>
+      <td>25</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>106</td>
+      <td>106</td>
+      <td>25</td>
+      <td>25</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10874,8 +13198,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -10907,9 +13230,24 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>1</td>
       <td>0</td>
-      <td>8320</td>
-      <td>162790</td>
+      <td>182221</td>
+      <td>192389</td>
+      <td>19343</td>
+      <td>20494</td>
+      <td>163961</td>
+      <td>182413</td>
+      <td>26449</td>
+      <td>29758</td>
+      <td>40663</td>
+      <td>41855</td>
+      <td>5974</td>
+      <td>6157</td>
+      <td>386845</td>
+      <td>416657</td>
+      <td>51766</td>
+      <td>56409</td>
       <td>False</td>
     </tr>
     <tr>
@@ -10975,6 +13313,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11040,6 +13392,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11103,8 +13469,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>33</td>
-      <td>844</td>
+      <td>854</td>
+      <td>860</td>
+      <td>110</td>
+      <td>111</td>
+      <td>79</td>
+      <td>79</td>
+      <td>15</td>
+      <td>15</td>
+      <td>274</td>
+      <td>274</td>
+      <td>13</td>
+      <td>13</td>
+      <td>1207</td>
+      <td>1213</td>
+      <td>138</td>
+      <td>139</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11150,7 +13530,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -11164,12 +13543,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>3</td>
-      <td>836</td>
+      <td>839</td>
+      <td>839</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>269</td>
+      <td>269</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1108</td>
+      <td>1108</td>
+      <td>17</td>
+      <td>17</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11199,8 +13593,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -11229,12 +13622,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2195</td>
-      <td>63235</td>
+      <td>99052</td>
+      <td>100009</td>
+      <td>5671</td>
+      <td>5755</td>
+      <td>40386</td>
+      <td>40386</td>
+      <td>3371</td>
+      <td>3371</td>
+      <td>17919</td>
+      <td>17919</td>
+      <td>2188</td>
+      <td>2188</td>
+      <td>157357</td>
+      <td>158314</td>
+      <td>11230</td>
+      <td>11314</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11264,10 +13672,9 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -11294,12 +13701,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>15</td>
-      <td>1074</td>
+      <td>1091</td>
+      <td>1091</td>
+      <td>44</td>
+      <td>44</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1091</td>
+      <td>1091</td>
+      <td>44</td>
+      <td>44</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11329,8 +13751,7 @@
       <td>16</td>
       <td>16</td>
       <td>16</td>
-      <td>16</td>
-      <td>16</td>
+      <td>0</td>
       <td>16</td>
       <td>16</td>
       <td>16</td>
@@ -11359,12 +13780,27 @@
       <td>0</td>
       <td>0</td>
       <td>16</td>
+      <td>15</td>
       <td>16</td>
       <td>16</td>
       <td>15</td>
       <td>0</td>
-      <td>4066</td>
-      <td>365597</td>
+      <td>391141</td>
+      <td>443752</td>
+      <td>9760</td>
+      <td>10546</td>
+      <td>306361</td>
+      <td>350178</td>
+      <td>11767</td>
+      <td>13684</td>
+      <td>227235</td>
+      <td>244814</td>
+      <td>3192</td>
+      <td>3617</td>
+      <td>924737</td>
+      <td>1038744</td>
+      <td>24719</td>
+      <td>27847</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11410,7 +13846,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -11429,7 +13864,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>125</td>
+      <td>125</td>
+      <td>26</td>
+      <td>26</td>
+      <td>2489</td>
+      <td>2489</td>
+      <td>139</td>
+      <td>139</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>2614</td>
+      <td>2614</td>
+      <td>165</td>
+      <td>165</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11459,8 +13909,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -11489,12 +13938,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>448</td>
-      <td>25505</td>
+      <td>33637</td>
+      <td>34195</td>
+      <td>1113</td>
+      <td>1172</td>
+      <td>16257</td>
+      <td>16257</td>
+      <td>1816</td>
+      <td>1816</td>
+      <td>7582</td>
+      <td>7582</td>
+      <td>899</td>
+      <td>899</td>
+      <td>57476</td>
+      <td>58034</td>
+      <td>3828</td>
+      <td>3887</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11524,11 +13988,10 @@
       <td>1</td>
       <td>1</td>
       <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11555,11 +14018,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>210</td>
-      <td>4080</td>
+      <td>4411</td>
+      <td>4411</td>
+      <td>396</td>
+      <td>396</td>
+      <td>9708</td>
+      <td>9708</td>
+      <td>279</td>
+      <td>279</td>
+      <td>2099</td>
+      <td>2099</td>
+      <td>212</td>
+      <td>212</td>
+      <td>16218</td>
+      <td>16218</td>
+      <td>887</td>
+      <td>887</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11586,11 +14064,11 @@
       <td>2.5.2</td>
       <td>De-novo assembly, Genome assembly</td>
       <td>Sequencing, Sequence assembly</td>
-      <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
+      <td>1</td>
       <td>0</td>
       <td>1</td>
       <td>0</td>
@@ -11623,8 +14101,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>84</td>
-      <td>268</td>
+      <td>391</td>
+      <td>391</td>
+      <td>158</td>
+      <td>158</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>391</td>
+      <td>391</td>
+      <td>158</td>
+      <td>158</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11654,10 +14146,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -11684,12 +14175,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5</td>
-      <td>142</td>
+      <td>107</td>
+      <td>143</td>
+      <td>13</td>
+      <td>15</td>
+      <td>148</td>
+      <td>148</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>255</td>
+      <td>291</td>
+      <td>33</td>
+      <td>35</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11753,8 +14259,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2</td>
-      <td>861</td>
+      <td>118</td>
+      <td>863</td>
+      <td>19</td>
+      <td>26</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>118</td>
+      <td>863</td>
+      <td>19</td>
+      <td>26</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11820,6 +14340,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11849,11 +14383,11 @@
       <td>1</td>
       <td>0</td>
       <td>2</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>2</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -11883,8 +14417,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
-      <td>45</td>
+      <td>352</td>
+      <td>352</td>
+      <td>42</td>
+      <td>42</td>
+      <td>8</td>
+      <td>8</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>360</td>
+      <td>360</td>
+      <td>48</td>
+      <td>48</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11914,9 +14462,8 @@
       <td>0</td>
       <td>10</td>
       <td>10</td>
-      <td>10</td>
       <td>0</td>
-      <td>10</td>
+      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
@@ -11945,11 +14492,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>0</td>
-      <td>503</td>
-      <td>26251</td>
+      <td>37598</td>
+      <td>37598</td>
+      <td>1277</td>
+      <td>1277</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3862</td>
+      <td>3862</td>
+      <td>280</td>
+      <td>280</td>
+      <td>41460</td>
+      <td>41460</td>
+      <td>1557</td>
+      <td>1557</td>
       <td>False</td>
     </tr>
     <tr>
@@ -11979,11 +14541,10 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -12014,7 +14575,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>12</td>
+      <td>12</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12078,8 +14654,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>53</td>
-      <td>774</td>
+      <td>897</td>
+      <td>897</td>
+      <td>99</td>
+      <td>99</td>
+      <td>1792</td>
+      <td>1792</td>
+      <td>239</td>
+      <td>239</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2689</td>
+      <td>2689</td>
+      <td>338</td>
+      <td>338</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12094,7 +14684,7 @@
       <td>OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.</td>
       <td>Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment</td>
       <td>Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/davidemms/OrthoFinder</td>
       <td>Phylogenetics, Sequence Analysis</td>
       <td>orthofinder</td>
@@ -12103,17 +14693,17 @@
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder</td>
       <td>2.5.5</td>
       <td>orthofinder</td>
-      <td>2.5.5</td>
+      <td>3.0.1b1</td>
       <td>Genome comparison, Genome alignment</td>
       <td>Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -12143,8 +14733,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>239</td>
-      <td>1333</td>
+      <td>2018</td>
+      <td>2018</td>
+      <td>419</td>
+      <td>419</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>438</td>
+      <td>438</td>
+      <td>58</td>
+      <td>58</td>
+      <td>2456</td>
+      <td>2456</td>
+      <td>477</td>
+      <td>477</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12174,8 +14778,7 @@
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
@@ -12204,12 +14807,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>4</td>
       <td>2</td>
       <td>0</td>
-      <td>485</td>
-      <td>17477</td>
+      <td>11986</td>
+      <td>17898</td>
+      <td>1046</td>
+      <td>1153</td>
+      <td>1314</td>
+      <td>1314</td>
+      <td>389</td>
+      <td>389</td>
+      <td>3034</td>
+      <td>3034</td>
+      <td>118</td>
+      <td>118</td>
+      <td>16334</td>
+      <td>22246</td>
+      <td>1553</td>
+      <td>1660</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12239,8 +14857,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -12270,11 +14887,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>19</td>
-      <td>165</td>
+      <td>773</td>
+      <td>773</td>
+      <td>60</td>
+      <td>60</td>
+      <td>495</td>
+      <td>495</td>
+      <td>72</td>
+      <td>72</td>
+      <td>246</td>
+      <td>246</td>
+      <td>17</td>
+      <td>17</td>
+      <td>1514</td>
+      <td>1514</td>
+      <td>149</td>
+      <td>149</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12320,7 +14952,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12335,11 +14966,26 @@
       <td>0</td>
       <td>1</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>74</td>
-      <td>2565</td>
+      <td>5462</td>
+      <td>5462</td>
+      <td>334</td>
+      <td>334</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>309</td>
+      <td>309</td>
+      <td>52</td>
+      <td>52</td>
+      <td>5771</td>
+      <td>5771</td>
+      <td>386</td>
+      <td>386</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12369,11 +15015,10 @@
       <td>0</td>
       <td>1</td>
       <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>0</td>
       <td>1</td>
       <td>4</td>
-      <td>4</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -12400,11 +15045,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>82</td>
-      <td>812</td>
+      <td>1199</td>
+      <td>1199</td>
+      <td>193</td>
+      <td>193</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1205</td>
+      <td>1205</td>
+      <td>194</td>
+      <td>194</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12434,9 +15094,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -12464,12 +15123,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>104</td>
-      <td>1770</td>
+      <td>1975</td>
+      <td>2034</td>
+      <td>246</td>
+      <td>258</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>553</td>
+      <td>564</td>
+      <td>140</td>
+      <td>144</td>
+      <td>2528</td>
+      <td>2598</td>
+      <td>386</td>
+      <td>402</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12499,11 +15173,10 @@
       <td>0</td>
       <td>6</td>
       <td>5</td>
-      <td>6</td>
+      <td>0</td>
       <td>0</td>
       <td>6</td>
       <td>5</td>
-      <td>6</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -12530,11 +15203,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>45</td>
-      <td>1095</td>
+      <td>867</td>
+      <td>1128</td>
+      <td>144</td>
+      <td>165</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2106</td>
+      <td>2106</td>
+      <td>121</td>
+      <td>121</td>
+      <td>2973</td>
+      <td>3234</td>
+      <td>265</td>
+      <td>286</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12598,8 +15286,22 @@
       <td>7</td>
       <td>0</td>
       <td>0</td>
-      <td>88</td>
-      <td>1000</td>
+      <td>2532</td>
+      <td>2532</td>
+      <td>382</td>
+      <td>382</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1311</td>
+      <td>1311</td>
+      <td>83</td>
+      <td>83</td>
+      <td>3844</td>
+      <td>3844</td>
+      <td>466</td>
+      <td>466</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12643,7 +15345,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -12659,12 +15360,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>278</td>
-      <td>22589</td>
+      <td>37086</td>
+      <td>37272</td>
+      <td>711</td>
+      <td>734</td>
+      <td>6346</td>
+      <td>6346</td>
+      <td>583</td>
+      <td>583</td>
+      <td>3065</td>
+      <td>3065</td>
+      <td>61</td>
+      <td>61</td>
+      <td>46497</td>
+      <td>46683</td>
+      <td>1355</td>
+      <td>1378</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12694,8 +15410,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -12725,17 +15440,32 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
-      <td>22</td>
-      <td>False</td>
-    </tr>
-    <tr>
-      <td></td>
-      <td>plasmidspades</td>
-      <td>plasmidspades</td>
+      <td>14652</td>
+      <td>14652</td>
+      <td>251</td>
+      <td>251</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>101</td>
+      <td>101</td>
+      <td>18</td>
+      <td>18</td>
+      <td>14753</td>
+      <td>14753</td>
+      <td>269</td>
+      <td>269</td>
+      <td>False</td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plasmidspades</td>
+      <td>plasmidspades</td>
       <td>Genome assembler for assemblying plasmid</td>
       <td></td>
       <td></td>
@@ -12774,7 +15504,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -12795,6 +15524,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12824,9 +15568,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -12855,11 +15598,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>24</td>
-      <td>239</td>
+      <td>731</td>
+      <td>731</td>
+      <td>86</td>
+      <td>86</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>4</td>
+      <td>4</td>
+      <td>773</td>
+      <td>773</td>
+      <td>90</td>
+      <td>90</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12889,9 +15647,8 @@
       <td>0</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -12902,7 +15659,7 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -12924,7 +15681,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>1902</td>
+      <td>1902</td>
+      <td>167</td>
+      <td>167</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>1902</td>
+      <td>1902</td>
+      <td>167</td>
+      <td>167</td>
       <td>False</td>
     </tr>
     <tr>
@@ -12954,8 +15726,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -12984,12 +15755,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3233</td>
-      <td>371445</td>
+      <td>464359</td>
+      <td>476554</td>
+      <td>7475</td>
+      <td>7721</td>
+      <td>313285</td>
+      <td>331256</td>
+      <td>11243</td>
+      <td>12384</td>
+      <td>131211</td>
+      <td>141875</td>
+      <td>4358</td>
+      <td>4947</td>
+      <td>908855</td>
+      <td>949685</td>
+      <td>23076</td>
+      <td>25052</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13055,6 +15841,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13100,7 +15900,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -13114,12 +15913,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>200</td>
-      <td>3320</td>
+      <td>3962</td>
+      <td>3962</td>
+      <td>501</td>
+      <td>501</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3962</td>
+      <td>3962</td>
+      <td>501</td>
+      <td>501</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13149,8 +15963,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -13180,11 +15993,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>350</td>
-      <td>21123</td>
+      <td>22742</td>
+      <td>22742</td>
+      <td>557</td>
+      <td>557</td>
+      <td>2159</td>
+      <td>2159</td>
+      <td>716</td>
+      <td>716</td>
+      <td>776</td>
+      <td>776</td>
+      <td>448</td>
+      <td>448</td>
+      <td>25677</td>
+      <td>25677</td>
+      <td>1721</td>
+      <td>1721</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13214,8 +16042,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -13244,12 +16071,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>377</td>
-      <td>11332</td>
+      <td>12858</td>
+      <td>13232</td>
+      <td>986</td>
+      <td>996</td>
+      <td>8092</td>
+      <td>8092</td>
+      <td>943</td>
+      <td>943</td>
+      <td>3238</td>
+      <td>3238</td>
+      <td>124</td>
+      <td>124</td>
+      <td>24188</td>
+      <td>24562</td>
+      <td>2053</td>
+      <td>2063</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13279,10 +16121,9 @@
       <td>0</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -13310,11 +16151,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
-      <td>68</td>
-      <td>1909</td>
+      <td>2092</td>
+      <td>2342</td>
+      <td>209</td>
+      <td>238</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2094</td>
+      <td>2344</td>
+      <td>210</td>
+      <td>239</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13344,10 +16200,9 @@
       <td>0</td>
       <td>0</td>
       <td>32</td>
-      <td>32</td>
       <td>0</td>
       <td>0</td>
-      <td>32</td>
+      <td>0</td>
       <td>32</td>
       <td>0</td>
       <td>0</td>
@@ -13375,11 +16230,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>31</td>
       <td>31</td>
       <td>0</td>
-      <td>1155</td>
-      <td>28681</td>
+      <td>31825</td>
+      <td>34677</td>
+      <td>3375</td>
+      <td>3785</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>14</td>
+      <td>14</td>
+      <td>4</td>
+      <td>4</td>
+      <td>31840</td>
+      <td>34692</td>
+      <td>3380</td>
+      <td>3790</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13409,11 +16279,10 @@
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>1</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -13439,12 +16308,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
       <td>0</td>
-      <td>1328</td>
-      <td>664470</td>
+      <td>684820</td>
+      <td>684820</td>
+      <td>3239</td>
+      <td>3239</td>
+      <td>90503</td>
+      <td>90503</td>
+      <td>3881</td>
+      <td>3881</td>
+      <td>29018</td>
+      <td>29018</td>
+      <td>826</td>
+      <td>826</td>
+      <td>804341</td>
+      <td>804341</td>
+      <td>7946</td>
+      <td>7946</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13474,8 +16358,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -13504,12 +16387,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>3567</td>
-      <td>51567</td>
+      <td>67737</td>
+      <td>69738</td>
+      <td>7787</td>
+      <td>7971</td>
+      <td>51925</td>
+      <td>56602</td>
+      <td>9692</td>
+      <td>10646</td>
+      <td>32003</td>
+      <td>34145</td>
+      <td>3890</td>
+      <td>4127</td>
+      <td>151665</td>
+      <td>160485</td>
+      <td>21369</td>
+      <td>22744</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13528,7 +16426,7 @@
       <td>https://github.com/mahulchak/quickmerge</td>
       <td>Assembly</td>
       <td>quickmerge</td>
-      <td>galaxy-australia</td>
+      <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge</td>
       <td>0.3</td>
@@ -13575,6 +16473,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13640,6 +16552,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13669,8 +16595,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -13699,12 +16624,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>309</td>
-      <td>21353</td>
+      <td>27113</td>
+      <td>27315</td>
+      <td>839</td>
+      <td>850</td>
+      <td>9089</td>
+      <td>9089</td>
+      <td>475</td>
+      <td>475</td>
+      <td>5452</td>
+      <td>5452</td>
+      <td>171</td>
+      <td>171</td>
+      <td>41654</td>
+      <td>41856</td>
+      <td>1485</td>
+      <td>1496</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13768,8 +16708,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>9</td>
+      <td>9</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13799,8 +16753,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -13829,12 +16782,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>383</td>
-      <td>6808</td>
+      <td>10905</td>
+      <td>10905</td>
+      <td>966</td>
+      <td>966</td>
+      <td>5100</td>
+      <td>5114</td>
+      <td>587</td>
+      <td>587</td>
+      <td>4955</td>
+      <td>6094</td>
+      <td>765</td>
+      <td>892</td>
+      <td>20960</td>
+      <td>22113</td>
+      <td>2318</td>
+      <td>2445</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13880,7 +16848,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -13895,11 +16862,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>71</td>
-      <td>3370</td>
+      <td>3710</td>
+      <td>3710</td>
+      <td>80</td>
+      <td>80</td>
+      <td>7</td>
+      <td>7</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3717</td>
+      <td>3717</td>
+      <td>86</td>
+      <td>86</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13965,6 +16947,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -13994,8 +16990,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -14025,11 +17020,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>48</td>
-      <td>331</td>
+      <td>472</td>
+      <td>472</td>
+      <td>92</td>
+      <td>92</td>
+      <td>32</td>
+      <td>32</td>
+      <td>13</td>
+      <td>13</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td>510</td>
+      <td>510</td>
+      <td>109</td>
+      <td>109</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14093,8 +17103,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>95</td>
+      <td>95</td>
+      <td>38</td>
+      <td>38</td>
       <td>0</td>
-      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>95</td>
+      <td>95</td>
+      <td>38</td>
+      <td>38</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14124,8 +17148,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -14154,12 +17177,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>656</td>
-      <td>12225</td>
+      <td>15196</td>
+      <td>15685</td>
+      <td>1459</td>
+      <td>1501</td>
+      <td>12188</td>
+      <td>12188</td>
+      <td>1768</td>
+      <td>1768</td>
+      <td>4881</td>
+      <td>5539</td>
+      <td>518</td>
+      <td>555</td>
+      <td>32265</td>
+      <td>33412</td>
+      <td>3745</td>
+      <td>3824</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14189,8 +17227,7 @@
       <td>22</td>
       <td>22</td>
       <td>22</td>
-      <td>22</td>
-      <td>22</td>
+      <td>0</td>
       <td>22</td>
       <td>22</td>
       <td>22</td>
@@ -14219,12 +17256,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>22</td>
       <td>22</td>
       <td>22</td>
       <td>0</td>
-      <td>3206</td>
-      <td>133498</td>
+      <td>136315</td>
+      <td>147595</td>
+      <td>8341</td>
+      <td>9385</td>
+      <td>138707</td>
+      <td>161046</td>
+      <td>10696</td>
+      <td>12789</td>
+      <td>22718</td>
+      <td>23767</td>
+      <td>1593</td>
+      <td>1695</td>
+      <td>297740</td>
+      <td>332408</td>
+      <td>20630</td>
+      <td>23869</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14254,11 +17306,10 @@
       <td>2</td>
       <td>2</td>
       <td>3</td>
-      <td>1</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>3</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -14284,12 +17335,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>969</td>
-      <td>61937</td>
+      <td>73085</td>
+      <td>77081</td>
+      <td>2243</td>
+      <td>2319</td>
+      <td>90634</td>
+      <td>122835</td>
+      <td>3402</td>
+      <td>4726</td>
+      <td>13371</td>
+      <td>15818</td>
+      <td>513</td>
+      <td>586</td>
+      <td>177090</td>
+      <td>215734</td>
+      <td>6158</td>
+      <td>7631</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14353,8 +17419,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>7</td>
-      <td>173</td>
+      <td>174</td>
+      <td>174</td>
+      <td>16</td>
+      <td>16</td>
+      <td>399</td>
+      <td>399</td>
+      <td>29</td>
+      <td>29</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>573</td>
+      <td>573</td>
+      <td>45</td>
+      <td>45</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14418,8 +17498,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1</td>
       <td>140</td>
+      <td>140</td>
+      <td>5</td>
+      <td>5</td>
+      <td>253</td>
+      <td>253</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>393</td>
+      <td>393</td>
+      <td>11</td>
+      <td>11</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14465,7 +17559,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -14480,11 +17573,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>61</td>
-      <td>676</td>
+      <td>901</td>
+      <td>901</td>
+      <td>90</td>
+      <td>90</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>901</td>
+      <td>901</td>
+      <td>90</td>
+      <td>90</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14514,11 +17622,11 @@
       <td>0</td>
       <td>0</td>
       <td>6</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>6</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -14548,8 +17656,22 @@
       <td>6</td>
       <td>0</td>
       <td>0</td>
-      <td>39</td>
-      <td>542</td>
+      <td>931</td>
+      <td>931</td>
+      <td>93</td>
+      <td>93</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>931</td>
+      <td>931</td>
+      <td>93</td>
+      <td>93</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14579,11 +17701,10 @@
       <td>0</td>
       <td>2</td>
       <td>5</td>
-      <td>3</td>
+      <td>0</td>
       <td>0</td>
       <td>2</td>
       <td>5</td>
-      <td>3</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -14610,11 +17731,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>129</td>
-      <td>1964</td>
+      <td>3364</td>
+      <td>3364</td>
+      <td>247</td>
+      <td>247</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>244</td>
+      <td>244</td>
+      <td>33</td>
+      <td>33</td>
+      <td>3608</td>
+      <td>3608</td>
+      <td>280</td>
+      <td>280</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14678,8 +17814,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>2424</td>
+      <td>2424</td>
+      <td>102</td>
+      <td>102</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>2424</td>
+      <td>2424</td>
+      <td>102</td>
+      <td>102</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14743,8 +17893,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>4182</td>
+      <td>4182</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
-      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4182</td>
+      <td>4182</td>
+      <td>42</td>
+      <td>42</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14790,7 +17954,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -14810,6 +17973,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14839,8 +18017,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -14869,12 +18046,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1008</td>
-      <td>41600</td>
+      <td>46125</td>
+      <td>47376</td>
+      <td>2273</td>
+      <td>2356</td>
+      <td>40577</td>
+      <td>40577</td>
+      <td>3971</td>
+      <td>3971</td>
+      <td>19960</td>
+      <td>21130</td>
+      <td>1085</td>
+      <td>1199</td>
+      <td>106662</td>
+      <td>109083</td>
+      <td>7329</td>
+      <td>7526</td>
       <td>False</td>
     </tr>
     <tr>
@@ -14920,7 +18112,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -14935,11 +18126,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>133</td>
-      <td>2489</td>
+      <td>3457</td>
+      <td>3457</td>
+      <td>301</td>
+      <td>301</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>556</td>
+      <td>556</td>
+      <td>65</td>
+      <td>65</td>
+      <td>4013</td>
+      <td>4013</td>
+      <td>366</td>
+      <td>366</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15003,8 +18209,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>6</td>
-      <td>121</td>
+      <td>158</td>
+      <td>158</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>8</td>
+      <td>8</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15050,7 +18270,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15070,6 +18289,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15133,8 +18367,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>133</td>
-      <td>1349</td>
+      <td>1499</td>
+      <td>1638</td>
+      <td>331</td>
+      <td>358</td>
+      <td>779</td>
+      <td>779</td>
+      <td>244</td>
+      <td>244</td>
+      <td>467</td>
+      <td>467</td>
+      <td>83</td>
+      <td>83</td>
+      <td>2745</td>
+      <td>2884</td>
+      <td>658</td>
+      <td>685</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15164,8 +18412,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -15194,12 +18441,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>2</td>
       <td>0</td>
-      <td>1372</td>
-      <td>105708</td>
+      <td>121363</td>
+      <td>124773</td>
+      <td>3448</td>
+      <td>3602</td>
+      <td>92504</td>
+      <td>92504</td>
+      <td>3945</td>
+      <td>3945</td>
+      <td>48068</td>
+      <td>52034</td>
+      <td>2705</td>
+      <td>3073</td>
+      <td>261935</td>
+      <td>269311</td>
+      <td>10098</td>
+      <td>10620</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15245,7 +18507,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15260,9 +18521,24 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>False</td>
@@ -15294,8 +18570,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -15324,12 +18599,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>376</td>
-      <td>18183</td>
+      <td>19865</td>
+      <td>21034</td>
+      <td>1047</td>
+      <td>1126</td>
+      <td>3141</td>
+      <td>3141</td>
+      <td>328</td>
+      <td>328</td>
+      <td>3304</td>
+      <td>3304</td>
+      <td>189</td>
+      <td>189</td>
+      <td>26310</td>
+      <td>27479</td>
+      <td>1564</td>
+      <td>1643</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15338,7 +18628,7 @@
       <td>spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades</td>
       <td>SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.</td>
       <td>spades</td>
-      <td>spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades</td>
+      <td>spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades</td>
       <td></td>
       <td>SPAdes</td>
       <td>St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.</td>
@@ -15359,8 +18649,7 @@
       <td>9</td>
       <td>9</td>
       <td>9</td>
-      <td>9</td>
-      <td>9</td>
+      <td>0</td>
       <td>9</td>
       <td>9</td>
       <td>9</td>
@@ -15389,12 +18678,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>9</td>
       <td>3</td>
       <td>0</td>
-      <td>3547</td>
-      <td>72953</td>
+      <td>82716</td>
+      <td>87113</td>
+      <td>8209</td>
+      <td>8526</td>
+      <td>120471</td>
+      <td>120475</td>
+      <td>14787</td>
+      <td>14790</td>
+      <td>54067</td>
+      <td>61541</td>
+      <td>5817</td>
+      <td>6653</td>
+      <td>257254</td>
+      <td>269129</td>
+      <td>28813</td>
+      <td>29969</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15458,8 +18762,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>12</td>
-      <td>1278</td>
+      <td>1436</td>
+      <td>1436</td>
+      <td>23</td>
+      <td>23</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1436</td>
+      <td>1436</td>
+      <td>23</td>
+      <td>23</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15504,7 +18822,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -15525,6 +18842,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>80</td>
+      <td>80</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>80</td>
+      <td>80</td>
+      <td>1</td>
+      <td>1</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15570,7 +18902,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15585,11 +18916,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>22</td>
-      <td>205</td>
+      <td>297</td>
+      <td>297</td>
+      <td>40</td>
+      <td>40</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>368</td>
+      <td>368</td>
+      <td>41</td>
+      <td>41</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15635,7 +18981,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15650,11 +18995,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>22</td>
-      <td>205</td>
+      <td>297</td>
+      <td>297</td>
+      <td>40</td>
+      <td>40</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>368</td>
+      <td>368</td>
+      <td>41</td>
+      <td>41</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15684,8 +19044,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -15714,12 +19073,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>889</td>
-      <td>12673</td>
+      <td>20778</td>
+      <td>20891</td>
+      <td>2030</td>
+      <td>2045</td>
+      <td>9520</td>
+      <td>9520</td>
+      <td>1424</td>
+      <td>1424</td>
+      <td>6753</td>
+      <td>6753</td>
+      <td>864</td>
+      <td>864</td>
+      <td>37051</td>
+      <td>37164</td>
+      <td>4318</td>
+      <td>4333</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15765,7 +19139,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -15785,6 +19158,21 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15814,11 +19202,11 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -15848,8 +19236,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>59</td>
-      <td>2623</td>
+      <td>2858</td>
+      <td>3001</td>
+      <td>118</td>
+      <td>123</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2858</td>
+      <td>3001</td>
+      <td>118</td>
+      <td>123</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15879,8 +19281,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -15910,11 +19311,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>6</td>
-      <td>13</td>
+      <td>249</td>
+      <td>249</td>
+      <td>32</td>
+      <td>32</td>
+      <td>16</td>
+      <td>16</td>
+      <td>10</td>
+      <td>10</td>
+      <td>102</td>
+      <td>102</td>
+      <td>16</td>
+      <td>16</td>
+      <td>367</td>
+      <td>367</td>
+      <td>58</td>
+      <td>58</td>
       <td>False</td>
     </tr>
     <tr>
@@ -15944,11 +19360,11 @@
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>2</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>2</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -15978,8 +19394,22 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>5</td>
+      <td>117</td>
+      <td>117</td>
+      <td>41</td>
+      <td>41</td>
+      <td>84</td>
+      <td>84</td>
+      <td>24</td>
+      <td>24</td>
+      <td>161</td>
+      <td>161</td>
+      <td>13</td>
+      <td>13</td>
+      <td>362</td>
+      <td>362</td>
+      <td>78</td>
+      <td>78</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16009,8 +19439,7 @@
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
@@ -16040,11 +19469,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>5</td>
-      <td>67</td>
+      <td>217</td>
+      <td>217</td>
+      <td>47</td>
+      <td>47</td>
+      <td>42</td>
+      <td>42</td>
+      <td>20</td>
+      <td>20</td>
+      <td>96</td>
+      <td>96</td>
+      <td>12</td>
+      <td>12</td>
+      <td>355</td>
+      <td>355</td>
+      <td>79</td>
+      <td>79</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16074,11 +19518,11 @@
       <td>4</td>
       <td>4</td>
       <td>4</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
-      <td>4</td>
-      <td>4</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -16108,8 +19552,22 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>31</td>
-      <td>202</td>
+      <td>721</td>
+      <td>721</td>
+      <td>160</td>
+      <td>160</td>
+      <td>350</td>
+      <td>350</td>
+      <td>91</td>
+      <td>91</td>
+      <td>214</td>
+      <td>214</td>
+      <td>35</td>
+      <td>35</td>
+      <td>1285</td>
+      <td>1285</td>
+      <td>286</td>
+      <td>286</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16139,11 +19597,11 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -16173,8 +19631,22 @@
       <td>3</td>
       <td>0</td>
       <td>0</td>
+      <td>125</td>
+      <td>125</td>
+      <td>30</td>
+      <td>30</td>
+      <td>13</td>
+      <td>13</td>
       <td>9</td>
-      <td>73</td>
+      <td>9</td>
+      <td>83</td>
+      <td>83</td>
+      <td>8</td>
+      <td>8</td>
+      <td>221</td>
+      <td>221</td>
+      <td>47</td>
+      <td>47</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16204,8 +19676,7 @@
       <td>6</td>
       <td>6</td>
       <td>6</td>
-      <td>6</td>
-      <td>6</td>
+      <td>0</td>
       <td>6</td>
       <td>6</td>
       <td>6</td>
@@ -16235,11 +19706,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>6</td>
       <td>0</td>
       <td>0</td>
-      <td>26</td>
-      <td>114</td>
+      <td>396</td>
+      <td>396</td>
+      <td>134</td>
+      <td>134</td>
+      <td>121</td>
+      <td>121</td>
+      <td>57</td>
+      <td>57</td>
+      <td>144</td>
+      <td>144</td>
+      <td>39</td>
+      <td>39</td>
+      <td>661</td>
+      <td>661</td>
+      <td>230</td>
+      <td>230</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16269,11 +19755,11 @@
       <td>21</td>
       <td>21</td>
       <td>22</td>
-      <td>21</td>
+      <td>0</td>
       <td>21</td>
       <td>21</td>
       <td>22</td>
-      <td>21</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -16303,8 +19789,22 @@
       <td>21</td>
       <td>0</td>
       <td>0</td>
-      <td>43</td>
-      <td>168</td>
+      <td>964</td>
+      <td>964</td>
+      <td>318</td>
+      <td>318</td>
+      <td>249</td>
+      <td>249</td>
+      <td>118</td>
+      <td>118</td>
+      <td>475</td>
+      <td>475</td>
+      <td>108</td>
+      <td>108</td>
+      <td>1688</td>
+      <td>1688</td>
+      <td>544</td>
+      <td>544</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16334,11 +19834,11 @@
       <td>12</td>
       <td>12</td>
       <td>12</td>
+      <td>0</td>
       <td>12</td>
       <td>12</td>
       <td>12</td>
-      <td>12</td>
-      <td>12</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -16368,8 +19868,22 @@
       <td>12</td>
       <td>0</td>
       <td>0</td>
-      <td>4</td>
-      <td>4</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>13</td>
+      <td>13</td>
+      <td>11</td>
+      <td>11</td>
+      <td>1302</td>
+      <td>1302</td>
+      <td>19</td>
+      <td>19</td>
+      <td>1323</td>
+      <td>1323</td>
+      <td>38</td>
+      <td>38</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16399,8 +19913,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -16430,11 +19943,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>2</td>
-      <td>6</td>
+      <td>58</td>
+      <td>58</td>
+      <td>23</td>
+      <td>23</td>
+      <td>24</td>
+      <td>24</td>
+      <td>11</td>
+      <td>11</td>
+      <td>92</td>
+      <td>92</td>
+      <td>11</td>
+      <td>11</td>
+      <td>174</td>
+      <td>174</td>
+      <td>45</td>
+      <td>45</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16464,8 +19992,7 @@
       <td>10</td>
       <td>10</td>
       <td>10</td>
-      <td>10</td>
-      <td>10</td>
+      <td>0</td>
       <td>10</td>
       <td>10</td>
       <td>10</td>
@@ -16495,11 +20022,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>10</td>
       <td>0</td>
       <td>0</td>
-      <td>48</td>
-      <td>263</td>
+      <td>863</td>
+      <td>863</td>
+      <td>220</td>
+      <td>220</td>
+      <td>237</td>
+      <td>237</td>
+      <td>98</td>
+      <td>98</td>
+      <td>181</td>
+      <td>181</td>
+      <td>41</td>
+      <td>41</td>
+      <td>1281</td>
+      <td>1281</td>
+      <td>359</td>
+      <td>359</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16529,8 +20071,7 @@
       <td>17</td>
       <td>17</td>
       <td>17</td>
-      <td>17</td>
-      <td>17</td>
+      <td>0</td>
       <td>17</td>
       <td>17</td>
       <td>17</td>
@@ -16560,11 +20101,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>17</td>
       <td>0</td>
       <td>0</td>
-      <td>59</td>
-      <td>213</td>
+      <td>983</td>
+      <td>983</td>
+      <td>287</td>
+      <td>287</td>
+      <td>375</td>
+      <td>375</td>
+      <td>144</td>
+      <td>144</td>
+      <td>907</td>
+      <td>907</td>
+      <td>106</td>
+      <td>106</td>
+      <td>2265</td>
+      <td>2265</td>
+      <td>537</td>
+      <td>537</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16594,8 +20150,7 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
@@ -16625,11 +20180,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>6</td>
-      <td>20</td>
+      <td>46</td>
+      <td>46</td>
+      <td>13</td>
+      <td>13</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>55</td>
+      <td>18</td>
+      <td>18</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16659,11 +20229,11 @@
       <td>11</td>
       <td>11</td>
       <td>11</td>
+      <td>0</td>
       <td>11</td>
       <td>11</td>
       <td>11</td>
-      <td>11</td>
-      <td>11</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -16693,8 +20263,22 @@
       <td>11</td>
       <td>0</td>
       <td>0</td>
-      <td>6</td>
+      <td>37</td>
+      <td>37</td>
+      <td>16</td>
+      <td>16</td>
+      <td>22</td>
+      <td>22</td>
+      <td>7</td>
+      <td>7</td>
+      <td>89</td>
+      <td>89</td>
       <td>14</td>
+      <td>14</td>
+      <td>148</td>
+      <td>148</td>
+      <td>37</td>
+      <td>37</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16724,11 +20308,11 @@
       <td>3</td>
       <td>3</td>
       <td>3</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
-      <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -16758,8 +20342,22 @@
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>40</td>
-      <td>232</td>
+      <td>615</td>
+      <td>615</td>
+      <td>143</td>
+      <td>143</td>
+      <td>246</td>
+      <td>246</td>
+      <td>75</td>
+      <td>75</td>
+      <td>115</td>
+      <td>115</td>
+      <td>27</td>
+      <td>27</td>
+      <td>976</td>
+      <td>976</td>
+      <td>245</td>
+      <td>245</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16789,11 +20387,11 @@
       <td>12</td>
       <td>12</td>
       <td>12</td>
+      <td>0</td>
       <td>12</td>
       <td>12</td>
       <td>12</td>
-      <td>12</td>
-      <td>12</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -16823,8 +20421,22 @@
       <td>12</td>
       <td>0</td>
       <td>0</td>
-      <td>12</td>
-      <td>37</td>
+      <td>330</td>
+      <td>330</td>
+      <td>83</td>
+      <td>83</td>
+      <td>64</td>
+      <td>64</td>
+      <td>40</td>
+      <td>40</td>
+      <td>195</td>
+      <td>195</td>
+      <td>49</td>
+      <td>49</td>
+      <td>589</td>
+      <td>589</td>
+      <td>172</td>
+      <td>172</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16854,8 +20466,7 @@
       <td>6</td>
       <td>6</td>
       <td>6</td>
-      <td>6</td>
-      <td>6</td>
+      <td>0</td>
       <td>6</td>
       <td>6</td>
       <td>6</td>
@@ -16885,11 +20496,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>6</td>
-      <td>0</td>
       <td>0</td>
+      <td>6</td>
       <td>0</td>
       <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
       <td>False</td>
     </tr>
     <tr>
@@ -16919,11 +20545,11 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -16953,8 +20579,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>14</td>
+      <td>14</td>
+      <td>16</td>
+      <td>16</td>
+      <td>6</td>
+      <td>6</td>
+      <td>37</td>
+      <td>37</td>
       <td>2</td>
-      <td>13</td>
+      <td>2</td>
+      <td>82</td>
+      <td>82</td>
+      <td>22</td>
+      <td>22</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17020,6 +20660,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17049,8 +20703,7 @@
       <td>15</td>
       <td>15</td>
       <td>15</td>
-      <td>15</td>
-      <td>15</td>
+      <td>0</td>
       <td>15</td>
       <td>15</td>
       <td>15</td>
@@ -17080,11 +20733,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>15</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
-      <td>1</td>
+      <td>10</td>
+      <td>10</td>
+      <td>3</td>
+      <td>3</td>
+      <td>14</td>
+      <td>14</td>
+      <td>10</td>
+      <td>10</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>29</td>
+      <td>29</td>
+      <td>18</td>
+      <td>18</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17110,12 +20778,11 @@
       <td></td>
       <td></td>
       <td></td>
-      <td></td>
-      <td>4</td>
-      <td>4</td>
+      <td></td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
+      <td>0</td>
       <td>4</td>
       <td>4</td>
       <td>4</td>
@@ -17145,11 +20812,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>22</td>
-      <td>172</td>
+      <td>664</td>
+      <td>664</td>
+      <td>145</td>
+      <td>145</td>
+      <td>113</td>
+      <td>113</td>
+      <td>43</td>
+      <td>43</td>
+      <td>255</td>
+      <td>255</td>
+      <td>50</td>
+      <td>50</td>
+      <td>1032</td>
+      <td>1032</td>
+      <td>238</td>
+      <td>238</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17179,11 +20861,11 @@
       <td>8</td>
       <td>8</td>
       <td>8</td>
-      <td>7</td>
+      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>8</td>
-      <td>7</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -17213,8 +20895,22 @@
       <td>8</td>
       <td>0</td>
       <td>0</td>
-      <td>8</td>
+      <td>84</td>
+      <td>84</td>
+      <td>52</td>
+      <td>52</td>
+      <td>25</td>
+      <td>25</td>
       <td>16</td>
+      <td>16</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>118</td>
+      <td>118</td>
+      <td>73</td>
+      <td>73</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17280,6 +20976,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17309,8 +21019,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -17340,11 +21049,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>124</td>
-      <td>7087</td>
+      <td>14941</td>
+      <td>14941</td>
+      <td>383</td>
+      <td>383</td>
+      <td>25941</td>
+      <td>25941</td>
+      <td>255</td>
+      <td>255</td>
+      <td>2856</td>
+      <td>2856</td>
+      <td>112</td>
+      <td>112</td>
+      <td>43738</td>
+      <td>43738</td>
+      <td>750</td>
+      <td>750</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17390,7 +21114,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -17404,12 +21127,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>31</td>
-      <td>457</td>
+      <td>411</td>
+      <td>472</td>
+      <td>68</td>
+      <td>90</td>
+      <td>102</td>
+      <td>7952</td>
+      <td>13</td>
+      <td>1240</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>513</td>
+      <td>8424</td>
+      <td>81</td>
+      <td>1330</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17455,7 +21193,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -17469,12 +21206,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>26</td>
-      <td>947</td>
+      <td>927</td>
+      <td>959</td>
+      <td>65</td>
+      <td>78</td>
+      <td>130</td>
+      <td>7194</td>
+      <td>18</td>
+      <td>1143</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1057</td>
+      <td>8153</td>
+      <td>83</td>
+      <td>1221</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17538,8 +21290,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>70</td>
-      <td>8690</td>
+      <td>3783</td>
+      <td>9125</td>
+      <td>211</td>
+      <td>229</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3784</td>
+      <td>9126</td>
+      <td>212</td>
+      <td>230</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17569,8 +21335,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -17599,12 +21364,27 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1801</td>
-      <td>27426</td>
+      <td>36069</td>
+      <td>36922</td>
+      <td>5257</td>
+      <td>5431</td>
+      <td>25255</td>
+      <td>30822</td>
+      <td>5066</td>
+      <td>5826</td>
+      <td>7949</td>
+      <td>7949</td>
+      <td>1584</td>
+      <td>1584</td>
+      <td>69273</td>
+      <td>75693</td>
+      <td>11907</td>
+      <td>12841</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17668,8 +21448,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>198</td>
-      <td>5161</td>
+      <td>6372</td>
+      <td>6395</td>
+      <td>372</td>
+      <td>379</td>
+      <td>7339</td>
+      <td>7339</td>
+      <td>378</td>
+      <td>378</td>
+      <td>6966</td>
+      <td>6966</td>
+      <td>154</td>
+      <td>154</td>
+      <td>20677</td>
+      <td>20700</td>
+      <td>904</td>
+      <td>911</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17699,10 +21493,9 @@
       <td>2</td>
       <td>0</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
       <td>0</td>
       <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
@@ -17734,7 +21527,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>9</td>
+      <td>9</td>
+      <td>6</td>
+      <td>6</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>71</td>
+      <td>71</td>
+      <td>14</td>
+      <td>14</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17798,8 +21606,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>84</td>
-      <td>907</td>
+      <td>1039</td>
+      <td>1039</td>
+      <td>189</td>
+      <td>189</td>
+      <td>2672</td>
+      <td>3349</td>
+      <td>467</td>
+      <td>485</td>
+      <td>358</td>
+      <td>358</td>
+      <td>47</td>
+      <td>47</td>
+      <td>4069</td>
+      <td>4746</td>
+      <td>703</td>
+      <td>721</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17863,8 +21685,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>5</td>
-      <td>229</td>
+      <td>250</td>
+      <td>254</td>
+      <td>31</td>
+      <td>31</td>
+      <td>174</td>
+      <td>174</td>
+      <td>45</td>
+      <td>45</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>424</td>
+      <td>428</td>
+      <td>76</td>
+      <td>76</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17894,8 +21730,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -17924,12 +21759,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>2334</td>
-      <td>238699</td>
+      <td>229489</td>
+      <td>275008</td>
+      <td>5733</td>
+      <td>6500</td>
+      <td>228708</td>
+      <td>324716</td>
+      <td>11708</td>
+      <td>16638</td>
+      <td>22644</td>
+      <td>23869</td>
+      <td>1439</td>
+      <td>1527</td>
+      <td>480841</td>
+      <td>623593</td>
+      <td>18880</td>
+      <td>24665</td>
       <td>False</td>
     </tr>
     <tr>
@@ -17959,9 +21809,8 @@
       <td>0</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
       <td>0</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
@@ -17990,11 +21839,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>5</td>
       <td>0</td>
       <td>0</td>
+      <td>14681</td>
+      <td>14681</td>
+      <td>265</td>
+      <td>265</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4488</td>
+      <td>4488</td>
       <td>147</td>
-      <td>8942</td>
+      <td>147</td>
+      <td>19169</td>
+      <td>19169</td>
+      <td>412</td>
+      <td>412</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18024,8 +21888,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -18054,12 +21917,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>1558</td>
-      <td>65732</td>
+      <td>74120</td>
+      <td>77648</td>
+      <td>3798</td>
+      <td>3963</td>
+      <td>64946</td>
+      <td>90075</td>
+      <td>5451</td>
+      <td>7380</td>
+      <td>19516</td>
+      <td>20422</td>
+      <td>2010</td>
+      <td>2080</td>
+      <td>158582</td>
+      <td>188145</td>
+      <td>11259</td>
+      <td>13423</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18103,7 +21981,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>1</td>
@@ -18119,12 +21996,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>115</td>
-      <td>5005</td>
+      <td>4900</td>
+      <td>5146</td>
+      <td>257</td>
+      <td>270</td>
+      <td>251</td>
+      <td>251</td>
+      <td>81</td>
+      <td>81</td>
+      <td>1069</td>
+      <td>1069</td>
+      <td>29</td>
+      <td>29</td>
+      <td>6220</td>
+      <td>6466</td>
+      <td>367</td>
+      <td>380</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18188,8 +22080,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>79</td>
-      <td>1360</td>
+      <td>1488</td>
+      <td>1596</td>
+      <td>230</td>
+      <td>266</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>743</td>
+      <td>743</td>
+      <td>35</td>
+      <td>35</td>
+      <td>2231</td>
+      <td>2339</td>
+      <td>265</td>
+      <td>301</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18253,8 +22159,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
+      <td>1060</td>
+      <td>1060</td>
       <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1060</td>
       <td>1060</td>
+      <td>5</td>
+      <td>5</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18284,10 +22204,9 @@
       <td>1</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -18314,12 +22233,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>20</td>
-      <td>637</td>
+      <td>518</td>
+      <td>677</td>
+      <td>75</td>
+      <td>87</td>
+      <td>234</td>
+      <td>234</td>
+      <td>65</td>
+      <td>65</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>752</td>
+      <td>911</td>
+      <td>140</td>
+      <td>152</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18368,7 +22302,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -18380,11 +22313,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>94</td>
-      <td>3164</td>
+      <td>5936</td>
+      <td>5936</td>
+      <td>147</td>
+      <td>147</td>
+      <td>523</td>
+      <td>523</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6459</td>
+      <td>6459</td>
+      <td>162</td>
+      <td>162</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18448,8 +22396,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>273</td>
+      <td>273</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>273</td>
+      <td>273</td>
+      <td>12</td>
+      <td>12</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18495,7 +22457,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>3</td>
       <td>0</td>
       <td>0</td>
@@ -18509,12 +22470,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>3</td>
       <td>3</td>
       <td>0</td>
-      <td>74</td>
-      <td>2020</td>
+      <td>2157</td>
+      <td>2287</td>
+      <td>198</td>
+      <td>209</td>
+      <td>3930</td>
+      <td>5591</td>
+      <td>446</td>
+      <td>744</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6087</td>
+      <td>7878</td>
+      <td>644</td>
+      <td>953</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18544,8 +22520,7 @@
       <td>2</td>
       <td>2</td>
       <td>2</td>
-      <td>2</td>
-      <td>2</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>2</td>
@@ -18574,12 +22549,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>2</td>
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>2083</td>
-      <td>25420</td>
+      <td>25171</td>
+      <td>27943</td>
+      <td>3899</td>
+      <td>4270</td>
+      <td>51187</td>
+      <td>51187</td>
+      <td>7557</td>
+      <td>7557</td>
+      <td>28546</td>
+      <td>28619</td>
+      <td>3585</td>
+      <td>3613</td>
+      <td>104904</td>
+      <td>107749</td>
+      <td>15041</td>
+      <td>15440</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18623,7 +22613,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
@@ -18639,12 +22628,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>255</td>
-      <td>4741</td>
+      <td>4715</td>
+      <td>5343</td>
+      <td>888</td>
+      <td>965</td>
+      <td>9575</td>
+      <td>9576</td>
+      <td>2117</td>
+      <td>2117</td>
+      <td>3271</td>
+      <td>5524</td>
+      <td>1050</td>
+      <td>1397</td>
+      <td>17561</td>
+      <td>20443</td>
+      <td>4055</td>
+      <td>4479</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18674,11 +22678,10 @@
       <td>0</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>3</td>
-      <td>3</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -18709,7 +22712,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>94</td>
+      <td>94</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>94</td>
+      <td>94</td>
+      <td>16</td>
+      <td>16</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18739,8 +22757,7 @@
       <td>8</td>
       <td>8</td>
       <td>8</td>
-      <td>8</td>
-      <td>8</td>
+      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>8</td>
@@ -18769,12 +22786,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>8</td>
       <td>8</td>
       <td>8</td>
       <td>0</td>
-      <td>182</td>
-      <td>8507</td>
+      <td>9694</td>
+      <td>10338</td>
+      <td>559</td>
+      <td>628</td>
+      <td>12282</td>
+      <td>53546</td>
+      <td>1031</td>
+      <td>2007</td>
+      <td>5334</td>
+      <td>5672</td>
+      <td>246</td>
+      <td>277</td>
+      <td>27310</td>
+      <td>69556</td>
+      <td>1836</td>
+      <td>2912</td>
       <td>False</td>
     </tr>
     <tr>
@@ -18804,10 +22836,9 @@
       <td>0</td>
       <td>0</td>
       <td>1</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -18835,11 +22866,26 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>116</td>
-      <td>1660</td>
+      <td>1619</td>
+      <td>1715</td>
+      <td>337</td>
+      <td>376</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1619</td>
+      <td>1715</td>
+      <td>337</td>
+      <td>376</td>
       <td>False</td>
     </tr>
   </tbody>
diff --git a/communities/microgalaxy/resources/tools.tsv b/communities/microgalaxy/resources/tools.tsv
index 9e964f17..31869869 100644
--- a/communities/microgalaxy/resources/tools.tsv
+++ b/communities/microgalaxy/resources/tools.tsv
@@ -1,291 +1,291 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004	True	False	True
-TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	984	True	False	True
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	1764	496717	True	False	True
-abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278	True	False	True
-aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	129	True	False	True
-amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	53	True	False	True
-amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	591	True	False	True
-ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	7	True	False	True
-antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	279	14596	True	False	True
-artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	123	8175	True	False	True
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	151	2982	True	False	True
-bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	208	14021	True	False	True
-bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	2016	44390	True	False	True
-bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	64	True	False	True
-bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.09	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	4	0	0	420	6381	True	False	True
-bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	81	True	False	True
-biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	98	3906	True	False	True
-biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	101	1232	True	False	True
-blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499	True	False	True
-blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	159	264558	True	False	True
-bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	326	18351	True	False	True
-busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1804	86180	True	False	True
-cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	268	2878	True	False	True
-cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474	True	False	True
-cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	98	True	False	True
-checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	390	5165	True	False	True
-clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	68	1856	True	False	True
-clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	651	46793	True	False	True
-cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	102	True	False	True
-codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	29	60901	True	False	True
-cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	2757	True	False	True
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	147	True	False	True
-compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	332	True	False	True
-compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	92	786	True	False	True
-coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	72	529	True	False	True
-cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	8518	True	False	True
-cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	5090	232004	True	False	True
-dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	10	10	10	0	1263	66609	True	False	True
-das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	24	706	True	False	True
-deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	4990	95752	True	False	True
-diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	3	3	0	963	49711	True	False	True
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369	True	False	True
-dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	39	6886	True	False	True
-drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	46	646	True	False	True
-ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	9907	True	False	True
-effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	1	3	1	0	510	30565	True	False	True
-emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	107	107	107	0	1816	89530	True	False	True
-ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	45	899	True	False	True
-export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	200	5265	True	False	True
-ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	52	459	True	False	True
-fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	250	3498	True	False	True
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	2803	1055760	True	False	True
-fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1266	4333	True	False	True
-fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	379	55434	True	False	True
-featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	4679	696399	True	False	True
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	617	30483	True	False	True
-flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	17	645	True	False	True
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904	True	False	True
-format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	166	5588	True	False	True
-fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	68	1102	True	False	True
-freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	55	20021	True	False	True
-frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	28	0	0	0	28	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	900	5906	True	False	True
-getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	5	5	5	0	1388	22148	True	False	True
-gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	27	660	True	False	True
-glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	0	187	3965	True	False	True
-glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	408	5484	True	False	True
-goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1210	19167	True	False	True
-graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	432	9277	True	False	True
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651	True	False	True
-gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	Up-to-date	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.4.0	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	145	3340	True	False	True
-hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	117	4459	True	False	True
-hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	339	True	False	True
-hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	137	True	False	True
-hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	12	12	12	0	439	33702	True	False	True
-humann	humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.9	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	10	10	10	6	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	1037	19490	True	False	True
-hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	2	17	2	17	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	12	17	12	0	161	10370	True	False	True
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	True	False	True
-icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127	True	False	True
-infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	67	100294	True	False	True
-instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	94	True	False	True
-integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	58	52965	True	False	True
-interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	677	35243	True	False	True
-iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	681	21598	True	False	True
-isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	57581	True	False	True
-itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	868	True	False	True
-ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	5	5	5	0	1171	1224275	True	False	True
-jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	2346	18229	True	False	True
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	True	False	True
-kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	363	True	False	True
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022	True	False	True
-kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.0.9	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	319	True	False	True
-kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	33	594	True	False	True
-kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	5	0	1209	33778	True	False	True
-kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	2367	185308	True	False	True
-kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	481	14683	True	False	True
-kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	182	1444	True	False	True
-kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	354	2527	True	False	True
-krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	703	16525	True	False	True
-krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	137	True	False	True
-legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	55	True	False	True
-lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152	True	False	True
-limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1012	20344	True	False	True
-lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	37	True	False	True
-lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	647	True	False	True
-lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	114	936	True	False	True
-m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	True	False	True
-maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	188	True	False	True
-mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	2	2	2	0	817	143045	True	False	True
-make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	554	5591	True	False	True
-mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	167	True	False	True
-mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	27	9763	True	False	True
-maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	118	2059	True	False	True
-maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	415	6078	True	False	True
-mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	29	True	False	True
-medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	3	3	3	0	768	99863	True	False	True
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530	True	False	True
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475	True	False	True
-megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	261	3610	True	False	True
-meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	True	False	True
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	2	2	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	192	4329	True	False	True
-metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	184	True	False	True
-metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	115	636	True	False	True
-metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	753	True	False	True
-metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	4181	True	False	True
-metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	4	1	2	4	4	0	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	499	11069	True	False	True
-metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	104	2522	True	False	True
-metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206	True	False	True
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938	True	False	True
-minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	185	True	False	True
-miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	30	842	True	False	True
-mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	0	236	100920	True	False	True
-mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	635	9304	True	False	True
-mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	322	89021	True	False	True
-mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	129	129	129	129	129	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	126	129	129	0	14353	302916	True	False	True
-mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	True	False	True
-msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	19958	True	False	True
-msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	726	True	False	True
-multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	53	True	False	True
-multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	8320	162790	True	False	True
-mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	844	True	False	True
-nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	3	836	True	False	True
-nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	2195	63235	True	False	True
-nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	15	1074	True	False	True
-ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	16	16	16	16	16	0	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	16	16	15	0	4066	365597	True	False	True
-ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	448	25505	True	False	True
-nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	2	1	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	2	0	0	210	4080	True	False	True
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	True	False	True
-nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	142	True	False	True
-nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	861	True	False	True
-nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45	True	False	True
-obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	503	26251	True	False	True
-omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	774	True	False	True
-orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	Up-to-date	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	2.5.5	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	239	1333	True	False	True
-peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.11			4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	2	0	485	17477	True	False	True
-pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	19	165	True	False	True
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	1038	1038	146	146	0	0	0	0	849	849	38	38	1887	1887	184	184	True	False	True
+TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1003	1022	48	52	0	0	0	0	0	0	0	0	1003	1022	48	52	True	False	True
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	619817	622353	4097	4130	320454	320454	2915	2915	496156	503743	2012	2227	1436427	1446550	9024	9272	True	False	True
+abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1139	1139	109	109	0	0	0	0	0	0	0	0	1139	1139	109	109	True	False	True
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5543	5543	1042	1042	1301	1305	413	414	2030	2030	299	299	8874	8878	1754	1755	True	False	True
+aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	262	36	36	0	0	0	0	0	0	0	0	262	262	36	36	True	False	True
+amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	81	81	17	17	0	0	0	0	0	0	0	0	81	81	17	17	True	False	True
+amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5734	5734	334	334	1035	1035	106	106	0	0	0	0	6769	6769	440	440	True	False	True
+ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	7	7	0	0	0	0	0	0	0	0	26	26	7	7	True	False	True
+antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15949	16490	726	811	5113	5113	649	649	6043	6043	169	169	27105	27646	1544	1629	True	False	True
+artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	9021	9021	238	238	0	0	0	0	0	0	0	0	9021	9021	238	238	True	False	True
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11117	11117	534	534	19	19	1	1	9601	9601	167	167	20737	20737	702	702	True	False	True
+bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	14693	15620	653	721	61872	101400	1656	5678	39	39	3	3	76604	117059	2312	6402	True	False	True
+bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	55392	56095	4951	5035	47603	47603	4916	4916	18089	18089	3121	3121	121084	121787	12988	13072	True	False	True
+bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	90	90	28	28	0	0	0	0	0	0	0	0	90	90	28	28	True	False	True
+bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.09	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	4	0	0	11989	11989	768	768	4458	4458	652	652	2507	2507	80	80	18954	18954	1500	1500	True	False	True
+bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	544	544	20	20	0	0	0	0	0	0	0	0	544	544	20	20	True	False	True
+binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	126	126	42	42	0	0	0	0	0	0	0	0	126	126	42	42	True	False	True
+biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12725	12725	297	297	2851	5049	450	638	2171	2371	214	239	17747	20145	961	1174	True	False	True
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6243	6243	375	375	0	0	0	0	6243	6243	375	375	True	False	True
+blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1063	1237	257	300	0	0	0	0	0	0	0	0	1063	1237	257	300	True	False	True
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24916	27120	283	347	0	0	0	0	0	0	0	0	24916	27120	283	347	True	False	True
+blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	264392	265217	483	552	0	0	0	0	0	0	0	0	264392	265217	483	552	True	False	True
+bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	51378	51378	775	775	3298	3298	160	160	1660	1660	63	63	56336	56336	998	998	True	False	True
+busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	102717	103051	3877	3926	34251	34251	3506	3506	33192	34369	2439	2525	170160	171671	9822	9957	True	False	True
+cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3835	3835	597	597	1359	1359	467	467	646	646	98	98	5840	5840	1162	1162	True	False	True
+cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5946	7379	407	628	0	0	0	0	5946	7379	407	628	True	False	True
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10414	10414	510	510	2	2	1	1	2	2	1	1	10418	10418	512	512	True	False	True
+cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	225	225	32	32	271	271	61	61	0	0	0	0	496	496	93	93	True	False	True
+checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	7500	7500	930	930	0	0	0	0	0	0	0	0	7500	7500	930	930	True	False	True
+clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3388	3388	187	187	1	1	1	1	1	1	1	1	3390	3390	189	189	True	False	True
+clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	548	548	18	18	0	0	0	0	548	548	18	18	True	False	True
+clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	79867	80817	1675	1785	49493	87884	3703	7380	8797	9713	670	728	138157	178414	6048	9893	True	False	True
+cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2609	2609	3	3	0	0	0	0	0	0	0	0	2609	2609	3	3	True	False	True
+codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	61197	61220	64	65	0	0	0	0	0	0	0	0	61197	61220	64	65	True	False	True
+cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2758	2758	22	22	20	20	10	10	0	0	0	0	2778	2778	32	32	True	False	True
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	530	530	65	65	8	8	6	6	0	0	0	0	538	538	71	71	True	False	True
+compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	332	28	32	0	0	0	0	0	0	0	0	306	332	28	32	True	False	True
+compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	266	266	39	39	28	28	15	15	0	0	0	0	294	294	54	54	True	False	True
+concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	2105	2105	155	155	0	0	0	0	0	0	0	0	2105	2105	155	155	True	False	True
+coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1081	1081	151	151	0	0	0	0	0	0	0	0	1081	1081	151	151	True	False	True
+cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9942	9942	26	26	0	0	0	0	0	0	0	0	9942	9942	26	26	True	False	True
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	259754	272370	11716	12601	334550	362356	18618	20162	64377	65986	3507	3627	658681	700712	33841	36390	True	False	True
+dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	0	10	10	10	0	92240	92240	2716	2716	179176	179176	5317	5317	12478	12478	394	394	283894	283894	8427	8427	True	False	True
+das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1323	1323	47	47	0	0	0	0	0	0	0	0	1323	1323	47	47	True	False	True
+deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	97434	109474	11355	12514	183905	246475	24951	31957	18551	20166	2647	2905	299890	376115	38953	47376	True	False	True
+diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	0	3	3	0	61376	61746	1847	1895	23164	28729	1140	1556	63034	63034	522	522	147574	153509	3509	3973	True	False	True
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	358	406	124	139	1361	1361	384	384	0	0	0	0	1719	1767	508	523	True	False	True
+dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	7358	7358	88	88	0	0	0	0	0	0	0	0	7358	7358	88	88	True	False	True
+drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	916	916	113	113	0	0	0	0	0	0	0	0	916	916	113	113	True	False	True
+ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12996	12996	137	137	10	10	1	1	0	0	0	0	13006	13006	138	138	True	False	True
+effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	1	3	1	0	34432	34437	1149	1152	42	42	2	2	21027	21027	413	413	55501	55506	1564	1567	True	False	True
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	0	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	107	107	107	0	143762	148864	4481	5039	151989	296028	13224	31140	24955	27001	2397	2705	320706	471893	20102	38884	True	False	True
+ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	820	966	89	106	0	0	0	0	0	0	0	0	820	966	89	106	True	False	True
+export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5396	5938	580	607	628	628	168	168	519	519	107	107	6543	7085	855	882	True	False	True
+ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	601	601	128	128	1165	1165	232	232	0	0	0	0	1766	1766	360	360	True	False	True
+fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6685	6685	603	603	0	0	0	0	0	0	0	0	6685	6685	603	603	True	False	True
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	136	11	11	0	0	0	0	0	0	0	0	136	136	11	11	True	False	True
+fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	1	1126086	1127111	6847	6909	422259	422259	10722	10722	76462	76462	2242	2242	1624807	1625832	19811	19873	True	False	True
+fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5162	5162	2350	2350	10176	10176	4714	4714	2610	2610	991	991	17948	17948	8055	8055	True	False	True
+fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	65542	65631	1049	1071	25992	25992	2147	2147	6733	7339	649	745	98267	98962	3845	3963	True	False	True
+featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	740719	770524	11699	12547	643892	784396	23272	27598	66108	68867	2348	2463	1450719	1623787	37319	42608	True	False	True
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	53310	53944	1499	1575	25043	25043	726	726	10824	10824	593	593	89177	89811	2818	2894	True	False	True
+flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	661	715	52	54	0	0	0	0	167	167	15	15	828	882	67	69	True	False	True
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32514	32675	3379	3422	19434	19434	2537	2537	9843	9843	1624	1624	61791	61952	7540	7583	True	False	True
+format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5940	6474	558	608	0	0	0	0	0	0	0	0	5940	6474	558	608	True	False	True
+fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1257	1450	150	162	0	0	0	0	1052	1052	45	45	2309	2502	195	207	True	False	True
+freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	21757	21757	101	101	217	217	21	21	0	0	0	0	21974	21974	122	122	True	False	True
+frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	8648	8648	1408	1408	32	32	6	6	6406	6406	597	597	15086	15086	2011	2011	True	False	True
+getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	0	5	5	5	0	24606	25662	3463	3630	26805	26808	5143	5144	8174	8237	1259	1279	59585	60707	9865	10053	True	False	True
+gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	490	682	74	109	127	14058	20	1798	0	0	0	0	617	14740	94	1907	True	False	True
+glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	0	4343	4343	407	407	0	0	0	0	0	0	0	0	4343	4343	407	407	True	False	True
+glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	5800	6212	826	871	7756	7756	1048	1048	1149	1149	215	215	14705	15117	2089	2134	True	False	True
+goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	20207	21960	2807	3139	24488	26198	3066	3321	4155	4155	545	545	48850	52313	6418	7005	True	False	True
+graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	9816	10927	1285	1350	1273	1273	368	368	1104	1104	242	242	12193	13304	1895	1960	True	False	True
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	7012	7344	323	338	0	0	0	0	0	0	0	0	7012	7344	323	338	True	False	True
+gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	Up-to-date	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.4.0	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	476	476	87	87	0	0	0	0	588	588	74	74	1064	1064	161	161	True	False	True
+gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3690	3811	326	336	3323	3323	235	235	1895	2429	234	258	8908	9563	795	829	True	False	True
+hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	7303	7303	222	222	20	20	2	2	0	0	0	0	7323	7323	224	224	True	False	True
+hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	349	359	32	33	364	364	53	53	0	0	0	0	713	723	85	86	True	False	True
+hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	156	156	20	20	0	0	0	0	220	220	11	11	376	376	31	31	True	False	True
+hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	0	0	12	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	12	0	35919	36952	1283	1321	0	0	0	0	3023	3023	180	180	38942	39975	1463	1501	True	False	True
+humann	humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.9	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	10	10	0	6	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	26659	26659	2067	2067	865	865	174	174	3238	3238	351	351	30762	30762	2592	2592	True	False	True
+hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	0	17	2	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	12	17	12	0	11429	11429	428	428	7751	7751	676	676	715	715	58	58	19895	19895	1162	1162	True	False	True
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	473	473	93	93	0	0	0	0	0	0	0	0	473	473	93	93	True	False	True
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	1200	1220	187	195	1588	1588	267	267	0	0	0	0	2788	2808	454	462	True	False	True
+infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	59700	112582	223	282	0	0	0	0	1157	1221	34	35	60857	113803	257	317	True	False	True
+instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	102	102	16	16	0	0	0	0	0	0	0	0	102	102	16	16	True	False	True
+integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55149	55149	161	161	0	0	0	0	6085	6085	73	73	61234	61234	234	234	True	False	True
+interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34689	55189	1634	1713	65	65	15	15	10897	10897	607	607	45651	66151	2256	2335	True	False	True
+iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	28279	28481	1623	1646	24662	24662	2093	2093	9780	10086	979	992	62721	63229	4695	4731	True	False	True
+isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	59386	59386	151	151	56	56	1	1	4741	4741	59	59	64183	64183	211	211	True	False	True
+itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1426	1426	71	71	0	0	0	0	0	0	0	0	1426	1426	71	71	True	False	True
+ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	0	5	5	5	0	1252220	1252220	2366	2366	126027	126027	2496	2496	41901	41901	993	993	1420148	1420148	5855	5855	True	False	True
+jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	21153	22174	5514	5779	17428	17428	6458	6458	15673	17267	3248	3786	54254	56869	15220	16023	True	False	True
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1825	1825	237	237	0	0	0	0	971	971	56	56	2796	2796	293	293	True	False	True
+kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	379	379	53	53	8259	8259	271	271	0	0	0	0	8638	8638	324	324	True	False	True
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	8	8	8	0	1995	2091	174	193	1430	1430	389	389	1580	1580	56	56	5005	5101	619	638	True	False	True
+kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.1.0	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	503	503	58	58	0	0	0	0	0	0	0	0	503	503	58	58	True	False	True
+kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1342	1342	63	63	0	0	0	0	0	0	0	0	1342	1342	63	63	True	False	True
+kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	5	5	5	0	48136	48164	2754	2760	59952	130398	5869	8654	29008	31148	1936	2200	137096	209710	10559	13614	True	False	True
+kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	271367	271786	6384	6409	101752	101752	4662	4662	53562	53562	1663	1663	426681	427100	12709	12734	True	False	True
+kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23008	23014	1060	1061	16194	24490	1719	2168	14898	14898	436	436	54100	62402	3215	3665	True	False	True
+kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3185	3185	495	495	0	0	0	0	385	385	48	48	3570	3570	543	543	True	False	True
+kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3981	3986	769	771	4087	5610	991	1284	88	88	41	41	8156	9684	1801	2096	True	False	True
+krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	48516	48516	2373	2373	8787	8787	943	943	4369	4369	393	393	61672	61672	3709	3709	True	False	True
+krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	89	137	4	20	118	6136	15	1112	0	0	0	0	207	6273	19	1132	True	False	True
+legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	92	92	8	8	0	0	0	0	0	0	0	0	92	92	8	8	True	False	True
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	171	27	30	0	0	0	0	0	0	0	0	149	171	27	30	True	False	True
+limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23442	24466	2379	2475	45734	49342	4565	5032	9327	9517	835	842	78503	83325	7779	8349	True	False	True
+lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	39	4	4	0	0	0	0	0	0	0	0	39	39	4	4	True	False	True
+lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	822	822	14	14	0	0	0	0	0	0	0	0	822	822	14	14	True	False	True
+lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1219	1219	182	182	0	0	0	0	37	37	4	4	1256	1256	186	186	True	False	True
+m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	44	44	11	11	0	0	0	0	0	0	0	0	44	44	11	11	True	False	True
+maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2835	2835	59	59	0	0	0	0	0	0	0	0	2835	2835	59	59	True	False	True
+mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	0	2	2	2	0	172433	174456	1865	1951	108640	122790	4266	5521	20027	20027	1172	1172	301100	317273	7303	8644	True	False	True
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6417	6861	1315	1366	7235	7235	1858	1858	4112	4112	902	902	17764	18208	4075	4126	True	False	True
+mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7871	7871	32	32	0	0	0	0	0	0	0	0	7871	7871	32	32	True	False	True
+mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	10119	10119	61	61	19	19	9	9	647	647	7	7	10785	10785	77	77	True	False	True
+maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	1	0	2798	2798	314	314	2452	2452	508	508	914	914	89	89	6164	6164	911	911	True	False	True
+maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6863	7021	1251	1264	2798	2798	543	543	3189	3189	352	352	12850	13008	2146	2159	True	False	True
+mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	35	13	13	0	0	0	0	0	0	0	0	35	35	13	13	True	False	True
+medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	0	3	3	3	0	117975	117975	1693	1693	55063	55063	796	796	9325	9325	639	639	182363	182363	3128	3128	True	False	True
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	12692	13292	1349	1400	16645	16645	2140	2140	6214	6214	431	431	35551	36151	3920	3971	True	False	True
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	513	557	152	155	74	74	35	35	10	10	4	4	597	641	191	194	True	False	True
+megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	4130	4130	447	447	0	0	0	0	0	0	0	0	4130	4130	447	447	True	False	True
+meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3150	3150	477	477	730	730	196	196	1183	1183	151	151	5063	5063	824	824	True	False	True
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	0	2	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	6135	6135	382	382	881	881	151	151	1094	1094	104	104	8110	8110	637	637	True	False	True
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	7.bba0d80	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	312	312	40	40	0	0	0	0	0	0	0	0	312	312	40	40	True	False	True
+metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	980	980	323	323	0	0	0	0	0	0	0	0	980	980	323	323	True	False	True
+metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	556	756	17	21	310	514	35	55	0	0	0	0	866	1270	52	76	True	False	True
+metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4471	4471	29	29	0	0	0	0	0	0	0	0	4471	4471	29	29	True	False	True
+metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	0	1	2	4	0	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	16629	16648	1183	1187	3983	3983	572	572	4747	4747	278	278	25359	25378	2033	2037	True	False	True
+metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	2730	2831	260	262	0	0	0	0	1540	1540	71	71	4270	4371	331	333	True	False	True
+metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	142	142	32	32	0	0	0	0	379	379	47	47	521	521	79	79	True	False	True
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7116	7116	256	256	0	0	0	0	278	278	60	60	7394	7394	316	316	True	False	True
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13357	13479	554	562	8416	8416	448	448	898	898	85	85	22671	22793	1087	1095	True	False	True
+minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	229	229	32	32	0	0	0	0	0	0	0	0	229	229	32	32	True	False	True
+miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1244	1244	86	86	24	24	15	15	0	0	0	0	1268	1268	101	101	True	False	True
+mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	0	191295	191295	1111	1111	42265	42265	320	320	10904	10904	83	83	244464	244464	1514	1514	True	False	True
+mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	13300	13471	1480	1501	6532	6532	1167	1167	10334	11841	1083	1300	30166	31844	3730	3968	True	False	True
+mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	119024	119024	628	628	42	42	2	2	36310	36310	191	191	155376	155376	821	821	True	False	True
+mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	0	129	129	129	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	126	129	129	0	297546	326056	37506	41763	565218	682083	72163	89926	167400	182490	26963	28404	1030164	1190629	136632	160093	True	False	True
+mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20749	22184	455	469	1239	1239	71	71	2666	2666	53	53	24654	26089	579	593	True	False	True
+msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	795	795	104	104	0	0	0	0	461	461	12	12	1256	1256	116	116	True	False	True
+multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	106	106	25	25	0	0	0	0	0	0	0	0	106	106	25	25	True	False	True
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	182221	192389	19343	20494	163961	182413	26449	29758	40663	41855	5974	6157	386845	416657	51766	56409	True	False	True
+mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	854	860	110	111	79	79	15	15	274	274	13	13	1207	1213	138	139	True	False	True
+nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	839	839	12	12	0	0	0	0	269	269	5	5	1108	1108	17	17	True	False	True
+nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	99052	100009	5671	5755	40386	40386	3371	3371	17919	17919	2188	2188	157357	158314	11230	11314	True	False	True
+nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1091	1091	44	44	0	0	0	0	0	0	0	0	1091	1091	44	44	True	False	True
+ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	15	16	16	15	0	391141	443752	9760	10546	306361	350178	11767	13684	227235	244814	3192	3617	924737	1038744	24719	27847	True	False	True
+ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	125	125	26	26	2489	2489	139	139	0	0	0	0	2614	2614	165	165	True	False	True
+newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33637	34195	1113	1172	16257	16257	1816	1816	7582	7582	899	899	57476	58034	3828	3887	True	False	True
+nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	0	2	0	0	4411	4411	396	396	9708	9708	279	279	2099	2099	212	212	16218	16218	887	887	True	False	True
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	391	391	158	158	0	0	0	0	0	0	0	0	391	391	158	158	True	False	True
+nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	107	143	13	15	148	148	20	20	0	0	0	0	255	291	33	35	True	False	True
+nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	118	863	19	26	0	0	0	0	0	0	0	0	118	863	19	26	True	False	True
+nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	352	352	42	42	8	8	6	6	0	0	0	0	360	360	48	48	True	False	True
+obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	37598	37598	1277	1277	0	0	0	0	3862	3862	280	280	41460	41460	1557	1557	True	False	True
+omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	158	158	12	12	0	0	0	0	0	0	0	0	158	158	12	12	True	False	True
+orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	897	897	99	99	1792	1792	239	239	0	0	0	0	2689	2689	338	338	True	False	True
+orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	To update	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	3.0.1b1	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2018	2018	419	419	0	0	0	0	438	438	58	58	2456	2456	477	477	True	False	True
+peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.11			4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	2	0	11986	17898	1046	1153	1314	1314	389	389	3034	3034	118	118	16334	22246	1553	1660	True	False	True
+pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	773	773	60	60	495	495	72	72	246	246	17	17	1514	1514	149	149	True	False	True
 pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
                 pharokka
-            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	74	2565	True	False	True
-phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	82	812	True	False	True
-phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	104	1770	True	False	True
-picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	6	0	6	5	6	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	45	1095	True	False	True
-picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	88	1000	True	False	True
-plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	278	22589	True	False	True
-plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	22	True	False	True
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	239	True	False	True
-prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	3233	371445	True	False	True
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	200	3320	True	False	True
-pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123	True	False	True
-pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	377	11332	True	False	True
-qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	68	1909	True	False	True
-qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	32	0	0	32	32	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	1155	28681	True	False	True
-qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	1	4	4	4	1	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	4	4	4	0	1328	664470	True	False	True
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567	True	False	True
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	True	False	True
-rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	309	21353	True	False	True
-rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	383	6808	True	False	True
-read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	3370	True	False	True
-reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.15.0	recentrifuge	1.15.0	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	331	True	False	True
-repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	True	False	True
-roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	656	12225	True	False	True
-rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	22	22	22	22	22	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	22	22	22	0	3206	133498	True	False	True
-salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	1	2	2	3	1	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	3	3	3	0	969	61937	True	False	True
-sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	173	True	False	True
-sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	140	True	False	True
-scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	61	676	True	False	True
-semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	1	0	0	6	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	39	542	True	False	True
-seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	3	0	2	5	3	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	129	1964	True	False	True
-seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	True	False	True
-shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600	True	False	True
-sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	133	2489	True	False	True
-smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	121	True	False	True
-smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	133	1349	True	False	True
-snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	0	1372	105708	True	False	True
-sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	True	False	True
-sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	376	18183	True	False	True
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953	True	False	True
-spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	1278	True	False	True
-sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205	True	False	True
-srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205	True	False	True
-staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	889	12673	True	False	True
-stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	2623	True	False	True
-suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	13	True	False	True
-suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	2	4	4	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	2	5	True	False	True
-suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	5	67	True	False	True
-suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	31	202	True	False	True
-suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	9	73	True	False	True
-suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	26	114	True	False	True
-suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	22	21	21	21	22	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	43	168	True	False	True
-suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	4	4	True	False	True
-suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2	6	True	False	True
-suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	48	263	True	False	True
-suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	17	17	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	59	213	True	False	True
-suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	20	True	False	True
-suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	6	14	True	False	True
-suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	40	232	True	False	True
-suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	12	37	True	False	True
-suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	True	False	True
-suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	13	True	False	True
-suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	1	1	True	False	True
-suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	22	172	True	False	True
-suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	7	8	8	8	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	8	16	True	False	True
-suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	124	7087	True	False	True
-t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	457	True	False	True
-t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26	947	True	False	True
-t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	70	8690	True	False	True
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426	True	False	True
-tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	198	5161	True	False	True
-tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9.1	tooldistillator	0.9.1	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	84	907	True	False	True
-transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	229	True	False	True
-trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	2334	238699	True	False	True
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	True	False	True
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732	True	False	True
-unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115	5005	True	False	True
-uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	79	1360	True	False	True
-usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	1060	True	False	True
-valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20	637	True	False	True
-vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	94	3164	True	False	True
-varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	74	2020	True	False	True
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420	True	False	True
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741	True	False	True
-virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.29.0	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	8	8	8	8	8	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	8	8	8	0	182	8507	True	False	True
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	True	False	True
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	5462	5462	334	334	0	0	0	0	309	309	52	52	5771	5771	386	386	True	False	True
+phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	0	0	1	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	1199	1199	193	193	0	0	0	0	6	6	1	1	1205	1205	194	194	True	False	True
+phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1975	2034	246	258	0	0	0	0	553	564	140	144	2528	2598	386	402	True	False	True
+picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	867	1128	144	165	0	0	0	0	2106	2106	121	121	2973	3234	265	286	True	False	True
+picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	2532	2532	382	382	1	1	1	1	1311	1311	83	83	3844	3844	466	466	True	False	True
+plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37086	37272	711	734	6346	6346	583	583	3065	3065	61	61	46497	46683	1355	1378	True	False	True
+plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14652	14652	251	251	0	0	0	0	101	101	18	18	14753	14753	269	269	True	False	True
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	731	731	86	86	0	0	0	0	42	42	4	4	773	773	90	90	True	False	True
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1902	1902	167	167	0	0	0	0	0	0	0	0	1902	1902	167	167	True	False	True
+prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	464359	476554	7475	7721	313285	331256	11243	12384	131211	141875	4358	4947	908855	949685	23076	25052	True	False	True
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3962	3962	501	501	0	0	0	0	0	0	0	0	3962	3962	501	501	True	False	True
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22742	22742	557	557	2159	2159	716	716	776	776	448	448	25677	25677	1721	1721	True	False	True
+pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12858	13232	986	996	8092	8092	943	943	3238	3238	124	124	24188	24562	2053	2063	True	False	True
+qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2092	2342	209	238	0	0	0	0	2	2	1	1	2094	2344	210	239	True	False	True
+qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	0	0	0	32	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	31825	34677	3375	3785	1	1	1	1	14	14	4	4	31840	34692	3380	3790	True	False	True
+qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	0	4	4	4	0	684820	684820	3239	3239	90503	90503	3881	3881	29018	29018	826	826	804341	804341	7946	7946	True	False	True
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	67737	69738	7787	7971	51925	56602	9692	10646	32003	34145	3890	4127	151665	160485	21369	22744	True	False	True
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	27113	27315	839	850	9089	9089	475	475	5452	5452	171	171	41654	41856	1485	1496	True	False	True
+rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	42	42	9	9	0	0	0	0	0	0	0	0	42	42	9	9	True	False	True
+raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10905	10905	966	966	5100	5114	587	587	4955	6094	765	892	20960	22113	2318	2445	True	False	True
+read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3710	3710	80	80	7	7	6	6	0	0	0	0	3717	3717	86	86	True	False	True
+reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.15.0	recentrifuge	1.15.0	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	472	472	92	92	32	32	13	13	6	6	4	4	510	510	109	109	True	False	True
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	95	38	38	0	0	0	0	0	0	0	0	95	95	38	38	True	False	True
+roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15196	15685	1459	1501	12188	12188	1768	1768	4881	5539	518	555	32265	33412	3745	3824	True	False	True
+rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	0	22	22	22	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	0	22	22	22	0	136315	147595	8341	9385	138707	161046	10696	12789	22718	23767	1593	1695	297740	332408	20630	23869	True	False	True
+salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	0	2	2	3	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	0	3	3	3	0	73085	77081	2243	2319	90634	122835	3402	4726	13371	15818	513	586	177090	215734	6158	7631	True	False	True
+sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	174	174	16	16	399	399	29	29	0	0	0	0	573	573	45	45	True	False	True
+sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	140	140	5	5	253	253	6	6	0	0	0	0	393	393	11	11	True	False	True
+scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	901	901	90	90	0	0	0	0	0	0	0	0	901	901	90	90	True	False	True
+semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	931	931	93	93	0	0	0	0	0	0	0	0	931	931	93	93	True	False	True
+seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	0	0	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3364	3364	247	247	0	0	0	0	244	244	33	33	3608	3608	280	280	True	False	True
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2424	2424	102	102	0	0	0	0	0	0	0	0	2424	2424	102	102	True	False	True
+seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4182	4182	42	42	0	0	0	0	0	0	0	0	4182	4182	42	42	True	False	True
+shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46125	47376	2273	2356	40577	40577	3971	3971	19960	21130	1085	1199	106662	109083	7329	7526	True	False	True
+sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3457	3457	301	301	0	0	0	0	556	556	65	65	4013	4013	366	366	True	False	True
+smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	158	158	8	8	0	0	0	0	0	0	0	0	158	158	8	8	True	False	True
+smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	1638	331	358	779	779	244	244	467	467	83	83	2745	2884	658	685	True	False	True
+snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	0	121363	124773	3448	3602	92504	92504	3945	3945	48068	52034	2705	3073	261935	269311	10098	10620	True	False	True
+sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	True	False	True
+sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19865	21034	1047	1126	3141	3141	328	328	3304	3304	189	189	26310	27479	1564	1643	True	False	True
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	3	9	3	0	82716	87113	8209	8526	120471	120475	14787	14790	54067	61541	5817	6653	257254	269129	28813	29969	True	False	True
+spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	23	23	0	0	0	0	0	0	0	0	1436	1436	23	23	True	False	True
+sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	80	80	1	1	0	0	0	0	80	80	1	1	True	False	True
+srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41	True	False	True
+srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41	True	False	True
+staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20778	20891	2030	2045	9520	9520	1424	1424	6753	6753	864	864	37051	37164	4318	4333	True	False	True
+stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2858	3001	118	123	0	0	0	0	0	0	0	0	2858	3001	118	123	True	False	True
+suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	249	249	32	32	16	16	10	10	102	102	16	16	367	367	58	58	True	False	True
+suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	117	117	41	41	84	84	24	24	161	161	13	13	362	362	78	78	True	False	True
+suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	217	217	47	47	42	42	20	20	96	96	12	12	355	355	79	79	True	False	True
+suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	721	721	160	160	350	350	91	91	214	214	35	35	1285	1285	286	286	True	False	True
+suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	125	125	30	30	13	13	9	9	83	83	8	8	221	221	47	47	True	False	True
+suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	396	396	134	134	121	121	57	57	144	144	39	39	661	661	230	230	True	False	True
+suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	22	0	21	21	22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	964	964	318	318	249	249	118	118	475	475	108	108	1688	1688	544	544	True	False	True
+suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	8	8	8	8	13	13	11	11	1302	1302	19	19	1323	1323	38	38	True	False	True
+suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	58	58	23	23	24	24	11	11	92	92	11	11	174	174	45	45	True	False	True
+suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	863	863	220	220	237	237	98	98	181	181	41	41	1281	1281	359	359	True	False	True
+suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	0	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	983	983	287	287	375	375	144	144	907	907	106	106	2265	2265	537	537	True	False	True
+suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	46	46	13	13	9	9	5	5	0	0	0	0	55	55	18	18	True	False	True
+suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	0	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	37	37	16	16	22	22	7	7	89	89	14	14	148	148	37	37	True	False	True
+suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	615	615	143	143	246	246	75	75	115	115	27	27	976	976	245	245	True	False	True
+suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	330	330	83	83	64	64	40	40	195	195	49	49	589	589	172	172	True	False	True
+suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	4	4	4	4	5	5	5	5	1	1	1	1	10	10	10	10	True	False	True
+suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	14	14	16	16	6	6	37	37	2	2	82	82	22	22	True	False	True
+suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	0	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	10	10	3	3	14	14	10	10	5	5	5	5	29	29	18	18	True	False	True
+suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	664	664	145	145	113	113	43	43	255	255	50	50	1032	1032	238	238	True	False	True
+suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	84	84	52	52	25	25	16	16	9	9	5	5	118	118	73	73	True	False	True
+suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14941	14941	383	383	25941	25941	255	255	2856	2856	112	112	43738	43738	750	750	True	False	True
+t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	411	472	68	90	102	7952	13	1240	0	0	0	0	513	8424	81	1330	True	False	True
+t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	927	959	65	78	130	7194	18	1143	0	0	0	0	1057	8153	83	1221	True	False	True
+t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3783	9125	211	229	1	1	1	1	0	0	0	0	3784	9126	212	230	True	False	True
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	36069	36922	5257	5431	25255	30822	5066	5826	7949	7949	1584	1584	69273	75693	11907	12841	True	False	True
+tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6372	6395	372	379	7339	7339	378	378	6966	6966	154	154	20677	20700	904	911	True	False	True
+tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9.1	tooldistillator	0.9.1	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	9	9	6	6	5	5	0	0	0	0	71	71	14	14	True	False	True
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	1039	1039	189	189	2672	3349	467	485	358	358	47	47	4069	4746	703	721	True	False	True
+transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	250	254	31	31	174	174	45	45	0	0	0	0	424	428	76	76	True	False	True
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	229489	275008	5733	6500	228708	324716	11708	16638	22644	23869	1439	1527	480841	623593	18880	24665	True	False	True
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	14681	14681	265	265	0	0	0	0	4488	4488	147	147	19169	19169	412	412	True	False	True
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	74120	77648	3798	3963	64946	90075	5451	7380	19516	20422	2010	2080	158582	188145	11259	13423	True	False	True
+unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4900	5146	257	270	251	251	81	81	1069	1069	29	29	6220	6466	367	380	True	False	True
+uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1488	1596	230	266	0	0	0	0	743	743	35	35	2231	2339	265	301	True	False	True
+usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1060	1060	5	5	0	0	0	0	0	0	0	0	1060	1060	5	5	True	False	True
+valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	518	677	75	87	234	234	65	65	0	0	0	0	752	911	140	152	True	False	True
+vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5936	5936	147	147	523	523	15	15	0	0	0	0	6459	6459	162	162	True	False	True
+varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	273	273	12	12	0	0	0	0	0	0	0	0	273	273	12	12	True	False	True
+vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	2157	2287	198	209	3930	5591	446	744	0	0	0	0	6087	7878	644	953	True	False	True
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	25171	27943	3899	4270	51187	51187	7557	7557	28546	28619	3585	3613	104904	107749	15041	15440	True	False	True
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4715	5343	888	965	9575	9576	2117	2117	3271	5524	1050	1397	17561	20443	4055	4479	True	False	True
+virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	94	94	16	16	0	0	0	0	0	0	0	0	94	94	16	16	True	False	True
+vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.29.0	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	0	8	8	8	0	9694	10338	559	628	12282	53546	1031	2007	5334	5672	246	277	27310	69556	1836	2912	True	False	True
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1619	1715	337	376	0	0	0	0	0	0	0	0	1619	1715	337	376	True	False	True
diff --git a/communities/microgalaxy/resources/tools_filtered_by_ts_categories.tsv b/communities/microgalaxy/resources/tools_filtered_by_ts_categories.tsv
index c54f0f36..80b89d4f 100644
--- a/communities/microgalaxy/resources/tools_filtered_by_ts_categories.tsv
+++ b/communities/microgalaxy/resources/tools_filtered_by_ts_categories.tsv
@@ -1,827 +1,827 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	116	True	False	False
-AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	10	3060	True	False	False
-CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	45191	True	False	False
-CollectResults	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	1961	True	False	False
-CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	108	True	False	False
-EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	9	0	0	11	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	102	True	False	False
-Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	82	True	False	False
-GAFA	gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	45	True	False	False
-GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	133	True	False	False
-Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	45325	True	False	False
-NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	28	62388	True	False	False
-PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	73	1004	True	False	True
-Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	68	True	False	False
-PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	1932	True	False	False
-Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	1758	True	False	False
-Structure_GSPAN	structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	2925	True	False	False
-ThermoRawFileParser	thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	2689	True	False	False
-TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	984	True	False	True
-TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	42	True	False	False
-abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	1764	496717	True	False	True
-abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	391	4278	True	False	True
-adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	37	217	True	False	False
-aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	4	1	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	47	168	True	False	False
-aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	129	True	False	True
-align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	329	True	False	False
-amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	53	True	False	True
-ampvis2	ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.9			Analysis, Visualisation	Biodiversity	0	0	19	0	0	0	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	42	267	True	False	False
-amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	591	True	False	True
-ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	7	True	False	True
-annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1175	25975	True	False	False
-antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	52	True	False	False
-antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	279	14596	True	False	True
-aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	65	True	False	False
-argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	38	3528	True	False	False
-art	art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/	Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	Conversion	Bioinformatics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	123	8175	True	False	True
-assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-astral	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees								Up-to-date	https://github.com/smirarab/ASTRAL	Phylogenetics	astral	iuc	https://github.com/usegalaxy-be/galaxytools/tree/main/astral	https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral	5.7.8	astral-tree	5.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	False		
-augustus	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	685	11245	True	False	False
-augustus	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	516	8864	True	False	False
-b2btools	b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.7	Protein disorder prediction, Protein secondary structure prediction		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	12	345	True	False	False
-bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	151	2982	True	False	True
-bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-bamclipper	bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-bamhash	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	169	True	False	False
-bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	208	14021	True	False	True
-bamtools_filter	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1195	114863	True	False	False
-bamtools_split	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	197	4328	True	False	False
-bamutil	bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	39	True	False	False
-bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	2016	44390	True	False	True
-barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	71	True	False	False
-barrnap	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update	https://github.com/tseemann/barrnap	Sequence Analysis	barrnap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	Gene prediction	Genomics, Model organisms, Model organisms	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	160	3938	True	False	False
-baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bax2bam	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	200	True	False	False
-bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	64	True	False	True
-bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.09	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	4	0	0	420	6381	True	False	True
-bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	7	0	87	2895	True	False	False
-bed_to_protein_map	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	49	385	True	False	False
-bellerophon	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	123	1194	True	False	False
-best_regression_subsets	BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	3	True	False	False
-bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-bigwig_outlier_bed	bigwig_outlier_bed	pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files	bigtools	bigtools		bigtools	Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.			To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	Sequence Analysis	bigwig_outlier_bed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed	0.2.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	81	True	False	True
-biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-bioinformatics_cafe	fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	978	True	False	False
-biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	98	3906	True	False	True
-bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	531	True	False	False
-bioperl	bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	Data handling, Service invocation	Genomics, Software engineering	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	240	6736	True	False	False
-biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	3	True	False	False
-bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	4	4	4	0	332	12876	True	False	False
-blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	101	1232	True	False	True
-blast_parser	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	296	True	False	False
-blast_plus_remote_blastp	blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.16.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	121	22499	True	False	True
-blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-blastxml_to_gapped_gff3	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	185	True	False	False
-blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	159	264558	True	False	True
-blat_coverage_report	generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-blat_mapping	blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	685	True	False	False
-blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	34	3009	True	False	False
-blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	15	1478	True	False	False
-bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	326	18351	True	False	True
-braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	17	109	True	False	False
-braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	567	True	False	False
-brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template	brew3r.r	brew3r.r		BREW3R.r	This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.	Genome annotation	Transcriptomics, Genomics	To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2			Genome annotation	Transcriptomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-bumbershoot	idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	3	1348	True	False	False
-bundle_collections	bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.58			0	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1804	86180	True	False	True
-bwameth	bwameth	Fast and accurate alignment of BS-seq reads								Up-to-date	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.7	bwameth	0.2.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	201	10619	True	False	False
-cactus	cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			Multiple sequence alignment, Genome alignment	Genomics, Sequence assembly, Mapping, Phylogenetics	0	2	2	1	0	2	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	26	234	True	False	False
-calculate_contrast_threshold	calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-calisp	calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	True	False	False
-cami_amber	biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert	Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments								Up-to-date	https://github.com/CAMI-challenge/AMBER	Metagenomics	cami_amber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber	2.0.7	cami-amber	2.0.7			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	101	7766	True	False	False
-cardinal	cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								Up-to-date	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	3.4.3	bioconductor-cardinal	3.4.3			0	9	11	11	0	9	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	9	11	9	0	277	48705	True	False	False
-cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	268	2878	True	False	True
-cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	280	4474	True	False	True
-cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	6	True	False	False
-cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	98	True	False	True
-champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	19	174	True	False	False
-charts	charts	Enables advanced visualization options in Galaxy Charts								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	287	3589	True	False	False
-checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	390	5165	True	False	True
-checkv	checkv_end_to_end	Assess quality of single-contig viral genomes	checkv	checkv		CheckV	CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	Up-to-date	https://bitbucket.org/berkeleylab/checkv/	Metagenomics	checkv	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv	1.0.3	checkv	1.0.3	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	207	True	False	False
-chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	418	15690	True	False	False
-chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	97	6418	True	False	False
-chromeister	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	182	2130	True	False	False
-chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-circexplorer	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	251	True	False	False
-circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	269	True	False	False
-cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18	False		
-clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	68	1856	True	False	True
-clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-climate-stripes	climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	237	True	False	False
-clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	651	46793	True	False	True
-cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	102	True	False	True
-cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	1	108	True	False	False
-codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	29	60901	True	False	True
-cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	8	342	True	False	False
-cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	2757	True	False	True
-colabfold	colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-colibread	commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								To update	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14+galaxy0	commet	24.7.14			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	251	True	False	False
-collapse_collection	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1583	33934	True	False	False
-combineJSON	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	147	True	False	True
-combine_tabular_collection	combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	220	True	False	False
-compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	332	True	False	True
-compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	94	True	False	False
-compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	65	True	False	False
-concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	92	786	True	False	True
-consensus_from_alignments	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55	585	True	False	False
-consolidate_vcfs	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	49	271	True	False	False
-count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-coverage_report	CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	72	529	True	False	True
-crispr_studio	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	Visualisation	Sequence analysis, Genomics, Data visualisation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	30	636	True	False	False
-crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	17	347	True	False	False
-crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	74	3389	True	False	False
-cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16	8518	True	False	True
-ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	203	True	False	False
-cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	1782	True	False	False
-custom_pro_db	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	57	1652	True	False	False
-custom_pro_db_annotation_data_manager		CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	5090	232004	True	False	True
-dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	10	10	10	0	1263	66609	True	False	True
-das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	24	706	True	False	True
-data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	439	True	False	False
-data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	99	799	True	False	False
-data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	146	658	True	False	False
-data_manager_eggnog_mapper		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-data_manager_eggnog_mapper_abspath		download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-dbbuilder	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	161	4758	True	False	False
-decoyfasta		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	True	False	False
-delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	39	True	False	False
-deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	4990	95752	True	False	True
-deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	72	True	False	False
-dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	218	16064	True	False	False
-dia_umpire	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	33	True	False	False
-dialignr	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	40	True	False	False
-diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	3	3	0	963	49711	True	False	True
-diann	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	15	True	False	False
-diapysef	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	245	True	False	False
-diffacto	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	7	True	False	False
-disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	369	True	False	True
-divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	32	True	False	False
-dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1576	True	False	False
-dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	83	True	False	False
-dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	39	6886	True	False	True
-drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	46	646	True	False	True
-droplet-barcode-plot	_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	973	True	False	False
-dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	201	1599	True	False	False
-dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	126	3934	True	False	False
-ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	9907	True	False	True
-edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	945	18117	True	False	False
-effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	1	3	1	0	510	30565	True	False	True
-egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	177	2524	True	False	False
-emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	107	107	107	0	1816	89530	True	False	True
-encyclopedia	encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30			2	4	7	0	2	4	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	48	706	True	False	False
-ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	45	899	True	False	True
-evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-exomedepth	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	29	410	True	False	False
-exonerate	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	988	True	False	False
-exparna	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	200	5265	True	False	True
-express	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	325	True	False	False
-ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-falco	falco	A high throughput sequence QC analysis tool	falco	falco		Falco	A high-speed FastQC emulation for quality control of sequencing data.	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	Up-to-date	https://github.com/smithlabcode/falco/	Sequence Analysis	falco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco	https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco	1.2.4	falco	1.2.4	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	52	459	True	False	True
-fasta2bed	fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fasta_extract	fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	10	True	False	False
-fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fasta_nucleotide_color_plot	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15	160	True	False	False
-fasta_stats	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1080	35336	True	False	False
-fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	250	3498	True	False	True
-fastg2protlib	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	28	True	False	False
-fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	2803	1055760	True	False	True
-fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fastqc_stats	FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1266	4333	True	False	True
-fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	379	55434	True	False	True
-feature_alignment	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18	True	False	False
-featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	22385	True	False	False
-featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	4679	696399	True	False	True
-feelnc	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	Annotation, Classification	Functional, regulatory and non-coding RNA	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46	1191	True	False	False
-feht	feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	307	5240	True	False	False
-filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	426	26274	True	False	False
-filter_density	filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-filter_stats	filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-filter_transcripts_via_tracking	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	20	True	False	False
-filter_vcf	filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	617	30483	True	False	True
-find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	69	True	False	False
-find_repeats	findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-fisher_test	fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	14	331	True	False	False
-flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	74	13759	True	False	False
-flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	17	645	True	False	True
-flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	20904	True	False	True
-format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	166	5588	True	False	True
-fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	68	1102	True	False	True
-fragpipe	fragpipe	Data analysis for mass spectrometry-based proteomics.								Up-to-date	https://fragpipe.nesvilab.org/	Proteomics	fragpipe	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	20.0	fragpipe	20.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	55	20021	True	False	True
-frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	28	0	0	0	28	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	900	5906	True	False	True
-garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	27	True	False	False
-gblocks	gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b			0	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	True	False	False
-gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	10	1475	True	False	False
-gecko	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	112	519	True	False	False
-gemini	gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	Sequence analysis, Genetic variation analysis	Sequence analysis	1	2	2	2	1	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	662	4916	True	False	False
-geneiobio	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	67	True	False	False
-generate_pc_lda_matrix	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	119	True	False	False
-genomad	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	genomad	genomad		geNomad	geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.	Sequence annotation, Taxonomic classification	Sequence analysis	Up-to-date	https://github.com/apcamargo/genomad/	Metagenomics	genomad	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad	1.8.0	genomad	1.8.0	Sequence annotation, Taxonomic classification	Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	46	True	False	False
-get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	0	15	186	True	False	False
-getindelrates_3way	indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-getindels_2way	getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	495	True	False	False
-gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	To update	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.7	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	418	8159	True	False	False
-gff3_rebase	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	135	True	False	False
-gffread	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	680	10995	True	False	False
-ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	5	5	5	0	1388	22148	True	False	True
-gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	27	660	True	False	True
-glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	0	187	3965	True	False	True
-glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4	11	True	False	False
-goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	408	5484	True	False	True
-goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1210	19167	True	False	True
-gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	71	True	False	False
-graphclust	graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	True	False	False
-graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	432	9277	True	False	True
-graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	136	6651	True	False	True
-graphprot	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy2	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	474	True	False	False
-gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-gtdb_to_taxdump	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	gtdb_to_taxdump	gtdb_to_taxdump		gtdb_to_taxdump	Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.	Data handling, Mapping, Generation	Computational biology	Up-to-date	https://github.com/nick-youngblut/gtdb_to_taxdump	Metagenomics	gtdb_to_taxdump	iuc	https://github.com/nick-youngblut/gtdb_to_taxdump	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	0.1.9	Data handling, Mapping, Generation	Computational biology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	Up-to-date	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.4.0	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-gtf-2-gene-list	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	155	1678	True	False	False
-gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	145	3340	True	False	True
-guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-gwastools	gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	Deposition, Analysis, Annotation	GWAS study	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	True	False	False
-hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	117	4459	True	False	True
-hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	339	True	False	True
-hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	295	True	False	False
-hardklor	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2	111	True	False	False
-hcluster_sg	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	238	True	False	False
-hcluster_sg_parser	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	290	True	False	False
-heatmap2	ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	1953	44240	True	False	False
-heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	heinz, bionet		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	242	1186	True	False	False
-helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	93	True	False	False
-hgv_fundo	hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	True	False	False
-hgv_hilbertvis	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	True	False	False
-hicexplorer	hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								Up-to-date	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.5	hicexplorer	3.7.5			38	38	38	4	38	38	38	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	33	36	33	0	1085	66003	True	False	False
-hicstuff	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices								To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	1410	True	False	False
-hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	137	True	False	True
-high_dim_heatmap	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	True	False	False
-hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	4183	299104	True	False	False
-hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	12	12	12	0	439	33702	True	False	True
-homer	homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	Sequence motif discovery		0	0	5	4	0	0	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	5	0	0	394	6937	True	False	False
-homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-htseq-clip	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	77	True	False	False
-htseq_count	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	Nucleic acid sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1419	154533	True	False	False
-humann	humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.9	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	10	10	10	6	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	1037	19490	True	False	True
-hybpiper	hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.3.0	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	2	17	2	17	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	12	17	12	0	161	10370	True	False	True
-hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	354	True	False	True
-icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	69	1127	True	False	True
-idconvert	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	275	True	False	False
-idr	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	30	2873	True	False	False
-iedb_api	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12	1506	True	False	False
-illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	22	True	False	False
-infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	67	100294	True	False	True
-inforna		INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	139	True	False	False
-instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	94	True	False	True
-intarna	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.1	intarna	3.4.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	7569	True	False	False
-integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	58	52965	True	False	True
-interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	677	35243	True	False	True
-iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	681	21598	True	False	True
-isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	57581	True	False	True
-isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	822	True	False	False
-isoplot	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	2	True	False	False
-itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	868	True	False	True
-ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	5	5	5	0	1171	1224275	True	False	True
-jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	2	2	2	0	2346	18229	True	False	True
-jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse_2	jbrowse_2		JBrowse 2	Modular genome browser with views of synteny and structural variation.	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.15.4	jbrowse2	2.15.4	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-jcvi_gff_stats	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.16			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	2469	True	False	False
-jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	91	1138	True	False	True
-kaptive	kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19	363	True	False	True
-khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	8	8	8	0	63	2022	True	False	True
-kinwalker		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.0.9	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	38	319	True	False	True
-kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	33	594	True	False	True
-kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	5	0	1209	33778	True	False	True
-kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	2367	185308	True	False	True
-kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	481	14683	True	False	True
-kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	182	1444	True	False	True
-kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	354	2527	True	False	True
-krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	703	16525	True	False	True
-krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-last	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1584	Sequence alignment	Comparative genomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	41	227	True	False	False
-lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2	137	True	False	True
-legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	55	True	False	True
-length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	322	4090	True	False	False
-lfq_protein_quant	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	111	True	False	False
-lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9	152	True	False	True
-limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1012	20344	True	False	True
-lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	37	True	False	True
-links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	77	405	True	False	False
-locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								Up-to-date	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	2.0.1	locarna	2.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	339	True	False	False
-logistic_regression_vif	LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-logol	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-longorf	longORF	obtain longest ORF in six-frame translations								To update		Sequence Analysis	longorf	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf	0.3.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	647	True	False	True
-lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	114	936	True	False	True
-m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	True	False	True
-maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	188	True	False	True
-macs2	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	0	0	9	0	0	0	0	0	9	9	9	0	1969	84521	True	False	False
-maf_cpg_filter	cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	2	2	2	0	817	143045	True	False	True
-make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	554	5591	True	False	True
-maldiquant	maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base				0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	2	2	0	25	3797	True	False	False
-map_peptides_to_bed	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	41	True	False	False
-mapping_quality_stats	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-mapping_to_ucsc	mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	167	True	False	True
-marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	27	9763	True	False	True
-mashmap	mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	576	True	False	False
-mauve_contig_mover	mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	118	2059	True	False	True
-maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	415	6078	True	False	True
-mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	29	True	False	True
-mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	85	True	False	False
-mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	24	True	False	False
-medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	3	3	3	0	768	99863	True	False	True
-medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	548	9530	True	False	True
-megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	54	475	True	False	True
-megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	261	3610	True	False	True
-meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	244	2483	True	False	True
-meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-meta_proteome_analyzer	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	123	True	False	False
-metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	2	2	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	192	4329	True	False	True
-metabuli	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	metabuli	metabuli		metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid	Taxonomic classification	Taxonomy	To update	https://github.com/steineggerlab/Metabuli	Sequence Analysis, Metagenomics	metabuli	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli	1.0.5	metabuli	1.0.8	Taxonomic classification	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	184	True	False	True
-metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	115	636	True	False	True
-metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	753	True	False	True
-metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	15	4181	True	False	True
-metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	4	1	2	4	4	0	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	499	11069	True	False	True
-metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	104	2522	True	False	True
-metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5461	True	False	False
-methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	200	16573	True	False	False
-metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	103	3966	True	False	False
-mg_toolkit	mg_toolkit_bulk_download, mg_toolkit_original_metadata	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	mg-toolkit	mg-toolkit		mg-toolkit	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	Data retrieval	Metagenomics	Up-to-date	https://github.com/EBI-Metagenomics/emg-toolkit	Metagenomics	mg_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	0.10.4	mg-toolkit	0.10.4	Data retrieval	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-microsatbed	microsatbed	Select microsatellites for a bed file								To update	https://github.com/lmdu/pytrf	Sequence Analysis	microsatbed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed	1.3.3	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-microsatellite_birthdeath	microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-microsats_alignment_level	microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-microsats_mutability	microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-migmap	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	Sequence analysis, Read mapping	Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	1226	True	False	False
-minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	53	895	True	False	False
-minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	109	2206	True	False	True
-miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	178	11938	True	False	True
-minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	185	True	False	True
-miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	30	842	True	False	True
-miranda	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	41	6076	True	False	False
-mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-mirmachine	mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-mirnature	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	10	True	False	False
-mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	66	881	True	False	False
-mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	56	613	True	False	False
-mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	0	236	100920	True	False	True
-mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	635	9304	True	False	True
-moFF	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	759	True	False	False
-mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	322	89021	True	False	True
-monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	264	3266	True	False	False
-morpheus	morpheus	Morpheus MS Search Application	morpheus	morpheus		Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.	Peptide database search	Proteomics	To update	https://cwenger.github.io/Morpheus	Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	288	morpheus	290	Peptide database search	Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	140	True	False	False
-mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	129	129	129	129	129	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	126	129	129	0	14353	302916	True	False	True
-motus	mereg_mOTUs_tables, motus_profiler	Tool for profiling the abundance of microbial taxa.	mOTUs	mOTUs		Metagenomic operational taxonomic units (mOTUs)	Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/motu-tool/mOTUs	Metagenomics	motus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs	https://github.com/bgruening/galaxytools/tree/master/tools/motus	3.1.0	motus	3.1.0	Taxonomic classification	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	76	True	False	False
-mqppep	mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2	True	False	False
-mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	True	False	True
-msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	19958	True	False	True
-msgfplus	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	507	True	False	False
-msms_extractor	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	110	True	False	False
-msstats	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	144	2036	True	False	False
-msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	726	True	False	True
-mt2mq	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	19	270	True	False	False
-multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	53	True	False	True
-multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	8320	162790	True	False	True
-multispecies_orthologous_microsats	multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-mummer	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	83	652	True	False	False
-mummer4	mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1			6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	6	3	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	669	18347	True	False	False
-mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	844	True	False	True
-mzml_validator	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-naltorfs	bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2			3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	3	836	True	False	True
-nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	2195	63235	True	False	True
-nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	15	1074	True	False	True
-nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	40	True	False	False
-ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	16	16	16	16	16	0	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	16	16	15	0	4066	365597	True	False	True
-ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ncbi_fcs_adaptor	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	95	667	True	False	False
-newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	448	25505	True	False	True
-nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	2	1	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	2	0	0	210	4080	True	False	True
-nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	84	268	True	False	True
-nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	142	True	False	True
-novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	162	6384	True	False	False
-nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	861	True	False	True
-nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	45	True	False	True
-obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	503	26251	True	False	True
-ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	True	False	False
-odgi	odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6			0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	2	25	True	False	False
-ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	39	2654	True	False	False
-openms	AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	3.1	openms	3.2.0			8	34	144	0	8	34	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	141	124	0	886	105432	True	False	False
-openms	AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.2.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	135	134	0	916	105743	True	False	False
-optitype	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	321	True	False	False
-orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	774	True	False	True
-orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	Up-to-date	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	2.5.5	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	239	1333	True	False	True
-pacu	pacu_map, pacu_snp	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.	pacu	pacu		PACU	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).	Clustering	Phylogenetics, Sequence analysis	Up-to-date	https://github.com/BioinformaticsPlatformWIV-ISP/PACU	Sequence Analysis, Phylogenetics	pacu	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu	0.0.5	pacu_snp	0.0.5	Clustering	Phylogenetics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-pairtools	pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0			5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-pangolin	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	0	0	259	7276	True	False	False
-pangolin	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	Tree-based sequence alignment, Variant classification	Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	0	0	259	7276	True	False	False
-paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	299	True	False	False
-parse_mito_blast	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	31	90	True	False	False
-pathview	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	565	5260	True	False	False
-pathwaymatcher	reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	238	True	False	False
-patrist	patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	78	3109	True	False	False
-pep_pointer	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	498	True	False	False
-pepquery	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	4862	True	False	False
-pepquery2	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2			0	1	3	0	0	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	13	717	True	False	False
-peptide_genomic_coordinate	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	468	True	False	False
-peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.11			4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	2	0	485	17477	True	False	True
-peptimapper	peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.1					0	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-pepxml_to_xls		Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-percolator	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.7.1			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	5	368	True	False	False
-pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	19	165	True	False	True
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	119	14	17	0	0	0	0	0	0	0	0	45	119	14	17	True	False	False
+AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	189	3094	23	25	0	0	0	0	0	0	0	0	189	3094	23	25	True	False	False
+CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25532	50045	45	57	0	0	0	0	0	0	0	0	25532	50045	45	57	True	False	False
+CollectResults	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1119	2115	50	62	0	0	0	0	0	0	0	0	1119	2115	50	62	True	False	False
+CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	108	1	3	0	0	0	0	0	0	0	0	37	108	1	3	True	False	False
+EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	516	516	128	128	0	0	0	0	0	0	0	0	516	516	128	128	True	False	False
+Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	352	352	36	36	0	0	0	0	0	0	0	0	352	352	36	36	True	False	False
+GAFA	gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	47	6	6	0	0	0	0	0	0	0	0	40	47	6	6	True	False	False
+GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	80	150	18	23	0	0	0	0	0	0	0	0	80	150	18	23	True	False	False
+Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	53	53	18	18	0	0	0	0	0	0	0	0	53	53	18	18	True	False	False
+LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25572	50177	45	57	0	0	0	0	0	0	0	0	25572	50177	45	57	True	False	False
+NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	3210	62854	96	124	0	0	0	0	0	0	0	0	3210	62854	96	124	True	False	False
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	1038	1038	146	146	0	0	0	0	849	849	38	38	1887	1887	184	184	True	False	True
+Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	71	9	10	0	0	0	0	0	0	0	0	45	71	9	10	True	False	False
+PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1202	2121	48	62	0	0	0	0	0	0	0	0	1202	2121	48	62	True	False	False
+Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1116	1897	57	71	0	0	0	0	0	0	0	0	1116	1897	57	71	True	False	False
+Structure_GSPAN	structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	991	3060	50	62	0	0	0	0	0	0	0	0	991	3060	50	62	True	False	False
+ThermoRawFileParser	thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2467	2959	88	124	0	0	0	0	1097	1097	18	18	3564	4056	106	142	True	False	False
+TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1003	1022	48	52	0	0	0	0	0	0	0	0	1003	1022	48	52	True	False	True
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	43	43	20	20	0	0	0	0	0	0	0	0	43	43	20	20	True	False	False
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	619817	622353	4097	4130	320454	320454	2915	2915	496156	503743	2012	2227	1436427	1446550	9024	9272	True	False	True
+abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1139	1139	109	109	0	0	0	0	0	0	0	0	1139	1139	109	109	True	False	True
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5543	5543	1042	1042	1301	1305	413	414	2030	2030	299	299	8874	8878	1754	1755	True	False	True
+adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	348	348	62	62	0	0	0	0	0	0	0	0	348	348	62	62	True	False	False
+aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	200	200	77	77	83	83	39	39	1747	1747	44	44	2030	2030	160	160	True	False	False
+aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	262	36	36	0	0	0	0	0	0	0	0	262	262	36	36	True	False	True
+align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	511	541	32	35	0	0	0	0	0	0	0	0	511	541	32	35	True	False	False
+amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	81	81	17	17	0	0	0	0	0	0	0	0	81	81	17	17	True	False	True
+ampvis2	ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.9			Analysis, Visualisation	Biodiversity	0	0	19	0	0	0	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	1213	1213	155	155	0	0	0	0	0	0	0	0	1213	1213	155	155	True	False	False
+amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5734	5734	334	334	1035	1035	106	106	0	0	0	0	6769	6769	440	440	True	False	True
+ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	7	7	0	0	0	0	0	0	0	0	26	26	7	7	True	False	True
+annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	29266	30655	2849	2973	59299	66180	5917	6355	5644	5644	1049	1049	94209	102479	9815	10377	True	False	False
+antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	292	306	5	7	0	0	0	0	0	0	0	0	292	306	5	7	True	False	False
+antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15949	16490	726	811	5113	5113	649	649	6043	6043	169	169	27105	27646	1544	1629	True	False	True
+aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	75	75	9	9	0	0	0	0	0	0	0	0	75	75	9	9	False		
+aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	59	74	10	12	0	0	0	0	0	0	0	0	59	74	10	12	True	False	False
+argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3670	3670	71	71	3	3	2	2	234	234	10	10	3907	3907	83	83	True	False	False
+art	art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/	Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	Conversion	Bioinformatics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	140	140	9	9	0	0	0	0	0	0	0	0	140	140	9	9	True	False	False
+artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	9021	9021	238	238	0	0	0	0	0	0	0	0	9021	9021	238	238	True	False	True
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+astral	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees								Up-to-date	https://github.com/smirarab/ASTRAL	Phylogenetics	astral	iuc	https://github.com/usegalaxy-be/galaxytools/tree/main/astral	https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral	5.7.8	astral-tree	5.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	151	151	5	5	151	151	5	5	False		
+augustus	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	12890	13988	1826	1988	14901	14901	2633	2633	6187	6187	511	511	33978	35076	4970	5132	True	False	False
+augustus	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10109	11052	1378	1509	12573	12573	2206	2206	5274	5274	369	369	27956	28899	3953	4084	True	False	False
+b2btools	b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.7	Protein disorder prediction, Protein secondary structure prediction		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	369	369	19	19	0	0	0	0	0	0	0	0	369	369	19	19	True	False	False
+bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11117	11117	534	534	19	19	1	1	9601	9601	167	167	20737	20737	702	702	True	False	True
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+bamclipper	bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+bamhash	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	158	181	40	44	0	0	0	0	0	0	0	0	158	181	40	44	True	False	False
+bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	14693	15620	653	721	61872	101400	1656	5678	39	39	3	3	76604	117059	2312	6402	True	False	True
+bamtools_filter	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115954	124795	2994	3180	95433	142254	6712	10660	5793	5793	497	497	217180	272842	10203	14337	True	False	False
+bamtools_split	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	9073	9073	401	401	2746	2746	224	224	103	103	10	10	11922	11922	635	635	True	False	False
+bamutil	bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	45	45	20	20	69	69	21	21	258	258	1	1	372	372	42	42	True	False	False
+bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	55392	56095	4951	5035	47603	47603	4916	4916	18089	18089	3121	3121	121084	121787	12988	13072	True	False	True
+barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	111	111	8	8	29	29	10	10	21	21	4	4	161	161	22	22	True	False	False
+barrnap	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update	https://github.com/tseemann/barrnap	Sequence Analysis	barrnap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	Gene prediction	Genomics, Model organisms, Model organisms	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6041	6041	316	316	0	0	0	0	6723	7273	240	322	12764	13314	556	638	True	False	False
+baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bax2bam	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	208	208	26	26	210	210	30	30	0	0	0	0	418	418	56	56	True	False	False
+bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	90	90	28	28	0	0	0	0	0	0	0	0	90	90	28	28	True	False	True
+bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.09	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	4	0	0	11989	11989	768	768	4458	4458	652	652	2507	2507	80	80	18954	18954	1500	1500	True	False	True
+bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	7	0	2352	3092	234	265	0	0	0	0	0	0	0	0	2352	3092	234	265	True	False	False
+bed_to_protein_map	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	410	419	134	137	363	363	99	99	158	158	13	13	931	940	246	249	True	False	False
+bellerophon	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1611	1611	262	262	763	763	67	67	543	543	30	30	2917	2917	359	359	True	False	False
+best_regression_subsets	BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3	4	3	4	14	253	7	72	0	0	0	0	17	257	10	76	True	False	False
+bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	544	544	20	20	0	0	0	0	0	0	0	0	544	544	20	20	True	False	True
+bigwig_outlier_bed	bigwig_outlier_bed	pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files	bigtools	bigtools		bigtools	Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.			To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	Sequence Analysis	bigwig_outlier_bed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed	0.2.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	218	218	5	5	0	0	0	0	0	0	0	0	218	218	5	5	False		
+binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	126	126	42	42	0	0	0	0	0	0	0	0	126	126	42	42	True	False	True
+biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+bioinformatics_cafe	fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1137	1137	97	97	1029	1029	71	71	0	0	0	0	2166	2166	168	168	True	False	False
+biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12725	12725	297	297	2851	5049	450	638	2171	2371	214	239	17747	20145	961	1174	True	False	True
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	151	151	143	143	43	43	596	596	22	22	1286	1286	216	216	True	False	False
+bioperl	bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	Data handling, Service invocation	Genomics, Software engineering	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7738	7931	478	508	8301	8301	849	849	1369	1369	154	154	17408	17601	1481	1511	True	False	False
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6243	6243	375	375	0	0	0	0	6243	6243	375	375	True	False	True
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	3	1	1	0	0	0	0	0	0	0	0	3	3	1	1	True	False	False
+bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	4	4	4	0	13715	14997	992	1099	0	0	0	0	197	197	22	22	13912	15194	1014	1121	True	False	False
+blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1063	1237	257	300	0	0	0	0	0	0	0	0	1063	1237	257	300	True	False	True
+blast_parser	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	417	438	99	104	0	0	0	0	0	0	0	0	417	438	99	104	True	False	False
+blast_plus_remote_blastp	blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.16.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24916	27120	283	347	0	0	0	0	0	0	0	0	24916	27120	283	347	True	False	True
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	True	False	False
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	True	False	False
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+blastxml_to_gapped_gff3	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	585	585	102	102	172	172	63	63	135	135	16	16	892	892	181	181	True	False	False
+blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	264392	265217	483	552	0	0	0	0	0	0	0	0	264392	265217	483	552	True	False	True
+blat_coverage_report	generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+blat_mapping	blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1527	1527	79	79	6	6	1	1	317	317	26	26	1850	1850	106	106	True	False	False
+blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	768	3043	97	119	14	14	11	11	276	276	9	9	1058	3333	117	139	True	False	False
+blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	811	1501	54	79	64	64	29	29	561	561	15	15	1436	2126	98	123	True	False	False
+bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	51378	51378	775	775	3298	3298	160	160	1660	1660	63	63	56336	56336	998	998	True	False	True
+braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	165	165	48	48	0	0	0	0	0	0	0	0	165	165	48	48	True	False	False
+braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1938	1938	294	294	0	0	0	0	412	412	71	71	2350	2350	365	365	True	False	False
+brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template	brew3r.r	brew3r.r		BREW3R.r	This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.	Genome annotation	Transcriptomics, Genomics	To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2			Genome annotation	Transcriptomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6	6	2	2	0	0	0	0	7	7	3	3	False		
+bumbershoot	idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	1186	1356	21	32	0	0	0	0	0	0	0	0	1186	1356	21	32	True	False	False
+bundle_collections	bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.58			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	1	1518	1526	73	76	1520	1528	74	77	True	False	False
+busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	102717	103051	3877	3926	34251	34251	3506	3506	33192	34369	2439	2525	170160	171671	9822	9957	True	False	True
+bwameth	bwameth	Fast and accurate alignment of BS-seq reads								Up-to-date	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.7	bwameth	0.2.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7970	11724	643	826	5524	5524	611	611	1242	1242	114	114	14736	18490	1368	1551	True	False	False
+cactus	cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			Multiple sequence alignment, Genome alignment	Genomics, Sequence assembly, Mapping, Phylogenetics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	299	299	61	61	0	0	0	0	1339	1339	95	95	1638	1638	156	156	True	False	False
+calculate_contrast_threshold	calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+calisp	calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	True	False	False
+cami_amber	biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert	Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments								Up-to-date	https://github.com/CAMI-challenge/AMBER	Metagenomics	cami_amber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber	2.0.7	cami-amber	2.0.7			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	195	195	4	4	0	0	0	0	0	0	0	0	195	195	4	4	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	9869	9869	158	158	0	0	0	0	6886	6886	146	146	16755	16755	304	304	True	False	False
+cardinal	cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								Up-to-date	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	3.4.3	bioconductor-cardinal	3.4.3			0	9	11	0	0	9	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	0	9	11	9	0	41875	50702	663	713	12	12	1	1	7512	7512	231	231	49399	58226	895	945	True	False	False
+cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3835	3835	597	597	1359	1359	467	467	646	646	98	98	5840	5840	1162	1162	True	False	True
+cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5946	7379	407	628	0	0	0	0	5946	7379	407	628	True	False	True
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10414	10414	510	510	2	2	1	1	2	2	1	1	10418	10418	512	512	True	False	True
+cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	4	4	0	0	0	0	0	0	0	0	8	8	4	4	True	False	False
+cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	225	225	32	32	271	271	61	61	0	0	0	0	496	496	93	93	True	False	True
+champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	183	183	20	20	0	0	0	0	0	0	0	0	183	183	20	20	True	False	False
+charts	charts	Enables advanced visualization options in Galaxy Charts								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3383	4001	1576	1822	7870	13727	3823	6880	249	350	108	145	11502	18078	5507	8847	True	False	False
+checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	7500	7500	930	930	0	0	0	0	0	0	0	0	7500	7500	930	930	True	False	True
+checkv	checkv_end_to_end	Assess quality of single-contig viral genomes	checkv	checkv		CheckV	CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	Up-to-date	https://bitbucket.org/berkeleylab/checkv/	Metagenomics	checkv	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv	1.0.3	checkv	1.0.3	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	207	207	1	1	0	0	0	0	0	0	0	0	207	207	1	1	True	False	False
+chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	16468	18344	956	991	33692	34453	2559	2625	2948	2948	104	104	53108	55745	3619	3720	True	False	False
+chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	16542	16542	287	287	1061	1061	102	102	27	27	5	5	17630	17630	394	394	True	False	False
+chromeister	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2696	2696	398	398	0	0	0	0	1235	1235	186	186	3931	3931	584	584	True	False	False
+chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+circexplorer	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	211	263	32	40	0	0	0	0	209	209	6	6	420	472	38	46	True	False	False
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	524	524	32	32	0	0	0	0	0	0	0	0	524	524	32	32	True	False	False
+cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	21	4	4	9	9	5	5	18	18	1	1	48	48	10	10	False		
+clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3388	3388	187	187	1	1	1	1	1	1	1	1	3390	3390	189	189	True	False	True
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+climate-stripes	climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	239	239	35	35	16	16	2	2	182	182	3	3	437	437	40	40	True	False	False
+clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	548	548	18	18	0	0	0	0	548	548	18	18	True	False	True
+clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	79867	80817	1675	1785	49493	87884	3703	7380	8797	9713	670	728	138157	178414	6048	9893	True	False	True
+cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2609	2609	3	3	0	0	0	0	0	0	0	0	2609	2609	3	3	True	False	True
+cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	90	112	11	14	0	0	0	0	0	0	0	0	90	112	11	14	True	False	False
+codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	61197	61220	64	65	0	0	0	0	0	0	0	0	61197	61220	64	65	True	False	True
+cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	316	355	25	29	0	0	0	0	0	0	0	0	316	355	25	29	True	False	False
+cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2758	2758	22	22	20	20	10	10	0	0	0	0	2778	2778	32	32	True	False	True
+colabfold	colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6771	6771	50	50	0	0	0	0	6771	6771	50	50	True	False	False
+colibread	commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								Up-to-date	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14	commet	24.7.14			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	273	273	40	40	0	0	0	0	0	0	0	0	273	273	40	40	True	False	False
+collapse_collection	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	39518	40471	3555	3629	22007	24841	3536	4045	3969	4101	814	835	65494	69413	7905	8509	True	False	False
+combineJSON	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	530	530	65	65	8	8	6	6	0	0	0	0	538	538	71	71	True	False	True
+combine_tabular_collection	combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	221	5	28	0	0	0	0	0	0	0	0	39	221	5	28	True	False	False
+compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	332	28	32	0	0	0	0	0	0	0	0	306	332	28	32	True	False	True
+compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	266	266	39	39	28	28	15	15	0	0	0	0	294	294	54	54	True	False	True
+compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	85	96	9	10	0	0	0	0	316	334	8	8	401	430	17	18	True	False	False
+compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	55	65	2	2	0	0	0	0	317	335	5	5	372	400	7	7	True	False	False
+concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	2105	2105	155	155	0	0	0	0	0	0	0	0	2105	2105	155	155	True	False	True
+consensus_from_alignments	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1184	1184	154	154	0	0	0	0	0	0	0	0	1184	1184	154	154	True	False	False
+consolidate_vcfs	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	280	307	110	124	712	1277	332	628	476	541	55	79	1468	2125	497	831	True	False	False
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+coverage_report	CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1081	1081	151	151	0	0	0	0	0	0	0	0	1081	1081	151	151	True	False	True
+crispr_studio	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	Visualisation	Sequence analysis, Genomics, Data visualisation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1052	1053	75	76	0	0	0	0	0	0	0	0	1052	1053	75	76	True	False	False
+crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	276	390	61	76	131	131	42	42	0	0	0	0	407	521	103	118	True	False	False
+crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4066	4139	166	180	0	0	0	0	0	0	0	0	4066	4139	166	180	True	False	False
+cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9942	9942	26	26	0	0	0	0	0	0	0	0	9942	9942	26	26	True	False	True
+ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	196	211	41	48	1	447	1	161	0	0	0	0	197	658	42	209	True	False	False
+cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1251	1803	98	166	3461	15159	486	2044	2425	3338	57	159	7137	20300	641	2369	True	False	False
+custom_pro_db	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1729	1744	144	146	450	450	72	72	361	361	12	12	2540	2555	228	230	True	False	False
+custom_pro_db_annotation_data_manager		CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	259754	272370	11716	12601	334550	362356	18618	20162	64377	65986	3507	3627	658681	700712	33841	36390	True	False	True
+dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	0	10	10	10	0	92240	92240	2716	2716	179176	179176	5317	5317	12478	12478	394	394	283894	283894	8427	8427	True	False	True
+das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1323	1323	47	47	0	0	0	0	0	0	0	0	1323	1323	47	47	True	False	True
+data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	441	451	83	87	3	3	2	2	0	0	0	0	444	454	85	89	True	False	False
+data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	867	877	213	216	339	339	94	94	64	64	5	5	1270	1280	312	315	True	False	False
+data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	967	967	308	308	0	0	0	0	0	0	0	0	967	967	308	308	True	False	False
+data_manager_eggnog_mapper		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+data_manager_eggnog_mapper_abspath		download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+dbbuilder	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4813	5555	687	805	0	0	0	0	961	961	87	87	5774	6516	774	892	True	False	False
+decoyfasta		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	37	37	0	0	0	0	0	0	0	0	65	65	37	37	True	False	False
+delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	40	6	7	0	0	0	0	0	0	0	0	33	40	6	7	True	False	False
+deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	97434	109474	11355	12514	183905	246475	24951	31957	18551	20166	2647	2905	299890	376115	38953	47376	True	False	True
+deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	18	18	0	0	0	0	0	0	0	0	89	89	18	18	True	False	False
+dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	14874	16927	533	837	18475	28854	1403	2568	3854	4271	141	163	37203	50052	2077	3568	True	False	False
+dia_umpire	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	28	33	4	4	0	0	0	0	134	134	4	4	162	167	8	8	True	False	False
+dialignr	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	40	2	2	0	0	0	0	0	0	0	0	40	40	2	2	True	False	False
+diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	0	3	3	0	61376	61746	1847	1895	23164	28729	1140	1556	63034	63034	522	522	147574	153509	3509	3973	True	False	True
+diann	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	72	72	14	14	0	0	0	0	171	171	14	14	243	243	28	28	True	False	False
+diapysef	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	262	262	38	38	0	0	0	0	256	256	6	6	518	518	44	44	True	False	False
+diffacto	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	11	7	7	0	0	0	0	0	0	0	0	11	11	7	7	True	False	False
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	358	406	124	139	1361	1361	384	384	0	0	0	0	1719	1767	508	523	True	False	True
+divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26	32	8	9	86	172	20	53	0	0	0	0	112	204	28	62	True	False	False
+dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	921	1626	4	31	0	0	0	0	0	0	0	0	921	1626	4	31	True	False	False
+dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	74	88	12	15	0	0	0	0	0	0	0	0	74	88	12	15	True	False	False
+dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	7358	7358	88	88	0	0	0	0	0	0	0	0	7358	7358	88	88	True	False	True
+drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	916	916	113	113	0	0	0	0	0	0	0	0	916	916	113	113	True	False	True
+droplet-barcode-plot	_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1151	1151	184	184	356	356	77	77	3	3	1	1	1510	1510	262	262	True	False	False
+dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1900	1901	412	413	609	609	131	131	0	0	0	0	2509	2510	543	544	True	False	False
+dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4413	4442	430	431	4403	4403	255	255	1816	1816	33	33	10632	10661	718	719	True	False	False
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	28	28	2	2	0	0	0	0	0	0	0	0	28	28	2	2	False		
+ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12996	12996	137	137	10	10	1	1	0	0	0	0	13006	13006	138	138	True	False	True
+edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	19294	20905	2423	2618	48876	58723	6341	7527	8010	8705	846	892	76180	88333	9610	11037	True	False	False
+effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	1	3	1	0	34432	34437	1149	1152	42	42	2	2	21027	21027	413	413	55501	55506	1564	1567	True	False	True
+egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2809	3060	371	402	5179	5179	759	759	1931	1931	226	226	9919	10170	1356	1387	True	False	False
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	0	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	107	107	107	0	143762	148864	4481	5039	151989	296028	13224	31140	24955	27001	2397	2705	320706	471893	20102	38884	True	False	True
+encyclopedia	encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30			2	4	7	0	2	4	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	738	738	98	98	1	1	1	1	42	42	4	4	781	781	103	103	True	False	False
+ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	820	966	89	106	0	0	0	0	0	0	0	0	820	966	89	106	True	False	True
+evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+exomedepth	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	517	517	61	61	2995	2995	184	184	0	0	0	0	3512	3512	245	245	True	False	False
+exonerate	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1030	1072	185	188	1058	1058	189	189	922	922	35	35	3010	3052	409	412	True	False	False
+exparna	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5396	5938	580	607	628	628	168	168	519	519	107	107	6543	7085	855	882	True	False	True
+express	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	278	337	34	45	0	1184	0	117	2402	2844	23	60	2680	4365	57	222	True	False	False
+ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+falco	falco	A high throughput sequence QC analysis tool	falco	falco		Falco	A high-speed FastQC emulation for quality control of sequencing data.	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	Up-to-date	https://github.com/smithlabcode/falco/	Sequence Analysis	falco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco	https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco	1.2.4	falco	1.2.4	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4298	4298	34	34	0	0	0	0	0	0	0	0	4298	4298	34	34	False		
+fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	601	601	128	128	1165	1165	232	232	0	0	0	0	1766	1766	360	360	True	False	True
+fasta2bed	fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fasta_extract	fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	10	10	1	1	0	0	0	0	1286	1827	144	181	1296	1837	145	182	True	False	False
+fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fasta_nucleotide_color_plot	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	164	179	42	47	758	905	128	170	0	0	0	0	922	1084	170	217	True	False	False
+fasta_stats	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	43726	44512	3104	3259	19941	19941	3693	3693	16788	18589	2467	2650	80455	83042	9264	9602	True	False	False
+fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6685	6685	603	603	0	0	0	0	0	0	0	0	6685	6685	603	603	True	False	True
+fastg2protlib	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	29	29	8	8	0	0	0	0	0	0	0	0	29	29	8	8	True	False	False
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	136	11	11	0	0	0	0	0	0	0	0	136	136	11	11	True	False	True
+fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	1	1126086	1127111	6847	6909	422259	422259	10722	10722	76462	76462	2242	2242	1624807	1625832	19811	19873	True	False	True
+fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fastqc_stats	FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5162	5162	2350	2350	10176	10176	4714	4714	2610	2610	991	991	17948	17948	8055	8055	True	False	True
+fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	65542	65631	1049	1071	25992	25992	2147	2147	6733	7339	649	745	98267	98962	3845	3963	True	False	True
+feature_alignment	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	18	18	1	1	0	0	0	0	0	0	0	0	18	18	1	1	True	False	False
+featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22308	22388	16	19	350	13711	54	349	0	0	0	0	22658	36099	70	368	True	False	False
+featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	740719	770524	11699	12547	643892	784396	23272	27598	66108	68867	2348	2463	1450719	1623787	37319	42608	True	False	True
+feelnc	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	Annotation, Classification	Functional, regulatory and non-coding RNA	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1375	1500	95	99	797	797	116	116	59	59	3	3	2231	2356	214	218	True	False	False
+feht	feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5618	5820	582	607	21673	21673	938	938	869	869	110	110	28160	28362	1630	1655	True	False	False
+filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	26717	29932	1026	1072	42990	42990	1176	1176	9619	9619	230	230	79326	82541	2432	2478	True	False	False
+filter_density	filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+filter_stats	filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+filter_transcripts_via_tracking	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23	24	9	10	62	635	26	241	2	2	2	2	87	661	37	253	True	False	False
+filter_vcf	filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	53310	53944	1499	1575	25043	25043	726	726	10824	10824	593	593	89177	89811	2818	2894	True	False	True
+find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	62	70	10	12	3	1787	1	204	0	0	0	0	65	1857	11	216	True	False	False
+find_repeats	findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+fisher_test	fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	1985	1985	41	41	0	0	0	0	0	0	0	0	1985	1985	41	41	True	False	False
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22017	22304	239	255	9399	14886	462	709	4	4	1	1	31420	37194	702	965	True	False	False
+flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	661	715	52	54	0	0	0	0	167	167	15	15	828	882	67	69	True	False	True
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32514	32675	3379	3422	19434	19434	2537	2537	9843	9843	1624	1624	61791	61952	7540	7583	True	False	True
+format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5940	6474	558	608	0	0	0	0	0	0	0	0	5940	6474	558	608	True	False	True
+fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1257	1450	150	162	0	0	0	0	1052	1052	45	45	2309	2502	195	207	True	False	True
+fragpipe	fragpipe	Data analysis for mass spectrometry-based proteomics.								Up-to-date	https://fragpipe.nesvilab.org/	Proteomics	fragpipe	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	20.0	fragpipe	20.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	64	64	9	9	0	0	0	0	0	0	0	0	64	64	9	9	False		
+freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	21757	21757	101	101	217	217	21	21	0	0	0	0	21974	21974	122	122	True	False	True
+frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	8648	8648	1408	1408	32	32	6	6	6406	6406	597	597	15086	15086	2011	2011	True	False	True
+garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	11	11	0	0	0	0	0	0	0	0	27	27	11	11	True	False	False
+gblocks	gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	466	466	62	62	466	466	62	62	True	False	False
+gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	1409	1498	39	42	0	0	0	0	0	0	0	0	1409	1498	39	42	True	False	False
+gecko	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	723	723	235	235	0	0	0	0	786	786	95	95	1509	1509	330	330	True	False	False
+gemini	gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	Sequence analysis, Genetic variation analysis	Sequence analysis	1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	4967	5475	1863	1992	992	1118	279	370	3756	3811	423	425	9715	10404	2565	2787	True	False	False
+geneiobio	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	101	101	25	25	0	0	0	0	59	59	6	6	160	160	31	31	True	False	False
+generate_pc_lda_matrix	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115	124	29	30	518	1029	102	261	184	198	14	17	817	1351	145	308	True	False	False
+genomad	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	genomad	genomad		geNomad	geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.	Sequence annotation, Taxonomic classification	Sequence analysis	To update	https://github.com/apcamargo/genomad/	Metagenomics	genomad	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad	1.8.0	genomad	1.8.1	Sequence annotation, Taxonomic classification	Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	47	47	13	13	0	0	0	0	0	0	0	0	47	47	13	13	True	False	False
+get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	746	746	136	136	0	0	0	0	1504	1504	244	244	2250	2250	380	380	True	False	False
+getindelrates_3way	indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	290	20	86	0	0	0	0	70	290	20	86	True	False	False
+getindels_2way	getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	74	237	24	61	0	0	0	0	74	237	24	61	True	False	False
+getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1542	1542	159	159	0	0	0	0	587	587	64	64	2129	2129	223	223	True	False	False
+gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	To update	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.7	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11748	11748	767	767	6560	6560	397	397	2556	2556	106	106	20864	20864	1270	1270	True	False	False
+gff3_rebase	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	806	812	68	68	197	197	37	37	132	132	12	12	1135	1141	117	117	True	False	False
+gffread	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12828	13716	1740	1829	15217	23818	2588	3486	4423	4423	732	732	32468	41957	5060	6047	True	False	False
+ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	0	5	5	5	0	24606	25662	3463	3630	26805	26808	5143	5144	8174	8237	1259	1279	59585	60707	9865	10053	True	False	True
+gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	490	682	74	109	127	14058	20	1798	0	0	0	0	617	14740	94	1907	True	False	True
+glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	0	4343	4343	407	407	0	0	0	0	0	0	0	0	4343	4343	407	407	True	False	True
+glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	11	6	6	85	984	29	230	10	11	7	8	106	1006	42	244	True	False	False
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	5800	6212	826	871	7756	7756	1048	1048	1149	1149	215	215	14705	15117	2089	2134	True	False	True
+goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	20207	21960	2807	3139	24488	26198	3066	3321	4155	4155	545	545	48850	52313	6418	7005	True	False	True
+gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	72	5	7	0	0	0	0	0	0	0	0	34	72	5	7	True	False	False
+graphclust	graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	1	0	0	0	0	0	0	0	0	0	6	0	1	True	False	False
+graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	9816	10927	1285	1350	1273	1273	368	368	1104	1104	242	242	12193	13304	1895	1960	True	False	True
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	7012	7344	323	338	0	0	0	0	0	0	0	0	7012	7344	323	338	True	False	True
+graphprot	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy2	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	463	484	18	19	0	0	0	0	0	0	0	0	463	484	18	19	True	False	False
+gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+gtdb_to_taxdump	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	gtdb_to_taxdump	gtdb_to_taxdump		gtdb_to_taxdump	Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.	Data handling, Mapping, Generation	Computational biology	Up-to-date	https://github.com/nick-youngblut/gtdb_to_taxdump	Metagenomics	gtdb_to_taxdump	iuc	https://github.com/nick-youngblut/gtdb_to_taxdump	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	0.1.9	Data handling, Mapping, Generation	Computational biology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	Up-to-date	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.4.0	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	476	476	87	87	0	0	0	0	588	588	74	74	1064	1064	161	161	True	False	True
+gtf-2-gene-list	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1982	1983	323	324	1040	1040	343	343	205	205	38	38	3227	3228	704	705	True	False	False
+gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3690	3811	326	336	3323	3323	235	235	1895	2429	234	258	8908	9563	795	829	True	False	True
+guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	1	1	7	7	1	1	True	False	False
+gwastools	gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	Deposition, Analysis, Annotation	GWAS study	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	7303	7303	222	222	20	20	2	2	0	0	0	0	7323	7323	224	224	True	False	True
+hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	349	359	32	33	364	364	53	53	0	0	0	0	713	723	85	86	True	False	True
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	103	103	4	4	103	103	4	4	True	False	False
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	502	502	66	66	0	0	0	0	0	0	0	0	502	502	66	66	True	False	False
+hardklor	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	98	111	5	8	0	0	0	0	0	0	0	0	98	111	5	8	True	False	False
+hcluster_sg	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	243	263	54	57	0	0	0	0	0	0	0	0	243	263	54	57	True	False	False
+hcluster_sg_parser	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	266	293	22	25	0	0	0	0	0	0	0	0	266	293	22	25	True	False	False
+heatmap2	ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	0	46700	50808	4645	5114	64214	70429	5799	6830	7783	7912	704	724	118697	129149	11148	12668	True	False	False
+heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	bionet, heinz		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	1281	1434	367	442	1559	1559	636	636	678	678	52	52	3518	3671	1055	1130	True	False	False
+helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	267	267	39	39	0	0	0	0	80	80	7	7	347	347	46	46	True	False	False
+hgv_fundo	hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	145	1794	33	397	0	0	0	0	145	1794	33	397	True	False	False
+hgv_hilbertvis	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	119	265	16	60	0	0	0	0	119	265	16	60	True	False	False
+hicexplorer	hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								Up-to-date	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.5	hicexplorer	3.7.5			38	38	38	0	38	38	38	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	33	36	33	0	44449	68602	3236	4177	46	46	21	21	1328	1328	67	67	45823	69976	3324	4265	True	False	False
+hicstuff	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices								To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1819	1819	539	539	1334	1334	389	389	2472	2472	137	137	5625	5625	1065	1065	True	False	False
+hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	156	156	20	20	0	0	0	0	220	220	11	11	376	376	31	31	True	False	True
+high_dim_heatmap	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	2	2	0	0	0	0	0	0	0	0	18	18	2	2	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	0	12	0	0	0	0	0	0	0	0	0	228	0	12	True	False	False
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	337151	353499	10046	10719	699868	896164	26656	34018	87016	94859	5302	5695	1124035	1344522	42004	50432	True	False	False
+hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	0	0	12	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	12	0	35919	36952	1283	1321	0	0	0	0	3023	3023	180	180	38942	39975	1463	1501	True	False	True
+homer	homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	Sequence motif discovery		0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	5	0	0	8531	8531	633	633	0	0	0	0	0	0	0	0	8531	8531	633	633	True	False	False
+homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+htseq-clip	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	98	98	19	19	0	0	0	0	0	0	0	0	98	98	19	19	True	False	False
+htseq_count	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	Nucleic acid sequence analysis	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	144907	168824	3703	4366	213407	346792	10798	16485	27209	33124	2613	2854	385523	548740	17114	23705	True	False	False
+humann	humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.9	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	10	10	0	6	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	26659	26659	2067	2067	865	865	174	174	3238	3238	351	351	30762	30762	2592	2592	True	False	True
+hybpiper	hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.3.0	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1571	1571	3	3	0	0	0	0	144	144	4	4	1715	1715	7	7	True	False	False
+hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	0	17	2	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	12	17	12	0	11429	11429	428	428	7751	7751	676	676	715	715	58	58	19895	19895	1162	1162	True	False	True
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	473	473	93	93	0	0	0	0	0	0	0	0	473	473	93	93	True	False	True
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	1200	1220	187	195	1588	1588	267	267	0	0	0	0	2788	2808	454	462	True	False	True
+idconvert	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	241	276	24	33	0	0	0	0	0	0	0	0	241	276	24	33	True	False	False
+idr	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2953	3027	109	114	1710	1710	199	199	0	0	0	0	4663	4737	308	313	True	False	False
+iedb_api	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1539	1539	35	35	0	0	0	0	0	0	0	0	1539	1539	35	35	True	False	False
+illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	22	1	1	44	292	3	21	0	0	0	0	62	314	4	22	True	False	False
+infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	59700	112582	223	282	0	0	0	0	1157	1221	34	35	60857	113803	257	317	True	False	True
+inforna		INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	157	157	14	14	0	0	0	0	0	0	0	0	157	157	14	14	True	False	False
+instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	102	102	16	16	0	0	0	0	0	0	0	0	102	102	16	16	True	False	True
+intarna	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.1	intarna	3.4.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3071	7652	41	47	0	0	0	0	0	0	0	0	3071	7652	41	47	True	False	False
+integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55149	55149	161	161	0	0	0	0	6085	6085	73	73	61234	61234	234	234	True	False	True
+interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	70	7	7	0	0	0	0	0	0	0	0	70	70	7	7	True	False	False
+interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34689	55189	1634	1713	65	65	15	15	10897	10897	607	607	45651	66151	2256	2335	True	False	True
+iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	28279	28481	1623	1646	24662	24662	2093	2093	9780	10086	979	992	62721	63229	4695	4731	True	False	True
+isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	59386	59386	151	151	56	56	1	1	4741	4741	59	59	64183	64183	211	211	True	False	True
+isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1301	1301	59	59	1331	1331	60	60	507	507	9	9	3139	3139	128	128	True	False	False
+isoplot	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	4	3	3	0	0	0	0	0	0	0	0	4	4	3	3	True	False	False
+itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1426	1426	71	71	0	0	0	0	0	0	0	0	1426	1426	71	71	True	False	True
+ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	0	5	5	5	0	1252220	1252220	2366	2366	126027	126027	2496	2496	41901	41901	993	993	1420148	1420148	5855	5855	True	False	True
+jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	21153	22174	5514	5779	17428	17428	6458	6458	15673	17267	3248	3786	54254	56869	15220	16023	True	False	True
+jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse_2	jbrowse_2		JBrowse 2	Modular genome browser with views of synteny and structural variation.	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.15.4	jbrowse2	2.15.4	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1312	1312	219	219	116	116	58	58	37	37	6	6	1465	1465	283	283	False		
+jcvi_gff_stats	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.16			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2747	2926	596	637	2311	2311	741	741	1145	1145	469	469	6203	6382	1806	1847	True	False	False
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1825	1825	237	237	0	0	0	0	971	971	56	56	2796	2796	293	293	True	False	True
+kaptive	kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	379	379	53	53	8259	8259	271	271	0	0	0	0	8638	8638	324	324	True	False	True
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	8	8	8	0	1995	2091	174	193	1430	1430	389	389	1580	1580	56	56	5005	5101	619	638	True	False	True
+kinwalker		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.1.0	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	503	503	58	58	0	0	0	0	0	0	0	0	503	503	58	58	True	False	True
+kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1342	1342	63	63	0	0	0	0	0	0	0	0	1342	1342	63	63	True	False	True
+kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	5	5	5	0	48136	48164	2754	2760	59952	130398	5869	8654	29008	31148	1936	2200	137096	209710	10559	13614	True	False	True
+kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	271367	271786	6384	6409	101752	101752	4662	4662	53562	53562	1663	1663	426681	427100	12709	12734	True	False	True
+kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23008	23014	1060	1061	16194	24490	1719	2168	14898	14898	436	436	54100	62402	3215	3665	True	False	True
+kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3185	3185	495	495	0	0	0	0	385	385	48	48	3570	3570	543	543	True	False	True
+kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3981	3986	769	771	4087	5610	991	1284	88	88	41	41	8156	9684	1801	2096	True	False	True
+krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	48516	48516	2373	2373	8787	8787	943	943	4369	4369	393	393	61672	61672	3709	3709	True	False	True
+krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+last	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1584	Sequence alignment	Comparative genomics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	329	329	94	94	0	0	0	0	0	0	0	0	329	329	94	94	True	False	False
+lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	89	137	4	20	118	6136	15	1112	0	0	0	0	207	6273	19	1132	True	False	True
+legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	92	92	8	8	0	0	0	0	0	0	0	0	92	92	8	8	True	False	True
+length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	4349	4466	666	698	2093	2286	928	998	201	201	77	77	6643	6953	1671	1773	True	False	False
+lfq_protein_quant	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	78	116	12	19	0	0	0	0	0	0	0	0	78	116	12	19	True	False	False
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	171	27	30	0	0	0	0	0	0	0	0	149	171	27	30	True	False	True
+limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23442	24466	2379	2475	45734	49342	4565	5032	9327	9517	835	842	78503	83325	7779	8349	True	False	True
+lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	39	4	4	0	0	0	0	0	0	0	0	39	39	4	4	True	False	True
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	512	512	126	126	0	0	0	0	480	480	65	65	992	992	191	191	True	False	False
+locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								Up-to-date	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	2.0.1	locarna	2.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	314	350	36	46	0	0	0	0	0	0	0	0	314	350	36	46	True	False	False
+logistic_regression_vif	LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	64	173	12	48	0	0	0	0	64	173	12	48	True	False	False
+logol	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+longorf	longORF	obtain longest ORF in six-frame translations								To update		Sequence Analysis	longorf	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf	0.3.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	822	822	14	14	0	0	0	0	0	0	0	0	822	822	14	14	True	False	True
+lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1219	1219	182	182	0	0	0	0	37	37	4	4	1256	1256	186	186	True	False	True
+m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	44	44	11	11	0	0	0	0	0	0	0	0	44	44	11	11	True	False	True
+maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2835	2835	59	59	0	0	0	0	0	0	0	0	2835	2835	59	59	True	False	True
+macs2	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	0	0	9	0	0	0	0	0	0	9	9	9	0	87810	96069	4980	5629	153500	227569	12946	18825	10988	12301	692	807	252298	335939	18618	25261	True	False	False
+maf_cpg_filter	cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	85	356	6	28	0	0	0	0	85	356	6	28	True	False	False
+mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	0	2	2	2	0	172433	174456	1865	1951	108640	122790	4266	5521	20027	20027	1172	1172	301100	317273	7303	8644	True	False	True
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6417	6861	1315	1366	7235	7235	1858	1858	4112	4112	902	902	17764	18208	4075	4126	True	False	True
+maldiquant	maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base				0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1452	3822	61	68	0	0	0	0	1065	1065	39	39	2517	4887	100	107	True	False	False
+map_peptides_to_bed	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	38	44	6	7	0	0	0	0	0	0	0	0	38	44	6	7	True	False	False
+mapping_quality_stats	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+mapping_to_ucsc	mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7871	7871	32	32	0	0	0	0	0	0	0	0	7871	7871	32	32	True	False	True
+marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	51	51	4	4	0	0	0	0	0	0	0	0	51	51	4	4	False		
+mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	10119	10119	61	61	19	19	9	9	647	647	7	7	10785	10785	77	77	True	False	True
+mashmap	mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	894	894	12	12	81	81	5	5	0	0	0	0	975	975	17	17	True	False	False
+masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	471	582	35	40	589	589	80	80	0	0	0	0	1060	1171	115	120	True	False	False
+mauve_contig_mover	mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	1	0	2798	2798	314	314	2452	2452	508	508	914	914	89	89	6164	6164	911	911	True	False	True
+maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6863	7021	1251	1264	2798	2798	543	543	3189	3189	352	352	12850	13008	2146	2159	True	False	True
+mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	35	13	13	0	0	0	0	0	0	0	0	35	35	13	13	True	False	True
+mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	73	86	5	5	0	0	0	0	0	0	0	0	73	86	5	5	True	False	False
+mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	3	3	0	0	0	0	0	0	0	0	20	25	3	3	True	False	False
+medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	0	3	3	3	0	117975	117975	1693	1693	55063	55063	796	796	9325	9325	639	639	182363	182363	3128	3128	True	False	True
+medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	9	9	0	0	0	0	0	0	0	0	27	27	9	9	True	False	False
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	12692	13292	1349	1400	16645	16645	2140	2140	6214	6214	431	431	35551	36151	3920	3971	True	False	True
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	513	557	152	155	74	74	35	35	10	10	4	4	597	641	191	194	True	False	True
+megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	4130	4130	447	447	0	0	0	0	0	0	0	0	4130	4130	447	447	True	False	True
+meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3150	3150	477	477	730	730	196	196	1183	1183	151	151	5063	5063	824	824	True	False	True
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+meta_proteome_analyzer	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	126	126	20	20	0	0	0	0	0	0	0	0	126	126	20	20	True	False	False
+metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	0	2	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	6135	6135	382	382	881	881	151	151	1094	1094	104	104	8110	8110	637	637	True	False	True
+metabuli	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	metabuli	metabuli		metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid	Taxonomic classification	Taxonomy	To update	https://github.com/steineggerlab/Metabuli	Sequence Analysis, Metagenomics	metabuli	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli	1.0.5	metabuli	1.0.8	Taxonomic classification	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	7.bba0d80	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	312	312	40	40	0	0	0	0	0	0	0	0	312	312	40	40	True	False	True
+metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	980	980	323	323	0	0	0	0	0	0	0	0	980	980	323	323	True	False	True
+metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	556	756	17	21	310	514	35	55	0	0	0	0	866	1270	52	76	True	False	True
+metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4471	4471	29	29	0	0	0	0	0	0	0	0	4471	4471	29	29	True	False	True
+metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	0	1	2	4	0	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	16629	16648	1183	1187	3983	3983	572	572	4747	4747	278	278	25359	25378	2033	2037	True	False	True
+metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	2730	2831	260	262	0	0	0	0	1540	1540	71	71	4270	4371	331	333	True	False	True
+metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	142	142	32	32	0	0	0	0	379	379	47	47	521	521	79	79	True	False	True
+methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	632	5461	155	453	0	0	0	0	0	0	0	0	632	5461	155	453	True	False	False
+methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	14907	18971	638	894	2677	2677	230	230	2313	2313	83	83	19897	23961	951	1207	True	False	False
+metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3209	4572	312	442	479	479	79	79	315	315	51	51	4003	5366	442	572	True	False	False
+mg_toolkit	mg_toolkit_bulk_download, mg_toolkit_original_metadata	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	mg-toolkit	mg-toolkit		mg-toolkit	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	Data retrieval	Metagenomics	Up-to-date	https://github.com/EBI-Metagenomics/emg-toolkit	Metagenomics	mg_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	0.10.4	mg-toolkit	0.10.4	Data retrieval	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	573	573	3	3	0	0	0	0	0	0	0	0	573	573	3	3	False		
+miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+microsatbed	microsatbed	Select microsatellites for a bed file								To update	https://github.com/lmdu/pytrf	Sequence Analysis	microsatbed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed	1.3.3	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	228	4	4	18	18	1	1	0	0	0	0	246	246	5	5	False		
+microsatellite_birthdeath	microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+microsats_alignment_level	microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	135	973	50	140	0	0	0	0	135	973	50	140	True	False	False
+microsats_mutability	microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	34	312	22	87	0	0	0	0	34	312	22	87	True	False	False
+migmap	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	Sequence analysis, Read mapping	Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1082	1229	25	33	1153	1376	70	89	0	0	0	0	2235	2605	95	122	True	False	False
+minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1213	1309	115	124	0	0	0	0	0	0	0	0	1213	1309	115	124	True	False	False
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7116	7116	256	256	0	0	0	0	278	278	60	60	7394	7394	316	316	True	False	True
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13357	13479	554	562	8416	8416	448	448	898	898	85	85	22671	22793	1087	1095	True	False	True
+minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	229	229	32	32	0	0	0	0	0	0	0	0	229	229	32	32	True	False	True
+miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1244	1244	86	86	24	24	15	15	0	0	0	0	1268	1268	101	101	True	False	True
+miranda	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6408	6514	94	99	0	0	0	0	0	0	0	0	6408	6514	94	99	True	False	False
+mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1458	1458	36	36	1458	1458	36	36	True	False	False
+mirmachine	mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	True	False	False
+mirnature	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	18	18	9	9	0	0	0	0	0	0	0	0	18	18	9	9	True	False	False
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1117	1117	116	116	0	0	0	0	295	295	25	25	1412	1412	141	141	True	False	False
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1020	1020	176	176	414	414	73	73	277	277	20	20	1711	1711	269	269	True	False	False
+mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	0	191295	191295	1111	1111	42265	42265	320	320	10904	10904	83	83	244464	244464	1514	1514	True	False	True
+mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	13300	13471	1480	1501	6532	6532	1167	1167	10334	11841	1083	1300	30166	31844	3730	3968	True	False	True
+moFF	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	331	762	20	34	0	0	0	0	137	137	4	4	468	899	24	38	True	False	False
+mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	119024	119024	628	628	42	42	2	2	36310	36310	191	191	155376	155376	821	821	True	False	True
+monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3610	3610	559	559	1728	1728	434	434	0	0	0	0	5338	5338	993	993	True	False	False
+morpheus	morpheus	Morpheus MS Search Application	morpheus	morpheus		Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.	Peptide database search	Proteomics	To update	https://cwenger.github.io/Morpheus	Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	288	morpheus	290	Peptide database search	Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	105	153	12	19	0	0	0	0	833	833	93	93	938	986	105	112	True	False	False
+mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	0	129	129	129	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	126	129	129	0	297546	326056	37506	41763	565218	682083	72163	89926	167400	182490	26963	28404	1030164	1190629	136632	160093	True	False	True
+motus	mereg_mOTUs_tables, motus_profiler	Tool for profiling the abundance of microbial taxa.	mOTUs	mOTUs		Metagenomic operational taxonomic units (mOTUs)	Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/motu-tool/mOTUs	Metagenomics	motus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs	https://github.com/bgruening/galaxytools/tree/master/tools/motus	3.1.0	motus	3.1.0	Taxonomic classification	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	76	9	9	0	0	0	0	0	0	0	0	71	76	9	9	True	False	False
+mqppep	mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	13	13	3	3	0	0	0	0	0	0	0	0	13	13	3	3	True	False	False
+mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20749	22184	455	469	1239	1239	71	71	2666	2666	53	53	24654	26089	579	593	True	False	True
+msgfplus	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	473	529	33	43	0	0	0	0	0	0	0	0	473	529	33	43	True	False	False
+msms_extractor	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	110	110	11	11	0	0	0	0	0	0	0	0	110	110	11	11	True	False	False
+msstats	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2353	2353	559	559	1122	1122	211	211	1091	1091	35	35	4566	4566	805	805	True	False	False
+msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	795	795	104	104	0	0	0	0	461	461	12	12	1256	1256	116	116	True	False	True
+mt2mq	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	275	275	38	38	0	0	0	0	0	0	0	0	275	275	38	38	True	False	False
+multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	106	106	25	25	0	0	0	0	0	0	0	0	106	106	25	25	True	False	True
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	182221	192389	19343	20494	163961	182413	26449	29758	40663	41855	5974	6157	386845	416657	51766	56409	True	False	True
+multispecies_orthologous_microsats	multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+mummer	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	883	921	199	211	730	730	199	199	136	202	34	49	1749	1853	432	459	True	False	False
+mummer4	mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1			6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	6	3	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	21587	22119	1940	2033	29284	29284	3626	3626	8194	8194	545	545	59065	59597	6111	6204	True	False	False
+mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	854	860	110	111	79	79	15	15	274	274	13	13	1207	1213	138	139	True	False	True
+mzml_validator	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+naltorfs	bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2			3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	204	204	75	75	0	0	0	0	204	204	75	75	True	False	False
+nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	839	839	12	12	0	0	0	0	269	269	5	5	1108	1108	17	17	True	False	True
+nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	99052	100009	5671	5755	40386	40386	3371	3371	17919	17919	2188	2188	157357	158314	11230	11314	True	False	True
+nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1091	1091	44	44	0	0	0	0	0	0	0	0	1091	1091	44	44	True	False	True
+nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	40	1	1	0	0	0	0	0	0	0	0	36	40	1	1	True	False	False
+ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	15	16	16	15	0	391141	443752	9760	10546	306361	350178	11767	13684	227235	244814	3192	3617	924737	1038744	24719	27847	True	False	True
+ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	6	6	0	0	0	0	15	15	6	6	False		
+ncbi_fcs_adaptor	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	842	842	93	93	0	0	0	0	842	842	93	93	True	False	False
+ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	125	125	26	26	2489	2489	139	139	0	0	0	0	2614	2614	165	165	True	False	True
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	790	790	160	160	0	0	0	0	0	0	0	0	790	790	160	160	True	False	False
+newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33637	34195	1113	1172	16257	16257	1816	1816	7582	7582	899	899	57476	58034	3828	3887	True	False	True
+nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	0	2	0	0	4411	4411	396	396	9708	9708	279	279	2099	2099	212	212	16218	16218	887	887	True	False	True
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	391	391	158	158	0	0	0	0	0	0	0	0	391	391	158	158	True	False	True
+nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	107	143	13	15	148	148	20	20	0	0	0	0	255	291	33	35	True	False	True
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	7780	7780	337	337	1	1	1	1	2323	2323	99	99	10104	10104	437	437	True	False	False
+nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	118	863	19	26	0	0	0	0	0	0	0	0	118	863	19	26	True	False	True
+nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	352	352	42	42	8	8	6	6	0	0	0	0	360	360	48	48	True	False	True
+obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	37598	37598	1277	1277	0	0	0	0	3862	3862	280	280	41460	41460	1557	1557	True	False	True
+ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	54	6	6	0	0	0	0	0	0	0	0	54	54	6	6	True	False	False
+odgi	odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	26	26	6	6	0	0	0	0	0	0	0	0	26	26	6	6	True	False	False
+ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	98	6	6	0	0	0	0	0	0	0	0	98	98	6	6	True	False	False
+ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	57	57	4	4	0	0	0	0	0	0	0	0	57	57	4	4	True	False	False
+omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	158	158	12	12	0	0	0	0	0	0	0	0	158	158	12	12	True	False	True
+ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	3051	3051	87	87	0	0	0	0	0	0	0	0	3051	3051	87	87	True	False	False
+openms	AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	3.1	openms	3.2.0			8	34	144	0	8	34	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	141	124	0	32169	108654	3316	4889	50	50	15	15	940	940	245	245	33159	109644	3576	5149	True	False	False
+openms	AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.2.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	135	134	0	31121	108907	3369	5029	50	50	15	15	933	933	242	242	32104	109890	3626	5286	True	False	False
+optitype	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	500	500	45	45	0	0	0	0	0	0	0	0	500	500	45	45	True	False	False
+orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	897	897	99	99	1792	1792	239	239	0	0	0	0	2689	2689	338	338	True	False	True
+orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	To update	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	3.0.1b1	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2018	2018	419	419	0	0	0	0	438	438	58	58	2456	2456	477	477	True	False	True
+pacu	pacu_map, pacu_snp	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.	pacu	pacu		PACU	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).	Clustering	Phylogenetics, Sequence analysis	Up-to-date	https://github.com/BioinformaticsPlatformWIV-ISP/PACU	Sequence Analysis, Phylogenetics	pacu	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu	0.0.5	pacu_snp	0.0.5	Clustering	Phylogenetics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pairtools	pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0			5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	196	196	16	16	19	19	14	14	0	0	0	0	215	215	30	30	True	False	False
+pangolin	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	0	0	7457	7457	508	508	8518	8518	377	377	2760	2760	259	259	18735	18735	1144	1144	True	False	False
+pangolin	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	Tree-based sequence alignment, Variant classification	Virology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	0	0	7457	7457	508	508	8518	8518	377	377	2760	2760	259	259	18735	18735	1144	1144	True	False	False
+paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	322	349	24	29	0	0	0	0	0	0	0	0	322	349	24	29	True	False	False
+parse_mito_blast	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	65	65	288	288	62	62	110	110	20	20	601	601	147	147	True	False	False
+pathview	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6204	6211	1261	1261	6667	6667	1143	1143	1160	1160	189	189	14031	14038	2593	2593	True	False	False
+pathwaymatcher	reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	174	244	65	76	0	0	0	0	0	0	0	0	174	244	65	76	True	False	False
+patrist	patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2807	3337	178	196	0	0	0	0	0	0	0	0	2807	3337	178	196	True	False	False
+pep_pointer	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	506	511	54	55	21	21	12	12	163	163	8	8	690	695	74	75	True	False	False
+pepquery	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7047	7047	76	76	0	0	0	0	0	0	0	0	7047	7047	76	76	True	False	False
+pepquery2	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2			0	1	3	0	0	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1222	1222	28	28	0	0	0	0	0	0	0	0	1222	1222	28	28	True	False	False
+peptide_genomic_coordinate	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	472	472	56	56	16	16	10	10	149	149	5	5	637	637	71	71	True	False	False
+peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.11			4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	2	0	11986	17898	1046	1153	1314	1314	389	389	3034	3034	118	118	16334	22246	1553	1660	True	False	True
+peptimapper	peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+pepxml_to_xls		Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+percolator	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.7.1			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	338	378	15	16	0	0	0	0	1059	1059	13	13	1397	1437	28	29	True	False	False
+pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	773	773	60	60	495	495	72	72	246	246	17	17	1514	1514	149	149	True	False	True
 pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
                 pharokka
-            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	74	2565	True	False	True
-phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	82	812	True	False	True
-phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	104	1770	True	False	True
-pi_db_tools	calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	6	0	6	5	6	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	45	1095	True	False	True
-picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	88	1000	True	False	True
-pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21	275	True	False	False
-piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	1809	True	False	False
-plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	278	22589	True	False	True
-plasmid_profiler_suite		Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	22	True	False	True
-plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.4	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	71	1323	True	False	False
-plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	652	True	False	False
-plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	79	843	True	False	False
-pmd_fdr	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6	116	True	False	False
-polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	239	True	False	True
-predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-presto	presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-pretext	pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6			3	2	3	0	3	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	254	2350	True	False	False
-prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	70	7881	True	False	False
-probecoverage	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-progressivemauve	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update	http://darlinglab.org/mauve/user-guide/progressivemauve.html	Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	286	1734	True	False	False
-prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	1	1	1	0	3233	371445	True	False	True
-promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-prot-scriber	prot_scriber	Protein annotation of short human readable descriptions								Up-to-date	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.6	prot-scriber	0.1.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	5	True	False	False
-protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7	154	True	False	False
-protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	451	6428	True	False	False
-protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30	604	True	False	False
-proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	200	3320	True	False	True
-proteomiqon_joinquantpepionswithproteins	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	366	True	False	False
-proteomiqon_labeledproteinquantification	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	14	True	False	False
-proteomiqon_labelfreeproteinquantification	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	6	True	False	False
-proteomiqon_mzmltomzlite	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	721	True	False	False
-proteomiqon_peptidedb	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	96	True	False	False
-proteomiqon_peptidespectrummatching	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	686	True	False	False
-proteomiqon_proteininference	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	89	True	False	False
-proteomiqon_psmbasedquantification	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	604	True	False	False
-proteomiqon_psmstatistics	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	694	True	False	False
-proteore_venn_diagram	proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	True	False	False
-pseudogenome	pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-psm2sam	PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-psm_validation	psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	20	True	False	False
-psy-maps	psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.3.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	46	469	True	False	False
-pureclip	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	1423	True	False	False
-purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	167	16800	True	False	False
-pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	350	21123	True	False	True
-pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	377	11332	True	False	True
-pyprophet	pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5			0	5	6	0	0	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	6	6	0	33	2509	True	False	False
-pyscenic	pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/								To update		Transcriptomics, RNA, Sequence Analysis	suite_pyscenic	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic	0.12.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-pysradb	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.1	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	26	144	True	False	False
-pyteomics	mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.4	Protein identification	Proteomics, Proteomics experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	81	True	False	False
-qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	68	1909	True	False	True
-qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	32	0	0	32	32	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	1155	28681	True	False	True
-qiime_extract_viz	qiime_extract_viz	Extract vizualization from QIIME artifacts								To update	http://www.qiime.org	Metagenomics	qiime_extract_viz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz	0.1.0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-qq_tools	qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	1	4	4	4	1	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	4	4	4	0	1328	664470	True	False	True
-quality_filter	qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.13.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-quantp	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6			0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	230	True	False	False
-quantwiz_iq	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	32	True	False	False
-quasitools	aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0			0	12	0	12	0	12	0	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	3567	51567	True	False	True
-quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	True	False	True
-rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	309	21353	True	False	True
-ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	237	2833	True	False	False
-rapidnj	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2		Phylogeny	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	176	True	False	False
-rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	6902	True	False	False
-rawtools	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	14	175	True	False	False
-raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	383	6808	True	False	True
-rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	1.0		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	36	True	False	False
-rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	38	1226	True	False	False
-rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	71	3370	True	False	True
-reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.15.0	recentrifuge	1.15.0	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	331	True	False	True
-red	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	88	578	True	False	False
-refseq_masher	refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2			2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	22	526	True	False	False
-remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2	42	True	False	False
-repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.0.9_p2			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	248	3750	True	False	False
-repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	True	False	True
-repeatmasker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.0.9_p2	Genome annotation	Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	248	3750	True	False	False
-repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	217	1177	True	False	False
-retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-revoluzer	revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	Structural variation detection	Molecular evolution, Phylogeny	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	44	628	True	False	False
-ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14	161	True	False	False
-rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11	129	True	False	False
-rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	164	True	False	False
-rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	1358	True	False	False
-rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	1074	True	False	False
-rnaformer	infer_rnaformer	RNAformer: RNA secondary structure prediction								To update	https://github.com/automl/RNAformer	RNA	rnaformer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	1.0.0	rnaformer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	33	True	False	False
-rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	109	1110	True	False	False
-rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	86	True	False	False
-rnaz	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	28	43279	True	False	False
-roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	656	12225	True	False	True
-rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	1	1	0	67	377	True	False	False
-rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	22	22	22	22	22	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	22	22	22	0	3206	133498	True	False	True
-ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	76	1236	True	False	False
-sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	55	4024	True	False	False
-salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	1	2	2	3	1	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	3	3	3	0	969	61937	True	False	True
-salmon-kallisto-mtx-to-10x	_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	86	561	True	False	False
-salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	84	454	True	False	False
-sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	3765	True	False	False
-samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	296	4948	True	False	False
-samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1450	48426	True	False	False
-sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	173	True	False	True
-sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	140	True	False	True
-sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	9	True	False	False
-scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			27	27	27	0	27	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	0	2185	39356	True	False	False
-scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			1	2	6	0	1	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	16	387	True	False	False
-scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	77	1365	True	False	False
-schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	23	779	True	False	False
-scikit-bio	scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	True	False	False
-scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	83	True	False	False
-scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	61	676	True	False	True
-scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	25	True	False	False
-sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	457	True	False	False
-semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	1	0	0	6	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	39	542	True	False	True
-seq2hla	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	16	288	True	False	False
-seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	874	True	False	False
-seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	25302	True	False	False
-seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	82	3784	True	False	False
-seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	True	False	False
-seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-seqcomplexity	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	16	68	True	False	False
-seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	3	0	2	5	3	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	129	1964	True	False	True
-seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	True	False	True
-seqtk	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	Data handling, Sequence file editing		15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	14	0	14	0	0	14	0	0	0	15	0	0	0	0	0	14	14	14	14	753	59668	True	False	False
-seqtk_nml	seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-seqwish	seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	271	True	False	False
-seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.4.0			14	14	14	11	14	14	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	181	1966	True	False	False
-seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	1	1	1	7	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	154	763	True	False	False
-shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-short_reads_figure_score	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13	163	True	False	False
-shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1008	41600	True	False	True
-sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	269	14982	True	False	False
-sina	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	42	1128	True	False	False
-sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	133	2489	True	False	True
-sixgill	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	24	293	True	False	False
-slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	2	361	True	False	False
-sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	64	True	False	False
-small_rna_clusters	small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-small_rna_maps	small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-small_rna_signatures	overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	121	True	False	True
-smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-smart_domains	smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	22	203	True	False	False
-snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	133	1349	True	False	True
-sniffles	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	Up-to-date	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	2.4	sniffles	2.4	Sequence analysis, Structural variation detection	Sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	58	919	True	False	False
-snipit	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	Base position variability plotting	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	22	669	True	False	False
-snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	0	1372	105708	True	False	True
-snv_matrix	snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-socru	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13	621	True	False	False
-sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	True	False	True
-sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	376	18183	True	False	True
-spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, rnaspades, metaplasmidspades, metaspades, metaviralspades, biosyntheticspades, rnaviralspades, coronaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	3	9	3	0	3547	72953	True	False	True
-spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	34	446	True	False	False
-spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-spatyper	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-spectrast2spectrast_irt	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-spectrast2tsv	gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	56	769	True	False	False
-spolpred	spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	1278	True	False	True
-sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-sr_bowtie_dataset_annotation	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	7	4	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	21	225	True	False	False
-srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205	True	False	True
-srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22	205	True	False	True
-sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5	223	True	False	False
-stacks	stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	Data handling	Mapping, Population genetics	0	13	13	12	0	13	13	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	13	0	152	11635	True	False	False
-stacks2	stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65			0	12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	238	7292	True	False	False
-star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update	https://github.com/STAR-Fusion/STAR-Fusion	Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	1212	True	False	False
-staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	889	12673	True	False	True
-stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	10	325	True	False	False
-stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	2623	True	False	True
-structureharvester	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date	http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/	Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-substitution_rates	subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-substitutions	substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	13	True	False	True
-suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	2	4	4	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	2	5	True	False	True
-suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	5	67	True	False	True
-suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	31	202	True	False	True
-suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	9	73	True	False	True
-suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	26	114	True	False	True
-suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	22	21	21	21	22	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	43	168	True	False	True
-suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	4	4	True	False	True
-suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2	6	True	False	True
-suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	48	263	True	False	True
-suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	17	17	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	59	213	True	False	True
-suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	6	20	True	False	True
-suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	6	14	True	False	True
-suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	40	232	True	False	True
-suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	12	37	True	False	True
-suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	True	False	True
-suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	13	True	False	True
-suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	1	1	True	False	True
-suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	22	172	True	False	True
-suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	7	8	8	8	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	8	16	True	False	True
-suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	124	7087	True	False	True
-suite_snvphyl		SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-syndiva	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	30	True	False	False
-t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	31	457	True	False	True
-t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26	947	True	False	True
-t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	70	8690	True	False	True
-tapscan	tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	713	True	False	False
-tasmanian_mismatch	tasmanian_mismatch	Analysis of positional mismatches								Up-to-date	https://github.com/nebiolabs/tasmanian-mismatch	Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-taxonkit	name2taxid, profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	taxonkit	taxonkit		TaxonKit	TaxonKit is a practical and efficient NCBI taxonomy toolkit.	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	Up-to-date	https://bioinf.shenwei.me/taxonkit/	Metagenomics	taxonkit	iuc	https://github.com/shenwei356/taxonkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit	0.17.0	taxonkit	0.17.0	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	1	1	1	0	1801	27426	True	False	True
-taxpasta	taxpasta	standardise taxonomic profiles	taxpasta	taxpasta		taxpasta	TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	Up-to-date	https://taxpasta.readthedocs.io/en/latest/	Sequence Analysis	taxpasta	iuc	https://github.com/taxprofiler/taxpasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta	0.7.0	taxpasta	0.7.0	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	198	5161	True	False	True
-tbl2gff3	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	229	1584	True	False	False
-te_finder	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.21	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	81	True	False	False
-telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-tetoolkit	tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	871	True	False	False
-tetyper	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8	69	True	False	False
-tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	460	True	False	False
-tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-tn93	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								Up-to-date	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.14	tn93	1.0.14			4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	4	0	0	17	1881	True	False	False
-tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9.1	tooldistillator	0.9.1	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	True	False	False
-tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	0	312	24167	True	False	False
-transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	348	5468	True	False	False
-transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	84	907	True	False	True
-translate_bed	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	49	643	True	False	False
-translate_bed_sequences	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	57	True	False	False
-transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5	229	True	False	True
-trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	2334	238699	True	False	True
-trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	To update	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.2	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	13	9	13	13	13	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	11	13	12	0	1762	31951	True	False	False
-trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	151	1796	True	False	False
-trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	0	236	2935	True	False	False
-trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	147	8942	True	False	True
-tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	True	False	False
-ucsc_axtchain	ucsc_axtchain	Chain together genome alignments	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_axtchain	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain	469	ucsc-axtchain	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ucsc_blat	ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	Up-to-date	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	469	ucsc-blat	469	Sequence alignment	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-ucsc_chainnet	ucsc_chainnet	Make alignment nets out of chains	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainnet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	469	ucsc-chainnet	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ucsc_chainprenet	ucsc_chainprenet	Remove chains that don't have a chance of being netted	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainprenet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet	469	ucsc-chainprenet	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ucsc_chainsort	ucsc_chainsort	Sort chains. By default sorts by score.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainsort	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort	469	ucsc-chainsort	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	45	394	True	False	False
-ucsc_netfilter	ucsc_netfilter	Filter out parts of net	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netfilter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter	469	ucsc-netfilter	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-ucsc_netsyntenic	ucsc_netsyntenic	Add synteny info to a net dataset	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netsyntenic	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic	469	ucsc-netsyntenic	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	3	5	5	0	379	61618	True	False	False
-unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	0	1558	65732	True	False	True
-unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115	5005	True	False	True
-uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.6	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	132	2406	True	False	False
-uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	79	1360	True	False	True
-usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	5	1060	True	False	True
-valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20	637	True	False	True
-validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	25	86	True	False	False
-vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	94	3164	True	False	True
-varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-vcf2snvalignment	vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	74	2020	True	False	True
-velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2083	25420	True	False	True
-velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	4741	True	False	True
-venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.1.5			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	248	5067	True	False	False
-verify_map	verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	22	True	False	False
-vg	vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.59.0			0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3	477	True	False	False
-vibrant	vibrant	Virus Identification By iteRative ANnoTation	VIBRANT	VIBRANT		VIBRANT	Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	Up-to-date	https://github.com/AnantharamanLab/VIBRANT	Metagenomics	vibrant	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant	1.2.1	vibrant	1.2.1	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-vienna_rna	viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	0	123	7864	True	False	False
-vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	351	12203	True	False	False
-virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
-virheat	virheat	generates a heatmap of allele frequencies from vcf files	virheat	virheat		virHEAT	VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.			Up-to-date	https://github.com/jonas-fuchs/virHEAT	Visualization, Variant Analysis	virheat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat	0.7.1	virheat	0.7.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-virsorter	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	virsorter	virsorter		virsorter	Identify DNA and RNA virus sequences.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/jiarong/VirSorter2/	Metagenomics	virsorter	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter	2.2.4	virsorter	2.2.4	Taxonomic classification	Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	1749	30946	True	False	False
-vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.29.0	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	8	8	8	8	8	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	8	8	8	0	182	8507	True	False	True
-vsnp	vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-wade	wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-weather_app	simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-weightedaverage	wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-windowmasker	windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.16.0			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	85	True	False	False
-windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	True	False	False
-wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	116	1660	True	False	True
-xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	5	5	2	6	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	175	5876	True	False	False
-xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	True	False	False
-yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	64	344	True	False	False
-zeiss_lmd_converter	ZeissLMDconverter	Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	2.0.4	shapely				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	5462	5462	334	334	0	0	0	0	309	309	52	52	5771	5771	386	386	True	False	True
+phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	0	0	1	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	1199	1199	193	193	0	0	0	0	6	6	1	1	1205	1205	194	194	True	False	True
+phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1975	2034	246	258	0	0	0	0	553	564	140	144	2528	2598	386	402	True	False	True
+pi_db_tools	calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	867	1128	144	165	0	0	0	0	2106	2106	121	121	2973	3234	265	286	True	False	True
+picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	2532	2532	382	382	1	1	1	1	1311	1311	83	83	3844	3844	466	466	True	False	True
+pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	238	283	42	45	0	0	0	0	0	0	0	0	238	283	42	45	True	False	False
+piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1408	2068	94	119	0	0	0	0	0	0	0	0	1408	2068	94	119	True	False	False
+plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37086	37272	711	734	6346	6346	583	583	3065	3065	61	61	46497	46683	1355	1378	True	False	True
+plasmid_profiler_suite		Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14652	14652	251	251	0	0	0	0	101	101	18	18	14753	14753	269	269	True	False	True
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.4	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1342	1472	184	197	902	902	156	156	630	630	24	24	2874	3004	364	377	True	False	False
+plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	408	664	91	122	627	627	118	118	605	605	26	26	1640	1896	235	266	True	False	False
+plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	764	879	213	237	304	304	95	95	193	193	26	26	1261	1376	334	358	True	False	False
+pmd_fdr	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	112	120	16	16	4	562	1	140	320	347	7	8	436	1029	24	164	True	False	False
+polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	731	731	86	86	0	0	0	0	42	42	4	4	773	773	90	90	True	False	True
+predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+presto	presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	63244	65177	1392	1599	0	0	0	0	63244	65177	1392	1599	True	False	False
+pretext	pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6			3	2	3	0	3	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	3463	3463	538	538	1853	1853	256	256	1097	1097	70	70	6413	6413	864	864	True	False	False
+prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10152	10626	253	281	10581	10581	1240	1240	0	0	0	0	20733	21207	1493	1521	True	False	False
+probecoverage	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1902	1902	167	167	0	0	0	0	0	0	0	0	1902	1902	167	167	True	False	True
+progressivemauve	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update	http://darlinglab.org/mauve/user-guide/progressivemauve.html	Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2064	2173	678	695	2900	2900	1034	1034	0	0	0	0	4964	5073	1712	1729	True	False	False
+prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	464359	476554	7475	7721	313285	331256	11243	12384	131211	141875	4358	4947	908855	949685	23076	25052	True	False	True
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+prot-scriber	prot_scriber	Protein annotation of short human readable descriptions								Up-to-date	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.6	prot-scriber	0.1.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	10	7	7	0	0	0	0	0	0	0	0	10	10	7	7	True	False	False
+protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	129	155	15	21	0	0	0	0	0	0	0	0	129	155	15	21	True	False	False
+protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	11743	12752	1137	1278	2	2	1	1	0	0	0	0	11745	12754	1138	1279	True	False	False
+protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	465	638	81	100	0	0	0	0	0	0	0	0	465	638	81	100	True	False	False
+proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3962	3962	501	501	0	0	0	0	0	0	0	0	3962	3962	501	501	True	False	True
+proteomiqon_joinquantpepionswithproteins	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	366	366	4	4	0	0	0	0	0	0	0	0	366	366	4	4	True	False	False
+proteomiqon_labeledproteinquantification	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	8	8	0	0	0	0	0	0	0	0	16	16	8	8	True	False	False
+proteomiqon_labelfreeproteinquantification	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	6	4	4	0	0	0	0	0	0	0	0	6	6	4	4	True	False	False
+proteomiqon_mzmltomzlite	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	721	721	8	8	0	0	0	0	0	0	0	0	721	721	8	8	True	False	False
+proteomiqon_peptidedb	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	96	96	12	12	0	0	0	0	0	0	0	0	96	96	12	12	True	False	False
+proteomiqon_peptidespectrummatching	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	686	686	5	5	0	0	0	0	0	0	0	0	686	686	5	5	True	False	False
+proteomiqon_proteininference	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	6	6	0	0	0	0	0	0	0	0	89	89	6	6	True	False	False
+proteomiqon_psmbasedquantification	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	604	604	4	4	0	0	0	0	0	0	0	0	604	604	4	4	True	False	False
+proteomiqon_psmstatistics	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	694	694	6	6	0	0	0	0	0	0	0	0	694	694	6	6	True	False	False
+proteore_venn_diagram	proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	1	1	0	0	0	0	0	0	0	0	15	15	1	1	True	False	False
+pseudogenome	pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+psm2sam	PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+psm_validation	psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	20	20	4	4	0	0	0	0	0	0	0	0	20	20	4	4	True	False	False
+psy-maps	psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.3.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	333	502	62	62	0	0	0	0	0	0	0	0	333	502	62	62	True	False	False
+pureclip	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1319	1507	81	92	0	0	0	0	0	0	0	0	1319	1507	81	92	True	False	False
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17782	17782	287	287	853	853	65	65	2224	2224	65	65	20859	20859	417	417	True	False	False
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22742	22742	557	557	2159	2159	716	716	776	776	448	448	25677	25677	1721	1721	True	False	True
+pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12858	13232	986	996	8092	8092	943	943	3238	3238	124	124	24188	24562	2053	2063	True	False	True
+pyprophet	pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5			0	5	6	0	0	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	6	6	0	2626	2626	150	150	0	0	0	0	609	609	9	9	3235	3235	159	159	True	False	False
+pyscenic	pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/								To update		Transcriptomics, RNA, Sequence Analysis	suite_pyscenic	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic	0.12.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pysradb	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.2	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	163	163	35	35	0	0	0	0	0	0	0	0	163	163	35	35	True	False	False
+pyteomics	mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.4	Protein identification	Proteomics, Proteomics experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	92	92	4	4	0	0	0	0	0	0	0	0	92	92	4	4	True	False	False
+qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2092	2342	209	238	0	0	0	0	2	2	1	1	2094	2344	210	239	True	False	True
+qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	0	0	0	32	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	31825	34677	3375	3785	1	1	1	1	14	14	4	4	31840	34692	3380	3790	True	False	True
+qiime_extract_viz	qiime_extract_viz	Extract vizualization from QIIME artifacts								To update	http://www.qiime.org	Metagenomics	qiime_extract_viz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz	0.1.0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	8	8	0	0	0	0	0	0	0	0	17	17	8	8	False		
+qq_tools	qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	0	4	4	4	0	684820	684820	3239	3239	90503	90503	3881	3881	29018	29018	826	826	804341	804341	7946	7946	True	False	True
+quality_filter	qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.13.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	724	35	62	0	0	0	0	98	724	35	62	True	False	False
+quantp	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	197	241	17	22	0	0	0	0	0	0	0	0	197	241	17	22	True	False	False
+quantwiz_iq	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	32	3	3	0	0	0	0	0	0	0	0	32	32	3	3	True	False	False
+quasitools	aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0			0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13483	13483	434	434	13483	13483	434	434	True	False	False
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	67737	69738	7787	7971	51925	56602	9692	10646	32003	34145	3890	4127	151665	160485	21369	22744	True	False	True
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	27113	27315	839	850	9089	9089	475	475	5452	5452	171	171	41654	41856	1485	1496	True	False	True
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4844	4844	480	480	0	0	0	0	7	7	3	3	4851	4851	483	483	True	False	False
+rapidnj	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2		Phylogeny	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	339	339	30	30	1737	1737	256	256	6	6	1	1	2082	2082	287	287	True	False	False
+rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	42	42	9	9	0	0	0	0	0	0	0	0	42	42	9	9	True	False	True
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9477	9477	438	438	0	0	0	0	10585	10585	182	182	20062	20062	620	620	True	False	False
+rawtools	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	166	179	32	33	0	0	0	0	414	414	13	13	580	593	45	46	True	False	False
+raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10905	10905	966	966	5100	5114	587	587	4955	6094	765	892	20960	22113	2318	2445	True	False	True
+rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	1.0		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	90	90	6	6	0	0	0	0	0	0	0	0	90	90	6	6	True	False	False
+rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	860	1257	88	98	0	0	0	0	0	0	0	0	860	1257	88	98	True	False	False
+rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	49	191	5	46	0	0	0	0	49	191	5	46	True	False	False
+read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3710	3710	80	80	7	7	6	6	0	0	0	0	3717	3717	86	86	True	False	True
+reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.15.0	recentrifuge	1.15.0	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	472	472	92	92	32	32	13	13	6	6	4	4	510	510	109	109	True	False	True
+red	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	859	859	203	203	305	305	142	142	227	227	58	58	1391	1391	403	403	True	False	False
+refseq_masher	refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	428	428	35	35	141	141	42	42	0	0	0	0	569	569	77	77	True	False	False
+regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	438	542	128	157	0	0	0	0	0	0	0	0	438	542	128	157	True	False	False
+remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	44	6	7	0	0	0	0	0	0	0	0	39	44	6	7	True	False	False
+repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.0.9_p2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5998	5998	810	810	7618	7618	803	803	3135	3135	292	292	16751	16751	1905	1905	True	False	False
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	95	38	38	0	0	0	0	0	0	0	0	95	95	38	38	True	False	True
+repeatmasker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.0.9_p2	Genome annotation	Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5998	5998	810	810	7618	7618	803	803	3135	3135	292	292	16751	16751	1905	1905	True	False	False
+repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7963	7963	413	413	1485	1485	220	220	8402	8402	168	168	17850	17850	801	801	True	False	False
+retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+revoluzer	revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	Structural variation detection	Molecular evolution, Phylogeny	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2444	2444	52	52	0	0	0	0	0	0	0	0	2444	2444	52	52	True	False	False
+ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	661	681	78	78	0	0	0	0	0	0	0	0	661	681	78	78	True	False	False
+ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	171	171	20	20	0	0	0	0	0	0	0	0	171	171	20	20	True	False	False
+rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	137	173	40	49	0	0	0	0	0	0	0	0	137	173	40	49	True	False	False
+rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	90	196	9	11	0	0	0	0	0	0	0	0	90	196	9	11	True	False	False
+rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	878	1363	29	35	0	0	0	0	0	0	0	0	878	1363	29	35	True	False	False
+rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1024	1077	18	21	0	0	0	0	0	0	0	0	1024	1077	18	21	True	False	False
+rnaformer	infer_rnaformer	RNAformer: RNA secondary structure prediction								To update	https://github.com/automl/RNAformer	RNA	rnaformer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	1.0.0	rnaformer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	6	6	0	0	0	0	0	0	0	0	26	26	6	6	False		
+rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	33	10	14	0	0	0	0	0	0	0	0	23	33	10	14	True	False	False
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1522	1522	254	254	372	372	75	75	5	5	1	1	1899	1899	330	330	True	False	False
+rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	65	89	14	18	0	0	0	0	0	0	0	0	65	89	14	18	True	False	False
+rnaz	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	1156	43309	93	121	0	0	0	0	0	0	0	0	1156	43309	93	121	True	False	False
+roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15196	15685	1459	1501	12188	12188	1768	1768	4881	5539	518	555	32265	33412	3745	3824	True	False	True
+rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	1	1	0	363	430	158	183	0	0	0	0	67	146	13	39	430	576	171	222	True	False	False
+rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	0	22	22	22	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	0	22	22	22	0	136315	147595	8341	9385	138707	161046	10696	12789	22718	23767	1593	1695	297740	332408	20630	23869	True	False	True
+ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1286	1364	178	193	2220	2220	299	299	0	0	0	0	3506	3584	477	492	True	False	False
+sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3628	4168	165	199	8399	14473	573	1147	2710	3000	151	175	14737	21641	889	1521	True	False	False
+salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	0	2	2	3	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	0	3	3	3	0	73085	77081	2243	2319	90634	122835	3402	4726	13371	15818	513	586	177090	215734	6158	7631	True	False	True
+salmon-kallisto-mtx-to-10x	_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	682	682	172	172	322	322	74	74	3	3	3	3	1007	1007	249	249	True	False	False
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	463	463	119	119	1038	1038	87	87	410	410	24	24	1911	1911	230	230	True	False	False
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3421	3859	340	382	883	883	109	109	1138	1138	15	15	5442	5880	464	506	True	False	False
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6485	6549	720	726	10127	10127	1518	1518	238	238	37	37	16850	16914	2275	2281	True	False	False
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	52099	55110	4053	4497	73194	108684	6930	9936	14771	15714	1222	1419	140064	179508	12205	15852	True	False	False
+sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	174	174	16	16	399	399	29	29	0	0	0	0	573	573	45	45	True	False	True
+sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	140	140	5	5	253	253	6	6	0	0	0	0	393	393	11	11	True	False	True
+sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	10	10	0	0	0	0	0	0	0	0	13	13	10	10	True	False	False
+scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			27	27	27	0	27	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	0	45501	45666	4832	4868	7304	7304	1846	1846	3106	3106	457	457	55911	56076	7135	7171	True	False	False
+scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			1	2	6	0	1	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	381	388	99	100	0	0	0	0	297	297	9	9	678	685	108	109	True	False	False
+scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	1345	1371	350	351	0	0	0	0	903	903	29	29	2248	2274	379	380	True	False	False
+schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	809	809	78	78	3	3	2	2	105	105	16	16	917	917	96	96	True	False	False
+scikit-bio	scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1503	1955	283	402	0	0	0	0	1504	1956	284	403	True	False	False
+scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	97	97	41	41	0	0	0	0	0	0	0	0	97	97	41	41	True	False	False
+scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	901	901	90	90	0	0	0	0	0	0	0	0	901	901	90	90	True	False	True
+scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	25	5	5	0	0	0	0	0	0	0	0	25	25	5	5	True	False	False
+sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	True	False	False
+selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	305	463	43	50	0	0	0	0	0	0	0	0	305	463	43	50	True	False	False
+semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	931	931	93	93	0	0	0	0	0	0	0	0	931	931	93	93	True	False	True
+seq2hla	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	342	342	40	40	0	0	0	0	0	0	0	0	342	342	40	40	True	False	False
+seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1053	1186	137	195	680	680	206	206	0	0	0	0	1733	1866	343	401	True	False	False
+seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30300	32553	732	799	21726	31891	619	621	2886	2886	144	144	54912	67330	1495	1564	True	False	False
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4322	4714	180	205	0	0	0	0	0	0	0	0	4322	4714	180	205	True	False	False
+seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2196	3529	260	289	2196	3529	260	289	True	False	False
+seqcomplexity	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	70	70	19	19	109	109	47	47	0	0	0	0	179	179	66	66	True	False	False
+seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	0	0	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3364	3364	247	247	0	0	0	0	244	244	33	33	3608	3608	280	280	True	False	True
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2424	2424	102	102	0	0	0	0	0	0	0	0	2424	2424	102	102	True	False	True
+seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4182	4182	42	42	0	0	0	0	0	0	0	0	4182	4182	42	42	True	False	True
+seqtk	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	Data handling, Sequence file editing		15	15	15	0	15	15	15	0	0	0	0	0	0	0	0	0	0	14	0	14	0	0	14	0	0	0	15	0	0	0	0	0	0	14	14	14	14	72816	73514	2210	2300	102777	107831	2313	2669	154613	154613	682	682	330206	335958	5205	5651	True	False	False
+seqtk_nml	seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+seqwish	seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	271	271	2	2	0	0	0	0	0	0	0	0	271	271	2	2	True	False	False
+seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.4.0			14	14	14	0	14	14	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	0	2296	2328	673	676	141	141	39	39	0	0	0	0	2437	2469	712	715	True	False	False
+seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	0	1	1	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	121	121	11	11	32	32	5	5	0	0	0	0	153	153	16	16	True	False	False
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	913	913	308	308	0	0	0	0	568	568	73	73	1481	1481	381	381	True	False	False
+shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+short_reads_figure_score	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	145	163	25	30	196	3360	23	711	0	0	0	0	341	3523	48	741	True	False	False
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46125	47376	2273	2356	40577	40577	3971	3971	19960	21130	1085	1199	106662	109083	7329	7526	True	False	True
+sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	0	18184	18937	555	608	10514	10514	1063	1063	0	0	0	0	28698	29451	1618	1671	True	False	False
+sina	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1369	1369	125	125	2398	2398	420	420	0	0	0	0	3767	3767	545	545	True	False	False
+sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3457	3457	301	301	0	0	0	0	556	556	65	65	4013	4013	366	366	True	False	True
+sixgill	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	312	312	71	71	0	0	0	0	0	0	0	0	312	312	71	71	True	False	False
+slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	346	362	16	16	872	872	67	67	0	0	0	0	1218	1234	83	83	True	False	False
+sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	141	141	26	26	0	0	0	0	0	0	0	0	141	141	26	26	True	False	False
+small_rna_clusters	small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+small_rna_maps	small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+small_rna_signatures	overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	158	158	8	8	0	0	0	0	0	0	0	0	158	158	8	8	True	False	True
+smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+smart_domains	smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	325	325	61	61	137	137	54	54	843	843	63	63	1305	1305	178	178	True	False	False
+snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	1638	331	358	779	779	244	244	467	467	83	83	2745	2884	658	685	True	False	True
+sniffles	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	Up-to-date	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	2.4	sniffles	2.4	Sequence analysis, Structural variation detection	Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1141	1141	134	134	606	606	156	156	2267	2267	80	80	4014	4014	370	370	True	False	False
+snipit	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	Base position variability plotting	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	905	905	44	44	0	0	0	0	0	0	0	0	905	905	44	44	True	False	False
+snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	0	121363	124773	3448	3602	92504	92504	3945	3945	48068	52034	2705	3073	261935	269311	10098	10620	True	False	True
+snv_matrix	snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+socru	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	659	659	42	42	296	296	92	92	0	0	0	0	955	955	134	134	True	False	False
+sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	True	False	True
+sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19865	21034	1047	1126	3141	3141	328	328	3304	3304	189	189	26310	27479	1564	1643	True	False	True
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	3	9	3	0	82716	87113	8209	8526	120471	120475	14787	14790	54067	61541	5817	6653	257254	269129	28813	29969	True	False	True
+spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	450	491	91	100	4270	4270	288	288	0	0	0	0	4720	4761	379	388	True	False	False
+spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spatyper	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+spectrast2spectrast_irt	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+spectrast2tsv	gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	789	840	130	134	0	0	0	0	0	0	0	0	789	840	130	134	True	False	False
+spolpred	spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	23	23	0	0	0	0	0	0	0	0	1436	1436	23	23	True	False	True
+sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	80	80	1	1	0	0	0	0	80	80	1	1	True	False	True
+sr_bowtie_dataset_annotation	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	0	4	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	239	239	34	34	44	44	13	13	0	0	0	0	283	283	47	47	True	False	False
+srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41	True	False	True
+srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41	True	False	True
+sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	214	225	17	18	0	0	0	0	0	0	0	0	214	225	17	18	True	False	False
+stacks	stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	Data handling	Mapping, Population genetics	0	13	13	0	0	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	13	0	6440	11998	465	593	0	0	0	0	4070	4070	76	76	10510	16068	541	669	True	False	False
+stacks2	stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65			0	12	12	0	0	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	8437	8592	626	646	0	0	0	0	18016	18016	270	270	26453	26608	896	916	True	False	False
+star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update	https://github.com/STAR-Fusion/STAR-Fusion	Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1312	1383	82	95	2198	3076	234	303	173	173	3	3	3683	4632	319	401	True	False	False
+staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20778	20891	2030	2045	9520	9520	1424	1424	6753	6753	864	864	37051	37164	4318	4333	True	False	True
+stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	328	328	38	38	0	0	0	0	0	0	0	0	328	328	38	38	True	False	False
+stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2858	3001	118	123	0	0	0	0	0	0	0	0	2858	3001	118	123	True	False	True
+structureharvester	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date	http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/	Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+substitution_rates	subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	121	3901	34	747	105	114	4	4	226	4015	38	751	True	False	False
+substitutions	substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	93	901	13	84	0	0	0	0	93	901	13	84	True	False	False
+suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	249	249	32	32	16	16	10	10	102	102	16	16	367	367	58	58	True	False	True
+suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	117	117	41	41	84	84	24	24	161	161	13	13	362	362	78	78	True	False	True
+suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	217	217	47	47	42	42	20	20	96	96	12	12	355	355	79	79	True	False	True
+suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	721	721	160	160	350	350	91	91	214	214	35	35	1285	1285	286	286	True	False	True
+suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	125	125	30	30	13	13	9	9	83	83	8	8	221	221	47	47	True	False	True
+suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	396	396	134	134	121	121	57	57	144	144	39	39	661	661	230	230	True	False	True
+suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	22	0	21	21	22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	964	964	318	318	249	249	118	118	475	475	108	108	1688	1688	544	544	True	False	True
+suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	8	8	8	8	13	13	11	11	1302	1302	19	19	1323	1323	38	38	True	False	True
+suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	58	58	23	23	24	24	11	11	92	92	11	11	174	174	45	45	True	False	True
+suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	863	863	220	220	237	237	98	98	181	181	41	41	1281	1281	359	359	True	False	True
+suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	0	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	983	983	287	287	375	375	144	144	907	907	106	106	2265	2265	537	537	True	False	True
+suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	46	46	13	13	9	9	5	5	0	0	0	0	55	55	18	18	True	False	True
+suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	0	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	37	37	16	16	22	22	7	7	89	89	14	14	148	148	37	37	True	False	True
+suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	615	615	143	143	246	246	75	75	115	115	27	27	976	976	245	245	True	False	True
+suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	330	330	83	83	64	64	40	40	195	195	49	49	589	589	172	172	True	False	True
+suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	4	4	4	4	5	5	5	5	1	1	1	1	10	10	10	10	True	False	True
+suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	14	14	16	16	6	6	37	37	2	2	82	82	22	22	True	False	True
+suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	0	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	10	10	3	3	14	14	10	10	5	5	5	5	29	29	18	18	True	False	True
+suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	664	664	145	145	113	113	43	43	255	255	50	50	1032	1032	238	238	True	False	True
+suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	84	84	52	52	25	25	16	16	9	9	5	5	118	118	73	73	True	False	True
+suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	True
+suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14941	14941	383	383	25941	25941	255	255	2856	2856	112	112	43738	43738	750	750	True	False	True
+suite_snvphyl		SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+syndiva	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	30	30	2	2	0	0	0	0	0	0	0	0	30	30	2	2	True	False	False
+t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	411	472	68	90	102	7952	13	1240	0	0	0	0	513	8424	81	1330	True	False	True
+t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	927	959	65	78	130	7194	18	1143	0	0	0	0	1057	8153	83	1221	True	False	True
+t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3783	9125	211	229	1	1	1	1	0	0	0	0	3784	9126	212	230	True	False	True
+tapscan	tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	19	6	6	0	0	0	0	0	0	0	0	19	19	6	6	True	False	False
+tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	827	838	89	92	114	114	41	41	900	900	29	29	1841	1852	159	162	True	False	False
+tasmanian_mismatch	tasmanian_mismatch	Analysis of positional mismatches								Up-to-date	https://github.com/nebiolabs/tasmanian-mismatch	Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	4	61	61	7	7	0	0	0	0	65	65	11	11	True	False	False
+taxonkit	name2taxid, profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	taxonkit	taxonkit		TaxonKit	TaxonKit is a practical and efficient NCBI taxonomy toolkit.	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	Up-to-date	https://bioinf.shenwei.me/taxonkit/	Metagenomics	taxonkit	iuc	https://github.com/shenwei356/taxonkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit	0.17.0	taxonkit	0.17.0	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	36069	36922	5257	5431	25255	30822	5066	5826	7949	7949	1584	1584	69273	75693	11907	12841	True	False	True
+taxpasta	taxpasta	standardise taxonomic profiles	taxpasta	taxpasta		taxpasta	TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	Up-to-date	https://taxpasta.readthedocs.io/en/latest/	Sequence Analysis	taxpasta	iuc	https://github.com/taxprofiler/taxpasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta	0.7.0	taxpasta	0.7.0	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	34	34	5	5	0	0	0	0	0	0	0	0	34	34	5	5	False		
+tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6372	6395	372	379	7339	7339	378	378	6966	6966	154	154	20677	20700	904	911	True	False	True
+tbl2gff3	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1941	1941	466	466	0	0	0	0	463	463	112	112	2404	2404	578	578	True	False	False
+te_finder	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.21	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	20	20	0	0	0	0	0	0	0	0	203	203	20	20	True	False	False
+telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+tetoolkit	tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1013	1013	74	74	0	0	0	0	70	70	4	4	1083	1083	78	78	True	False	False
+tetyper	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	106	106	16	16	155	155	47	47	0	0	0	0	261	261	63	63	True	False	False
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	51	51	0	0	0	0	0	0	0	0	547	547	51	51	True	False	False
+tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	8	8	0	0	0	0	0	0	0	0	15	15	8	8	False		
+tn93	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								Up-to-date	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.14	tn93	1.0.14			4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1915	1915	42	42	1972	1972	225	225	0	0	0	0	3887	3887	267	267	True	False	False
+tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9.1	tooldistillator	0.9.1	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	9	9	6	6	5	5	0	0	0	0	71	71	14	14	True	False	True
+tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	158	66524	28	7228	0	0	0	0	158	66525	28	7229	True	False	False
+tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	15496	26623	1076	1664	83063	343017	8372	27829	5388	14057	508	1012	103947	383697	9956	30505	True	False	False
+transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5964	6418	944	970	5450	5450	1066	1066	2610	2796	317	344	14024	14664	2327	2380	True	False	False
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	1039	1039	189	189	2672	3349	467	485	358	358	47	47	4069	4746	703	721	True	False	True
+translate_bed	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	649	685	138	142	473	473	105	105	761	761	18	18	1883	1919	261	265	True	False	False
+translate_bed_sequences	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	69	16	21	0	0	0	0	0	0	0	0	57	69	16	21	True	False	False
+transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	250	254	31	31	174	174	45	45	0	0	0	0	424	428	76	76	True	False	True
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	229489	275008	5733	6500	228708	324716	11708	16638	22644	23869	1439	1527	480841	623593	18880	24665	True	False	True
+trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	To update	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.2	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	0	9	13	13	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	0	11	13	12	0	35698	39132	4376	4632	44509	44509	6714	6714	21883	23889	1924	2070	102090	107530	13014	13416	True	False	False
+trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1968	2080	374	390	1825	1825	527	527	862	1060	161	195	4655	4965	1062	1112	True	False	False
+trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	4361	4601	741	807	0	0	0	0	2469	2469	190	190	6830	7070	931	997	True	False	False
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	14681	14681	265	265	0	0	0	0	4488	4488	147	147	19169	19169	412	412	True	False	True
+tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	7	7	0	0	0	0	0	0	0	0	17	17	7	7	True	False	False
+ucsc_axtchain	ucsc_axtchain	Chain together genome alignments	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_axtchain	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain	469	ucsc-axtchain	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_blat	ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	Up-to-date	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	469	ucsc-blat	469	Sequence alignment	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+ucsc_chainnet	ucsc_chainnet	Make alignment nets out of chains	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainnet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	469	ucsc-chainnet	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainprenet	ucsc_chainprenet	Remove chains that don't have a chance of being netted	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainprenet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet	469	ucsc-chainprenet	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainsort	ucsc_chainsort	Sort chains. By default sorts by score.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainsort	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort	469	ucsc-chainsort	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	373	463	134	151	2249	18611	638	4080	0	0	0	0	2622	19074	772	4231	True	False	False
+ucsc_netfilter	ucsc_netfilter	Filter out parts of net	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netfilter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter	469	ucsc-netfilter	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_netsyntenic	ucsc_netsyntenic	Add synteny info to a net dataset	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netsyntenic	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic	469	ucsc-netsyntenic	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	0	3	5	5	0	55050	68123	1090	1223	9001	9001	906	906	12444	12444	187	187	76495	89568	2183	2316	True	False	False
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	74120	77648	3798	3963	64946	90075	5451	7380	19516	20422	2010	2080	158582	188145	11259	13423	True	False	True
+unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4900	5146	257	270	251	251	81	81	1069	1069	29	29	6220	6466	367	380	True	False	True
+uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.6	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2117	2725	341	412	3111	5779	594	1011	806	806	50	50	6034	9310	985	1473	True	False	False
+uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1488	1596	230	266	0	0	0	0	743	743	35	35	2231	2339	265	301	True	False	True
+usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1060	1060	5	5	0	0	0	0	0	0	0	0	1060	1060	5	5	True	False	True
+valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	518	677	75	87	234	234	65	65	0	0	0	0	752	911	140	152	True	False	True
+validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	112	38	38	0	0	0	0	0	0	0	0	112	112	38	38	True	False	False
+vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5936	5936	147	147	523	523	15	15	0	0	0	0	6459	6459	162	162	True	False	True
+varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	273	273	12	12	0	0	0	0	0	0	0	0	273	273	12	12	True	False	True
+vcf2snvalignment	vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	2157	2287	198	209	3930	5591	446	744	0	0	0	0	6087	7878	644	953	True	False	True
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	25171	27943	3899	4270	51187	51187	7557	7557	28546	28619	3585	3613	104904	107749	15041	15440	True	False	True
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4715	5343	888	965	9575	9576	2117	2117	3271	5524	1050	1397	17561	20443	4055	4479	True	False	True
+venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4519	5476	667	730	9858	18420	986	2010	0	0	0	0	14377	23896	1653	2740	True	False	False
+verify_map	verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	48	25	25	0	0	0	0	0	0	0	0	48	48	25	25	True	False	False
+vg	vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.59.0			0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	478	478	17	17	0	0	0	0	0	0	0	0	478	478	17	17	True	False	False
+vibrant	vibrant	Virus Identification By iteRative ANnoTation	VIBRANT	VIBRANT		VIBRANT	Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	Up-to-date	https://github.com/AnantharamanLab/VIBRANT	Metagenomics	vibrant	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant	1.2.1	vibrant	1.2.1	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vienna_rna	viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	0	3197	8107	344	415	0	0	0	0	0	0	0	0	3197	8107	344	415	True	False	False
+vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	14412	14590	722	732	0	0	0	0	0	0	0	0	14412	14590	722	732	True	False	False
+virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	94	94	16	16	0	0	0	0	0	0	0	0	94	94	16	16	True	False	True
+virheat	virheat	generates a heatmap of allele frequencies from vcf files	virheat	virheat		virHEAT	VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.			Up-to-date	https://github.com/jonas-fuchs/virHEAT	Visualization, Variant Analysis	virheat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat	0.7.1	virheat	0.7.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	2	2	0	0	0	0	0	0	0	0	12	12	2	2	False		
+virsorter	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	virsorter	virsorter		virsorter	Identify DNA and RNA virus sequences.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/jiarong/VirSorter2/	Metagenomics	virsorter	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter	2.2.4	virsorter	2.2.4	Taxonomic classification	Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	34917	36852	3670	3786	54931	54931	5597	5597	7183	7183	905	905	97031	98966	10172	10288	True	False	False
+vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.29.0	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	0	8	8	8	0	9694	10338	559	628	12282	53546	1031	2007	5334	5672	246	277	27310	69556	1836	2912	True	False	True
+vsnp	vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+wade	wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+weather_app	simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+weightedaverage	wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	227	2307	17	75	0	0	0	0	227	2307	17	75	True	False	False
+windowmasker	windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.16.0			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	537	537	19	19	12	12	7	7	297	297	2	2	846	846	28	28	True	False	False
+windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	2	171	3961	34	328	0	0	0	0	171	3972	34	330	True	False	False
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1619	1715	337	376	0	0	0	0	0	0	0	0	1619	1715	337	376	True	False	True
+xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	0	5	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	5995	5995	275	275	66	66	23	23	295	295	3	3	6356	6356	301	301	True	False	False
+xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	True	False	False
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	618	618	176	176	336	336	62	62	588	588	25	25	1542	1542	263	263	True	False	False
+zeiss_lmd_converter	ZeissLMDconverter	Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	2.0.4	shapely				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	1	1	0	0	0	0	0	0	0	0	4	4	1	1	False		
+zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	4	4	0	0	0	0	0	0	0	0	26	26	4	4	True	False	False
diff --git a/communities/microgalaxy/resources/tools_wordcloud.png b/communities/microgalaxy/resources/tools_wordcloud.png
index 6e436d5c..b0725ad8 100644
Binary files a/communities/microgalaxy/resources/tools_wordcloud.png and b/communities/microgalaxy/resources/tools_wordcloud.png differ
diff --git a/communities/microgalaxy/resources/tutorials.html b/communities/microgalaxy/resources/tutorials.html
index eb1038d1..ffe71adc 100644
--- a/communities/microgalaxy/resources/tutorials.html
+++ b/communities/microgalaxy/resources/tutorials.html
@@ -87,7 +87,7 @@
       <td>Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data</td>
       <td>https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html</td>
       <td>Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology</td>
-      <td>Sequence assembly validation, Statistical calculation, Sequence assembly visualisation, Visualisation, Genome assembly, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering</td>
+      <td>Sequence contamination filtering, Genome assembly, Sequence assembly validation, Sequencing quality control, Visualisation, Sequence assembly visualisation, Sequence composition calculation, Statistical calculation</td>
       <td>2021-03-24</td>
       <td>2024-09-18</td>
       <td>15</td>
@@ -95,13 +95,13 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>fastp, bandage_image, upload1, bandage_info, quast, fastqc, shovill</td>
-      <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)</td>
+      <td>bandage_image, shovill, fastqc, bandage_info, upload1, fastp, quast</td>
+      <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main)</td>
       <td>Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.no</td>
       <td>0</td>
       <td></td>
-      <td>6735</td>
-      <td>10837</td>
+      <td>6791</td>
+      <td>10915</td>
       <td>3.783333</td>
       <td>0</td>
     </tr>
@@ -111,7 +111,7 @@
       <td>Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)</td>
       <td>https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html</td>
       <td>Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance</td>
-      <td>Scatter plot plotting, Sequencing error detection, Sequence alignment, Visualisation, Cross-assembly, Read mapping, Sequencing quality control, Genome assembly, De-novo assembly, Box-Whisker plot plotting, Sequence contamination filtering, Sequence assembly validation, Mapping assembly, Statistical calculation, Sequence assembly visualisation, Filtering, Sequence composition calculation</td>
+      <td>Genome assembly, Sequencing error detection, Sequence assembly visualisation, De-novo assembly, Filtering, Mapping assembly, Scatter plot plotting, Sequence assembly validation, Visualisation, Cross-assembly, Sequence alignment, Sequence composition calculation, Box-Whisker plot plotting, Sequencing quality control, Read mapping, Sequence contamination filtering, Statistical calculation</td>
       <td>2021-03-24</td>
       <td>2024-03-13</td>
       <td>14</td>
@@ -119,14 +119,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>CONVERTER_bz2_to_uncompressed, fastp, filtlong, bandage_image, porechop, upload1, quast, flye, nanoplot, bwa_mem2, polypolish, fastqc</td>
+      <td>bandage_image, polypolish, filtlong, fastqc, nanoplot, upload1, bwa_mem2, fastp, porechop, CONVERTER_bz2_to_uncompressed, quast, flye</td>
       <td>UseGalaxy.eu</td>
       <td>UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>7147</td>
-      <td>10976</td>
-      <td>3.400000</td>
+      <td>7215</td>
+      <td>11067</td>
+      <td>3.383333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -135,22 +135,22 @@
       <td>Assembly of metagenomic sequencing data</td>
       <td>https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html</td>
       <td>Metagenomics, Sequence assembly</td>
-      <td>Data handling, Visualisation, Sequence trimming, Read mapping, Sequencing quality control, Genome assembly, Sequence alignment analysis, Sequence contamination filtering, Sequence assembly validation, Variant calling, Statistical calculation, Sequence assembly visualisation, Sequence file editing, Local alignment, Sequence composition calculation, Read pre-processing, Primer removal, Formatting</td>
-      <td>2024-10-02</td>
-      <td>2024-10-02</td>
+      <td>Variant calling, Genome assembly, Sequence assembly visualisation, Sequence assembly validation, Visualisation, Sequence trimming, Local alignment, Sequence file editing, Data handling, Sequence alignment analysis, Primer removal, Formatting, Sequence composition calculation, Sequencing quality control, Read mapping, Read pre-processing, Sequence contamination filtering, Statistical calculation</td>
+      <td>2024-10-08</td>
+      <td>2024-10-08</td>
       <td>0</td>
       <td>True</td>
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>ngsutils_bam_filter, tp_cat, bamtools, bandage_image, filter_tabular, megahit_contig2fastg, bandage_info, bg_uniq, quast, seqtk_subseq, cutadapt, random_lines1, collection_column_join, megahit, coverm_contig, fastqc, metaspades, bowtie2</td>
+      <td>bandage_image, seqtk_subseq, megahit_contig2fastg, cutadapt, random_lines1, tp_cat, megahit, fastqc, bg_uniq, collection_column_join, bandage_info, metaspades, coverm_contig, bowtie2, filter_tabular, quast, bamtools, ngsutils_bam_filter</td>
       <td></td>
       <td>UseGalaxy.cz, UseGalaxy.eu</td>
       <td>0</td>
       <td></td>
       <td>6</td>
-      <td>7</td>
-      <td>0.383333</td>
+      <td>14</td>
+      <td>7.100000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -159,7 +159,7 @@
       <td>Unicycler Assembly</td>
       <td>https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html</td>
       <td>Sequence assembly, Genomics, Microbiology</td>
-      <td>Genome annotation, Visualisation, Genome assembly, Sequencing quality control, Sequence assembly validation, Gene prediction, Statistical calculation, Aggregation, Validation, Sequence composition calculation, Coding region prediction</td>
+      <td>Genome assembly, Coding region prediction, Sequence composition calculation, Genome annotation, Sequence assembly validation, Validation, Sequencing quality control, Gene prediction, Visualisation, Aggregation, Statistical calculation</td>
       <td>2017-10-11</td>
       <td>2024-03-13</td>
       <td>23</td>
@@ -167,14 +167,14 @@
       <td>True</td>
       <td>False</td>
       <td>True</td>
-      <td>prokka, unicycler, quast, multiqc, fastqc</td>
+      <td>unicycler, fastqc, multiqc, prokka, quast</td>
       <td>UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au</td>
-      <td>GalaxyTrakr, HyPhy HIV NGS Tools, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no</td>
+      <td>GalaxyTrakr, HyPhy HIV NGS Tools, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no</td>
       <td>0</td>
       <td></td>
-      <td>2144791</td>
-      <td>5917098</td>
-      <td>4.566667</td>
+      <td>2155238</td>
+      <td>5948759</td>
+      <td>4.583333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -183,7 +183,7 @@
       <td>Making sense of a newly assembled genome</td>
       <td>https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html</td>
       <td>Sequence assembly, Genomics, Microbiology</td>
-      <td>Sequence alignment, Sequence visualisation, Read mapping, Genome visualisation, Mapping</td>
+      <td>Read mapping, Sequence alignment, Sequence visualisation, Genome visualisation, Mapping</td>
       <td>2018-06-14</td>
       <td>2024-06-24</td>
       <td>29</td>
@@ -191,13 +191,13 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>join1, tp_sed_tool, lastz_wrapper_2, upload1, fasta_filter_by_length, bedtools_intersectbed, datamash_ops, circos_interval_to_tiles, jbrowse, tp_cat, mergeCols1, Filter1, bedtools_sortbed, tp_sort_header_tool, Grep1, Cut1, collapse_dataset, cat1, tp_replace_in_column, addValue, circos_aln_to_links, fasta_compute_length, circos, tp_grep_tool, tp_replace_in_line, random_lines1, bedtools_complementbed</td>
+      <td>cat1, tp_sed_tool, lastz_wrapper_2, jbrowse, circos_interval_to_tiles, tp_grep_tool, circos, bedtools_complementbed, collapse_dataset, bedtools_intersectbed, upload1, datamash_ops, tp_replace_in_column, addValue, Filter1, tp_replace_in_line, random_lines1, tp_sort_header_tool, Grep1, fasta_compute_length, mergeCols1, Cut1, fasta_filter_by_length, tp_cat, join1, bedtools_sortbed, circos_aln_to_links</td>
       <td></td>
       <td></td>
       <td>0</td>
       <td></td>
-      <td>6026</td>
-      <td>12166</td>
+      <td>6047</td>
+      <td>12192</td>
       <td>3.016667</td>
       <td>0</td>
     </tr>
@@ -207,7 +207,7 @@
       <td>Checking expected species and contamination in bacterial isolate</td>
       <td>https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html</td>
       <td>Whole genome sequencing, Genomics, Microbiology, Microbial ecology</td>
-      <td>Statistical calculation, Taxonomic classification, Cross-assembly, Expression analysis</td>
+      <td>Expression analysis, Cross-assembly, Statistical calculation, Taxonomic classification</td>
       <td>2024-03-04</td>
       <td>2024-06-27</td>
       <td>4</td>
@@ -215,14 +215,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>recentrifuge, kraken2, upload1, est_abundance</td>
-      <td>UseGalaxy.eu, UseGalaxy.fr</td>
+      <td>kraken2, upload1, recentrifuge, est_abundance</td>
+      <td>UseGalaxy.eu</td>
       <td>Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>260</td>
-      <td>343</td>
-      <td>3.533333</td>
+      <td>267</td>
+      <td>352</td>
+      <td>3.366667</td>
       <td>0</td>
     </tr>
     <tr>
@@ -239,14 +239,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>upload1, interactive_tool_rstudio, raxml</td>
+      <td>interactive_tool_rstudio, upload1, raxml</td>
       <td>UseGalaxy.eu</td>
-      <td>UseGalaxy.fr, UseGalaxy.org (Main)</td>
+      <td>UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>1373</td>
-      <td>2071</td>
-      <td>2.233333</td>
+      <td>1378</td>
+      <td>2078</td>
+      <td>2.250000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -255,7 +255,7 @@
       <td>Identifying tuberculosis transmission links: from SNPs to transmission clusters</td>
       <td>https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html</td>
       <td>Genomics, Microbiology, Infectious disease, DNA polymorphism</td>
-      <td>Phylogenetic tree visualisation, Variant calling, Antimicrobial resistance prediction, Phylogenetic tree generation</td>
+      <td>Variant calling, Antimicrobial resistance prediction, Phylogenetic tree visualisation, Phylogenetic tree generation</td>
       <td>2022-03-16</td>
       <td>2024-07-12</td>
       <td>12</td>
@@ -263,14 +263,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>tp_sed_tool, tp_easyjoin_tool, tp_cat, bcftools_consensus, samtools_view, upload1, snippy, tp_grep_tool, tp_replace_in_line, snp_dists, Grep1, tb_variant_filter, tb_profiler_profile, collapse_dataset, snp_sites, trimmomatic, __MERGE_COLLECTION__, addName</td>
+      <td>samtools_view, tp_replace_in_line, tp_sed_tool, bcftools_consensus, snippy, snp_sites, collapse_dataset, trimmomatic, tp_cat, tp_easyjoin_tool, tp_grep_tool, Grep1, tb_variant_filter, addName, tb_profiler_profile, upload1, __MERGE_COLLECTION__, snp_dists</td>
       <td>UseGalaxy.eu</td>
       <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>1605</td>
-      <td>2499</td>
-      <td>3.050000</td>
+      <td>1610</td>
+      <td>2504</td>
+      <td>3.033333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -279,7 +279,7 @@
       <td>Genome annotation with Prokka</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html</td>
       <td>Genomics, Microbiology, Gene and protein families, Sequence analysis</td>
-      <td>Genome visualisation, Gene prediction, Genome annotation, Coding region prediction</td>
+      <td>Coding region prediction, Gene prediction, Genome visualisation, Genome annotation</td>
       <td>2018-03-06</td>
       <td>2024-08-08</td>
       <td>25</td>
@@ -287,13 +287,13 @@
       <td>True</td>
       <td>True</td>
       <td>True</td>
-      <td>jbrowse, prokka</td>
+      <td>prokka, jbrowse</td>
       <td>UseGalaxy.eu, UseGalaxy.org (Main)</td>
-      <td>Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>2149523</td>
-      <td>5925124</td>
+      <td>2160036</td>
+      <td>5956792</td>
       <td>4.316667</td>
       <td>0</td>
     </tr>
@@ -303,7 +303,7 @@
       <td>Identification of AMR genes in an assembled bacterial genome</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html</td>
       <td>Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance</td>
-      <td>Genome visualisation, Genome annotation, Read mapping</td>
+      <td>Genome visualisation, Read mapping, Genome annotation</td>
       <td>2024-01-23</td>
       <td>2024-09-27</td>
       <td>6</td>
@@ -311,14 +311,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>jbrowse, tbl2gff3, upload1, Grep1, staramr_search, bakta, bowtie2</td>
-      <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr</td>
+      <td>jbrowse, Grep1, tbl2gff3, bakta, upload1, bowtie2, staramr_search</td>
+      <td>UseGalaxy.cz, UseGalaxy.eu</td>
       <td>Galaxy@AuBi, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>1138</td>
-      <td>1576</td>
-      <td>2.750000</td>
+      <td>1181</td>
+      <td>1633</td>
+      <td>2.966667</td>
       <td>0</td>
     </tr>
     <tr>
@@ -335,14 +335,14 @@
       <td>True</td>
       <td>True</td>
       <td>True</td>
-      <td>jbrowse, create_or_update, iframe, list_organism, create_account</td>
+      <td>jbrowse, create_or_update, create_account, iframe, list_organism</td>
       <td></td>
       <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no</td>
       <td>0</td>
       <td></td>
-      <td>1906178</td>
-      <td>5119567</td>
-      <td>4.983333</td>
+      <td>1916586</td>
+      <td>5151189</td>
+      <td>5.000000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -351,7 +351,7 @@
       <td>Bacterial Genome Annotation</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html</td>
       <td>Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements</td>
-      <td>Genome annotation, Nucleic acid feature detection, Multilocus sequence typing, Genome visualisation, Genome assembly, Sequence motif recognition, Structural variation detection, Scaffolding, Protein feature detection</td>
+      <td>Sequence motif recognition, Genome assembly, Genome visualisation, Protein feature detection, Genome annotation, Multilocus sequence typing, Nucleic acid feature detection, Scaffolding, Structural variation detection</td>
       <td>2024-02-01</td>
       <td>2024-09-08</td>
       <td>5</td>
@@ -359,14 +359,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>jbrowse, tbl2gff3, plasmidfinder, integron_finder, upload1, isescan, tp_tail_tool, bakta, tp_replace_in_column, Grouping1</td>
-      <td>UseGalaxy.eu, UseGalaxy.fr</td>
+      <td>integron_finder, jbrowse, tp_tail_tool, bakta, tbl2gff3, upload1, tp_replace_in_column, Grouping1, isescan, plasmidfinder</td>
+      <td>UseGalaxy.eu</td>
       <td>Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>2243</td>
-      <td>2969</td>
-      <td>2.333333</td>
+      <td>2301</td>
+      <td>3039</td>
+      <td>2.300000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -375,7 +375,7 @@
       <td>Comparative gene analysis in unannotated genomes</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html</td>
       <td>Genomics, Gene and protein families, Sequence analysis, Phylogeny</td>
-      <td>Database search, Transcriptome assembly, Phylogenetic tree generation, De-novo assembly, Sequence alignment analysis, Multiple sequence alignment, Coding region prediction</td>
+      <td>Multiple sequence alignment, Sequence alignment analysis, Transcriptome assembly, Coding region prediction, Database search, De-novo assembly, Phylogenetic tree generation</td>
       <td>2022-09-08</td>
       <td>2024-03-18</td>
       <td>8</td>
@@ -383,14 +383,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>orfipy, rapidnj, join1, bg_diamond_makedb, Filter1, tp_split_on_column, tab2fasta, collapse_dataset, rbc_mafft, bg_diamond_view, Cut1, Add_a_column1, bg_diamond, regexColumn1, gops_intersect_1, cat1</td>
+      <td>Cut1, cat1, bg_diamond_view, tp_split_on_column, collapse_dataset, rbc_mafft, tab2fasta, regexColumn1, gops_intersect_1, join1, rapidnj, bg_diamond, orfipy, Add_a_column1, bg_diamond_makedb, Filter1</td>
       <td>UseGalaxy.eu, UseGalaxy.org (Main)</td>
       <td>UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>1045</td>
-      <td>1602</td>
-      <td>3.583333</td>
+      <td>1051</td>
+      <td>1608</td>
+      <td>3.550000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -399,7 +399,7 @@
       <td>Essential genes detection with Transposon insertion sequencing</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html</td>
       <td>Genomics, Microbiology, Sequence analysis, Mobile genetic elements</td>
-      <td>Sequence trimming, Transposon prediction, Read pre-processing, Primer removal</td>
+      <td>Read pre-processing, Sequence trimming, Primer removal, Transposon prediction</td>
       <td>2019-07-02</td>
       <td>2024-03-18</td>
       <td>12</td>
@@ -407,13 +407,13 @@
       <td>True</td>
       <td>False</td>
       <td>True</td>
-      <td>__EXTRACT_DATASET__, bowtie_wrapper, gff_to_prot, tp_easyjoin_tool, Filter1, transit_gumbel, bg_find_subsequences, tp_sort_header_tool, cutadapt, Cut1, Add_a_column1, deeptools_bam_coverage</td>
+      <td>Cut1, transit_gumbel, cutadapt, tp_easyjoin_tool, bg_find_subsequences, tp_sort_header_tool, deeptools_bam_coverage, bowtie_wrapper, __EXTRACT_DATASET__, Add_a_column1, gff_to_prot, Filter1</td>
       <td>UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>UseGalaxy.cz, UseGalaxy.eu</td>
       <td>0</td>
       <td></td>
-      <td>2140389</td>
-      <td>5910080</td>
+      <td>2150876</td>
+      <td>5941722</td>
       <td>4.266667</td>
       <td>0</td>
     </tr>
@@ -423,7 +423,7 @@
       <td>Genome annotation with Prokka</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html</td>
       <td>Genomics, Microbiology, Gene and protein families, Sequence analysis</td>
-      <td>Genome visualisation, Gene prediction, Genome annotation, Coding region prediction</td>
+      <td>Coding region prediction, Gene prediction, Genome visualisation, Genome annotation</td>
       <td>2018-03-06</td>
       <td>2024-08-08</td>
       <td>25</td>
@@ -431,13 +431,13 @@
       <td>True</td>
       <td>True</td>
       <td>True</td>
-      <td>jbrowse, prokka</td>
+      <td>prokka, jbrowse</td>
       <td>UseGalaxy.eu, UseGalaxy.org (Main)</td>
-      <td>Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>2149523</td>
-      <td>5925127</td>
+      <td>2160036</td>
+      <td>5956800</td>
       <td>4.316667</td>
       <td>0</td>
     </tr>
@@ -447,7 +447,7 @@
       <td>Identification of AMR genes in an assembled bacterial genome</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html</td>
       <td>Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance</td>
-      <td>Genome visualisation, Genome annotation, Read mapping</td>
+      <td>Genome visualisation, Read mapping, Genome annotation</td>
       <td>2024-01-23</td>
       <td>2024-09-27</td>
       <td>6</td>
@@ -455,14 +455,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>jbrowse, tbl2gff3, upload1, Grep1, staramr_search, bakta, bowtie2</td>
-      <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr</td>
+      <td>jbrowse, Grep1, tbl2gff3, bakta, upload1, bowtie2, staramr_search</td>
+      <td>UseGalaxy.cz, UseGalaxy.eu</td>
       <td>Galaxy@AuBi, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>1138</td>
-      <td>1576</td>
-      <td>2.750000</td>
+      <td>1181</td>
+      <td>1633</td>
+      <td>2.966667</td>
       <td>0</td>
     </tr>
     <tr>
@@ -479,14 +479,14 @@
       <td>True</td>
       <td>True</td>
       <td>True</td>
-      <td>jbrowse, create_or_update, iframe, list_organism, create_account</td>
+      <td>jbrowse, create_or_update, create_account, iframe, list_organism</td>
       <td></td>
       <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no</td>
       <td>0</td>
       <td></td>
-      <td>1906178</td>
-      <td>5119570</td>
-      <td>4.983333</td>
+      <td>1916586</td>
+      <td>5151198</td>
+      <td>5.000000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -495,7 +495,7 @@
       <td>Bacterial Genome Annotation</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html</td>
       <td>Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements</td>
-      <td>Genome annotation, Nucleic acid feature detection, Multilocus sequence typing, Genome visualisation, Genome assembly, Sequence motif recognition, Structural variation detection, Scaffolding, Protein feature detection</td>
+      <td>Sequence motif recognition, Genome assembly, Genome visualisation, Protein feature detection, Genome annotation, Multilocus sequence typing, Nucleic acid feature detection, Scaffolding, Structural variation detection</td>
       <td>2024-02-01</td>
       <td>2024-09-08</td>
       <td>5</td>
@@ -503,14 +503,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>jbrowse, tbl2gff3, plasmidfinder, integron_finder, upload1, isescan, tp_tail_tool, bakta, tp_replace_in_column, Grouping1</td>
-      <td>UseGalaxy.eu, UseGalaxy.fr</td>
+      <td>integron_finder, jbrowse, tp_tail_tool, bakta, tbl2gff3, upload1, tp_replace_in_column, Grouping1, isescan, plasmidfinder</td>
+      <td>UseGalaxy.eu</td>
       <td>Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>2243</td>
-      <td>2969</td>
-      <td>2.333333</td>
+      <td>2301</td>
+      <td>3039</td>
+      <td>2.300000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -519,7 +519,7 @@
       <td>Microbial Variant Calling</td>
       <td>https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html</td>
       <td>Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation</td>
-      <td>Genome visualisation, Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation</td>
+      <td>Variant calling, Phylogenetic tree visualisation, Genome visualisation, Phylogenetic tree generation</td>
       <td>2018-02-26</td>
       <td>2024-03-15</td>
       <td>23</td>
@@ -529,11 +529,11 @@
       <td>True</td>
       <td>jbrowse, snippy</td>
       <td>UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)</td>
-      <td>GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>GalaxyTrakr, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>12475</td>
-      <td>20692</td>
+      <td>12499</td>
+      <td>20722</td>
       <td>1.983333</td>
       <td>0</td>
     </tr>
@@ -543,7 +543,7 @@
       <td>Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)</td>
       <td>https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html</td>
       <td>Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance</td>
-      <td>Scatter plot plotting, Sequencing error detection, Sequence alignment, Visualisation, Cross-assembly, Read mapping, Sequencing quality control, Genome assembly, De-novo assembly, Box-Whisker plot plotting, Sequence contamination filtering, Sequence assembly validation, Mapping assembly, Statistical calculation, Sequence assembly visualisation, Filtering, Sequence composition calculation</td>
+      <td>Genome assembly, Sequencing error detection, Sequence assembly visualisation, De-novo assembly, Filtering, Mapping assembly, Scatter plot plotting, Sequence assembly validation, Visualisation, Cross-assembly, Sequence alignment, Sequence composition calculation, Box-Whisker plot plotting, Sequencing quality control, Read mapping, Sequence contamination filtering, Statistical calculation</td>
       <td>2021-03-24</td>
       <td>2024-03-13</td>
       <td>14</td>
@@ -551,14 +551,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>CONVERTER_bz2_to_uncompressed, fastp, filtlong, bandage_image, porechop, upload1, quast, flye, nanoplot, bwa_mem2, polypolish, fastqc</td>
+      <td>bandage_image, polypolish, filtlong, fastqc, nanoplot, upload1, bwa_mem2, fastp, porechop, CONVERTER_bz2_to_uncompressed, quast, flye</td>
       <td>UseGalaxy.eu</td>
       <td>UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>7148</td>
-      <td>10977</td>
-      <td>3.400000</td>
+      <td>7215</td>
+      <td>11067</td>
+      <td>3.383333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -567,7 +567,7 @@
       <td>Making sense of a newly assembled genome</td>
       <td>https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html</td>
       <td>Sequence assembly, Genomics, Microbiology</td>
-      <td>Sequence alignment, Sequence visualisation, Read mapping, Genome visualisation, Mapping</td>
+      <td>Read mapping, Sequence alignment, Sequence visualisation, Genome visualisation, Mapping</td>
       <td>2018-06-14</td>
       <td>2024-06-24</td>
       <td>29</td>
@@ -575,13 +575,13 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>join1, tp_sed_tool, lastz_wrapper_2, upload1, fasta_filter_by_length, bedtools_intersectbed, datamash_ops, circos_interval_to_tiles, jbrowse, tp_cat, mergeCols1, Filter1, bedtools_sortbed, tp_sort_header_tool, Grep1, Cut1, collapse_dataset, cat1, tp_replace_in_column, addValue, circos_aln_to_links, fasta_compute_length, circos, tp_grep_tool, tp_replace_in_line, random_lines1, bedtools_complementbed</td>
+      <td>cat1, tp_sed_tool, lastz_wrapper_2, jbrowse, circos_interval_to_tiles, tp_grep_tool, circos, bedtools_complementbed, collapse_dataset, bedtools_intersectbed, upload1, datamash_ops, tp_replace_in_column, addValue, Filter1, tp_replace_in_line, random_lines1, tp_sort_header_tool, Grep1, fasta_compute_length, mergeCols1, Cut1, fasta_filter_by_length, tp_cat, join1, bedtools_sortbed, circos_aln_to_links</td>
       <td></td>
       <td></td>
       <td>0</td>
       <td></td>
-      <td>6026</td>
-      <td>12166</td>
+      <td>6047</td>
+      <td>12192</td>
       <td>3.016667</td>
       <td>0</td>
     </tr>
@@ -591,7 +591,7 @@
       <td>Analyses of metagenomics data - The global picture</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html</td>
       <td>Metagenomics, Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>DNA barcoding, Visualisation, Phylogenetic analysis, Sequencing quality control, Taxonomic classification, Sequence read processing, Sequence clustering</td>
+      <td>Sequence read processing, DNA barcoding, Taxonomic classification, Sequencing quality control, Visualisation, Phylogenetic analysis, Sequence clustering</td>
       <td>2017-06-22</td>
       <td>2024-08-09</td>
       <td>4</td>
@@ -599,14 +599,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>humann2_regroup_table, mothur_summary_seqs, humann2_renorm_table, mothur_make_biom, mothur_count_seqs, mothur_classify_seqs, mothur_make_group, mothur_make_shared, mothur_filter_seqs, mothur_merge_files, mothur_classify_otu, mothur_align_seqs, humann2, mothur_cluster_split, mothur_screen_seqs, metaphlan2, mothur_pre_cluster, mothur_unique_seqs, taxonomy_krona_chart, krona-text, metaphlan2krona</td>
+      <td>krona-text, mothur_merge_files, mothur_count_seqs, mothur_screen_seqs, mothur_summary_seqs, mothur_classify_otu, mothur_unique_seqs, mothur_make_biom, mothur_classify_seqs, mothur_pre_cluster, metaphlan2, metaphlan2krona, humann2_renorm_table, mothur_make_group, humann2_regroup_table, mothur_filter_seqs, mothur_align_seqs, humann2, mothur_make_shared, mothur_cluster_split, taxonomy_krona_chart</td>
       <td>UseGalaxy.be</td>
-      <td>UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>3586</td>
-      <td>4852</td>
-      <td>2.783333</td>
+      <td>3689</td>
+      <td>4998</td>
+      <td>2.800000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -615,7 +615,7 @@
       <td>Identification of the micro-organisms in a beer using Nanopore sequencing</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html</td>
       <td>Metagenomics, Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Taxonomic classification, Statistical calculation, Aggregation, Visualisation, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering</td>
+      <td>Sequence composition calculation, Sequence contamination filtering, Sequencing quality control, Visualisation, Aggregation, Statistical calculation, Taxonomic classification</td>
       <td>2022-09-29</td>
       <td>2024-06-14</td>
       <td>4</td>
@@ -623,14 +623,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>porechop, fastp, Filter1, taxonomy_krona_chart, kraken2, krakentools_kreport2krona, fastqc</td>
+      <td>krakentools_kreport2krona, fastqc, fastp, porechop, kraken2, taxonomy_krona_chart, Filter1</td>
       <td>GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au</td>
       <td>UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>1239</td>
-      <td>1942</td>
-      <td>2.966667</td>
+      <td>1249</td>
+      <td>1962</td>
+      <td>2.950000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -639,7 +639,7 @@
       <td>Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html</td>
       <td>Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis</td>
-      <td>Scatter plot plotting, Visualisation, Cross-assembly, Phylogenetic tree generation, Genome assembly, Sequencing quality control, Box-Whisker plot plotting, Multiple sequence alignment, Mapping assembly, Base-calling, Aggregation, Statistical calculation, Pairwise sequence alignment, Validation, Taxonomic classification, Sequence composition calculation, Mapping, Antimicrobial resistance prediction, Phylogenetic tree analysis, Data handling, Multilocus sequence typing, De-novo assembly, Sequence alignment analysis, Phylogenetic tree reconstruction, Sequence contamination filtering, Sequence assembly, Variant calling, Sequence assembly visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)</td>
+      <td>Variant calling, Genome assembly, Sequence assembly visualisation, Base-calling, De-novo assembly, Antimicrobial resistance prediction, Mapping assembly, Taxonomic classification, Multilocus sequence typing, Multiple sequence alignment, Validation, Scatter plot plotting, Visualisation, Cross-assembly, Aggregation, Pairwise sequence alignment, Data handling, Sequence alignment analysis, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation, Sequence composition calculation, Box-Whisker plot plotting, Sequence assembly, Sequencing quality control, Phylogenetic tree reconstruction, Sequence contamination filtering, Statistical calculation, Mapping</td>
       <td>2023-01-26</td>
       <td>2024-09-27</td>
       <td>11</td>
@@ -647,14 +647,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>__FILTER_FAILED_DATASETS__, Count1, minimap2, snpSift_filter, compose_text_param, tab2fasta, tp_find_and_replace, tp_head_tool, tp_multijoin_tool, param_value_from_file, collection_column_join, collection_element_identifiers, bcftools_norm, krakentools_kreport2krona, krakentools_extract_kraken_reads, ggplot2_heatmap, bamtools_split_mapped, fasta_merge_files_and_filter_unique_sequences, barchart_gnuplot, samtools_fastx, flye, medaka_consensus_pipeline, tp_cut_tool, fastqc, snpSift_extractFields, regex1, Grouping1, tp_sorted_uniq, porechop, table_compute, bcftools_consensus, split_file_to_collection, bandage_image, abricate, Paste1, add_line_to_file, tp_split_on_column, multiqc, Grep1, Cut1, collapse_dataset, Remove beginning1, clustalw, bedtools_getfastabed, tp_replace_in_column, fasttree, newick_display, fastp, samtools_coverage, samtools_depth, clair3, taxonomy_krona_chart, __FILTER_EMPTY_DATASETS__, kraken2, __BUILD_LIST__, Add_a_column1, mlst, nanoplot, regexColumn1, CONVERTER_gz_to_uncompressed, fasta2tab</td>
+      <td>regex1, regexColumn1, CONVERTER_gz_to_uncompressed, mlst, __BUILD_LIST__, Remove beginning1, fasta2tab, fastp, abricate, collapse_dataset, __FILTER_EMPTY_DATASETS__, samtools_depth, tab2fasta, tp_sorted_uniq, snpSift_filter, samtools_fastx, tp_replace_in_column, clair3, porechop, __FILTER_FAILED_DATASETS__, Paste1, ggplot2_heatmap, bandage_image, bcftools_norm, Count1, compose_text_param, krakentools_extract_kraken_reads, krakentools_kreport2krona, medaka_consensus_pipeline, minimap2, newick_display, clustalw, collection_element_identifiers, barchart_gnuplot, tp_find_and_replace, fasta_merge_files_and_filter_unique_sequences, collection_column_join, snpSift_extractFields, Grep1, add_line_to_file, bamtools_split_mapped, multiqc, kraken2, Add_a_column1, tp_cut_tool, Cut1, tp_split_on_column, bcftools_consensus, tp_multijoin_tool, samtools_coverage, bedtools_getfastabed, param_value_from_file, fastqc, nanoplot, table_compute, split_file_to_collection, fasttree, Grouping1, taxonomy_krona_chart, flye, tp_head_tool</td>
       <td>UseGalaxy.eu</td>
       <td>UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>1964</td>
-      <td>2918</td>
-      <td>3.000000</td>
+      <td>2001</td>
+      <td>2968</td>
+      <td>2.966667</td>
       <td>0</td>
     </tr>
     <tr>
@@ -663,7 +663,7 @@
       <td>Metatranscriptomics analysis using microbiome RNA-seq data</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html</td>
       <td>Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis</td>
-      <td>Visualisation, Sequencing quality control, Phylogenetic inference, Phylogenetic tree editing, Statistical calculation, Taxonomic classification, Validation, Sequence composition calculation, Sequence comparison, Sequence similarity search, Phylogenetic tree analysis, Sequence trimming, Phylogenetic analysis, Phylogenetic tree visualisation, Sequence alignment analysis, Species frequency estimation, Conversion, Nucleic acid sequence analysis, Read pre-processing, Primer removal</td>
+      <td>Sequence comparison, Taxonomic classification, Validation, Conversion, Visualisation, Sequence trimming, Phylogenetic analysis, Phylogenetic tree visualisation, Phylogenetic inference, Nucleic acid sequence analysis, Sequence alignment analysis, Species frequency estimation, Phylogenetic tree analysis, Primer removal, Sequence composition calculation, Phylogenetic tree editing, Sequencing quality control, Sequence similarity search, Read pre-processing, Statistical calculation</td>
       <td>2019-11-21</td>
       <td>2024-06-14</td>
       <td>4</td>
@@ -671,13 +671,13 @@
       <td>True</td>
       <td>False</td>
       <td>True</td>
-      <td>fastq_paired_end_interlacer, tp_find_and_replace, metaphlan, fastqc, humann, graphlan_annotate, graphlan, humann_split_stratified_table, humann_renorm_table, humann_regroup_table, humann_rename_table, cutadapt, combine_metaphlan2_humann2, multiqc, bg_sortmerna, Grep1, Cut1, export2graphlan, humann_unpack_pathways, taxonomy_krona_chart</td>
+      <td>humann, bg_sortmerna, combine_metaphlan2_humann2, metaphlan, cutadapt, humann_renorm_table, graphlan_annotate, fastq_paired_end_interlacer, humann_unpack_pathways, export2graphlan, humann_regroup_table, tp_find_and_replace, Grep1, multiqc, Cut1, humann_split_stratified_table, fastqc, humann_rename_table, graphlan, taxonomy_krona_chart</td>
       <td>UseGalaxy.org (Main), UseGalaxy.org.au</td>
       <td>UseGalaxy.cz, UseGalaxy.no</td>
       <td>0</td>
       <td></td>
-      <td>2136358</td>
-      <td>5901051</td>
+      <td>2147260</td>
+      <td>5933139</td>
       <td>4.266667</td>
       <td>0</td>
     </tr>
@@ -687,7 +687,7 @@
       <td>Taxonomic Profiling and Visualization of Metagenomic Data</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html</td>
       <td>Metagenomics, Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Phylogenetic tree analysis, Statistical calculation, Taxonomic classification, Aggregation, Visualisation, Nucleic acid sequence analysis</td>
+      <td>Taxonomic classification, Visualisation, Phylogenetic tree analysis, Aggregation, Statistical calculation, Nucleic acid sequence analysis</td>
       <td>2023-05-03</td>
       <td>2024-06-14</td>
       <td>4</td>
@@ -695,13 +695,13 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>interactive_tool_phinch, est_abundance, taxonomy_krona_chart, interactive_tool_pavian, kraken2, kraken_biom, __UNZIP_COLLECTION__, krakentools_kreport2krona, metaphlan</td>
+      <td>krakentools_kreport2krona, metaphlan, interactive_tool_phinch, interactive_tool_pavian, est_abundance, kraken_biom, __UNZIP_COLLECTION__, taxonomy_krona_chart, kraken2</td>
       <td>UseGalaxy.eu</td>
-      <td>UseGalaxy.fr, UseGalaxy.org.au</td>
+      <td>UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>4443</td>
-      <td>6096</td>
+      <td>4540</td>
+      <td>6233</td>
       <td>1.966667</td>
       <td>0</td>
     </tr>
@@ -711,7 +711,7 @@
       <td>Metatranscriptomics analysis using microbiome RNA-seq data (short)</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html</td>
       <td>Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis</td>
-      <td>Visualisation, Sequencing quality control, Phylogenetic inference, Phylogenetic tree editing, Statistical calculation, Taxonomic classification, Validation, Sequence composition calculation, Sequence comparison, Sequence similarity search, Phylogenetic tree analysis, Sequence trimming, Phylogenetic analysis, Phylogenetic tree visualisation, Sequence alignment analysis, Species frequency estimation, Conversion, Nucleic acid sequence analysis, Read pre-processing, Primer removal</td>
+      <td>Sequence comparison, Taxonomic classification, Validation, Conversion, Visualisation, Sequence trimming, Phylogenetic analysis, Phylogenetic tree visualisation, Phylogenetic inference, Nucleic acid sequence analysis, Sequence alignment analysis, Species frequency estimation, Phylogenetic tree analysis, Primer removal, Sequence composition calculation, Phylogenetic tree editing, Sequencing quality control, Sequence similarity search, Read pre-processing, Statistical calculation</td>
       <td>2020-02-13</td>
       <td>2024-06-14</td>
       <td>4</td>
@@ -719,14 +719,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>fastq_paired_end_interlacer, tp_find_and_replace, metaphlan, fastqc, humann, graphlan_annotate, graphlan, humann_split_stratified_table, humann_renorm_table, humann_regroup_table, humann_rename_table, cutadapt, combine_metaphlan2_humann2, multiqc, bg_sortmerna, Grep1, Cut1, export2graphlan, humann_unpack_pathways, taxonomy_krona_chart</td>
+      <td>humann, bg_sortmerna, combine_metaphlan2_humann2, metaphlan, cutadapt, humann_renorm_table, graphlan_annotate, fastq_paired_end_interlacer, humann_unpack_pathways, export2graphlan, humann_regroup_table, tp_find_and_replace, Grep1, multiqc, Cut1, humann_split_stratified_table, fastqc, humann_rename_table, graphlan, taxonomy_krona_chart</td>
       <td>UseGalaxy.org (Main), UseGalaxy.org.au</td>
       <td>UseGalaxy.cz, UseGalaxy.no</td>
       <td>0</td>
       <td></td>
-      <td>274</td>
-      <td>351</td>
-      <td>1.433333</td>
+      <td>280</td>
+      <td>357</td>
+      <td>1.400000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -735,7 +735,7 @@
       <td>Antibiotic resistance detection</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html</td>
       <td>Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial Resistance</td>
-      <td>Scatter plot plotting, Genome assembly, Box-Whisker plot plotting, De-novo assembly, Sequence analysis, Mapping assembly, Aggregation, Sequence assembly visualisation, Pairwise sequence alignment</td>
+      <td>Genome assembly, Sequence assembly visualisation, De-novo assembly, Mapping assembly, Sequence analysis, Box-Whisker plot plotting, Scatter plot plotting, Aggregation, Pairwise sequence alignment</td>
       <td>2019-06-25</td>
       <td>2024-06-14</td>
       <td>4</td>
@@ -743,14 +743,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>unicycler, minimap2, bandage_image, PlasFlow, racon, nanoplot, gfa_to_fa, staramr_search, miniasm</td>
+      <td>bandage_image, minimap2, unicycler, nanoplot, PlasFlow, gfa_to_fa, miniasm, racon, staramr_search</td>
       <td>UseGalaxy.eu</td>
       <td>UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>1281</td>
-      <td>1950</td>
-      <td>4.033333</td>
+      <td>1301</td>
+      <td>1976</td>
+      <td>4.050000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -759,7 +759,7 @@
       <td>16S Microbial analysis with Nanopore data</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html</td>
       <td>Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Taxonomic classification, Statistical calculation, Visualisation, Validation, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering</td>
+      <td>Sequence contamination filtering, Validation, Sequencing quality control, Visualisation, Sequence composition calculation, Statistical calculation, Taxonomic classification</td>
       <td>2020-11-24</td>
       <td>2024-07-31</td>
       <td>5</td>
@@ -767,14 +767,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>porechop, fastp, tp_replace_in_line, taxonomy_krona_chart, multiqc, kraken2, datamash_reverse, fastqc, Remove beginning1</td>
+      <td>tp_replace_in_line, datamash_reverse, multiqc, fastqc, Remove beginning1, fastp, porechop, kraken2, taxonomy_krona_chart</td>
       <td>UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
       <td>GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>2758</td>
-      <td>3844</td>
-      <td>2.716667</td>
+      <td>2802</td>
+      <td>3894</td>
+      <td>2.733333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -783,7 +783,7 @@
       <td>Building an amplicon sequence variant (ASV) table from 16S data using DADA2</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html</td>
       <td>Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Variant calling, DNA barcoding, Visualisation, Analysis, Deposition</td>
+      <td>Variant calling, DNA barcoding, Visualisation, Deposition, Analysis</td>
       <td>2024-06-05</td>
       <td>2024-09-26</td>
       <td>8</td>
@@ -791,13 +791,13 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>tp_head_tool, collection_element_identifiers, __UNZIP_COLLECTION__, interactive_tool_phyloseq, dada2_mergePairs, dada2_removeBimeraDenovo, dada2_assignTaxonomyAddspecies, Grouping1, dada2_plotQualityProfile, dada2_filterAndTrim, cat1, tp_replace_in_column, dada2_seqCounts, dada2_makeSequenceTable, tp_replace_in_line, Add_a_column1, dada2_dada, __SORTLIST__, dada2_learnErrors, phyloseq_from_dada2</td>
+      <td>cat1, dada2_makeSequenceTable, dada2_filterAndTrim, __SORTLIST__, tp_replace_in_column, __UNZIP_COLLECTION__, tp_replace_in_line, dada2_assignTaxonomyAddspecies, dada2_mergePairs, phyloseq_from_dada2, dada2_plotQualityProfile, collection_element_identifiers, interactive_tool_phyloseq, dada2_learnErrors, dada2_removeBimeraDenovo, dada2_dada, Add_a_column1, dada2_seqCounts, Grouping1, tp_head_tool</td>
       <td>UseGalaxy.eu</td>
       <td></td>
       <td>0</td>
       <td></td>
-      <td>1089</td>
-      <td>1460</td>
+      <td>1162</td>
+      <td>1566</td>
       <td>1.833333</td>
       <td>0</td>
     </tr>
@@ -807,7 +807,7 @@
       <td>Assembly of metagenomic sequencing data</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html</td>
       <td>Metagenomics, Sequence assembly</td>
-      <td>Data handling, Visualisation, Sequence trimming, Read mapping, Sequencing quality control, Genome assembly, Sequence alignment analysis, Sequence contamination filtering, Sequence assembly validation, Variant calling, Statistical calculation, Sequence assembly visualisation, Sequence file editing, Local alignment, Sequence composition calculation, Read pre-processing, Primer removal, Formatting</td>
+      <td>Variant calling, Genome assembly, Sequence assembly visualisation, Sequence assembly validation, Visualisation, Sequence trimming, Local alignment, Sequence file editing, Data handling, Sequence alignment analysis, Primer removal, Formatting, Sequence composition calculation, Sequencing quality control, Read mapping, Read pre-processing, Sequence contamination filtering, Statistical calculation</td>
       <td>2022-12-05</td>
       <td>2024-06-14</td>
       <td>4</td>
@@ -815,14 +815,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>ngsutils_bam_filter, tp_cat, bamtools, bandage_image, filter_tabular, megahit_contig2fastg, bandage_info, bg_uniq, quast, seqtk_subseq, cutadapt, random_lines1, collection_column_join, megahit, coverm_contig, fastqc, metaspades, bowtie2</td>
+      <td>bandage_image, seqtk_subseq, megahit_contig2fastg, cutadapt, random_lines1, tp_cat, megahit, fastqc, bg_uniq, collection_column_join, bandage_info, metaspades, coverm_contig, bowtie2, filter_tabular, quast, bamtools, ngsutils_bam_filter</td>
       <td></td>
       <td>UseGalaxy.cz, UseGalaxy.eu</td>
       <td>0</td>
       <td></td>
-      <td>1613</td>
-      <td>2258</td>
-      <td>2.950000</td>
+      <td>1671</td>
+      <td>2337</td>
+      <td>2.983333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -844,9 +844,9 @@
       <td>UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr</td>
       <td>0</td>
       <td></td>
-      <td>131</td>
-      <td>195</td>
-      <td>3.383333</td>
+      <td>136</td>
+      <td>201</td>
+      <td>3.350000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -855,7 +855,7 @@
       <td>Binning of metagenomic sequencing data</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html</td>
       <td>Metagenomics, Sequence assembly</td>
-      <td>Sequence assembly validation, Statistical calculation, Sequencing quality control, Validation, Genome assembly, Sequence composition calculation</td>
+      <td>Sequence assembly validation, Genome assembly, Validation, Sequencing quality control, Statistical calculation, Sequence composition calculation</td>
       <td>2023-12-05</td>
       <td>2024-09-12</td>
       <td>4</td>
@@ -864,12 +864,12 @@
       <td>False</td>
       <td>False</td>
       <td>megahit, checkm_lineage_wf</td>
-      <td>GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr</td>
+      <td>GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu</td>
       <td>UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>2076</td>
-      <td>2537</td>
+      <td>2123</td>
+      <td>2591</td>
       <td>1.416667</td>
       <td>0</td>
     </tr>
@@ -892,8 +892,8 @@
       <td>UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr</td>
       <td>0</td>
       <td></td>
-      <td>153</td>
-      <td>281</td>
+      <td>154</td>
+      <td>283</td>
       <td>3.483333</td>
       <td>0</td>
     </tr>
@@ -903,7 +903,7 @@
       <td>16S Microbial Analysis with mothur (extended)</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html</td>
       <td>Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Phylogenetic tree analysis, DNA barcoding, Visualisation, Phylogenetic analysis, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Taxonomic classification, Sequence read processing, Sequence clustering</td>
+      <td>Sequence read processing, DNA barcoding, Phylogenetic tree analysis, Phylogenetic tree generation, Taxonomic classification, Sequencing quality control, Visualisation, Phylogenetic tree reconstruction, Phylogenetic analysis, Sequence clustering</td>
       <td>2017-02-12</td>
       <td>2024-03-14</td>
       <td>4</td>
@@ -911,14 +911,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>mothur_dist_shared, mothur_seq_error, mothur_summary_seqs, mothur_remove_lineage, mothur_make_biom, mothur_count_seqs, mothur_get_groups, mothur_classify_seqs, mothur_remove_groups, mothur_make_shared, mothur_filter_seqs, mothur_dist_seqs, mothur_remove_seqs, mothur_rarefaction_single, mothur_venn, mothur_classify_otu, mothur_count_groups, mothur_align_seqs, mothur_taxonomy_to_krona, mothur_heatmap_sim, mothur_chimera_vsearch, mothur_cluster_split, mothur_screen_seqs, newick_display, mothur_pre_cluster, mothur_make_contigs, mothur_unique_seqs, XY_Plot_1, taxonomy_krona_chart, mothur_cluster, mothur_tree_shared, mothur_summary_single, mothur_sub_sample</td>
+      <td>mothur_make_contigs, mothur_chimera_vsearch, mothur_count_seqs, mothur_screen_seqs, mothur_cluster, mothur_classify_otu, mothur_summary_seqs, mothur_unique_seqs, mothur_dist_shared, mothur_make_biom, mothur_classify_seqs, mothur_dist_seqs, mothur_pre_cluster, XY_Plot_1, mothur_remove_seqs, mothur_remove_groups, mothur_sub_sample, newick_display, mothur_venn, mothur_rarefaction_single, mothur_tree_shared, mothur_summary_single, mothur_remove_lineage, mothur_filter_seqs, mothur_seq_error, mothur_get_groups, mothur_heatmap_sim, mothur_align_seqs, mothur_count_groups, mothur_taxonomy_to_krona, mothur_make_shared, mothur_cluster_split, taxonomy_krona_chart</td>
       <td>UseGalaxy.be, UseGalaxy.eu</td>
-      <td>UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
+      <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>5448</td>
-      <td>8271</td>
-      <td>2.983333</td>
+      <td>5547</td>
+      <td>8409</td>
+      <td>2.966667</td>
       <td>0</td>
     </tr>
     <tr>
@@ -927,7 +927,7 @@
       <td>16S Microbial Analysis with mothur (short)</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html</td>
       <td>Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Phylogenetic tree analysis, DNA barcoding, Visualisation, Phylogenetic analysis, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Taxonomic classification, Sequence read processing, Sequence clustering</td>
+      <td>Sequence read processing, DNA barcoding, Phylogenetic tree analysis, Phylogenetic tree generation, Taxonomic classification, Sequencing quality control, Visualisation, Phylogenetic tree reconstruction, Phylogenetic analysis, Sequence clustering</td>
       <td>2019-05-13</td>
       <td>2024-06-14</td>
       <td>5</td>
@@ -935,13 +935,13 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>mothur_dist_shared, mothur_summary_seqs, mothur_remove_lineage, mothur_count_seqs, mothur_classify_seqs, mothur_remove_groups, mothur_make_shared, mothur_filter_seqs, mothur_dist_seqs, mothur_remove_seqs, mothur_rarefaction_single, mothur_venn, mothur_classify_otu, mothur_count_groups, mothur_heatmap_sim, mothur_chimera_vsearch, mothur_cluster_split, mothur_screen_seqs, collapse_dataset, newick_display, mothur_pre_cluster, mothur_unique_seqs, XY_Plot_1, mothur_cluster, mothur_tree_shared, mothur_summary_single, mothur_sub_sample</td>
+      <td>mothur_chimera_vsearch, mothur_count_seqs, mothur_screen_seqs, mothur_cluster, mothur_classify_otu, mothur_summary_seqs, mothur_unique_seqs, mothur_dist_shared, collapse_dataset, mothur_classify_seqs, mothur_dist_seqs, mothur_pre_cluster, XY_Plot_1, mothur_remove_seqs, mothur_remove_groups, mothur_sub_sample, newick_display, mothur_venn, mothur_rarefaction_single, mothur_tree_shared, mothur_summary_single, mothur_remove_lineage, mothur_filter_seqs, mothur_heatmap_sim, mothur_count_groups, mothur_make_shared, mothur_cluster_split</td>
       <td>UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
-      <td>UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr</td>
+      <td>UseGalaxy.be, UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>1985</td>
-      <td>3572</td>
+      <td>2011</td>
+      <td>3607</td>
       <td>5.616667</td>
       <td>0</td>
     </tr>
@@ -959,14 +959,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>upload1, interactive_tool_rstudio, raxml</td>
+      <td>interactive_tool_rstudio, upload1, raxml</td>
       <td>UseGalaxy.eu</td>
-      <td>UseGalaxy.fr, UseGalaxy.org (Main)</td>
+      <td>UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>1374</td>
-      <td>2072</td>
-      <td>2.216667</td>
+      <td>1379</td>
+      <td>2079</td>
+      <td>2.250000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -975,7 +975,7 @@
       <td>Identifying tuberculosis transmission links: from SNPs to transmission clusters</td>
       <td>https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html</td>
       <td>Genomics, Microbiology, Infectious disease, DNA polymorphism</td>
-      <td>Phylogenetic tree visualisation, Variant calling, Antimicrobial resistance prediction, Phylogenetic tree generation</td>
+      <td>Variant calling, Antimicrobial resistance prediction, Phylogenetic tree visualisation, Phylogenetic tree generation</td>
       <td>2022-03-16</td>
       <td>2024-07-12</td>
       <td>12</td>
@@ -983,14 +983,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>tp_sed_tool, tp_easyjoin_tool, tp_cat, bcftools_consensus, samtools_view, upload1, snippy, tp_grep_tool, tp_replace_in_line, snp_dists, Grep1, tb_variant_filter, tb_profiler_profile, collapse_dataset, snp_sites, trimmomatic, __MERGE_COLLECTION__, addName</td>
+      <td>samtools_view, tp_replace_in_line, tp_sed_tool, bcftools_consensus, snippy, snp_sites, collapse_dataset, trimmomatic, tp_cat, tp_easyjoin_tool, tp_grep_tool, Grep1, tb_variant_filter, addName, tb_profiler_profile, upload1, __MERGE_COLLECTION__, snp_dists</td>
       <td>UseGalaxy.eu</td>
       <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>1605</td>
-      <td>2499</td>
-      <td>3.050000</td>
+      <td>1610</td>
+      <td>2504</td>
+      <td>3.033333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -999,7 +999,7 @@
       <td>Identification of AMR genes in an assembled bacterial genome</td>
       <td>https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html</td>
       <td>Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance</td>
-      <td>Genome visualisation, Genome annotation, Read mapping</td>
+      <td>Genome visualisation, Read mapping, Genome annotation</td>
       <td>2024-01-23</td>
       <td>2024-09-27</td>
       <td>6</td>
@@ -1007,14 +1007,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>jbrowse, tbl2gff3, upload1, Grep1, staramr_search, bakta, bowtie2</td>
-      <td>UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr</td>
+      <td>jbrowse, Grep1, tbl2gff3, bakta, upload1, bowtie2, staramr_search</td>
+      <td>UseGalaxy.cz, UseGalaxy.eu</td>
       <td>Galaxy@AuBi, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>1138</td>
-      <td>1576</td>
-      <td>2.750000</td>
+      <td>1183</td>
+      <td>1635</td>
+      <td>2.950000</td>
       <td>0</td>
     </tr>
     <tr>
@@ -1023,7 +1023,7 @@
       <td>M. tuberculosis Variant Analysis</td>
       <td>https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html</td>
       <td>Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease</td>
-      <td>Sequence alignment, Phylogenetic tree generation, Phylogenetic tree visualisation, Sequencing quality control, Sequence alignment analysis, Genome visualisation, Sequence analysis, Sequence contamination filtering, Variant calling, Global alignment, Statistical calculation, Taxonomic classification, Validation, Local alignment, Sequence composition calculation, Antimicrobial resistance prediction</td>
+      <td>Variant calling, Sequence alignment analysis, Antimicrobial resistance prediction, Sequence analysis, Phylogenetic tree generation, Genome visualisation, Sequence composition calculation, Taxonomic classification, Statistical calculation, Validation, Sequencing quality control, Global alignment, Sequence alignment, Sequence contamination filtering, Phylogenetic tree visualisation, Local alignment</td>
       <td>2020-07-25</td>
       <td>2024-07-26</td>
       <td>30</td>
@@ -1031,14 +1031,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>tp_sed_tool, upload1, snippy, qualimap_bamqc, tb_variant_filter, EMBOSS: seqret84, tb_profiler_profile, mosdepth, jvarkit_wgscoverageplotter, tbvcfreport, tp_awk_tool, fastqc, jbrowse, samtools_stats, bcftools_consensus, multiqc, fastp, kraken2, EMBOSS:%20seqret84, __FLATTEN__</td>
+      <td>mosdepth, tp_sed_tool, qualimap_bamqc, jbrowse, snippy, jvarkit_wgscoverageplotter, samtools_stats, fastp, upload1, EMBOSS:%20seqret84, tp_awk_tool, tb_variant_filter, tb_profiler_profile, multiqc, kraken2, tbvcfreport, EMBOSS: seqret84, bcftools_consensus, __FLATTEN__, fastqc</td>
       <td></td>
       <td></td>
       <td>0</td>
       <td></td>
-      <td>5788</td>
-      <td>9172</td>
-      <td>2.950000</td>
+      <td>5800</td>
+      <td>9186</td>
+      <td>2.933333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -1047,7 +1047,7 @@
       <td>16S Microbial analysis with Nanopore data</td>
       <td>https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html</td>
       <td>Microbial ecology, Taxonomy, Sequence analysis</td>
-      <td>Taxonomic classification, Statistical calculation, Visualisation, Validation, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering</td>
+      <td>Sequence contamination filtering, Validation, Sequencing quality control, Visualisation, Sequence composition calculation, Statistical calculation, Taxonomic classification</td>
       <td>2020-11-24</td>
       <td>2024-07-31</td>
       <td>5</td>
@@ -1055,14 +1055,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>porechop, fastp, tp_replace_in_line, taxonomy_krona_chart, multiqc, kraken2, datamash_reverse, fastqc, Remove beginning1</td>
+      <td>tp_replace_in_line, datamash_reverse, multiqc, fastqc, Remove beginning1, fastp, porechop, kraken2, taxonomy_krona_chart</td>
       <td>UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
       <td>GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>2758</td>
-      <td>3844</td>
-      <td>2.716667</td>
+      <td>2802</td>
+      <td>3894</td>
+      <td>2.733333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -1079,13 +1079,13 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>query_tabular, peptide_shaker, search_gui, unipept, sqlite_to_tabular</td>
+      <td>sqlite_to_tabular, query_tabular, search_gui, peptide_shaker, unipept</td>
       <td>UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au</td>
       <td>UseGalaxy.be, UseGalaxy.cz</td>
       <td>0</td>
       <td></td>
-      <td>2310</td>
-      <td>3828</td>
+      <td>2320</td>
+      <td>3839</td>
       <td>2.633333</td>
       <td>0</td>
     </tr>
@@ -1095,7 +1095,7 @@
       <td>metaQuantome 3: Taxonomy</td>
       <td>https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html</td>
       <td>Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy</td>
-      <td>Visualisation, Indexing, Differential protein expression analysis, Functional clustering, Statistical inference, Principal component visualisation, Query and retrieval, Heat map generation, Quantification, Filtering</td>
+      <td>Differential protein expression analysis, Filtering, Heat map generation, Indexing, Query and retrieval, Visualisation, Principal component visualisation, Quantification, Functional clustering, Statistical inference</td>
       <td>2020-10-29</td>
       <td>2024-03-15</td>
       <td>14</td>
@@ -1103,13 +1103,13 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_viz, metaquantome_db</td>
+      <td>metaquantome_db, metaquantome_stat, metaquantome_sample, metaquantome_viz, metaquantome_expand, metaquantome_filter</td>
       <td>UseGalaxy.be, UseGalaxy.eu</td>
       <td>UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>377</td>
-      <td>509</td>
+      <td>378</td>
+      <td>510</td>
       <td>2.733333</td>
       <td>0</td>
     </tr>
@@ -1119,7 +1119,7 @@
       <td>metaQuantome 2: Function</td>
       <td>https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html</td>
       <td>Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics</td>
-      <td>Visualisation, Indexing, Differential protein expression analysis, Functional clustering, Statistical inference, Principal component visualisation, Query and retrieval, Heat map generation, Quantification, Filtering</td>
+      <td>Differential protein expression analysis, Filtering, Heat map generation, Indexing, Query and retrieval, Visualisation, Principal component visualisation, Quantification, Functional clustering, Statistical inference</td>
       <td>2020-10-29</td>
       <td>2024-03-15</td>
       <td>14</td>
@@ -1127,13 +1127,13 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_viz, metaquantome_db</td>
+      <td>metaquantome_db, metaquantome_stat, metaquantome_sample, metaquantome_viz, metaquantome_expand, metaquantome_filter</td>
       <td>UseGalaxy.eu</td>
       <td>UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>352</td>
-      <td>508</td>
+      <td>353</td>
+      <td>509</td>
       <td>3.766667</td>
       <td>0</td>
     </tr>
@@ -1143,7 +1143,7 @@
       <td>metaQuantome 1: Data creation</td>
       <td>https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html</td>
       <td>Proteomics, Proteogenomics, Biodiversity, Taxonomy</td>
-      <td>Prediction and recognition, Visualisation, Filtering, Label-free quantification, Formatting</td>
+      <td>Prediction and recognition, Visualisation, Filtering, Formatting, Label-free quantification</td>
       <td>2020-10-16</td>
       <td>2024-03-14</td>
       <td>20</td>
@@ -1151,14 +1151,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>query_tabular, flashlfq, Filter1, peptide_shaker, regex1, tp_replace_in_line, msconvert, search_gui, unipept, Grep1, Cut1, Remove beginning1, tp_replace_in_column</td>
+      <td>Cut1, tp_replace_in_line, flashlfq, regex1, query_tabular, search_gui, peptide_shaker, Grep1, Remove beginning1, msconvert, tp_replace_in_column, unipept, Filter1</td>
       <td>UseGalaxy.eu</td>
       <td>UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>781</td>
-      <td>1353</td>
-      <td>3.816667</td>
+      <td>782</td>
+      <td>1355</td>
+      <td>3.833333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -1167,7 +1167,7 @@
       <td>Quality and contamination control in bacterial isolate using Illumina MiSeq Data</td>
       <td>https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html</td>
       <td>Whole genome sequencing, Genomics, Microbiology, Microbial ecology</td>
-      <td>Cross-assembly, Sequencing quality control, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Expression analysis, Sequence composition calculation</td>
+      <td>Expression analysis, Sequence contamination filtering, Sequencing quality control, Cross-assembly, Sequence composition calculation, Statistical calculation, Taxonomic classification</td>
       <td>2024-07-15</td>
       <td>2024-09-02</td>
       <td>2</td>
@@ -1175,14 +1175,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>fastp, est_abundance, recentrifuge, upload1, kraken2, fastqc</td>
-      <td>UseGalaxy.eu, UseGalaxy.fr</td>
+      <td>fastqc, upload1, recentrifuge, est_abundance, fastp, kraken2</td>
+      <td>UseGalaxy.eu</td>
       <td>Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)</td>
       <td>0</td>
       <td></td>
-      <td>185</td>
-      <td>225</td>
-      <td>2.516667</td>
+      <td>229</td>
+      <td>296</td>
+      <td>2.716667</td>
       <td>0</td>
     </tr>
     <tr>
@@ -1191,7 +1191,7 @@
       <td>Calling variants in non-diploid systems</td>
       <td>https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html</td>
       <td>Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation</td>
-      <td>Data handling, Sequence alignment, Read mapping, Sequencing quality control, Sequence alignment analysis, Generation, Statistical calculation, Variant calling, Sequence composition calculation, Formatting, Genome indexing</td>
+      <td>Variant calling, Data handling, Sequence alignment analysis, Genome indexing, Formatting, Sequence composition calculation, Generation, Sequencing quality control, Read mapping, Sequence alignment, Statistical calculation</td>
       <td>2017-02-16</td>
       <td>2024-03-15</td>
       <td>23</td>
@@ -1199,13 +1199,13 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>bwa_mem, picard_MarkDuplicates, vcffilter2, bamFilter, picard_MergeSamFiles, Cut1, bamleftalign, fastqc, vcf2tsv, freebayes</td>
-      <td>UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main)</td>
+      <td>Cut1, bamFilter, fastqc, freebayes, picard_MergeSamFiles, vcf2tsv, bwa_mem, vcffilter2, picard_MarkDuplicates, bamleftalign</td>
+      <td>UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main)</td>
       <td>UseGalaxy.cz, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>7149</td>
-      <td>13577</td>
+      <td>7181</td>
+      <td>13614</td>
       <td>2.050000</td>
       <td>0</td>
     </tr>
@@ -1215,7 +1215,7 @@
       <td>M. tuberculosis Variant Analysis</td>
       <td>https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html</td>
       <td>Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease</td>
-      <td>Sequence alignment, Phylogenetic tree generation, Phylogenetic tree visualisation, Sequencing quality control, Sequence alignment analysis, Genome visualisation, Sequence analysis, Sequence contamination filtering, Variant calling, Global alignment, Statistical calculation, Taxonomic classification, Validation, Local alignment, Sequence composition calculation, Antimicrobial resistance prediction</td>
+      <td>Variant calling, Sequence alignment analysis, Antimicrobial resistance prediction, Sequence analysis, Phylogenetic tree generation, Genome visualisation, Sequence composition calculation, Taxonomic classification, Statistical calculation, Validation, Sequencing quality control, Global alignment, Sequence alignment, Sequence contamination filtering, Phylogenetic tree visualisation, Local alignment</td>
       <td>2020-07-25</td>
       <td>2024-07-26</td>
       <td>30</td>
@@ -1223,14 +1223,14 @@
       <td>False</td>
       <td>False</td>
       <td>True</td>
-      <td>tp_sed_tool, upload1, snippy, qualimap_bamqc, tb_variant_filter, EMBOSS: seqret84, tb_profiler_profile, mosdepth, jvarkit_wgscoverageplotter, tbvcfreport, tp_awk_tool, fastqc, jbrowse, samtools_stats, bcftools_consensus, multiqc, fastp, kraken2, EMBOSS:%20seqret84, __FLATTEN__</td>
+      <td>mosdepth, tp_sed_tool, qualimap_bamqc, jbrowse, snippy, jvarkit_wgscoverageplotter, samtools_stats, fastp, upload1, EMBOSS:%20seqret84, tp_awk_tool, tb_variant_filter, tb_profiler_profile, multiqc, kraken2, tbvcfreport, EMBOSS: seqret84, bcftools_consensus, __FLATTEN__, fastqc</td>
       <td></td>
       <td></td>
       <td>0</td>
       <td></td>
-      <td>5788</td>
-      <td>9172</td>
-      <td>2.950000</td>
+      <td>5800</td>
+      <td>9186</td>
+      <td>2.933333</td>
       <td>0</td>
     </tr>
     <tr>
@@ -1239,7 +1239,7 @@
       <td>Microbial Variant Calling</td>
       <td>https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html</td>
       <td>Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation</td>
-      <td>Genome visualisation, Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation</td>
+      <td>Variant calling, Phylogenetic tree visualisation, Genome visualisation, Phylogenetic tree generation</td>
       <td>2018-02-26</td>
       <td>2024-03-15</td>
       <td>23</td>
@@ -1249,11 +1249,11 @@
       <td>True</td>
       <td>jbrowse, snippy</td>
       <td>UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)</td>
-      <td>GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au</td>
+      <td>GalaxyTrakr, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au</td>
       <td>0</td>
       <td></td>
-      <td>12476</td>
-      <td>20693</td>
+      <td>12499</td>
+      <td>20722</td>
       <td>1.983333</td>
       <td>0</td>
     </tr>
diff --git a/communities/microgalaxy/resources/tutorials.tsv b/communities/microgalaxy/resources/tutorials.tsv
index ef7358df..d8a37750 100644
--- a/communities/microgalaxy/resources/tutorials.tsv
+++ b/communities/microgalaxy/resources/tutorials.tsv
@@ -1,50 +1,50 @@
 Topic	Title	Link	EDAM topic	EDAM operation	Creation	Last modification	Version	Tutorial	Slides	Video	Workflows	Tools	Servers with precise tool versions	Servers with tool but different versions	Feedback number	Feedback mean note	Visitors	Page views	Visit duration	Video views
-Assembly	Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology	Sequence assembly validation, Statistical calculation, Sequence assembly visualisation, Visualisation, Genome assembly, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering	2021-03-24	2024-09-18	15	True	False	False	True	fastp, bandage_image, upload1, bandage_info, quast, fastqc, shovill	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.no	0		6735	10837	3.783333333333333	0
-Assembly	Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance	Scatter plot plotting, Sequencing error detection, Sequence alignment, Visualisation, Cross-assembly, Read mapping, Sequencing quality control, Genome assembly, De-novo assembly, Box-Whisker plot plotting, Sequence contamination filtering, Sequence assembly validation, Mapping assembly, Statistical calculation, Sequence assembly visualisation, Filtering, Sequence composition calculation	2021-03-24	2024-03-13	14	True	False	False	True	CONVERTER_bz2_to_uncompressed, fastp, filtlong, bandage_image, porechop, upload1, quast, flye, nanoplot, bwa_mem2, polypolish, fastqc	UseGalaxy.eu	UseGalaxy.cz	0		7147	10976	3.4	0
-Assembly	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Data handling, Visualisation, Sequence trimming, Read mapping, Sequencing quality control, Genome assembly, Sequence alignment analysis, Sequence contamination filtering, Sequence assembly validation, Variant calling, Statistical calculation, Sequence assembly visualisation, Sequence file editing, Local alignment, Sequence composition calculation, Read pre-processing, Primer removal, Formatting	2024-10-02	2024-10-02	0	True	False	False	True	ngsutils_bam_filter, tp_cat, bamtools, bandage_image, filter_tabular, megahit_contig2fastg, bandage_info, bg_uniq, quast, seqtk_subseq, cutadapt, random_lines1, collection_column_join, megahit, coverm_contig, fastqc, metaspades, bowtie2		UseGalaxy.cz, UseGalaxy.eu	0		6	7	0.38333333333333336	0
-Assembly	Unicycler Assembly	https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html	Sequence assembly, Genomics, Microbiology	Genome annotation, Visualisation, Genome assembly, Sequencing quality control, Sequence assembly validation, Gene prediction, Statistical calculation, Aggregation, Validation, Sequence composition calculation, Coding region prediction	2017-10-11	2024-03-13	23	True	True	False	True	prokka, unicycler, quast, multiqc, fastqc	UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, HyPhy HIV NGS Tools, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no	0		2144791	5917098	4.566666666666666	0
-Assembly	Making sense of a newly assembled genome	https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html	Sequence assembly, Genomics, Microbiology	Sequence alignment, Sequence visualisation, Read mapping, Genome visualisation, Mapping	2018-06-14	2024-06-24	29	True	False	False	True	join1, tp_sed_tool, lastz_wrapper_2, upload1, fasta_filter_by_length, bedtools_intersectbed, datamash_ops, circos_interval_to_tiles, jbrowse, tp_cat, mergeCols1, Filter1, bedtools_sortbed, tp_sort_header_tool, Grep1, Cut1, collapse_dataset, cat1, tp_replace_in_column, addValue, circos_aln_to_links, fasta_compute_length, circos, tp_grep_tool, tp_replace_in_line, random_lines1, bedtools_complementbed			0		6026	12166	3.0166666666666666	0
-Ecology	Checking expected species and contamination in bacterial isolate	https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html	Whole genome sequencing, Genomics, Microbiology, Microbial ecology	Statistical calculation, Taxonomic classification, Cross-assembly, Expression analysis	2024-03-04	2024-06-27	4	True	False	False	True	recentrifuge, kraken2, upload1, est_abundance	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)	0		260	343	3.533333333333333	0
-Evolution	Tree thinking for tuberculosis evolution and epidemiology	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html	Genomics, Microbiology, Phylogeny, Infectious disease	Phylogenetic tree analysis, Sequence analysis	2022-03-16	2024-03-12	11	True	False	False	True	upload1, interactive_tool_rstudio, raxml	UseGalaxy.eu	UseGalaxy.fr, UseGalaxy.org (Main)	0		1373	2071	2.2333333333333334	0
-Evolution	Identifying tuberculosis transmission links: from SNPs to transmission clusters	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html	Genomics, Microbiology, Infectious disease, DNA polymorphism	Phylogenetic tree visualisation, Variant calling, Antimicrobial resistance prediction, Phylogenetic tree generation	2022-03-16	2024-07-12	12	True	False	False	True	tp_sed_tool, tp_easyjoin_tool, tp_cat, bcftools_consensus, samtools_view, upload1, snippy, tp_grep_tool, tp_replace_in_line, snp_dists, Grep1, tb_variant_filter, tb_profiler_profile, collapse_dataset, snp_sites, trimmomatic, __MERGE_COLLECTION__, addName	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)	0		1605	2499	3.05	0
-Genome Annotation	Genome annotation with Prokka	https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation, Gene prediction, Genome annotation, Coding region prediction	2018-03-06	2024-08-08	25	True	True	True	True	jbrowse, prokka	UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		2149523	5925124	4.316666666666666	0
-Genome Annotation	Identification of AMR genes in an assembled bacterial genome	https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html	Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance	Genome visualisation, Genome annotation, Read mapping	2024-01-23	2024-09-27	6	True	False	False	True	jbrowse, tbl2gff3, upload1, Grep1, staramr_search, bakta, bowtie2	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.org (Main)	0		1138	1576	2.75	0
-Genome Annotation	Refining Genome Annotations with Apollo (prokaryotes)	https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation	2021-06-04	2024-08-08	20	True	True	True	True	jbrowse, create_or_update, iframe, list_organism, create_account		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no	0		1906178	5119567	4.983333333333333	0
-Genome Annotation	Bacterial Genome Annotation	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements	Genome annotation, Nucleic acid feature detection, Multilocus sequence typing, Genome visualisation, Genome assembly, Sequence motif recognition, Structural variation detection, Scaffolding, Protein feature detection	2024-02-01	2024-09-08	5	True	False	False	True	jbrowse, tbl2gff3, plasmidfinder, integron_finder, upload1, isescan, tp_tail_tool, bakta, tp_replace_in_column, Grouping1	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)	0		2243	2969	2.3333333333333335	0
-Genome Annotation	Comparative gene analysis in unannotated genomes	https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html	Genomics, Gene and protein families, Sequence analysis, Phylogeny	Database search, Transcriptome assembly, Phylogenetic tree generation, De-novo assembly, Sequence alignment analysis, Multiple sequence alignment, Coding region prediction	2022-09-08	2024-03-18	8	True	False	False	True	orfipy, rapidnj, join1, bg_diamond_makedb, Filter1, tp_split_on_column, tab2fasta, collapse_dataset, rbc_mafft, bg_diamond_view, Cut1, Add_a_column1, bg_diamond, regexColumn1, gops_intersect_1, cat1	UseGalaxy.eu, UseGalaxy.org (Main)	UseGalaxy.cz	0		1045	1602	3.5833333333333335	0
-Genome Annotation	Essential genes detection with Transposon insertion sequencing	https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html	Genomics, Microbiology, Sequence analysis, Mobile genetic elements	Sequence trimming, Transposon prediction, Read pre-processing, Primer removal	2019-07-02	2024-03-18	12	True	True	False	True	__EXTRACT_DATASET__, bowtie_wrapper, gff_to_prot, tp_easyjoin_tool, Filter1, transit_gumbel, bg_find_subsequences, tp_sort_header_tool, cutadapt, Cut1, Add_a_column1, deeptools_bam_coverage	UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.eu	0		2140389	5910080	4.266666666666667	0
-Genome Annotation	Genome annotation with Prokka	https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation, Gene prediction, Genome annotation, Coding region prediction	2018-03-06	2024-08-08	25	True	True	True	True	jbrowse, prokka	UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		2149523	5925127	4.316666666666666	0
-Genome Annotation	Identification of AMR genes in an assembled bacterial genome	https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html	Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance	Genome visualisation, Genome annotation, Read mapping	2024-01-23	2024-09-27	6	True	False	False	True	jbrowse, tbl2gff3, upload1, Grep1, staramr_search, bakta, bowtie2	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.org (Main)	0		1138	1576	2.75	0
-Genome Annotation	Refining Genome Annotations with Apollo (prokaryotes)	https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation	2021-06-04	2024-08-08	20	True	True	True	True	jbrowse, create_or_update, iframe, list_organism, create_account		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no	0		1906178	5119570	4.983333333333333	0
-Genome Annotation	Bacterial Genome Annotation	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements	Genome annotation, Nucleic acid feature detection, Multilocus sequence typing, Genome visualisation, Genome assembly, Sequence motif recognition, Structural variation detection, Scaffolding, Protein feature detection	2024-02-01	2024-09-08	5	True	False	False	True	jbrowse, tbl2gff3, plasmidfinder, integron_finder, upload1, isescan, tp_tail_tool, bakta, tp_replace_in_column, Grouping1	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)	0		2243	2969	2.3333333333333335	0
-Variant Analysis	Microbial Variant Calling	https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Genome visualisation, Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation	2018-02-26	2024-03-15	23	True	False	False	True	jbrowse, snippy	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		12475	20692	1.9833333333333334	0
-Assembly	Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance	Scatter plot plotting, Sequencing error detection, Sequence alignment, Visualisation, Cross-assembly, Read mapping, Sequencing quality control, Genome assembly, De-novo assembly, Box-Whisker plot plotting, Sequence contamination filtering, Sequence assembly validation, Mapping assembly, Statistical calculation, Sequence assembly visualisation, Filtering, Sequence composition calculation	2021-03-24	2024-03-13	14	True	False	False	True	CONVERTER_bz2_to_uncompressed, fastp, filtlong, bandage_image, porechop, upload1, quast, flye, nanoplot, bwa_mem2, polypolish, fastqc	UseGalaxy.eu	UseGalaxy.cz	0		7148	10977	3.4	0
-Assembly	Making sense of a newly assembled genome	https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html	Sequence assembly, Genomics, Microbiology	Sequence alignment, Sequence visualisation, Read mapping, Genome visualisation, Mapping	2018-06-14	2024-06-24	29	True	False	False	True	join1, tp_sed_tool, lastz_wrapper_2, upload1, fasta_filter_by_length, bedtools_intersectbed, datamash_ops, circos_interval_to_tiles, jbrowse, tp_cat, mergeCols1, Filter1, bedtools_sortbed, tp_sort_header_tool, Grep1, Cut1, collapse_dataset, cat1, tp_replace_in_column, addValue, circos_aln_to_links, fasta_compute_length, circos, tp_grep_tool, tp_replace_in_line, random_lines1, bedtools_complementbed			0		6026	12166	3.0166666666666666	0
-Microbiome	Analyses of metagenomics data - The global picture	https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	DNA barcoding, Visualisation, Phylogenetic analysis, Sequencing quality control, Taxonomic classification, Sequence read processing, Sequence clustering	2017-06-22	2024-08-09	4	True	False	False	True	humann2_regroup_table, mothur_summary_seqs, humann2_renorm_table, mothur_make_biom, mothur_count_seqs, mothur_classify_seqs, mothur_make_group, mothur_make_shared, mothur_filter_seqs, mothur_merge_files, mothur_classify_otu, mothur_align_seqs, humann2, mothur_cluster_split, mothur_screen_seqs, metaphlan2, mothur_pre_cluster, mothur_unique_seqs, taxonomy_krona_chart, krona-text, metaphlan2krona	UseGalaxy.be	UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		3586	4852	2.783333333333333	0
-Microbiome	Identification of the micro-organisms in a beer using Nanopore sequencing	https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	Taxonomic classification, Statistical calculation, Aggregation, Visualisation, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering	2022-09-29	2024-06-14	4	True	False	False	True	porechop, fastp, Filter1, taxonomy_krona_chart, kraken2, krakentools_kreport2krona, fastqc	GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz	0		1239	1942	2.966666666666667	0
-Microbiome	Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition	https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html	Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis	Scatter plot plotting, Visualisation, Cross-assembly, Phylogenetic tree generation, Genome assembly, Sequencing quality control, Box-Whisker plot plotting, Multiple sequence alignment, Mapping assembly, Base-calling, Aggregation, Statistical calculation, Pairwise sequence alignment, Validation, Taxonomic classification, Sequence composition calculation, Mapping, Antimicrobial resistance prediction, Phylogenetic tree analysis, Data handling, Multilocus sequence typing, De-novo assembly, Sequence alignment analysis, Phylogenetic tree reconstruction, Sequence contamination filtering, Sequence assembly, Variant calling, Sequence assembly visualisation, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	2023-01-26	2024-09-27	11	True	False	False	True	__FILTER_FAILED_DATASETS__, Count1, minimap2, snpSift_filter, compose_text_param, tab2fasta, tp_find_and_replace, tp_head_tool, tp_multijoin_tool, param_value_from_file, collection_column_join, collection_element_identifiers, bcftools_norm, krakentools_kreport2krona, krakentools_extract_kraken_reads, ggplot2_heatmap, bamtools_split_mapped, fasta_merge_files_and_filter_unique_sequences, barchart_gnuplot, samtools_fastx, flye, medaka_consensus_pipeline, tp_cut_tool, fastqc, snpSift_extractFields, regex1, Grouping1, tp_sorted_uniq, porechop, table_compute, bcftools_consensus, split_file_to_collection, bandage_image, abricate, Paste1, add_line_to_file, tp_split_on_column, multiqc, Grep1, Cut1, collapse_dataset, Remove beginning1, clustalw, bedtools_getfastabed, tp_replace_in_column, fasttree, newick_display, fastp, samtools_coverage, samtools_depth, clair3, taxonomy_krona_chart, __FILTER_EMPTY_DATASETS__, kraken2, __BUILD_LIST__, Add_a_column1, mlst, nanoplot, regexColumn1, CONVERTER_gz_to_uncompressed, fasta2tab	UseGalaxy.eu	UseGalaxy.org.au	0		1964	2918	3.0	0
-Microbiome	Metatranscriptomics analysis using microbiome RNA-seq data	https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html	Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis	Visualisation, Sequencing quality control, Phylogenetic inference, Phylogenetic tree editing, Statistical calculation, Taxonomic classification, Validation, Sequence composition calculation, Sequence comparison, Sequence similarity search, Phylogenetic tree analysis, Sequence trimming, Phylogenetic analysis, Phylogenetic tree visualisation, Sequence alignment analysis, Species frequency estimation, Conversion, Nucleic acid sequence analysis, Read pre-processing, Primer removal	2019-11-21	2024-06-14	4	True	True	False	True	fastq_paired_end_interlacer, tp_find_and_replace, metaphlan, fastqc, humann, graphlan_annotate, graphlan, humann_split_stratified_table, humann_renorm_table, humann_regroup_table, humann_rename_table, cutadapt, combine_metaphlan2_humann2, multiqc, bg_sortmerna, Grep1, Cut1, export2graphlan, humann_unpack_pathways, taxonomy_krona_chart	UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.no	0		2136358	5901051	4.266666666666667	0
-Microbiome	Taxonomic Profiling and Visualization of Metagenomic Data	https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	Phylogenetic tree analysis, Statistical calculation, Taxonomic classification, Aggregation, Visualisation, Nucleic acid sequence analysis	2023-05-03	2024-06-14	4	True	False	False	True	interactive_tool_phinch, est_abundance, taxonomy_krona_chart, interactive_tool_pavian, kraken2, kraken_biom, __UNZIP_COLLECTION__, krakentools_kreport2krona, metaphlan	UseGalaxy.eu	UseGalaxy.fr, UseGalaxy.org.au	0		4443	6096	1.9666666666666666	0
-Microbiome	Metatranscriptomics analysis using microbiome RNA-seq data (short)	https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html	Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis	Visualisation, Sequencing quality control, Phylogenetic inference, Phylogenetic tree editing, Statistical calculation, Taxonomic classification, Validation, Sequence composition calculation, Sequence comparison, Sequence similarity search, Phylogenetic tree analysis, Sequence trimming, Phylogenetic analysis, Phylogenetic tree visualisation, Sequence alignment analysis, Species frequency estimation, Conversion, Nucleic acid sequence analysis, Read pre-processing, Primer removal	2020-02-13	2024-06-14	4	True	False	False	True	fastq_paired_end_interlacer, tp_find_and_replace, metaphlan, fastqc, humann, graphlan_annotate, graphlan, humann_split_stratified_table, humann_renorm_table, humann_regroup_table, humann_rename_table, cutadapt, combine_metaphlan2_humann2, multiqc, bg_sortmerna, Grep1, Cut1, export2graphlan, humann_unpack_pathways, taxonomy_krona_chart	UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.no	0		274	351	1.4333333333333333	0
-Microbiome	Antibiotic resistance detection	https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html	Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial Resistance	Scatter plot plotting, Genome assembly, Box-Whisker plot plotting, De-novo assembly, Sequence analysis, Mapping assembly, Aggregation, Sequence assembly visualisation, Pairwise sequence alignment	2019-06-25	2024-06-14	4	True	False	False	True	unicycler, minimap2, bandage_image, PlasFlow, racon, nanoplot, gfa_to_fa, staramr_search, miniasm	UseGalaxy.eu	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	0		1281	1950	4.033333333333333	0
-Microbiome	16S Microbial analysis with Nanopore data	https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Taxonomic classification, Statistical calculation, Visualisation, Validation, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering	2020-11-24	2024-07-31	5	True	False	False	True	porechop, fastp, tp_replace_in_line, taxonomy_krona_chart, multiqc, kraken2, datamash_reverse, fastqc, Remove beginning1	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz	0		2758	3844	2.716666666666667	0
-Microbiome	Building an amplicon sequence variant (ASV) table from 16S data using DADA2	https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Variant calling, DNA barcoding, Visualisation, Analysis, Deposition	2024-06-05	2024-09-26	8	True	False	False	True	tp_head_tool, collection_element_identifiers, __UNZIP_COLLECTION__, interactive_tool_phyloseq, dada2_mergePairs, dada2_removeBimeraDenovo, dada2_assignTaxonomyAddspecies, Grouping1, dada2_plotQualityProfile, dada2_filterAndTrim, cat1, tp_replace_in_column, dada2_seqCounts, dada2_makeSequenceTable, tp_replace_in_line, Add_a_column1, dada2_dada, __SORTLIST__, dada2_learnErrors, phyloseq_from_dada2	UseGalaxy.eu		0		1089	1460	1.8333333333333333	0
-Microbiome	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Data handling, Visualisation, Sequence trimming, Read mapping, Sequencing quality control, Genome assembly, Sequence alignment analysis, Sequence contamination filtering, Sequence assembly validation, Variant calling, Statistical calculation, Sequence assembly visualisation, Sequence file editing, Local alignment, Sequence composition calculation, Read pre-processing, Primer removal, Formatting	2022-12-05	2024-06-14	4	True	False	False	True	ngsutils_bam_filter, tp_cat, bamtools, bandage_image, filter_tabular, megahit_contig2fastg, bandage_info, bg_uniq, quast, seqtk_subseq, cutadapt, random_lines1, collection_column_join, megahit, coverm_contig, fastqc, metaspades, bowtie2		UseGalaxy.cz, UseGalaxy.eu	0		1613	2258	2.95	0
-Microbiome	QIIME 2 Moving Pictures	https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis		2024-03-14	2024-03-14	1	external	False	False	False			UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr	0		131	195	3.3833333333333333	0
-Microbiome	Binning of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html	Metagenomics, Sequence assembly	Sequence assembly validation, Statistical calculation, Sequencing quality control, Validation, Genome assembly, Sequence composition calculation	2023-12-05	2024-09-12	4	True	False	False	False	megahit, checkm_lineage_wf	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	UseGalaxy.org.au	0		2076	2537	1.4166666666666667	0
-Microbiome	QIIME 2 Cancer Microbiome Intervention	https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis		2024-02-12	2024-03-14	3	external	False	False	False			UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr	0		153	281	3.4833333333333334	0
-Microbiome	16S Microbial Analysis with mothur (extended)	https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Phylogenetic tree analysis, DNA barcoding, Visualisation, Phylogenetic analysis, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Taxonomic classification, Sequence read processing, Sequence clustering	2017-02-12	2024-03-14	4	True	False	False	True	mothur_dist_shared, mothur_seq_error, mothur_summary_seqs, mothur_remove_lineage, mothur_make_biom, mothur_count_seqs, mothur_get_groups, mothur_classify_seqs, mothur_remove_groups, mothur_make_shared, mothur_filter_seqs, mothur_dist_seqs, mothur_remove_seqs, mothur_rarefaction_single, mothur_venn, mothur_classify_otu, mothur_count_groups, mothur_align_seqs, mothur_taxonomy_to_krona, mothur_heatmap_sim, mothur_chimera_vsearch, mothur_cluster_split, mothur_screen_seqs, newick_display, mothur_pre_cluster, mothur_make_contigs, mothur_unique_seqs, XY_Plot_1, taxonomy_krona_chart, mothur_cluster, mothur_tree_shared, mothur_summary_single, mothur_sub_sample	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	0		5448	8271	2.9833333333333334	0
-Microbiome	16S Microbial Analysis with mothur (short)	https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Phylogenetic tree analysis, DNA barcoding, Visualisation, Phylogenetic analysis, Sequencing quality control, Phylogenetic tree generation, Phylogenetic tree reconstruction, Taxonomic classification, Sequence read processing, Sequence clustering	2019-05-13	2024-06-14	5	True	False	False	True	mothur_dist_shared, mothur_summary_seqs, mothur_remove_lineage, mothur_count_seqs, mothur_classify_seqs, mothur_remove_groups, mothur_make_shared, mothur_filter_seqs, mothur_dist_seqs, mothur_remove_seqs, mothur_rarefaction_single, mothur_venn, mothur_classify_otu, mothur_count_groups, mothur_heatmap_sim, mothur_chimera_vsearch, mothur_cluster_split, mothur_screen_seqs, collapse_dataset, newick_display, mothur_pre_cluster, mothur_unique_seqs, XY_Plot_1, mothur_cluster, mothur_tree_shared, mothur_summary_single, mothur_sub_sample	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.fr	0		1985	3572	5.616666666666666	0
-Evolution	Tree thinking for tuberculosis evolution and epidemiology	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html	Genomics, Microbiology, Phylogeny, Infectious disease	Phylogenetic tree analysis, Sequence analysis	2022-03-16	2024-03-12	11	True	False	False	True	upload1, interactive_tool_rstudio, raxml	UseGalaxy.eu	UseGalaxy.fr, UseGalaxy.org (Main)	0		1374	2072	2.216666666666667	0
-Evolution	Identifying tuberculosis transmission links: from SNPs to transmission clusters	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html	Genomics, Microbiology, Infectious disease, DNA polymorphism	Phylogenetic tree visualisation, Variant calling, Antimicrobial resistance prediction, Phylogenetic tree generation	2022-03-16	2024-07-12	12	True	False	False	True	tp_sed_tool, tp_easyjoin_tool, tp_cat, bcftools_consensus, samtools_view, upload1, snippy, tp_grep_tool, tp_replace_in_line, snp_dists, Grep1, tb_variant_filter, tb_profiler_profile, collapse_dataset, snp_sites, trimmomatic, __MERGE_COLLECTION__, addName	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)	0		1605	2499	3.05	0
-Genome Annotation	Identification of AMR genes in an assembled bacterial genome	https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html	Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance	Genome visualisation, Genome annotation, Read mapping	2024-01-23	2024-09-27	6	True	False	False	True	jbrowse, tbl2gff3, upload1, Grep1, staramr_search, bakta, bowtie2	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, UseGalaxy.org (Main)	0		1138	1576	2.75	0
-Variant Analysis	M. tuberculosis Variant Analysis	https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html	Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease	Sequence alignment, Phylogenetic tree generation, Phylogenetic tree visualisation, Sequencing quality control, Sequence alignment analysis, Genome visualisation, Sequence analysis, Sequence contamination filtering, Variant calling, Global alignment, Statistical calculation, Taxonomic classification, Validation, Local alignment, Sequence composition calculation, Antimicrobial resistance prediction	2020-07-25	2024-07-26	30	True	False	False	True	tp_sed_tool, upload1, snippy, qualimap_bamqc, tb_variant_filter, EMBOSS: seqret84, tb_profiler_profile, mosdepth, jvarkit_wgscoverageplotter, tbvcfreport, tp_awk_tool, fastqc, jbrowse, samtools_stats, bcftools_consensus, multiqc, fastp, kraken2, EMBOSS:%20seqret84, __FLATTEN__			0		5788	9172	2.95	0
-Microbiome	16S Microbial analysis with Nanopore data	https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Taxonomic classification, Statistical calculation, Visualisation, Validation, Sequencing quality control, Sequence composition calculation, Sequence contamination filtering	2020-11-24	2024-07-31	5	True	False	False	True	porechop, fastp, tp_replace_in_line, taxonomy_krona_chart, multiqc, kraken2, datamash_reverse, fastqc, Remove beginning1	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz	0		2758	3844	2.716666666666667	0
-Proteomics	Metaproteomics tutorial	https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Prediction and recognition, Visualisation	2017-06-28	2024-06-14	41	True	False	False	True	query_tabular, peptide_shaker, search_gui, unipept, sqlite_to_tabular	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.be, UseGalaxy.cz	0		2310	3828	2.6333333333333333	0
-Proteomics	metaQuantome 3: Taxonomy	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy	Visualisation, Indexing, Differential protein expression analysis, Functional clustering, Statistical inference, Principal component visualisation, Query and retrieval, Heat map generation, Quantification, Filtering	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_viz, metaquantome_db	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		377	509	2.7333333333333334	0
-Proteomics	metaQuantome 2: Function	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics	Visualisation, Indexing, Differential protein expression analysis, Functional clustering, Statistical inference, Principal component visualisation, Query and retrieval, Heat map generation, Quantification, Filtering	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_expand, metaquantome_viz, metaquantome_db	UseGalaxy.eu	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		352	508	3.7666666666666666	0
-Proteomics	metaQuantome 1: Data creation	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Prediction and recognition, Visualisation, Filtering, Label-free quantification, Formatting	2020-10-16	2024-03-14	20	True	False	False	True	query_tabular, flashlfq, Filter1, peptide_shaker, regex1, tp_replace_in_line, msconvert, search_gui, unipept, Grep1, Cut1, Remove beginning1, tp_replace_in_column	UseGalaxy.eu	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		781	1353	3.816666666666667	0
-Sequence analysis	Quality and contamination control in bacterial isolate using Illumina MiSeq Data	https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html	Whole genome sequencing, Genomics, Microbiology, Microbial ecology	Cross-assembly, Sequencing quality control, Sequence contamination filtering, Statistical calculation, Taxonomic classification, Expression analysis, Sequence composition calculation	2024-07-15	2024-09-02	2	True	False	False	True	fastp, est_abundance, recentrifuge, upload1, kraken2, fastqc	UseGalaxy.eu, UseGalaxy.fr	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)	0		185	225	2.5166666666666666	0
-Variant Analysis	Calling variants in non-diploid systems	https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Data handling, Sequence alignment, Read mapping, Sequencing quality control, Sequence alignment analysis, Generation, Statistical calculation, Variant calling, Sequence composition calculation, Formatting, Genome indexing	2017-02-16	2024-03-15	23	True	False	False	True	bwa_mem, picard_MarkDuplicates, vcffilter2, bamFilter, picard_MergeSamFiles, Cut1, bamleftalign, fastqc, vcf2tsv, freebayes	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org (Main)	UseGalaxy.cz, UseGalaxy.org.au	0		7149	13577	2.05	0
-Variant Analysis	M. tuberculosis Variant Analysis	https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html	Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease	Sequence alignment, Phylogenetic tree generation, Phylogenetic tree visualisation, Sequencing quality control, Sequence alignment analysis, Genome visualisation, Sequence analysis, Sequence contamination filtering, Variant calling, Global alignment, Statistical calculation, Taxonomic classification, Validation, Local alignment, Sequence composition calculation, Antimicrobial resistance prediction	2020-07-25	2024-07-26	30	True	False	False	True	tp_sed_tool, upload1, snippy, qualimap_bamqc, tb_variant_filter, EMBOSS: seqret84, tb_profiler_profile, mosdepth, jvarkit_wgscoverageplotter, tbvcfreport, tp_awk_tool, fastqc, jbrowse, samtools_stats, bcftools_consensus, multiqc, fastp, kraken2, EMBOSS:%20seqret84, __FLATTEN__			0		5788	9172	2.95	0
-Variant Analysis	Microbial Variant Calling	https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Genome visualisation, Variant calling, Phylogenetic tree visualisation, Phylogenetic tree generation	2018-02-26	2024-03-15	23	True	False	False	True	jbrowse, snippy	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.fr, UseGalaxy.no, UseGalaxy.org.au	0		12476	20693	1.9833333333333334	0
+Assembly	Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-illumina/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology	Sequence contamination filtering, Genome assembly, Sequence assembly validation, Sequencing quality control, Visualisation, Sequence assembly visualisation, Sequence composition calculation, Statistical calculation	2021-03-24	2024-09-18	15	True	False	False	True	bandage_image, shovill, fastqc, bandage_info, upload1, fastp, quast	UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.be, UseGalaxy.no	0		6791	10915	3.783333333333333	0
+Assembly	Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance	Genome assembly, Sequencing error detection, Sequence assembly visualisation, De-novo assembly, Filtering, Mapping assembly, Scatter plot plotting, Sequence assembly validation, Visualisation, Cross-assembly, Sequence alignment, Sequence composition calculation, Box-Whisker plot plotting, Sequencing quality control, Read mapping, Sequence contamination filtering, Statistical calculation	2021-03-24	2024-03-13	14	True	False	False	True	bandage_image, polypolish, filtlong, fastqc, nanoplot, upload1, bwa_mem2, fastp, porechop, CONVERTER_bz2_to_uncompressed, quast, flye	UseGalaxy.eu	UseGalaxy.cz	0		7215	11067	3.3833333333333333	0
+Assembly	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/assembly/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Variant calling, Genome assembly, Sequence assembly visualisation, Sequence assembly validation, Visualisation, Sequence trimming, Local alignment, Sequence file editing, Data handling, Sequence alignment analysis, Primer removal, Formatting, Sequence composition calculation, Sequencing quality control, Read mapping, Read pre-processing, Sequence contamination filtering, Statistical calculation	2024-10-08	2024-10-08	0	True	False	False	True	bandage_image, seqtk_subseq, megahit_contig2fastg, cutadapt, random_lines1, tp_cat, megahit, fastqc, bg_uniq, collection_column_join, bandage_info, metaspades, coverm_contig, bowtie2, filter_tabular, quast, bamtools, ngsutils_bam_filter		UseGalaxy.cz, UseGalaxy.eu	0		6	14	7.1	0
+Assembly	Unicycler Assembly	https://training.galaxyproject.org//topics/assembly/tutorials/unicycler-assembly/tutorial.html	Sequence assembly, Genomics, Microbiology	Genome assembly, Coding region prediction, Sequence composition calculation, Genome annotation, Sequence assembly validation, Validation, Sequencing quality control, Gene prediction, Visualisation, Aggregation, Statistical calculation	2017-10-11	2024-03-13	23	True	True	False	True	unicycler, fastqc, multiqc, prokka, quast	UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, HyPhy HIV NGS Tools, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no	0		2155238	5948759	4.583333333333333	0
+Assembly	Making sense of a newly assembled genome	https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html	Sequence assembly, Genomics, Microbiology	Read mapping, Sequence alignment, Sequence visualisation, Genome visualisation, Mapping	2018-06-14	2024-06-24	29	True	False	False	True	cat1, tp_sed_tool, lastz_wrapper_2, jbrowse, circos_interval_to_tiles, tp_grep_tool, circos, bedtools_complementbed, collapse_dataset, bedtools_intersectbed, upload1, datamash_ops, tp_replace_in_column, addValue, Filter1, tp_replace_in_line, random_lines1, tp_sort_header_tool, Grep1, fasta_compute_length, mergeCols1, Cut1, fasta_filter_by_length, tp_cat, join1, bedtools_sortbed, circos_aln_to_links			0		6047	12192	3.0166666666666666	0
+Ecology	Checking expected species and contamination in bacterial isolate	https://training.galaxyproject.org//topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/tutorial.html	Whole genome sequencing, Genomics, Microbiology, Microbial ecology	Expression analysis, Cross-assembly, Statistical calculation, Taxonomic classification	2024-03-04	2024-06-27	4	True	False	False	True	kraken2, upload1, recentrifuge, est_abundance	UseGalaxy.eu	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)	0		267	352	3.3666666666666667	0
+Evolution	Tree thinking for tuberculosis evolution and epidemiology	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html	Genomics, Microbiology, Phylogeny, Infectious disease	Phylogenetic tree analysis, Sequence analysis	2022-03-16	2024-03-12	11	True	False	False	True	interactive_tool_rstudio, upload1, raxml	UseGalaxy.eu	UseGalaxy.org (Main)	0		1378	2078	2.25	0
+Evolution	Identifying tuberculosis transmission links: from SNPs to transmission clusters	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html	Genomics, Microbiology, Infectious disease, DNA polymorphism	Variant calling, Antimicrobial resistance prediction, Phylogenetic tree visualisation, Phylogenetic tree generation	2022-03-16	2024-07-12	12	True	False	False	True	samtools_view, tp_replace_in_line, tp_sed_tool, bcftools_consensus, snippy, snp_sites, collapse_dataset, trimmomatic, tp_cat, tp_easyjoin_tool, tp_grep_tool, Grep1, tb_variant_filter, addName, tb_profiler_profile, upload1, __MERGE_COLLECTION__, snp_dists	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)	0		1610	2504	3.033333333333333	0
+Genome Annotation	Genome annotation with Prokka	https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Coding region prediction, Gene prediction, Genome visualisation, Genome annotation	2018-03-06	2024-08-08	25	True	True	True	True	prokka, jbrowse	UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		2160036	5956792	4.316666666666666	0
+Genome Annotation	Identification of AMR genes in an assembled bacterial genome	https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html	Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance	Genome visualisation, Read mapping, Genome annotation	2024-01-23	2024-09-27	6	True	False	False	True	jbrowse, Grep1, tbl2gff3, bakta, upload1, bowtie2, staramr_search	UseGalaxy.cz, UseGalaxy.eu	Galaxy@AuBi, UseGalaxy.org (Main)	0		1181	1633	2.966666666666667	0
+Genome Annotation	Refining Genome Annotations with Apollo (prokaryotes)	https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation	2021-06-04	2024-08-08	20	True	True	True	True	jbrowse, create_or_update, create_account, iframe, list_organism		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no	0		1916586	5151189	5.0	0
+Genome Annotation	Bacterial Genome Annotation	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements	Sequence motif recognition, Genome assembly, Genome visualisation, Protein feature detection, Genome annotation, Multilocus sequence typing, Nucleic acid feature detection, Scaffolding, Structural variation detection	2024-02-01	2024-09-08	5	True	False	False	True	integron_finder, jbrowse, tp_tail_tool, bakta, tbl2gff3, upload1, tp_replace_in_column, Grouping1, isescan, plasmidfinder	UseGalaxy.eu	Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)	0		2301	3039	2.3	0
+Genome Annotation	Comparative gene analysis in unannotated genomes	https://training.galaxyproject.org//topics/genome-annotation/tutorials/gene-centric/tutorial.html	Genomics, Gene and protein families, Sequence analysis, Phylogeny	Multiple sequence alignment, Sequence alignment analysis, Transcriptome assembly, Coding region prediction, Database search, De-novo assembly, Phylogenetic tree generation	2022-09-08	2024-03-18	8	True	False	False	True	Cut1, cat1, bg_diamond_view, tp_split_on_column, collapse_dataset, rbc_mafft, tab2fasta, regexColumn1, gops_intersect_1, join1, rapidnj, bg_diamond, orfipy, Add_a_column1, bg_diamond_makedb, Filter1	UseGalaxy.eu, UseGalaxy.org (Main)	UseGalaxy.cz	0		1051	1608	3.55	0
+Genome Annotation	Essential genes detection with Transposon insertion sequencing	https://training.galaxyproject.org//topics/genome-annotation/tutorials/tnseq/tutorial.html	Genomics, Microbiology, Sequence analysis, Mobile genetic elements	Read pre-processing, Sequence trimming, Primer removal, Transposon prediction	2019-07-02	2024-03-18	12	True	True	False	True	Cut1, transit_gumbel, cutadapt, tp_easyjoin_tool, bg_find_subsequences, tp_sort_header_tool, deeptools_bam_coverage, bowtie_wrapper, __EXTRACT_DATASET__, Add_a_column1, gff_to_prot, Filter1	UseGalaxy.be, UseGalaxy.no, UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.eu	0		2150876	5941722	4.266666666666667	0
+Genome Annotation	Genome annotation with Prokka	https://training.galaxyproject.org//topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Coding region prediction, Gene prediction, Genome visualisation, Genome annotation	2018-03-06	2024-08-08	25	True	True	True	True	prokka, jbrowse	UseGalaxy.eu, UseGalaxy.org (Main)	Galaxy@AuBi, GalaxyTrakr, MISSISSIPPI, UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		2160036	5956800	4.316666666666666	0
+Genome Annotation	Identification of AMR genes in an assembled bacterial genome	https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html	Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance	Genome visualisation, Read mapping, Genome annotation	2024-01-23	2024-09-27	6	True	False	False	True	jbrowse, Grep1, tbl2gff3, bakta, upload1, bowtie2, staramr_search	UseGalaxy.cz, UseGalaxy.eu	Galaxy@AuBi, UseGalaxy.org (Main)	0		1181	1633	2.966666666666667	0
+Genome Annotation	Refining Genome Annotations with Apollo (prokaryotes)	https://training.galaxyproject.org//topics/genome-annotation/tutorials/apollo/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis	Genome visualisation	2021-06-04	2024-08-08	20	True	True	True	True	jbrowse, create_or_update, create_account, iframe, list_organism		UseGalaxy.cz, UseGalaxy.eu, UseGalaxy.no	0		1916586	5151198	5.0	0
+Genome Annotation	Bacterial Genome Annotation	https://training.galaxyproject.org//topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.html	Genomics, Microbiology, Gene and protein families, Sequence analysis, Whole genome sequencing, Functional genomics, Mobile genetic elements	Sequence motif recognition, Genome assembly, Genome visualisation, Protein feature detection, Genome annotation, Multilocus sequence typing, Nucleic acid feature detection, Scaffolding, Structural variation detection	2024-02-01	2024-09-08	5	True	False	False	True	integron_finder, jbrowse, tp_tail_tool, bakta, tbl2gff3, upload1, tp_replace_in_column, Grouping1, isescan, plasmidfinder	UseGalaxy.eu	Galaxy@AuBi, UseGalaxy.cz, UseGalaxy.org (Main)	0		2301	3039	2.3	0
+Variant Analysis	Microbial Variant Calling	https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Variant calling, Phylogenetic tree visualisation, Genome visualisation, Phylogenetic tree generation	2018-02-26	2024-03-15	23	True	False	False	True	jbrowse, snippy	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		12499	20722	1.9833333333333334	0
+Assembly	Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)	https://training.galaxyproject.org//topics/assembly/tutorials/mrsa-nanopore/tutorial.html	Sequence assembly, Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Antimicrobial Resistance	Genome assembly, Sequencing error detection, Sequence assembly visualisation, De-novo assembly, Filtering, Mapping assembly, Scatter plot plotting, Sequence assembly validation, Visualisation, Cross-assembly, Sequence alignment, Sequence composition calculation, Box-Whisker plot plotting, Sequencing quality control, Read mapping, Sequence contamination filtering, Statistical calculation	2021-03-24	2024-03-13	14	True	False	False	True	bandage_image, polypolish, filtlong, fastqc, nanoplot, upload1, bwa_mem2, fastp, porechop, CONVERTER_bz2_to_uncompressed, quast, flye	UseGalaxy.eu	UseGalaxy.cz	0		7215	11067	3.3833333333333333	0
+Assembly	Making sense of a newly assembled genome	https://training.galaxyproject.org//topics/assembly/tutorials/ecoli_comparison/tutorial.html	Sequence assembly, Genomics, Microbiology	Read mapping, Sequence alignment, Sequence visualisation, Genome visualisation, Mapping	2018-06-14	2024-06-24	29	True	False	False	True	cat1, tp_sed_tool, lastz_wrapper_2, jbrowse, circos_interval_to_tiles, tp_grep_tool, circos, bedtools_complementbed, collapse_dataset, bedtools_intersectbed, upload1, datamash_ops, tp_replace_in_column, addValue, Filter1, tp_replace_in_line, random_lines1, tp_sort_header_tool, Grep1, fasta_compute_length, mergeCols1, Cut1, fasta_filter_by_length, tp_cat, join1, bedtools_sortbed, circos_aln_to_links			0		6047	12192	3.0166666666666666	0
+Microbiome	Analyses of metagenomics data - The global picture	https://training.galaxyproject.org//topics/microbiome/tutorials/general-tutorial/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	Sequence read processing, DNA barcoding, Taxonomic classification, Sequencing quality control, Visualisation, Phylogenetic analysis, Sequence clustering	2017-06-22	2024-08-09	4	True	False	False	True	krona-text, mothur_merge_files, mothur_count_seqs, mothur_screen_seqs, mothur_summary_seqs, mothur_classify_otu, mothur_unique_seqs, mothur_make_biom, mothur_classify_seqs, mothur_pre_cluster, metaphlan2, metaphlan2krona, humann2_renorm_table, mothur_make_group, humann2_regroup_table, mothur_filter_seqs, mothur_align_seqs, humann2, mothur_make_shared, mothur_cluster_split, taxonomy_krona_chart	UseGalaxy.be	UseGalaxy.no, UseGalaxy.org.au	0		3689	4998	2.8	0
+Microbiome	Identification of the micro-organisms in a beer using Nanopore sequencing	https://training.galaxyproject.org//topics/microbiome/tutorials/beer-data-analysis/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	Sequence composition calculation, Sequence contamination filtering, Sequencing quality control, Visualisation, Aggregation, Statistical calculation, Taxonomic classification	2022-09-29	2024-06-14	4	True	False	False	True	krakentools_kreport2krona, fastqc, fastp, porechop, kraken2, taxonomy_krona_chart, Filter1	GalaxyTrakr, UseGalaxy.eu, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz	0		1249	1962	2.95	0
+Microbiome	Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition	https://training.galaxyproject.org//topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html	Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis	Variant calling, Genome assembly, Sequence assembly visualisation, Base-calling, De-novo assembly, Antimicrobial resistance prediction, Mapping assembly, Taxonomic classification, Multilocus sequence typing, Multiple sequence alignment, Validation, Scatter plot plotting, Visualisation, Cross-assembly, Aggregation, Pairwise sequence alignment, Data handling, Sequence alignment analysis, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation, Sequence composition calculation, Box-Whisker plot plotting, Sequence assembly, Sequencing quality control, Phylogenetic tree reconstruction, Sequence contamination filtering, Statistical calculation, Mapping	2023-01-26	2024-09-27	11	True	False	False	True	regex1, regexColumn1, CONVERTER_gz_to_uncompressed, mlst, __BUILD_LIST__, Remove beginning1, fasta2tab, fastp, abricate, collapse_dataset, __FILTER_EMPTY_DATASETS__, samtools_depth, tab2fasta, tp_sorted_uniq, snpSift_filter, samtools_fastx, tp_replace_in_column, clair3, porechop, __FILTER_FAILED_DATASETS__, Paste1, ggplot2_heatmap, bandage_image, bcftools_norm, Count1, compose_text_param, krakentools_extract_kraken_reads, krakentools_kreport2krona, medaka_consensus_pipeline, minimap2, newick_display, clustalw, collection_element_identifiers, barchart_gnuplot, tp_find_and_replace, fasta_merge_files_and_filter_unique_sequences, collection_column_join, snpSift_extractFields, Grep1, add_line_to_file, bamtools_split_mapped, multiqc, kraken2, Add_a_column1, tp_cut_tool, Cut1, tp_split_on_column, bcftools_consensus, tp_multijoin_tool, samtools_coverage, bedtools_getfastabed, param_value_from_file, fastqc, nanoplot, table_compute, split_file_to_collection, fasttree, Grouping1, taxonomy_krona_chart, flye, tp_head_tool	UseGalaxy.eu	UseGalaxy.org.au	0		2001	2968	2.966666666666667	0
+Microbiome	Metatranscriptomics analysis using microbiome RNA-seq data	https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics/tutorial.html	Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis	Sequence comparison, Taxonomic classification, Validation, Conversion, Visualisation, Sequence trimming, Phylogenetic analysis, Phylogenetic tree visualisation, Phylogenetic inference, Nucleic acid sequence analysis, Sequence alignment analysis, Species frequency estimation, Phylogenetic tree analysis, Primer removal, Sequence composition calculation, Phylogenetic tree editing, Sequencing quality control, Sequence similarity search, Read pre-processing, Statistical calculation	2019-11-21	2024-06-14	4	True	True	False	True	humann, bg_sortmerna, combine_metaphlan2_humann2, metaphlan, cutadapt, humann_renorm_table, graphlan_annotate, fastq_paired_end_interlacer, humann_unpack_pathways, export2graphlan, humann_regroup_table, tp_find_and_replace, Grep1, multiqc, Cut1, humann_split_stratified_table, fastqc, humann_rename_table, graphlan, taxonomy_krona_chart	UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.no	0		2147260	5933139	4.266666666666667	0
+Microbiome	Taxonomic Profiling and Visualization of Metagenomic Data	https://training.galaxyproject.org//topics/microbiome/tutorials/taxonomic-profiling/tutorial.html	Metagenomics, Microbial ecology, Taxonomy, Sequence analysis	Taxonomic classification, Visualisation, Phylogenetic tree analysis, Aggregation, Statistical calculation, Nucleic acid sequence analysis	2023-05-03	2024-06-14	4	True	False	False	True	krakentools_kreport2krona, metaphlan, interactive_tool_phinch, interactive_tool_pavian, est_abundance, kraken_biom, __UNZIP_COLLECTION__, taxonomy_krona_chart, kraken2	UseGalaxy.eu	UseGalaxy.org.au	0		4540	6233	1.9666666666666666	0
+Microbiome	Metatranscriptomics analysis using microbiome RNA-seq data (short)	https://training.galaxyproject.org//topics/microbiome/tutorials/metatranscriptomics-short/tutorial.html	Metatranscriptomics, Microbial ecology, Taxonomy, Function analysis, Sequence analysis	Sequence comparison, Taxonomic classification, Validation, Conversion, Visualisation, Sequence trimming, Phylogenetic analysis, Phylogenetic tree visualisation, Phylogenetic inference, Nucleic acid sequence analysis, Sequence alignment analysis, Species frequency estimation, Phylogenetic tree analysis, Primer removal, Sequence composition calculation, Phylogenetic tree editing, Sequencing quality control, Sequence similarity search, Read pre-processing, Statistical calculation	2020-02-13	2024-06-14	4	True	False	False	True	humann, bg_sortmerna, combine_metaphlan2_humann2, metaphlan, cutadapt, humann_renorm_table, graphlan_annotate, fastq_paired_end_interlacer, humann_unpack_pathways, export2graphlan, humann_regroup_table, tp_find_and_replace, Grep1, multiqc, Cut1, humann_split_stratified_table, fastqc, humann_rename_table, graphlan, taxonomy_krona_chart	UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.cz, UseGalaxy.no	0		280	357	1.4	0
+Microbiome	Antibiotic resistance detection	https://training.galaxyproject.org//topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.html	Metagenomic sequencing, Public health and epidemiology, Metagenomics, Microbiology, Infectious disease, Sequence analysis, Antimicrobial Resistance	Genome assembly, Sequence assembly visualisation, De-novo assembly, Mapping assembly, Sequence analysis, Box-Whisker plot plotting, Scatter plot plotting, Aggregation, Pairwise sequence alignment	2019-06-25	2024-06-14	4	True	False	False	True	bandage_image, minimap2, unicycler, nanoplot, PlasFlow, gfa_to_fa, miniasm, racon, staramr_search	UseGalaxy.eu	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	0		1301	1976	4.05	0
+Microbiome	16S Microbial analysis with Nanopore data	https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Sequence contamination filtering, Validation, Sequencing quality control, Visualisation, Sequence composition calculation, Statistical calculation, Taxonomic classification	2020-11-24	2024-07-31	5	True	False	False	True	tp_replace_in_line, datamash_reverse, multiqc, fastqc, Remove beginning1, fastp, porechop, kraken2, taxonomy_krona_chart	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz	0		2802	3894	2.7333333333333334	0
+Microbiome	Building an amplicon sequence variant (ASV) table from 16S data using DADA2	https://training.galaxyproject.org//topics/microbiome/tutorials/dada-16S/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Variant calling, DNA barcoding, Visualisation, Deposition, Analysis	2024-06-05	2024-09-26	8	True	False	False	True	cat1, dada2_makeSequenceTable, dada2_filterAndTrim, __SORTLIST__, tp_replace_in_column, __UNZIP_COLLECTION__, tp_replace_in_line, dada2_assignTaxonomyAddspecies, dada2_mergePairs, phyloseq_from_dada2, dada2_plotQualityProfile, collection_element_identifiers, interactive_tool_phyloseq, dada2_learnErrors, dada2_removeBimeraDenovo, dada2_dada, Add_a_column1, dada2_seqCounts, Grouping1, tp_head_tool	UseGalaxy.eu		0		1162	1566	1.8333333333333333	0
+Microbiome	Assembly of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-assembly/tutorial.html	Metagenomics, Sequence assembly	Variant calling, Genome assembly, Sequence assembly visualisation, Sequence assembly validation, Visualisation, Sequence trimming, Local alignment, Sequence file editing, Data handling, Sequence alignment analysis, Primer removal, Formatting, Sequence composition calculation, Sequencing quality control, Read mapping, Read pre-processing, Sequence contamination filtering, Statistical calculation	2022-12-05	2024-06-14	4	True	False	False	True	bandage_image, seqtk_subseq, megahit_contig2fastg, cutadapt, random_lines1, tp_cat, megahit, fastqc, bg_uniq, collection_column_join, bandage_info, metaspades, coverm_contig, bowtie2, filter_tabular, quast, bamtools, ngsutils_bam_filter		UseGalaxy.cz, UseGalaxy.eu	0		1671	2337	2.9833333333333334	0
+Microbiome	QIIME 2 Moving Pictures	https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis		2024-03-14	2024-03-14	1	external	False	False	False			UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr	0		136	201	3.35	0
+Microbiome	Binning of metagenomic sequencing data	https://training.galaxyproject.org//topics/microbiome/tutorials/metagenomics-binning/tutorial.html	Metagenomics, Sequence assembly	Sequence assembly validation, Genome assembly, Validation, Sequencing quality control, Statistical calculation, Sequence composition calculation	2023-12-05	2024-09-12	4	True	False	False	False	megahit, checkm_lineage_wf	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.eu	UseGalaxy.org.au	0		2123	2591	1.4166666666666667	0
+Microbiome	QIIME 2 Cancer Microbiome Intervention	https://training.galaxyproject.org//topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis		2024-02-12	2024-03-14	3	external	False	False	False			UseGalaxy.eu, UseGalaxy.org, UseGalaxy.org.au, UseGalaxy.fr	0		154	283	3.4833333333333334	0
+Microbiome	16S Microbial Analysis with mothur (extended)	https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Sequence read processing, DNA barcoding, Phylogenetic tree analysis, Phylogenetic tree generation, Taxonomic classification, Sequencing quality control, Visualisation, Phylogenetic tree reconstruction, Phylogenetic analysis, Sequence clustering	2017-02-12	2024-03-14	4	True	False	False	True	mothur_make_contigs, mothur_chimera_vsearch, mothur_count_seqs, mothur_screen_seqs, mothur_cluster, mothur_classify_otu, mothur_summary_seqs, mothur_unique_seqs, mothur_dist_shared, mothur_make_biom, mothur_classify_seqs, mothur_dist_seqs, mothur_pre_cluster, XY_Plot_1, mothur_remove_seqs, mothur_remove_groups, mothur_sub_sample, newick_display, mothur_venn, mothur_rarefaction_single, mothur_tree_shared, mothur_summary_single, mothur_remove_lineage, mothur_filter_seqs, mothur_seq_error, mothur_get_groups, mothur_heatmap_sim, mothur_align_seqs, mothur_count_groups, mothur_taxonomy_to_krona, mothur_make_shared, mothur_cluster_split, taxonomy_krona_chart	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	0		5547	8409	2.966666666666667	0
+Microbiome	16S Microbial Analysis with mothur (short)	https://training.galaxyproject.org//topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Sequence read processing, DNA barcoding, Phylogenetic tree analysis, Phylogenetic tree generation, Taxonomic classification, Sequencing quality control, Visualisation, Phylogenetic tree reconstruction, Phylogenetic analysis, Sequence clustering	2019-05-13	2024-06-14	5	True	False	False	True	mothur_chimera_vsearch, mothur_count_seqs, mothur_screen_seqs, mothur_cluster, mothur_classify_otu, mothur_summary_seqs, mothur_unique_seqs, mothur_dist_shared, collapse_dataset, mothur_classify_seqs, mothur_dist_seqs, mothur_pre_cluster, XY_Plot_1, mothur_remove_seqs, mothur_remove_groups, mothur_sub_sample, newick_display, mothur_venn, mothur_rarefaction_single, mothur_tree_shared, mothur_summary_single, mothur_remove_lineage, mothur_filter_seqs, mothur_heatmap_sim, mothur_count_groups, mothur_make_shared, mothur_cluster_split	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.be, UseGalaxy.cz	0		2011	3607	5.616666666666666	0
+Evolution	Tree thinking for tuberculosis evolution and epidemiology	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_phylogeny/tutorial.html	Genomics, Microbiology, Phylogeny, Infectious disease	Phylogenetic tree analysis, Sequence analysis	2022-03-16	2024-03-12	11	True	False	False	True	interactive_tool_rstudio, upload1, raxml	UseGalaxy.eu	UseGalaxy.org (Main)	0		1379	2079	2.25	0
+Evolution	Identifying tuberculosis transmission links: from SNPs to transmission clusters	https://training.galaxyproject.org//topics/evolution/tutorials/mtb_transmission/tutorial.html	Genomics, Microbiology, Infectious disease, DNA polymorphism	Variant calling, Antimicrobial resistance prediction, Phylogenetic tree visualisation, Phylogenetic tree generation	2022-03-16	2024-07-12	12	True	False	False	True	samtools_view, tp_replace_in_line, tp_sed_tool, bcftools_consensus, snippy, snp_sites, collapse_dataset, trimmomatic, tp_cat, tp_easyjoin_tool, tp_grep_tool, Grep1, tb_variant_filter, addName, tb_profiler_profile, upload1, __MERGE_COLLECTION__, snp_dists	UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org (Main)	0		1610	2504	3.033333333333333	0
+Genome Annotation	Identification of AMR genes in an assembled bacterial genome	https://training.galaxyproject.org//topics/genome-annotation/tutorials/amr-gene-detection/tutorial.html	Whole genome sequencing, Public health and epidemiology, Genomics, Microbiology, Sequence analysis, Infectious disease, Antimicrobial Resistance	Genome visualisation, Read mapping, Genome annotation	2024-01-23	2024-09-27	6	True	False	False	True	jbrowse, Grep1, tbl2gff3, bakta, upload1, bowtie2, staramr_search	UseGalaxy.cz, UseGalaxy.eu	Galaxy@AuBi, UseGalaxy.org (Main)	0		1183	1635	2.95	0
+Variant Analysis	M. tuberculosis Variant Analysis	https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html	Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease	Variant calling, Sequence alignment analysis, Antimicrobial resistance prediction, Sequence analysis, Phylogenetic tree generation, Genome visualisation, Sequence composition calculation, Taxonomic classification, Statistical calculation, Validation, Sequencing quality control, Global alignment, Sequence alignment, Sequence contamination filtering, Phylogenetic tree visualisation, Local alignment	2020-07-25	2024-07-26	30	True	False	False	True	mosdepth, tp_sed_tool, qualimap_bamqc, jbrowse, snippy, jvarkit_wgscoverageplotter, samtools_stats, fastp, upload1, EMBOSS:%20seqret84, tp_awk_tool, tb_variant_filter, tb_profiler_profile, multiqc, kraken2, tbvcfreport, EMBOSS: seqret84, bcftools_consensus, __FLATTEN__, fastqc			0		5800	9186	2.933333333333333	0
+Microbiome	16S Microbial analysis with Nanopore data	https://training.galaxyproject.org//topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.html	Microbial ecology, Taxonomy, Sequence analysis	Sequence contamination filtering, Validation, Sequencing quality control, Visualisation, Sequence composition calculation, Statistical calculation, Taxonomic classification	2020-11-24	2024-07-31	5	True	False	False	True	tp_replace_in_line, datamash_reverse, multiqc, fastqc, Remove beginning1, fastp, porechop, kraken2, taxonomy_krona_chart	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	GalaxyTrakr, UseGalaxy.be, UseGalaxy.cz	0		2802	3894	2.7333333333333334	0
+Proteomics	Metaproteomics tutorial	https://training.galaxyproject.org//topics/proteomics/tutorials/metaproteomics/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Prediction and recognition, Visualisation	2017-06-28	2024-06-14	41	True	False	False	True	sqlite_to_tabular, query_tabular, search_gui, peptide_shaker, unipept	UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main), UseGalaxy.org.au	UseGalaxy.be, UseGalaxy.cz	0		2320	3839	2.6333333333333333	0
+Proteomics	metaQuantome 3: Taxonomy	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics, Taxonomy	Differential protein expression analysis, Filtering, Heat map generation, Indexing, Query and retrieval, Visualisation, Principal component visualisation, Quantification, Functional clustering, Statistical inference	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_db, metaquantome_stat, metaquantome_sample, metaquantome_viz, metaquantome_expand, metaquantome_filter	UseGalaxy.be, UseGalaxy.eu	UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		378	510	2.7333333333333334	0
+Proteomics	metaQuantome 2: Function	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-function/tutorial.html	Proteomics, Proteogenomics, Metatranscriptomics, Microbial ecology, Metagenomics	Differential protein expression analysis, Filtering, Heat map generation, Indexing, Query and retrieval, Visualisation, Principal component visualisation, Quantification, Functional clustering, Statistical inference	2020-10-29	2024-03-15	14	True	False	False	True	metaquantome_db, metaquantome_stat, metaquantome_sample, metaquantome_viz, metaquantome_expand, metaquantome_filter	UseGalaxy.eu	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		353	509	3.7666666666666666	0
+Proteomics	metaQuantome 1: Data creation	https://training.galaxyproject.org//topics/proteomics/tutorials/metaquantome-data-creation/tutorial.html	Proteomics, Proteogenomics, Biodiversity, Taxonomy	Prediction and recognition, Visualisation, Filtering, Formatting, Label-free quantification	2020-10-16	2024-03-14	20	True	False	False	True	Cut1, tp_replace_in_line, flashlfq, regex1, query_tabular, search_gui, peptide_shaker, Grep1, Remove beginning1, msconvert, tp_replace_in_column, unipept, Filter1	UseGalaxy.eu	UseGalaxy.be, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		782	1355	3.8333333333333335	0
+Sequence analysis	Quality and contamination control in bacterial isolate using Illumina MiSeq Data	https://training.galaxyproject.org//topics/sequence-analysis/tutorials/quality-contamination-control/tutorial.html	Whole genome sequencing, Genomics, Microbiology, Microbial ecology	Expression analysis, Sequence contamination filtering, Sequencing quality control, Cross-assembly, Sequence composition calculation, Statistical calculation, Taxonomic classification	2024-07-15	2024-09-02	2	True	False	False	True	fastqc, upload1, recentrifuge, est_abundance, fastp, kraken2	UseGalaxy.eu	Galaxy@AuBi, GalaxyTrakr, UseGalaxy.cz, UseGalaxy.org (Main)	0		229	296	2.716666666666667	0
+Variant Analysis	Calling variants in non-diploid systems	https://training.galaxyproject.org//topics/variant-analysis/tutorials/non-dip/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Variant calling, Data handling, Sequence alignment analysis, Genome indexing, Formatting, Sequence composition calculation, Generation, Sequencing quality control, Read mapping, Sequence alignment, Statistical calculation	2017-02-16	2024-03-15	23	True	False	False	True	Cut1, bamFilter, fastqc, freebayes, picard_MergeSamFiles, vcf2tsv, bwa_mem, vcffilter2, picard_MarkDuplicates, bamleftalign	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.no, UseGalaxy.org (Main)	UseGalaxy.cz, UseGalaxy.org.au	0		7181	13614	2.05	0
+Variant Analysis	M. tuberculosis Variant Analysis	https://training.galaxyproject.org//topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.html	Genomics, Microbiology, Sequence assembly, Genetic variation, Public health and epidemiology, Infectious disease	Variant calling, Sequence alignment analysis, Antimicrobial resistance prediction, Sequence analysis, Phylogenetic tree generation, Genome visualisation, Sequence composition calculation, Taxonomic classification, Statistical calculation, Validation, Sequencing quality control, Global alignment, Sequence alignment, Sequence contamination filtering, Phylogenetic tree visualisation, Local alignment	2020-07-25	2024-07-26	30	True	False	False	True	mosdepth, tp_sed_tool, qualimap_bamqc, jbrowse, snippy, jvarkit_wgscoverageplotter, samtools_stats, fastp, upload1, EMBOSS:%20seqret84, tp_awk_tool, tb_variant_filter, tb_profiler_profile, multiqc, kraken2, tbvcfreport, EMBOSS: seqret84, bcftools_consensus, __FLATTEN__, fastqc			0		5800	9186	2.933333333333333	0
+Variant Analysis	Microbial Variant Calling	https://training.galaxyproject.org//topics/variant-analysis/tutorials/microbial-variants/tutorial.html	Genomics, Sequence assembly, DNA polymorphism, Microbiology, Sequence analysis, Genetic variation	Variant calling, Phylogenetic tree visualisation, Genome visualisation, Phylogenetic tree generation	2018-02-26	2024-03-15	23	True	False	False	True	jbrowse, snippy	UseGalaxy.be, UseGalaxy.eu, UseGalaxy.org (Main)	GalaxyTrakr, UseGalaxy.cz, UseGalaxy.no, UseGalaxy.org.au	0		12499	20722	1.9833333333333334	0
diff --git a/communities/proteomics/resources/tools.html b/communities/proteomics/resources/tools.html
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--- /dev/null
+++ b/communities/proteomics/resources/tools.html
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+
+<div class="display nowrap" style="width:80%" width="100%">
+
+<table class="dataframe display nowrap" id="dataframe">
+  <thead>
+    <tr style="text-align: right;">
+      <th>Expand</th>
+      <th>Galaxy wrapper id</th>
+      <th>Galaxy tool ids</th>
+      <th>Description</th>
+      <th>bio.tool id</th>
+      <th>bio.tool ids</th>
+      <th>biii</th>
+      <th>bio.tool name</th>
+      <th>bio.tool description</th>
+      <th>EDAM operation</th>
+      <th>EDAM topic</th>
+      <th>Status</th>
+      <th>Source</th>
+      <th>ToolShed categories</th>
+      <th>ToolShed id</th>
+      <th>Galaxy wrapper owner</th>
+      <th>Galaxy wrapper source</th>
+      <th>Galaxy wrapper parsed folder</th>
+      <th>Galaxy wrapper version</th>
+      <th>Conda id</th>
+      <th>Conda version</th>
+      <th>EDAM operation (no superclasses)</th>
+      <th>EDAM topic (no superclasses)</th>
+      <th>Available on UseGalaxy.org (Main)</th>
+      <th>Available on UseGalaxy.org.au</th>
+      <th>Available on UseGalaxy.eu</th>
+      <th>Available on UseGalaxy.fr</th>
+      <th>Tools available on UseGalaxy.org (Main)</th>
+      <th>Tools available on UseGalaxy.org.au</th>
+      <th>Tools available on UseGalaxy.eu</th>
+      <th>Tools available on UseGalaxy.fr</th>
+      <th>Tools available on APOSTL</th>
+      <th>Tools available on ARGs-OAP</th>
+      <th>Tools available on CIRM-CFBP</th>
+      <th>Tools available on ChemFlow</th>
+      <th>Tools available on Coloc-stats</th>
+      <th>Tools available on CoralSNP</th>
+      <th>Tools available on CropGalaxy</th>
+      <th>Tools available on Dintor</th>
+      <th>Tools available on GASLINI</th>
+      <th>Tools available on Galaxy@AuBi</th>
+      <th>Tools available on Galaxy@Pasteur</th>
+      <th>Tools available on GalaxyTrakr</th>
+      <th>Tools available on Genomic Hyperbrowser</th>
+      <th>Tools available on GigaGalaxy</th>
+      <th>Tools available on HyPhy HIV NGS Tools</th>
+      <th>Tools available on IPK Galaxy Blast Suite</th>
+      <th>Tools available on ImmPort Galaxy</th>
+      <th>Tools available on InteractoMIX</th>
+      <th>Tools available on MISSISSIPPI</th>
+      <th>Tools available on Mandoiu Lab</th>
+      <th>Tools available on MiModD NacreousMap</th>
+      <th>Tools available on Oqtans</th>
+      <th>Tools available on Palfinder</th>
+      <th>Tools available on PepSimili</th>
+      <th>Tools available on PhagePromotor</th>
+      <th>Tools available on UseGalaxy.be</th>
+      <th>Tools available on UseGalaxy.cz</th>
+      <th>Tools available on UseGalaxy.no</th>
+      <th>Tools available on Viral Variant Visualizer (VVV)</th>
+      <th>No. of tool users (5 years) (usegalaxy.eu)</th>
+      <th>No. of tool users (all time) (usegalaxy.eu)</th>
+      <th>Tool usage (5 years) (usegalaxy.eu)</th>
+      <th>Tool usage (all time) (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org)</th>
+      <th>No. of tool users (all time) (usegalaxy.org)</th>
+      <th>Tool usage (5 years) (usegalaxy.org)</th>
+      <th>Tool usage (all time) (usegalaxy.org)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org.au)</th>
+      <th>No. of tool users (all time) (usegalaxy.org.au)</th>
+      <th>Tool usage (5 years) (usegalaxy.org.au)</th>
+      <th>Tool usage (all time) (usegalaxy.org.au)</th>
+      <th>No. of tool users (5 years) - all main servers</th>
+      <th>No. of tool users (all time) - all main servers</th>
+      <th>Tool usage (5 years) - all main servers</th>
+      <th>Tool usage (all time) - all main servers</th>
+      <th>Deprecated</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <td></td>
+      <td>10x_bamtofastq</td>
+      <td>10x_bamtofastq</td>
+      <td>Converts 10x Genomics BAM to FASTQ</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/10XGenomics/bamtofastq</td>
+      <td>Convert Formats</td>
+      <td>10x_bamtofastq</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq</td>
+      <td>1.4.1</td>
+      <td>10x_bamtofastq</td>
+      <td>1.4.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>307</td>
+      <td>307</td>
+      <td>80</td>
+      <td>80</td>
+      <td>8</td>
+      <td>8</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1</td>
+      <td>1</td>
+      <td>318</td>
+      <td>318</td>
+      <td>84</td>
+      <td>84</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>2d_auto_threshold</td>
+      <td>ip_threshold</td>
+      <td>Automatic thresholding</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.</td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>2d_auto_threshold</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold</td>
+      <td>0.18.1</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1434</td>
+      <td>6746</td>
+      <td>120</td>
+      <td>122</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>305</td>
+      <td>305</td>
+      <td>11</td>
+      <td>11</td>
+      <td>1739</td>
+      <td>7051</td>
+      <td>131</td>
+      <td>133</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>2d_feature_extraction</td>
+      <td>ip_2d_feature_extraction</td>
+      <td>2D feature extraction</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.</td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>2d_feature_extraction</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction</td>
+      <td>0.18.1</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1156</td>
+      <td>13842</td>
+      <td>40</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1277</td>
+      <td>13963</td>
+      <td>44</td>
+      <td>46</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>2d_filter_segmentation_by_features</td>
+      <td>ip_2d_filter_segmentation_by_features</td>
+      <td>filter segmentation by rules</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>2d_filter_segmentation_by_features</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features</td>
+      <td>0.0.1-4</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>591</td>
+      <td>6863</td>
+      <td>38</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>119</td>
+      <td>3</td>
+      <td>3</td>
+      <td>710</td>
+      <td>6982</td>
+      <td>41</td>
+      <td>43</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>2d_histogram_equalization</td>
+      <td>ip_histogram_equalization</td>
+      <td>2d histogram equalization</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.</td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>2d_histogram_equalization</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization</td>
+      <td>0.18.1</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>762</td>
+      <td>782</td>
+      <td>100</td>
+      <td>101</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>230</td>
+      <td>230</td>
+      <td>14</td>
+      <td>14</td>
+      <td>992</td>
+      <td>1012</td>
+      <td>114</td>
+      <td>115</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>2d_simple_filter</td>
+      <td>ip_filter_standard</td>
+      <td>2d simple filter</td>
+      <td></td>
+      <td></td>
+      <td>scipy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>2d_simple_filter</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter</td>
+      <td>1.12.0</td>
+      <td>scipy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>948</td>
+      <td>6261</td>
+      <td>98</td>
+      <td>100</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>153</td>
+      <td>153</td>
+      <td>13</td>
+      <td>13</td>
+      <td>1101</td>
+      <td>6414</td>
+      <td>111</td>
+      <td>113</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>AggregateAlignments</td>
+      <td>graphclust_aggregate_alignments</td>
+      <td>Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_aggregate_alignments</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments</td>
+      <td>0.6.0</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>45</td>
+      <td>119</td>
+      <td>14</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45</td>
+      <td>119</td>
+      <td>14</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>AlignCluster</td>
+      <td>graphclust_align_cluster</td>
+      <td>Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_align_cluster</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster</td>
+      <td>0.1</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>189</td>
+      <td>3094</td>
+      <td>23</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>189</td>
+      <td>3094</td>
+      <td>23</td>
+      <td>25</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>CMFinder</td>
+      <td>cmFinder</td>
+      <td>Determines consensus motives for sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_cmfinder</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder</td>
+      <td>0.4</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>25532</td>
+      <td>50045</td>
+      <td>45</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25532</td>
+      <td>50045</td>
+      <td>45</td>
+      <td>57</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>CollectResults</td>
+      <td>glob_report</td>
+      <td>Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_postprocessing</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults</td>
+      <td>0.5</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1119</td>
+      <td>2115</td>
+      <td>50</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1119</td>
+      <td>2115</td>
+      <td>50</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>CollectResultsNoAlign</td>
+      <td>graphclust_glob_report_no_align</td>
+      <td>Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_postprocessing_no_align</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign</td>
+      <td>0.5</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>37</td>
+      <td>108</td>
+      <td>1</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>108</td>
+      <td>1</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>EMLassemblyline</td>
+      <td>annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template</td>
+      <td>Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/EDIorg/EMLassemblyline</td>
+      <td>Ecology</td>
+      <td>emlassemblyline</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline</td>
+      <td>0.1.0+galaxy0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>516</td>
+      <td>516</td>
+      <td>128</td>
+      <td>128</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>516</td>
+      <td>516</td>
+      <td>128</td>
+      <td>128</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>Ecoregionalization_workflow</td>
+      <td>ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker</td>
+      <td>Tools to compute ecoregionalization with BRT model predictions and clustering.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/PaulineSGN/Workflow_Galaxy</td>
+      <td>Ecology</td>
+      <td>ecoregionalization</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow</td>
+      <td>0.1.0+galaxy0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>352</td>
+      <td>352</td>
+      <td>36</td>
+      <td>36</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>352</td>
+      <td>352</td>
+      <td>36</td>
+      <td>36</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>Ensembl-REST</td>
+      <td>get_feature_info, get_genetree, get_sequences</td>
+      <td>A suite of Galaxy tools designed to work with Ensembl REST API.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://rest.ensembl.org</td>
+      <td>Data Source</td>
+      <td></td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST</td>
+      <td>0.1.2</td>
+      <td>requests</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>474</td>
+      <td>2914</td>
+      <td>132</td>
+      <td>163</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>474</td>
+      <td>2914</td>
+      <td>132</td>
+      <td>163</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>GAFA</td>
+      <td>gafa</td>
+      <td>Gene Align and Family Aggregator</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://aequatus.tgac.ac.uk</td>
+      <td>Visualization</td>
+      <td>gafa</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA</td>
+      <td>0.3.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>40</td>
+      <td>47</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>47</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>GSPAN</td>
+      <td>gspan</td>
+      <td>Second step of GraphClust</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_fasta_to_gspan</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN</td>
+      <td>0.4</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>80</td>
+      <td>150</td>
+      <td>18</td>
+      <td>23</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>80</td>
+      <td>150</td>
+      <td>18</td>
+      <td>23</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>Geom_mean_workflow</td>
+      <td>Map_shp, Mean_geom, bar_plot</td>
+      <td>Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom</td>
+      <td>Ecology</td>
+      <td>Geometric means (Dead wood)</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow</td>
+      <td>0.1.0+galaxy0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>53</td>
+      <td>53</td>
+      <td>18</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>53</td>
+      <td>53</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>LocARNAGraphClust</td>
+      <td>locarna_best_subtree</td>
+      <td>MLocARNA computes a multiple sequence-structure alignment of RNA sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_mlocarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust</td>
+      <td>0.4</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>25572</td>
+      <td>50177</td>
+      <td>45</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25572</td>
+      <td>50177</td>
+      <td>45</td>
+      <td>57</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>NSPDK</td>
+      <td>NSPDK_candidateClust, nspdk_sparse</td>
+      <td>Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_nspdk</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK</td>
+      <td>9.2.3.1</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>3210</td>
+      <td>62854</td>
+      <td>96</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3210</td>
+      <td>62854</td>
+      <td>96</td>
+      <td>124</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>PAMPA</td>
+      <td>pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm</td>
+      <td>Tools to compute and analyse biodiversity metrics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Ecology</td>
+      <td>pampa</td>
+      <td>ecology</td>
+      <td>https://github.com/ColineRoyaux/PAMPA-Galaxy</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA</td>
+      <td>0.0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>4</td>
+      <td>0</td>
+      <td>1038</td>
+      <td>1038</td>
+      <td>146</td>
+      <td>146</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>849</td>
+      <td>849</td>
+      <td>38</td>
+      <td>38</td>
+      <td>1887</td>
+      <td>1887</td>
+      <td>184</td>
+      <td>184</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>Plotting</td>
+      <td>motifFinderPlot</td>
+      <td>Plotting results for GraphClust</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_motif_finder_plot</td>
+      <td>rnateam</td>
+      <td>https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting</td>
+      <td>0.4</td>
+      <td>seaborn</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>45</td>
+      <td>71</td>
+      <td>9</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45</td>
+      <td>71</td>
+      <td>9</td>
+      <td>10</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>PrepareForMlocarna</td>
+      <td>preMloc</td>
+      <td>This tool prepares files for locarna step.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_prepocessing_for_mlocarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna</td>
+      <td>0.4</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1202</td>
+      <td>2121</td>
+      <td>48</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1202</td>
+      <td>2121</td>
+      <td>48</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>Preprocessing</td>
+      <td>preproc</td>
+      <td>Preprocessing input for GraphClust</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>graphclust_preprocessing</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing</td>
+      <td>0.5</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1116</td>
+      <td>1897</td>
+      <td>57</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1116</td>
+      <td>1897</td>
+      <td>57</td>
+      <td>71</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>Structure_GSPAN</td>
+      <td>structure_to_gspan</td>
+      <td>Convert RNA structure to GSPAN graphs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>structure_to_gspan</td>
+      <td>rnateam</td>
+      <td>https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN</td>
+      <td>0.4</td>
+      <td>graphclust-wrappers</td>
+      <td>0.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>991</td>
+      <td>3060</td>
+      <td>50</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>991</td>
+      <td>3060</td>
+      <td>50</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ThermoRawFileParser</td>
+      <td>thermo_raw_file_converter</td>
+      <td>Thermo RAW file converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/compomics/ThermoRawFileParser</td>
+      <td>Proteomics</td>
+      <td>thermo_raw_file_converter</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser</td>
+      <td>1.3.4</td>
+      <td>thermorawfileparser</td>
+      <td>1.4.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2467</td>
+      <td>2959</td>
+      <td>88</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1097</td>
+      <td>1097</td>
+      <td>18</td>
+      <td>18</td>
+      <td>3564</td>
+      <td>4056</td>
+      <td>106</td>
+      <td>142</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>TreeBest</td>
+      <td>treebest_best</td>
+      <td>TreeBeST best</td>
+      <td>treebest</td>
+      <td>treebest</td>
+      <td></td>
+      <td>TreeBeST</td>
+      <td>TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.</td>
+      <td>Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)</td>
+      <td>Phylogenetics</td>
+      <td>To update</td>
+      <td>http://treesoft.sourceforge.net/treebest.shtml</td>
+      <td>Phylogenetics</td>
+      <td>treebest_best</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest</td>
+      <td>1.9.2.post0</td>
+      <td>treebest</td>
+      <td>1.9.2.post1</td>
+      <td>Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)</td>
+      <td>Phylogenetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1003</td>
+      <td>1022</td>
+      <td>48</td>
+      <td>52</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1003</td>
+      <td>1022</td>
+      <td>48</td>
+      <td>52</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>TrimNs</td>
+      <td>trimns</td>
+      <td>TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs</td>
+      <td>Assembly</td>
+      <td>trimns</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs</td>
+      <td>0.1.0</td>
+      <td>trimns_vgp</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ab1_fastq</td>
+      <td>ab1_fastq_converter</td>
+      <td>Tool to convert ab1 files into FASTQ files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats</td>
+      <td>ab1fastq</td>
+      <td>ecology</td>
+      <td>https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq</td>
+      <td>1.20.0</td>
+      <td>bioconductor-sangerseqr</td>
+      <td>1.38.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>49465</td>
+      <td>49465</td>
+      <td>281</td>
+      <td>281</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>49465</td>
+      <td>49465</td>
+      <td>281</td>
+      <td>281</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>abacas</td>
+      <td>abacas</td>
+      <td>Order and Orientate Contigs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/abacas</td>
+      <td>Assembly</td>
+      <td>abacas</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/abacas</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas</td>
+      <td>1.1</td>
+      <td>mummer</td>
+      <td>3.23</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>abricate</td>
+      <td>abricate, abricate_list, abricate_summary</td>
+      <td>Mass screening of contigs for antiobiotic resistance genes</td>
+      <td>ABRicate</td>
+      <td>ABRicate</td>
+      <td></td>
+      <td>ABRicate</td>
+      <td>Mass screening of contigs for antimicrobial resistance or virulence genes.</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Genomics, Microbiology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tseemann/abricate</td>
+      <td>Sequence Analysis</td>
+      <td>abricate</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate</td>
+      <td>1.0.1</td>
+      <td>abricate</td>
+      <td>1.0.1</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Genomics, Microbiology</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>619817</td>
+      <td>622353</td>
+      <td>4097</td>
+      <td>4130</td>
+      <td>320454</td>
+      <td>320454</td>
+      <td>2915</td>
+      <td>2915</td>
+      <td>496156</td>
+      <td>503743</td>
+      <td>2012</td>
+      <td>2227</td>
+      <td>1436427</td>
+      <td>1446550</td>
+      <td>9024</td>
+      <td>9272</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>abritamr</td>
+      <td>abritamr</td>
+      <td>A pipeline for running AMRfinderPlus and collating results into functional classes</td>
+      <td>abritamr</td>
+      <td>abritamr</td>
+      <td></td>
+      <td>abriTAMR</td>
+      <td>an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Microbiology, Public health and epidemiology, Infectious disease</td>
+      <td>Up-to-date</td>
+      <td>https://zenodo.org/record/7370628</td>
+      <td>Sequence Analysis</td>
+      <td>abritamr</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr</td>
+      <td>1.0.19</td>
+      <td>abritamr</td>
+      <td>1.0.19</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Microbiology, Public health and epidemiology, Infectious disease</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>109</td>
+      <td>109</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>109</td>
+      <td>109</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>abyss</td>
+      <td>abyss-pe</td>
+      <td>Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler</td>
+      <td>abyss</td>
+      <td>abyss</td>
+      <td></td>
+      <td>ABySS</td>
+      <td>De novo genome sequence assembler using short reads.</td>
+      <td>Genome assembly, De-novo assembly, Scaffolding</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>http://www.bcgsc.ca/platform/bioinfo/software/abyss</td>
+      <td>Assembly</td>
+      <td>abyss</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss</td>
+      <td>2.3.9</td>
+      <td>abyss</td>
+      <td>2.3.9</td>
+      <td>Genome assembly, De-novo assembly, Scaffolding</td>
+      <td>Sequence assembly</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5543</td>
+      <td>5543</td>
+      <td>1042</td>
+      <td>1042</td>
+      <td>1301</td>
+      <td>1305</td>
+      <td>413</td>
+      <td>414</td>
+      <td>2030</td>
+      <td>2030</td>
+      <td>299</td>
+      <td>299</td>
+      <td>8874</td>
+      <td>8878</td>
+      <td>1754</td>
+      <td>1755</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>adapter_removal</td>
+      <td>adapter_removal</td>
+      <td>Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.</td>
+      <td>adapterremoval</td>
+      <td>adapterremoval</td>
+      <td></td>
+      <td>AdapterRemoval</td>
+      <td>AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.</td>
+      <td>Sequence trimming, Sequence merging, Primer removal</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/MikkelSchubert/adapterremoval</td>
+      <td>Fasta Manipulation, Sequence Analysis</td>
+      <td>adapter_removal</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal</td>
+      <td>2.3.4</td>
+      <td>adapterremoval</td>
+      <td>2.3.4</td>
+      <td>Sequence trimming, Sequence merging, Primer removal</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>348</td>
+      <td>348</td>
+      <td>62</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>348</td>
+      <td>348</td>
+      <td>62</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>add_input_name_as_column</td>
+      <td>addName</td>
+      <td>Add input name as column on an existing tabular file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column</td>
+      <td>Text Manipulation</td>
+      <td>add_input_name_as_column</td>
+      <td>mvdbeek</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column</td>
+      <td>0.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>76834</td>
+      <td>86002</td>
+      <td>227</td>
+      <td>246</td>
+      <td>20174</td>
+      <td>20953</td>
+      <td>312</td>
+      <td>395</td>
+      <td>11</td>
+      <td>11</td>
+      <td>2</td>
+      <td>2</td>
+      <td>97019</td>
+      <td>106966</td>
+      <td>541</td>
+      <td>643</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>add_line_to_file</td>
+      <td>add_line_to_file</td>
+      <td>Adds a text line to the beginning or end of a file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>add_line_to_file</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file</td>
+      <td>0.1.0</td>
+      <td>coreutils</td>
+      <td>8.25</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15933</td>
+      <td>15933</td>
+      <td>378</td>
+      <td>378</td>
+      <td>1736</td>
+      <td>1736</td>
+      <td>214</td>
+      <td>214</td>
+      <td>380</td>
+      <td>380</td>
+      <td>28</td>
+      <td>28</td>
+      <td>18049</td>
+      <td>18049</td>
+      <td>620</td>
+      <td>620</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>add_value</td>
+      <td>addValue</td>
+      <td>Add a value as a new column.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>add_value</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value</td>
+      <td>1.0.1</td>
+      <td>perl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>37860</td>
+      <td>374587</td>
+      <td>1293</td>
+      <td>1610</td>
+      <td>17588</td>
+      <td>293713</td>
+      <td>1243</td>
+      <td>6197</td>
+      <td>3873</td>
+      <td>4397</td>
+      <td>202</td>
+      <td>229</td>
+      <td>59321</td>
+      <td>672697</td>
+      <td>2738</td>
+      <td>8036</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>aegean</td>
+      <td>aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval</td>
+      <td>AEGeAn toolkit wrappers</td>
+      <td>gaeval</td>
+      <td>gaeval</td>
+      <td></td>
+      <td>GAEVAL</td>
+      <td>Gene Annotation EVAluation.</td>
+      <td>Sequence annotation</td>
+      <td>Sequence analysis, Gene structure</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BrendelGroup/AEGeAn</td>
+      <td>Transcriptomics, Sequence Analysis</td>
+      <td>aegean</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean</td>
+      <td>0.16.0</td>
+      <td>aegean</td>
+      <td>0.16.0</td>
+      <td>Sequence annotation</td>
+      <td>Sequence analysis, Gene structure</td>
+      <td>1</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>1</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>200</td>
+      <td>200</td>
+      <td>77</td>
+      <td>77</td>
+      <td>83</td>
+      <td>83</td>
+      <td>39</td>
+      <td>39</td>
+      <td>1747</td>
+      <td>1747</td>
+      <td>44</td>
+      <td>44</td>
+      <td>2030</td>
+      <td>2030</td>
+      <td>160</td>
+      <td>160</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>agat</td>
+      <td>agat</td>
+      <td>GTF/GFF analysis toolkit</td>
+      <td>agat</td>
+      <td>agat</td>
+      <td></td>
+      <td>AGAT</td>
+      <td>Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.</td>
+      <td>Data handling, Genome annotation</td>
+      <td>Genomics</td>
+      <td>To update</td>
+      <td>https://github.com/NBISweden/AGAT</td>
+      <td>Convert Formats, Statistics, Fasta Manipulation</td>
+      <td>agat</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/agat</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/agat</td>
+      <td>1.4.0</td>
+      <td>agat</td>
+      <td>1.4.1</td>
+      <td>Data handling, Genome annotation</td>
+      <td>Genomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1436</td>
+      <td>1436</td>
+      <td>244</td>
+      <td>244</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>119</td>
+      <td>10</td>
+      <td>10</td>
+      <td>1555</td>
+      <td>1555</td>
+      <td>254</td>
+      <td>254</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>aldex2</td>
+      <td>aldex2</td>
+      <td>Performs analysis Of differential abundance taking sample variation into account</td>
+      <td>aldex2</td>
+      <td>aldex2</td>
+      <td></td>
+      <td>ALDEx2</td>
+      <td>A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.</td>
+      <td>Statistical inference</td>
+      <td>Gene expression, Statistics and probability</td>
+      <td>To update</td>
+      <td>https://github.com/ggloor/ALDEx_bioc</td>
+      <td>Metagenomics</td>
+      <td>aldex2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2</td>
+      <td>1.26.0</td>
+      <td>bioconductor-aldex2</td>
+      <td>1.34.0</td>
+      <td>Statistical inference</td>
+      <td>Gene expression, Statistics and probability</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>262</td>
+      <td>262</td>
+      <td>36</td>
+      <td>36</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>262</td>
+      <td>262</td>
+      <td>36</td>
+      <td>36</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>align_back_trans</td>
+      <td>align_back_trans</td>
+      <td>Thread nucleotides onto a protein alignment (back-translation)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans</td>
+      <td>Fasta Manipulation, Sequence Analysis</td>
+      <td>align_back_trans</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans</td>
+      <td>0.0.10</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>511</td>
+      <td>541</td>
+      <td>32</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>511</td>
+      <td>541</td>
+      <td>32</td>
+      <td>35</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>allegro</td>
+      <td>allegro</td>
+      <td>Linkage and haplotype analysis from deCODE</td>
+      <td>allegro</td>
+      <td>allegro</td>
+      <td></td>
+      <td>Allegro</td>
+      <td>It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.</td>
+      <td>Sequence motif discovery</td>
+      <td>Sequence analysis, Transcription factors and regulatory sites, DNA</td>
+      <td>To update</td>
+      <td>http://www.decode.com/software/</td>
+      <td>Variant Analysis</td>
+      <td>allegro</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro</td>
+      <td>@VER@.0</td>
+      <td>allegro</td>
+      <td>3</td>
+      <td>Sequence motif discovery</td>
+      <td>Sequence analysis, Transcription factors and regulatory sites, DNA</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ambertools</td>
+      <td>ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap</td>
+      <td>Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://ambermd.org/AmberTools.php</td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>ambertools</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools</td>
+      <td>21.10</td>
+      <td>ambertools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>7</td>
+      <td>2</td>
+      <td>7</td>
+      <td>0</td>
+      <td>7</td>
+      <td>2</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>7</td>
+      <td>5</td>
+      <td>0</td>
+      <td>41793</td>
+      <td>41881</td>
+      <td>510</td>
+      <td>511</td>
+      <td>1126</td>
+      <td>1126</td>
+      <td>159</td>
+      <td>159</td>
+      <td>1552</td>
+      <td>1552</td>
+      <td>85</td>
+      <td>85</td>
+      <td>44471</td>
+      <td>44559</td>
+      <td>754</td>
+      <td>755</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>amplican</td>
+      <td>amplican</td>
+      <td>AmpliCan is an analysis tool for genome editing.</td>
+      <td>amplican</td>
+      <td>amplican</td>
+      <td></td>
+      <td>amplican</td>
+      <td>It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.</td>
+      <td>Alignment, Standardisation and normalisation</td>
+      <td>PCR experiment, Statistics and probability</td>
+      <td>To update</td>
+      <td>https://github.com/valenlab/amplican</td>
+      <td>Sequence Analysis</td>
+      <td>amplican</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican</td>
+      <td>1.14.0</td>
+      <td>bioconductor-amplican</td>
+      <td>1.24.0</td>
+      <td>Alignment, Standardisation and normalisation</td>
+      <td>PCR experiment, Statistics and probability</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>81</td>
+      <td>81</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>81</td>
+      <td>81</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ampvis2</td>
+      <td>ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn</td>
+      <td>ampvis2</td>
+      <td>ampvis</td>
+      <td>ampvis</td>
+      <td></td>
+      <td>ampvis</td>
+      <td>ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.</td>
+      <td>Analysis, Visualisation</td>
+      <td>Biodiversity</td>
+      <td>To update</td>
+      <td>https://github.com/MadsAlbertsen/ampvis2/</td>
+      <td>Metagenomics</td>
+      <td>ampvis2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2</td>
+      <td>2.8.9</td>
+      <td></td>
+      <td></td>
+      <td>Analysis, Visualisation</td>
+      <td>Biodiversity</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1213</td>
+      <td>1213</td>
+      <td>155</td>
+      <td>155</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1213</td>
+      <td>1213</td>
+      <td>155</td>
+      <td>155</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>amrfinderplus</td>
+      <td>amrfinderplus</td>
+      <td>"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms.</td>
+      <td>amrfinderplus</td>
+      <td>amrfinderplus</td>
+      <td></td>
+      <td>AMRFinderPlus</td>
+      <td>AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Microbiology, Public health and epidemiology, Infectious disease</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/ncbi/amr</td>
+      <td>Sequence Analysis</td>
+      <td>AMRFinderPlus</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus</td>
+      <td>3.12.8</td>
+      <td>ncbi-amrfinderplus</td>
+      <td>3.12.8</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Microbiology, Public health and epidemiology, Infectious disease</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5734</td>
+      <td>5734</td>
+      <td>334</td>
+      <td>334</td>
+      <td>1035</td>
+      <td>1035</td>
+      <td>106</td>
+      <td>106</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6769</td>
+      <td>6769</td>
+      <td>440</td>
+      <td>440</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ancombc</td>
+      <td>ancombc</td>
+      <td>Performs analysis of compositions of microbiomes with bias correction.</td>
+      <td>ancombc</td>
+      <td>ancombc</td>
+      <td></td>
+      <td>ANCOMBC</td>
+      <td>Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.</td>
+      <td>DNA barcoding</td>
+      <td>Microbial ecology, Metagenomics, Taxonomy</td>
+      <td>To update</td>
+      <td>https://github.com/FrederickHuangLin/ANCOMBC</td>
+      <td>Metagenomics</td>
+      <td>ancombc</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc</td>
+      <td>1.4.0</td>
+      <td>bioconductor-ancombc</td>
+      <td>2.4.0</td>
+      <td>DNA barcoding</td>
+      <td>Microbial ecology, Metagenomics, Taxonomy</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>anisotropic_diffusion</td>
+      <td>ip_anisotropic_diffusion</td>
+      <td>Anisotropic image diffusion</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>anisotropic_diffusion</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion</td>
+      <td>0.4.0</td>
+      <td>medpy</td>
+      <td>0.4.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>36</td>
+      <td>41</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>36</td>
+      <td>41</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>anndata</td>
+      <td>anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom</td>
+      <td>Import, Export, Inspect and Manipulate Anndata and Loom objects</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://anndata.readthedocs.io</td>
+      <td>Single Cell, Spatial Omics</td>
+      <td>anndata</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata</td>
+      <td>0.10.9</td>
+      <td>anndata</td>
+      <td>0.6.22.post1</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>43047</td>
+      <td>43139</td>
+      <td>1826</td>
+      <td>1827</td>
+      <td>17240</td>
+      <td>17240</td>
+      <td>878</td>
+      <td>878</td>
+      <td>9309</td>
+      <td>9309</td>
+      <td>298</td>
+      <td>298</td>
+      <td>69596</td>
+      <td>69688</td>
+      <td>3002</td>
+      <td>3003</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>annotatemyids</td>
+      <td>annotatemyids</td>
+      <td>annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages</td>
+      <td>annotatemyids</td>
+      <td>annotatemyids</td>
+      <td></td>
+      <td>annotatemyids</td>
+      <td>This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.</td>
+      <td>Annotation</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids</td>
+      <td>Genome annotation</td>
+      <td>annotatemyids</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids</td>
+      <td>3.18.0</td>
+      <td>bioconductor-org.hs.eg.db</td>
+      <td>3.18.0</td>
+      <td>Annotation</td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>29266</td>
+      <td>30655</td>
+      <td>2849</td>
+      <td>2973</td>
+      <td>59299</td>
+      <td>66180</td>
+      <td>5917</td>
+      <td>6355</td>
+      <td>5644</td>
+      <td>5644</td>
+      <td>1049</td>
+      <td>1049</td>
+      <td>94209</td>
+      <td>102479</td>
+      <td>9815</td>
+      <td>10377</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>antarna</td>
+      <td>antarna</td>
+      <td>antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>antarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna</td>
+      <td>1.1</td>
+      <td>antarna</td>
+      <td>2.0.1.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>292</td>
+      <td>306</td>
+      <td>5</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>292</td>
+      <td>306</td>
+      <td>5</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>antismash</td>
+      <td>antismash</td>
+      <td>Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters</td>
+      <td>antismash</td>
+      <td>antismash</td>
+      <td></td>
+      <td>antiSMASH</td>
+      <td>Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.</td>
+      <td>Sequence clustering, Gene prediction, Differential gene expression analysis</td>
+      <td>Molecular interactions, pathways and networks, Gene and protein families</td>
+      <td>To update</td>
+      <td>https://antismash.secondarymetabolites.org</td>
+      <td>Sequence Analysis</td>
+      <td>antismash</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/antismash</td>
+      <td>6.1.1</td>
+      <td>antismash</td>
+      <td>7.1.0</td>
+      <td>Sequence clustering, Gene prediction, Differential gene expression analysis</td>
+      <td>Molecular interactions, pathways and networks, Gene and protein families</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15949</td>
+      <td>16490</td>
+      <td>726</td>
+      <td>811</td>
+      <td>5113</td>
+      <td>5113</td>
+      <td>649</td>
+      <td>649</td>
+      <td>6043</td>
+      <td>6043</td>
+      <td>169</td>
+      <td>169</td>
+      <td>27105</td>
+      <td>27646</td>
+      <td>1544</td>
+      <td>1629</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>apoc</td>
+      <td>apoc</td>
+      <td>Large-scale structural comparison of protein pockets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://cssb.biology.gatech.edu/APoc</td>
+      <td>Computational chemistry</td>
+      <td>apoc</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc</td>
+      <td>1.0+galaxy1</td>
+      <td>apoc</td>
+      <td>1b16</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>apollo</td>
+      <td>create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism</td>
+      <td>Access an Apollo instance from Galaxy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxy-genome-annotation/python-apollo</td>
+      <td>Web Services</td>
+      <td></td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo</td>
+      <td></td>
+      <td>apollo</td>
+      <td>4.2.13</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>3600</td>
+      <td>3760</td>
+      <td>883</td>
+      <td>911</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3606</td>
+      <td>3766</td>
+      <td>887</td>
+      <td>915</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>appendfdr</td>
+      <td>append_fdr</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>appendfdr</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>aquainfra_importer</td>
+      <td>aquainfra_importer</td>
+      <td>A data source tool for downloading datasets via the AquaINFRA Interaction Platform.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AquaINFRA/galaxy</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>75</td>
+      <td>75</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>75</td>
+      <td>75</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>aresite2</td>
+      <td>AREsite2_REST</td>
+      <td>AREsite2 REST Interface</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rna.tbi.univie.ac.at/AREsite</td>
+      <td>RNA, Data Source, Sequence Analysis</td>
+      <td>aresite2</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2</td>
+      <td>0.1.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>59</td>
+      <td>74</td>
+      <td>10</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59</td>
+      <td>74</td>
+      <td>10</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>argnorm</td>
+      <td>argnorm</td>
+      <td>argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database</td>
+      <td>argnorm</td>
+      <td>argnorm</td>
+      <td></td>
+      <td>argNorm</td>
+      <td>argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.</td>
+      <td>Gene functional annotation</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BigDataBiology/argNorm</td>
+      <td>Genome annotation</td>
+      <td>argnorm</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm</td>
+      <td>0.6.0</td>
+      <td>argnorm</td>
+      <td>0.6.0</td>
+      <td>Gene functional annotation</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>arriba</td>
+      <td>arriba, arriba_draw_fusions, arriba_get_filters</td>
+      <td>Arriba detects fusion genes in RNA-Seq data after running RNA-STAR</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/suhrig/arriba</td>
+      <td>Sequence Analysis, Transcriptomics</td>
+      <td>arriba</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba</td>
+      <td>2.4.0</td>
+      <td>arriba</td>
+      <td>2.4.0</td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3670</td>
+      <td>3670</td>
+      <td>71</td>
+      <td>71</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>234</td>
+      <td>234</td>
+      <td>10</td>
+      <td>10</td>
+      <td>3907</td>
+      <td>3907</td>
+      <td>83</td>
+      <td>83</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>art</td>
+      <td>art_454, art_illumina, art_solid</td>
+      <td>Simulator for Illumina, 454, and SOLiD sequencing data</td>
+      <td>art</td>
+      <td>art</td>
+      <td></td>
+      <td>ART</td>
+      <td>ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD</td>
+      <td>Conversion</td>
+      <td>Bioinformatics</td>
+      <td>To update</td>
+      <td>http://www.niehs.nih.gov/research/resources/software/biostatistics/art/</td>
+      <td>Sequence Analysis, Data Source</td>
+      <td>art</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/art</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/art</td>
+      <td>2014.11.03.0</td>
+      <td>art</td>
+      <td>2016.06.05</td>
+      <td>Conversion</td>
+      <td>Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>140</td>
+      <td>140</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>140</td>
+      <td>140</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>artbio_bam_cleaning</td>
+      <td>artbio_bam_cleaning</td>
+      <td>filter bam files before somatic-varscan or lumpy-smoove analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>SAM, Variant Analysis</td>
+      <td>artbio_bam_cleaning</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning</td>
+      <td>1.10+galaxy0</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>artic</td>
+      <td>artic_guppyplex, artic_minion</td>
+      <td>The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building</td>
+      <td>artic</td>
+      <td>artic</td>
+      <td></td>
+      <td>ARTIC</td>
+      <td>A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore</td>
+      <td>Sequence alignment</td>
+      <td>Genomics</td>
+      <td>To update</td>
+      <td>https://github.com/artic-network/fieldbioinformatics</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic</td>
+      <td></td>
+      <td>artic</td>
+      <td>1.2.4</td>
+      <td>Sequence alignment</td>
+      <td>Genomics</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9021</td>
+      <td>9021</td>
+      <td>238</td>
+      <td>238</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9021</td>
+      <td>9021</td>
+      <td>238</td>
+      <td>238</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>askomics</td>
+      <td>askomics_integrate</td>
+      <td>Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/askomics/</td>
+      <td>Web Services</td>
+      <td></td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics</td>
+      <td></td>
+      <td>askocli</td>
+      <td>0.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>askor</td>
+      <td>askor_de</td>
+      <td>AskoR links EdgeR and AskOmics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/askomics/askoR</td>
+      <td>Transcriptomics</td>
+      <td>askor_de</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/askor</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/askor</td>
+      <td>0.2</td>
+      <td>bioconductor-limma</td>
+      <td>3.58.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>assembly-stats</td>
+      <td>assembly_stats</td>
+      <td>Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/rjchallis/assembly-stats</td>
+      <td>Assembly</td>
+      <td>assembly_stats</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats</td>
+      <td>17.02</td>
+      <td>rjchallis-assembly-stats</td>
+      <td>17.02</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>assemblystats</td>
+      <td>assemblystats</td>
+      <td>Summarise an assembly (e.g. N50 metrics)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Assembly</td>
+      <td>assemblystats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats</td>
+      <td>1.1.0</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>astral</td>
+      <td>astral</td>
+      <td>Tool for estimating an unrooted species tree given a set of unrooted gene trees</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/smirarab/ASTRAL</td>
+      <td>Phylogenetics</td>
+      <td>astral</td>
+      <td>iuc</td>
+      <td>https://github.com/usegalaxy-be/galaxytools/tree/main/astral</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral</td>
+      <td>5.7.8</td>
+      <td>astral-tree</td>
+      <td>5.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>151</td>
+      <td>151</td>
+      <td>5</td>
+      <td>5</td>
+      <td>151</td>
+      <td>151</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>astropytools</td>
+      <td>astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo</td>
+      <td>AstropyTools library contains Galaxy tools for elementary Astrophysical operations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/astropy/astropy</td>
+      <td>Astronomy</td>
+      <td>astropytools</td>
+      <td>volodymyrss</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools</td>
+      <td>0.1.0+galaxy0</td>
+      <td>astropy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>atactk_trim_adapters</td>
+      <td>atactk_trim_adapters</td>
+      <td>Trim adapters from paired-end HTS reads.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ParkerLab/atactk/</td>
+      <td>Fastq Manipulation</td>
+      <td>atactk_trim_adapters</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters</td>
+      <td>0.1.6</td>
+      <td>atactk</td>
+      <td>0.1.9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>232</td>
+      <td>279</td>
+      <td>62</td>
+      <td>72</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>232</td>
+      <td>279</td>
+      <td>62</td>
+      <td>72</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>augustus</td>
+      <td>augustus, augustus_training</td>
+      <td>AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.</td>
+      <td>augustus</td>
+      <td>augustus</td>
+      <td></td>
+      <td>AUGUSTUS</td>
+      <td>AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.</td>
+      <td>Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation</td>
+      <td>Gene transcripts, Gene and protein families</td>
+      <td>To update</td>
+      <td>http://bioinf.uni-greifswald.de/augustus/</td>
+      <td>Sequence Analysis</td>
+      <td>augustus</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus</td>
+      <td>3.4.0</td>
+      <td>augustus</td>
+      <td>3.5.0</td>
+      <td>Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation</td>
+      <td>Gene transcripts, Gene and protein families</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>12890</td>
+      <td>13988</td>
+      <td>1826</td>
+      <td>1988</td>
+      <td>14901</td>
+      <td>14901</td>
+      <td>2633</td>
+      <td>2633</td>
+      <td>6187</td>
+      <td>6187</td>
+      <td>511</td>
+      <td>511</td>
+      <td>33978</td>
+      <td>35076</td>
+      <td>4970</td>
+      <td>5132</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>augustus</td>
+      <td>augustus</td>
+      <td>AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://bioinf.uni-greifswald.de/augustus/</td>
+      <td>Sequence Analysis</td>
+      <td>augustus</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/augustus</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/augustus</td>
+      <td>3.1.0</td>
+      <td>augustus</td>
+      <td>3.5.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>10109</td>
+      <td>11052</td>
+      <td>1378</td>
+      <td>1509</td>
+      <td>12573</td>
+      <td>12573</td>
+      <td>2206</td>
+      <td>2206</td>
+      <td>5274</td>
+      <td>5274</td>
+      <td>369</td>
+      <td>369</td>
+      <td>27956</td>
+      <td>28899</td>
+      <td>3953</td>
+      <td>4084</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>b2btools</td>
+      <td>b2btools_single_sequence</td>
+      <td>This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.</td>
+      <td>b2btools</td>
+      <td>b2btools</td>
+      <td></td>
+      <td>b2bTools</td>
+      <td>The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA</td>
+      <td>Protein disorder prediction, Protein secondary structure prediction, Protein feature detection</td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bio2byte.be</td>
+      <td>Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools</td>
+      <td>3.0.5+galaxy0</td>
+      <td>b2btools</td>
+      <td>3.0.7</td>
+      <td>Protein disorder prediction, Protein secondary structure prediction</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>369</td>
+      <td>369</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>369</td>
+      <td>369</td>
+      <td>19</td>
+      <td>19</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>background_removal</td>
+      <td>background_removal</td>
+      <td>Background removal filters using scikit-image</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>background_removal</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tools/background_removal</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal</td>
+      <td>0.24.0</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bakta</td>
+      <td>bakta</td>
+      <td>"Bakta is a tool for the rapid &amp; standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON &amp; bioinformatics standard file formats for automatic downstream analysis."</td>
+      <td>bakta</td>
+      <td>bakta</td>
+      <td></td>
+      <td>Bakta</td>
+      <td>Rapid &amp; standardized annotation of bacterial genomes, MAGs &amp; plasmids</td>
+      <td>Genome annotation</td>
+      <td>Genomics, Data submission, annotation and curation, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/oschwengers/bakta</td>
+      <td>Sequence Analysis</td>
+      <td>bakta</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta</td>
+      <td>1.9.4</td>
+      <td>bakta</td>
+      <td>1.9.4</td>
+      <td>Genome annotation</td>
+      <td>Genomics, Data submission, annotation and curation, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>11117</td>
+      <td>11117</td>
+      <td>534</td>
+      <td>534</td>
+      <td>19</td>
+      <td>19</td>
+      <td>1</td>
+      <td>1</td>
+      <td>9601</td>
+      <td>9601</td>
+      <td>167</td>
+      <td>167</td>
+      <td>20737</td>
+      <td>20737</td>
+      <td>702</td>
+      <td>702</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bam2mappingstats</td>
+      <td>bam2mappingstats</td>
+      <td>Generates mapping stats from a bam file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Assembly</td>
+      <td>bam2mappingstats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats</td>
+      <td>1.1.0</td>
+      <td>perl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bam_to_scidx</td>
+      <td>bam_to_scidx</td>
+      <td>Contains a tool that converts a BAM file to an ScIdx file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx</td>
+      <td>Convert Formats</td>
+      <td>bam_to_scidx</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx</td>
+      <td>1.0.1</td>
+      <td>openjdk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>83</td>
+      <td>131</td>
+      <td>15</td>
+      <td>20</td>
+      <td>329</td>
+      <td>785</td>
+      <td>50</td>
+      <td>210</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>412</td>
+      <td>916</td>
+      <td>65</td>
+      <td>230</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamclipper</td>
+      <td>bamclipper</td>
+      <td>Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tommyau/bamclipper</td>
+      <td>Sequence Analysis</td>
+      <td>bamclipper</td>
+      <td>nml</td>
+      <td>https://github.com/tommyau/bamclipper</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper</td>
+      <td>1.0.0</td>
+      <td>bamclipper</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamhash</td>
+      <td>bamhash</td>
+      <td>Hash BAM and FASTQ files to verify data integrity</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/DecodeGenetics/BamHash</td>
+      <td>Sequence Analysis</td>
+      <td>bamhash</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bamhash</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bamhash</td>
+      <td>1.1</td>
+      <td>bamhash</td>
+      <td>1.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>158</td>
+      <td>181</td>
+      <td>40</td>
+      <td>44</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>181</td>
+      <td>40</td>
+      <td>44</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamparse</td>
+      <td>bamparse</td>
+      <td>Generates hit count lists from bam alignments.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Transcriptomics</td>
+      <td>bamparse</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse</td>
+      <td>4.1.1</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamtools</td>
+      <td>bamtools</td>
+      <td>Operate on and transform BAM datasets in various ways using bamtools</td>
+      <td>bamtools</td>
+      <td>bamtools</td>
+      <td></td>
+      <td>BamTools</td>
+      <td>BamTools provides a fast, flexible C++ API &amp; toolkit for reading, writing, and managing BAM files.</td>
+      <td>Data handling, Sequence alignment analysis</td>
+      <td>Sequencing, Data management, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pezmaster31/bamtools</td>
+      <td>Sequence Analysis, SAM</td>
+      <td>bamtools</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools</td>
+      <td>2.5.2</td>
+      <td>bamtools</td>
+      <td>2.5.2</td>
+      <td>Data handling, Sequence alignment analysis</td>
+      <td>Sequencing, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>14693</td>
+      <td>15620</td>
+      <td>653</td>
+      <td>721</td>
+      <td>61872</td>
+      <td>101400</td>
+      <td>1656</td>
+      <td>5678</td>
+      <td>39</td>
+      <td>39</td>
+      <td>3</td>
+      <td>3</td>
+      <td>76604</td>
+      <td>117059</td>
+      <td>2312</td>
+      <td>6402</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamtools_filter</td>
+      <td>bamFilter</td>
+      <td>Filter BAM datasets on various attributes using bamtools filter</td>
+      <td>bamtools</td>
+      <td>bamtools</td>
+      <td></td>
+      <td>BamTools</td>
+      <td>BamTools provides a fast, flexible C++ API &amp; toolkit for reading, writing, and managing BAM files.</td>
+      <td>Data handling, Sequence alignment analysis</td>
+      <td>Sequencing, Data management, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pezmaster31/bamtools</td>
+      <td>Sequence Analysis, SAM</td>
+      <td>bamtools_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter</td>
+      <td>2.5.2</td>
+      <td>bamtools</td>
+      <td>2.5.2</td>
+      <td>Data handling, Sequence alignment analysis</td>
+      <td>Sequencing, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>115954</td>
+      <td>124795</td>
+      <td>2994</td>
+      <td>3180</td>
+      <td>95433</td>
+      <td>142254</td>
+      <td>6712</td>
+      <td>10660</td>
+      <td>5793</td>
+      <td>5793</td>
+      <td>497</td>
+      <td>497</td>
+      <td>217180</td>
+      <td>272842</td>
+      <td>10203</td>
+      <td>14337</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamtools_split</td>
+      <td>bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag</td>
+      <td>Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.</td>
+      <td>bamtools</td>
+      <td>bamtools</td>
+      <td></td>
+      <td>BamTools</td>
+      <td>BamTools provides a fast, flexible C++ API &amp; toolkit for reading, writing, and managing BAM files.</td>
+      <td>Data handling, Sequence alignment analysis</td>
+      <td>Sequencing, Data management, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pezmaster31/bamtools</td>
+      <td>Sequence Analysis, SAM</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split</td>
+      <td>2.5.2</td>
+      <td>bamtools</td>
+      <td>2.5.2</td>
+      <td>Data handling, Sequence alignment analysis</td>
+      <td>Sequencing, Sequence analysis</td>
+      <td>4</td>
+      <td>3</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>3</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9073</td>
+      <td>9073</td>
+      <td>401</td>
+      <td>401</td>
+      <td>2746</td>
+      <td>2746</td>
+      <td>224</td>
+      <td>224</td>
+      <td>103</td>
+      <td>103</td>
+      <td>10</td>
+      <td>10</td>
+      <td>11922</td>
+      <td>11922</td>
+      <td>635</td>
+      <td>635</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bamutil</td>
+      <td>bamutil_clip_overlap, bamutil_diff</td>
+      <td>bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/statgen/bamUtil</td>
+      <td>Sequence Analysis</td>
+      <td>bamutil</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil</td>
+      <td></td>
+      <td>bamutil</td>
+      <td>1.0.15</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45</td>
+      <td>45</td>
+      <td>20</td>
+      <td>20</td>
+      <td>69</td>
+      <td>69</td>
+      <td>21</td>
+      <td>21</td>
+      <td>258</td>
+      <td>258</td>
+      <td>1</td>
+      <td>1</td>
+      <td>372</td>
+      <td>372</td>
+      <td>42</td>
+      <td>42</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bandage</td>
+      <td>bandage_image, bandage_info</td>
+      <td>Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily</td>
+      <td>bandage</td>
+      <td>bandage</td>
+      <td></td>
+      <td>Bandage</td>
+      <td>GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.</td>
+      <td>Sequence assembly visualisation</td>
+      <td>Genomics, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/rrwick/Bandage</td>
+      <td>Visualization</td>
+      <td>bandage</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage</td>
+      <td>2022.09</td>
+      <td>bandage_ng</td>
+      <td>2022.09</td>
+      <td>Sequence assembly visualisation</td>
+      <td>Genomics, Sequence assembly</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>55392</td>
+      <td>56095</td>
+      <td>4951</td>
+      <td>5035</td>
+      <td>47603</td>
+      <td>47603</td>
+      <td>4916</td>
+      <td>4916</td>
+      <td>18089</td>
+      <td>18089</td>
+      <td>3121</td>
+      <td>3121</td>
+      <td>121084</td>
+      <td>121787</td>
+      <td>12988</td>
+      <td>13072</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>barcode_collapse</td>
+      <td>barcode_collapse</td>
+      <td>Paired End randomer aware duplicate removal algorithm</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/YeoLab/gscripts</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>barcode_collapse</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse</td>
+      <td>0.1.0</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>barcode_splitter</td>
+      <td>barcode_splitter</td>
+      <td>A utility to split sequence files using multiple sets of barcodes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/princeton_genomics/barcode_splitter/</td>
+      <td>Fastq Manipulation</td>
+      <td>barcode_splitter</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter</td>
+      <td>0.18.4.0</td>
+      <td>barcode_splitter</td>
+      <td>0.18.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>baredsc</td>
+      <td>baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d</td>
+      <td>baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.</td>
+      <td>baredsc</td>
+      <td>baredsc</td>
+      <td></td>
+      <td>baredSC</td>
+      <td>The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.</td>
+      <td>Data retrieval, Expression correlation analysis, Differential gene expression profiling</td>
+      <td>RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lldelisle/baredSC</td>
+      <td>Single Cell, Transcriptomics, Visualization</td>
+      <td>baredsc</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc</td>
+      <td>1.1.3</td>
+      <td>baredsc</td>
+      <td>1.1.3</td>
+      <td>Data retrieval, Expression correlation analysis, Differential gene expression profiling</td>
+      <td>RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>111</td>
+      <td>111</td>
+      <td>8</td>
+      <td>8</td>
+      <td>29</td>
+      <td>29</td>
+      <td>10</td>
+      <td>10</td>
+      <td>21</td>
+      <td>21</td>
+      <td>4</td>
+      <td>4</td>
+      <td>161</td>
+      <td>161</td>
+      <td>22</td>
+      <td>22</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>baric_archive</td>
+      <td>baric_archive_rennes, baric_archive_toulouse</td>
+      <td>A data source tool to fetch data from a BARIC Archive server.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.cesgo.org/catibaric/</td>
+      <td>Data Source</td>
+      <td></td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>barrnap</td>
+      <td>barrnap</td>
+      <td>Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.</td>
+      <td>barrnap</td>
+      <td>barrnap</td>
+      <td></td>
+      <td>Barrnap</td>
+      <td>Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).</td>
+      <td>Gene prediction</td>
+      <td>Genomics, Model organisms, Model organisms</td>
+      <td>To update</td>
+      <td>https://github.com/tseemann/barrnap</td>
+      <td>Sequence Analysis</td>
+      <td>barrnap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap</td>
+      <td>1.2.2</td>
+      <td>barrnap</td>
+      <td>0.9</td>
+      <td>Gene prediction</td>
+      <td>Genomics, Model organisms, Model organisms</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6041</td>
+      <td>6041</td>
+      <td>316</td>
+      <td>316</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6723</td>
+      <td>7273</td>
+      <td>240</td>
+      <td>322</td>
+      <td>12764</td>
+      <td>13314</td>
+      <td>556</td>
+      <td>638</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>basecoverage</td>
+      <td>gops_basecoverage_1</td>
+      <td>Base Coverage of all intervals</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>basecoverage</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>226</td>
+      <td>308</td>
+      <td>27</td>
+      <td>35</td>
+      <td>2615</td>
+      <td>45557</td>
+      <td>302</td>
+      <td>2284</td>
+      <td>482</td>
+      <td>522</td>
+      <td>32</td>
+      <td>36</td>
+      <td>3323</td>
+      <td>46387</td>
+      <td>361</td>
+      <td>2355</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>baseline_calculator</td>
+      <td>tt_baseline</td>
+      <td>Toxicity prediction using QSAR models</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools</td>
+      <td>Ecology, Text Manipulation</td>
+      <td>baseline_toxicity_calculator</td>
+      <td>mbernt</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator</td>
+      <td>0.1.0+galaxy0</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>basil</td>
+      <td>basil</td>
+      <td>Breakpoint detection, including large insertions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/seqan/anise_basil</td>
+      <td>Variant Analysis</td>
+      <td>basil</td>
+      <td>iuc</td>
+      <td></td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil</td>
+      <td>1.2.0</td>
+      <td>anise_basil</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>306</td>
+      <td>311</td>
+      <td>82</td>
+      <td>83</td>
+      <td>467</td>
+      <td>467</td>
+      <td>99</td>
+      <td>99</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>773</td>
+      <td>778</td>
+      <td>181</td>
+      <td>182</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>batched_lastz</td>
+      <td>batched_lastz</td>
+      <td>Galaxy wrapper for the batching Lastz runs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/galaxyproject/KegAlign</td>
+      <td>Next Gen Mappers</td>
+      <td>batched_lastz</td>
+      <td>richard-burhans</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz</td>
+      <td>1.04.22</td>
+      <td>lastz</td>
+      <td>1.04.22</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>123</td>
+      <td>123</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>123</td>
+      <td>123</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bax2bam</td>
+      <td>bax2bam</td>
+      <td>BAX to BAM converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pacificbiosciences/bax2bam/</td>
+      <td>Convert Formats, Sequence Analysis</td>
+      <td>bax2bam</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam</td>
+      <td>0.0.11</td>
+      <td>bax2bam</td>
+      <td>0.0.11</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>208</td>
+      <td>208</td>
+      <td>26</td>
+      <td>26</td>
+      <td>210</td>
+      <td>210</td>
+      <td>30</td>
+      <td>30</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>418</td>
+      <td>418</td>
+      <td>56</td>
+      <td>56</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bayescan</td>
+      <td>BayeScan</td>
+      <td>Detecting natural selection from population-based genetic data</td>
+      <td>bayescan</td>
+      <td>bayescan</td>
+      <td></td>
+      <td>BayeScan</td>
+      <td>BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.</td>
+      <td>Statistical inference</td>
+      <td>Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism</td>
+      <td>To update</td>
+      <td>http://cmpg.unibe.ch/software/BayeScan/index.html</td>
+      <td>Sequence Analysis</td>
+      <td>bayescan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan</td>
+      <td>2.1</td>
+      <td>bayescan</td>
+      <td>2.0.1</td>
+      <td>Statistical inference</td>
+      <td>Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>90</td>
+      <td>90</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>90</td>
+      <td>90</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bbgbigwig</td>
+      <td>bbgtobigwig</td>
+      <td>Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file.</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://www.encodeproject.org/software/bedgraphtobigwig/</td>
+      <td>Convert Formats</td>
+      <td>bbgbigwig</td>
+      <td>iuc</td>
+      <td>https://www.encodeproject.org/software/bedgraphtobigwig/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig</td>
+      <td>0.1</td>
+      <td>ucsc-bedgraphtobigwig</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>7</td>
+      <td>7</td>
+      <td>175</td>
+      <td>175</td>
+      <td>26</td>
+      <td>26</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>217</td>
+      <td>217</td>
+      <td>33</td>
+      <td>33</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bbtools</td>
+      <td>bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole</td>
+      <td>BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.</td>
+      <td>bbmap</td>
+      <td>bbtools, bbmap</td>
+      <td></td>
+      <td>BBMap</td>
+      <td>BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.</td>
+      <td>RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment</td>
+      <td>Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq</td>
+      <td>To update</td>
+      <td>https://jgi.doe.gov/data-and-tools/bbtools/</td>
+      <td>Sequence Analysis</td>
+      <td>bbtools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools</td>
+      <td>39.08</td>
+      <td>bbmap</td>
+      <td>39.09</td>
+      <td>RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment</td>
+      <td>RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq</td>
+      <td>6</td>
+      <td>3</td>
+      <td>5</td>
+      <td>0</td>
+      <td>6</td>
+      <td>3</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11989</td>
+      <td>11989</td>
+      <td>768</td>
+      <td>768</td>
+      <td>4458</td>
+      <td>4458</td>
+      <td>652</td>
+      <td>652</td>
+      <td>2507</td>
+      <td>2507</td>
+      <td>80</td>
+      <td>80</td>
+      <td>18954</td>
+      <td>18954</td>
+      <td>1500</td>
+      <td>1500</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bcftools</td>
+      <td>bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@</td>
+      <td>BCFtools toolkit wrappers</td>
+      <td>bcftools</td>
+      <td>bcftools</td>
+      <td></td>
+      <td>BCFtools</td>
+      <td>BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</td>
+      <td>Data handling, Variant calling</td>
+      <td>Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment</td>
+      <td>To update</td>
+      <td>https://samtools.github.io/bcftools/</td>
+      <td>Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools</td>
+      <td>1.15.1</td>
+      <td>bcftools</td>
+      <td>1.21</td>
+      <td>Data handling, Variant calling</td>
+      <td>DNA polymorphism, GWAS study, Genotyping experiment</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bctools</td>
+      <td>bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events</td>
+      <td>bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/dmaticzka/bctools</td>
+      <td>Sequence Analysis, Transcriptomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools</td>
+      <td>0.2.2</td>
+      <td>bctools</td>
+      <td>0.2.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>2352</td>
+      <td>3092</td>
+      <td>234</td>
+      <td>265</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2352</td>
+      <td>3092</td>
+      <td>234</td>
+      <td>265</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>beacon2</td>
+      <td>beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff</td>
+      <td>beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).</td>
+      <td>ga4gh_beacon</td>
+      <td>ga4gh_beacon</td>
+      <td></td>
+      <td>GA4GH Beacon</td>
+      <td>A global search engine for genetic mutations.</td>
+      <td>Service discovery, Database search, Genetic variation analysis</td>
+      <td>Genetic variation, Population genetics, Data security, Rare diseases</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/EGA-archive/beacon2-ri-tools/tree/main</td>
+      <td>Variant Analysis</td>
+      <td>beacon2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2</td>
+      <td>2.0.0</td>
+      <td>beacon2-ri-tools</td>
+      <td>2.0.0</td>
+      <td>Service discovery, Database search, Genetic variation analysis</td>
+      <td>Genetic variation, Population genetics, Data security, Rare diseases</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>beacon2-import</td>
+      <td>beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence</td>
+      <td>Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants.</td>
+      <td>ga4gh_beacon</td>
+      <td>ga4gh_beacon</td>
+      <td></td>
+      <td>GA4GH Beacon</td>
+      <td>A global search engine for genetic mutations.</td>
+      <td>Service discovery, Database search, Genetic variation analysis</td>
+      <td>Genetic variation, Population genetics, Data security, Rare diseases</td>
+      <td>Up-to-date</td>
+      <td>https://pypi.org/project/beacon2-import/</td>
+      <td>Variant Analysis</td>
+      <td>Beacon2_Import</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import</td>
+      <td>2.2.4</td>
+      <td>beacon2-import</td>
+      <td>2.2.4</td>
+      <td>Service discovery, Database search, Genetic variation analysis</td>
+      <td>Genetic variation, Population genetics, Data security, Rare diseases</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22</td>
+      <td>22</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22</td>
+      <td>22</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>beagle</td>
+      <td>beagle</td>
+      <td>Beagle is a program for phasing and imputing missing genotypes.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://faculty.washington.edu/browning/beagle/beagle.html</td>
+      <td>Variant Analysis</td>
+      <td>beagle</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle</td>
+      <td>5.2_21Apr21.304</td>
+      <td>beagle</td>
+      <td>5.4_22Jul22.46e</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>88</td>
+      <td>88</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>88</td>
+      <td>88</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bed_to_protein_map</td>
+      <td>bed_to_protein_map</td>
+      <td>Converts a BED file to a tabular list of exon locations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>bed_to_protein_map</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map</td>
+      <td>0.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>410</td>
+      <td>419</td>
+      <td>134</td>
+      <td>137</td>
+      <td>363</td>
+      <td>363</td>
+      <td>99</td>
+      <td>99</td>
+      <td>158</td>
+      <td>158</td>
+      <td>13</td>
+      <td>13</td>
+      <td>931</td>
+      <td>940</td>
+      <td>246</td>
+      <td>249</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bedops</td>
+      <td>bedops-sort-bed</td>
+      <td>BEDOPS: high-performance genomic feature operations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://bedops.readthedocs.io/en/latest/</td>
+      <td>Genomic Interval Operations</td>
+      <td>bedops_sortbed</td>
+      <td>iuc</td>
+      <td>https://bedops.readthedocs.io/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops</td>
+      <td>2.4.41</td>
+      <td>bedops</td>
+      <td>2.4.41</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>93</td>
+      <td>93</td>
+      <td>36</td>
+      <td>36</td>
+      <td>181</td>
+      <td>181</td>
+      <td>62</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>274</td>
+      <td>274</td>
+      <td>98</td>
+      <td>98</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bedtools</td>
+      <td>bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed</td>
+      <td>bedtools is a powerful toolset for genome arithmetic</td>
+      <td>bedtools</td>
+      <td>bedtools</td>
+      <td></td>
+      <td>BEDTools</td>
+      <td>BEDTools is an extensive suite of utilities for comparing genomic features in BED format.</td>
+      <td>Mapping</td>
+      <td>Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/arq5x/bedtools2</td>
+      <td>Genomic Interval Operations, Text Manipulation</td>
+      <td>bedtools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools</td>
+      <td>2.31.1</td>
+      <td>bedtools</td>
+      <td>2.31.1</td>
+      <td>Mapping</td>
+      <td>Genomics</td>
+      <td>37</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>37</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>6</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>916111</td>
+      <td>962278</td>
+      <td>13235</td>
+      <td>14525</td>
+      <td>407944</td>
+      <td>647621</td>
+      <td>25849</td>
+      <td>41751</td>
+      <td>84008</td>
+      <td>89233</td>
+      <td>2486</td>
+      <td>2832</td>
+      <td>1408063</td>
+      <td>1699132</td>
+      <td>41570</td>
+      <td>59108</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bellerophon</td>
+      <td>bellerophon</td>
+      <td>Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/davebx/bellerophon</td>
+      <td>Sequence Analysis</td>
+      <td>bellerophon</td>
+      <td>iuc</td>
+      <td>https://github.com/davebx/bellerophon</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon</td>
+      <td>1.0</td>
+      <td>bellerophon</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1611</td>
+      <td>1611</td>
+      <td>262</td>
+      <td>262</td>
+      <td>763</td>
+      <td>763</td>
+      <td>67</td>
+      <td>67</td>
+      <td>543</td>
+      <td>543</td>
+      <td>30</td>
+      <td>30</td>
+      <td>2917</td>
+      <td>2917</td>
+      <td>359</td>
+      <td>359</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>berokka</td>
+      <td>berokka</td>
+      <td>Berokka is used to trim, circularise, orient &amp; filter long read bacterial genome assemblies.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tseemann/berokka</td>
+      <td>Fasta Manipulation</td>
+      <td>berokka</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka</td>
+      <td>0.2.3</td>
+      <td>berokka</td>
+      <td>0.2.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>617</td>
+      <td>617</td>
+      <td>63</td>
+      <td>63</td>
+      <td>617</td>
+      <td>617</td>
+      <td>63</td>
+      <td>63</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>best_regression_subsets</td>
+      <td>BestSubsetsRegression1</td>
+      <td>Perform Best-subsets Regression</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>best_regression_subsets</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets</td>
+      <td>1.0.0</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3</td>
+      <td>4</td>
+      <td>3</td>
+      <td>4</td>
+      <td>14</td>
+      <td>253</td>
+      <td>7</td>
+      <td>72</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>257</td>
+      <td>10</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bfconvert</td>
+      <td>ip_convertimage</td>
+      <td>Convert image</td>
+      <td></td>
+      <td></td>
+      <td>python-bioformats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging, Convert Formats</td>
+      <td>bfconvert</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert</td>
+      <td>6.7.0</td>
+      <td>bftools</td>
+      <td>6.7.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1635</td>
+      <td>1671</td>
+      <td>123</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>334</td>
+      <td>334</td>
+      <td>21</td>
+      <td>21</td>
+      <td>1969</td>
+      <td>2005</td>
+      <td>144</td>
+      <td>145</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bia-ftplinks</td>
+      <td>bia_download</td>
+      <td>Tool to query ftp links for study from bioimage archive</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>bia_download</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks</td>
+      <td>0.1.0</td>
+      <td>wget</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bigscape</td>
+      <td>bigscape</td>
+      <td>Construct sequence similarity networks of BGCs and groups them into GCF</td>
+      <td>BiG-SCAPE</td>
+      <td>BiG-SCAPE</td>
+      <td></td>
+      <td>BiG-SCAPE</td>
+      <td>A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.</td>
+      <td>Clustering, Global alignment, Fold recognition</td>
+      <td>Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/medema-group/BiG-SCAPE</td>
+      <td>Metagenomics</td>
+      <td>bigscape</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape</td>
+      <td>1.1.9</td>
+      <td>bigscape</td>
+      <td>1.1.9</td>
+      <td>Clustering, Global alignment, Fold recognition</td>
+      <td>Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>544</td>
+      <td>544</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>544</td>
+      <td>544</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bigwig_outlier_bed</td>
+      <td>bigwig_outlier_bed</td>
+      <td>pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files</td>
+      <td>bigtools</td>
+      <td>bigtools</td>
+      <td></td>
+      <td>bigtools</td>
+      <td>Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.</td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed</td>
+      <td>Sequence Analysis</td>
+      <td>bigwig_outlier_bed</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed</td>
+      <td>0.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bigwig_to_bedgraph</td>
+      <td>bigwig_to_bedgraph</td>
+      <td>Convert from bigWig to bedGraph format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats</td>
+      <td>bigwig_to_bedgraph</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph</td>
+      <td>0.1.0</td>
+      <td>ucsc_tools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5769</td>
+      <td>6802</td>
+      <td>567</td>
+      <td>650</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1</td>
+      <td>5769</td>
+      <td>6805</td>
+      <td>567</td>
+      <td>651</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bigwig_to_bedgraph</td>
+      <td>bigwig_to_bedgraph</td>
+      <td>Converts a bigWig file to bedGraph format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Convert Formats</td>
+      <td>bigwig_to_bedgraph</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph</td>
+      <td>377+galaxy1</td>
+      <td>ucsc-bigwigtobedgraph</td>
+      <td>469</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5769</td>
+      <td>6802</td>
+      <td>567</td>
+      <td>650</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1</td>
+      <td>5769</td>
+      <td>6805</td>
+      <td>567</td>
+      <td>651</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bigwig_to_wig</td>
+      <td>bigwig_to_wig</td>
+      <td>Converts a bigWig file to Wiggle (WIG) format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://artbio.fr</td>
+      <td>Convert Formats</td>
+      <td>bigwig_to_wig</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig</td>
+      <td>3+galaxy0</td>
+      <td>ucsc-bigwiginfo</td>
+      <td>469</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>binary2labelimage</td>
+      <td>ip_binary_to_labelimage</td>
+      <td>Binary 2 label image</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>binary2labelimage</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage</td>
+      <td>0.5</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>401</td>
+      <td>1385</td>
+      <td>87</td>
+      <td>88</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>188</td>
+      <td>188</td>
+      <td>9</td>
+      <td>9</td>
+      <td>589</td>
+      <td>1573</td>
+      <td>96</td>
+      <td>97</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>binaryimage2points</td>
+      <td>ip_binaryimage_to_points</td>
+      <td>Binary Image to Points</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>binaryimage2points</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points</td>
+      <td>0.1-2</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>24</td>
+      <td>29</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>29</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>binning_refiner</td>
+      <td>bin_refiner</td>
+      <td>Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.</td>
+      <td>binning_refiner</td>
+      <td>binning_refiner</td>
+      <td></td>
+      <td>Binning_refiner</td>
+      <td>Improving genome bins through the combination of different binning programs</td>
+      <td>Read binning, Sequence clustering</td>
+      <td>Metagenomics, Sequence assembly, Microbial ecology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/songweizhi/Binning_refiner</td>
+      <td>Metagenomics</td>
+      <td>binning_refiner</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner</td>
+      <td>1.4.3</td>
+      <td>binning_refiner</td>
+      <td>1.4.3</td>
+      <td>Read binning, Sequence clustering</td>
+      <td>Metagenomics, Sequence assembly, Microbial ecology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>126</td>
+      <td>126</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>126</td>
+      <td>126</td>
+      <td>42</td>
+      <td>42</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bio3d</td>
+      <td>bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize</td>
+      <td>Bio3d is a program that can be used to analyse molecular dynamics trajectories.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://thegrantlab.org/bio3d/index.php</td>
+      <td>Computational chemistry</td>
+      <td>bio3d</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d</td>
+      <td>2.4_1</td>
+      <td>r-bio3d</td>
+      <td>2.3_3</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>4</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>4</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>10600</td>
+      <td>10729</td>
+      <td>1150</td>
+      <td>1159</td>
+      <td>1042</td>
+      <td>1042</td>
+      <td>255</td>
+      <td>255</td>
+      <td>2756</td>
+      <td>2756</td>
+      <td>215</td>
+      <td>215</td>
+      <td>14398</td>
+      <td>14527</td>
+      <td>1620</td>
+      <td>1629</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bioext</td>
+      <td>bioext_bam2msa, bioext_bealign</td>
+      <td>A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://pypi.python.org/pypi/biopython-extensions/</td>
+      <td>Next Gen Mappers</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/davebx/bioext-gx/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext</td>
+      <td>0.21.9</td>
+      <td>python-bioext</td>
+      <td>0.21.9</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17413</td>
+      <td>17413</td>
+      <td>822</td>
+      <td>822</td>
+      <td>15349</td>
+      <td>15349</td>
+      <td>2020</td>
+      <td>2020</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>32764</td>
+      <td>32764</td>
+      <td>2843</td>
+      <td>2843</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bioformats2raw</td>
+      <td>bf2raw</td>
+      <td>Convert image to OME-Zarr</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/Euro-BioImaging</td>
+      <td>Imaging, Convert Formats</td>
+      <td>bioformats2raw</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw</td>
+      <td>0.7.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>61</td>
+      <td>61</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>61</td>
+      <td>61</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biohansel</td>
+      <td>biohansel</td>
+      <td>Heidelberg and Enteritidis SNP Elucidation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/biohansel</td>
+      <td>Sequence Analysis</td>
+      <td>biohansel</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/biohansel</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel</td>
+      <td>2.4.0</td>
+      <td>bio_hansel</td>
+      <td>2.6.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biohansel_bionumeric_converter</td>
+      <td>bionumeric_convert</td>
+      <td>Convert BioHansel output data to a Bionumerics friendly form</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Text Manipulation</td>
+      <td>biohansel_bionumeric_converter</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter</td>
+      <td>0.2.0</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bioimaging</td>
+      <td>bioimage_inference</td>
+      <td>Load model from BioImage.IO and make inferences</td>
+      <td>pytorch</td>
+      <td>pytorch</td>
+      <td>pytorch</td>
+      <td>PyTorch</td>
+      <td>PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.</td>
+      <td></td>
+      <td>Machine learning, Computer science</td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools</td>
+      <td>Imaging</td>
+      <td>bioimage_inference</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging</td>
+      <td>2.4.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td>Machine learning</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bioinformatics_cafe</td>
+      <td>fasta_regex_finder</td>
+      <td>Miscellanea of scripts for bioinformatics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/dariober/bioinformatics-cafe/</td>
+      <td>Sequence Analysis</td>
+      <td>bioinformatics_cafe</td>
+      <td>mbernt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe</td>
+      <td>0.1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1137</td>
+      <td>1137</td>
+      <td>97</td>
+      <td>97</td>
+      <td>1029</td>
+      <td>1029</td>
+      <td>71</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2166</td>
+      <td>2166</td>
+      <td>168</td>
+      <td>168</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biom_format</td>
+      <td>biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table</td>
+      <td>The biom-format package provides a command line interface and Python API for working with BIOM files.</td>
+      <td>biomformat</td>
+      <td>biomformat</td>
+      <td></td>
+      <td>biomformat</td>
+      <td>This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.</td>
+      <td>Formatting</td>
+      <td>Laboratory information management, Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/biocore/biom-format</td>
+      <td>Metagenomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format</td>
+      <td>2.1.15</td>
+      <td>biom-format</td>
+      <td>2.1.7</td>
+      <td>Formatting</td>
+      <td>Laboratory information management, Sequence analysis</td>
+      <td>2</td>
+      <td>2</td>
+      <td>6</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>12725</td>
+      <td>12725</td>
+      <td>297</td>
+      <td>297</td>
+      <td>2851</td>
+      <td>5049</td>
+      <td>450</td>
+      <td>638</td>
+      <td>2171</td>
+      <td>2371</td>
+      <td>214</td>
+      <td>239</td>
+      <td>17747</td>
+      <td>20145</td>
+      <td>961</td>
+      <td>1174</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biomodelsML</td>
+      <td>biomodels_biomd0000001066, biomodels_biomd0000001076</td>
+      <td>Wrappers for tools to bring BioModels AI models into Galaxy.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.ebi.ac.uk/biomodels/</td>
+      <td>Machine Learning</td>
+      <td>biomodels</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML</td>
+      <td>1.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25</td>
+      <td>25</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25</td>
+      <td>25</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biomoldyn</td>
+      <td>biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering</td>
+      <td>Tools for MD analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/moldyn/</td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>biomoldyn</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn</td>
+      <td>1.5.2</td>
+      <td>scipy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>3</td>
+      <td>0</td>
+      <td>493</td>
+      <td>493</td>
+      <td>119</td>
+      <td>119</td>
+      <td>441</td>
+      <td>441</td>
+      <td>148</td>
+      <td>148</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>934</td>
+      <td>934</td>
+      <td>267</td>
+      <td>267</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bionano</td>
+      <td>bionano_scaffold</td>
+      <td>Bionano Solve is a set of tools for analyzing Bionano data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bionanogenomics.com/</td>
+      <td>Assembly</td>
+      <td>bionano</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bionano</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bionano</td>
+      <td>3.7.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>547</td>
+      <td>547</td>
+      <td>151</td>
+      <td>151</td>
+      <td>143</td>
+      <td>143</td>
+      <td>43</td>
+      <td>43</td>
+      <td>596</td>
+      <td>596</td>
+      <td>22</td>
+      <td>22</td>
+      <td>1286</td>
+      <td>1286</td>
+      <td>216</td>
+      <td>216</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bioperl</td>
+      <td>bp_genbank2gff3</td>
+      <td>Converts GenBank format files to GFF3</td>
+      <td>bioperl</td>
+      <td>bioperl</td>
+      <td></td>
+      <td>BioPerl</td>
+      <td>A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.</td>
+      <td>Data handling, Service invocation</td>
+      <td>Genomics, Software engineering, Data management</td>
+      <td>To update</td>
+      <td>https://bioperl.org/</td>
+      <td>Sequence Analysis</td>
+      <td>bp_genbank2gff3</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl</td>
+      <td>1.1</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td>Data handling, Service invocation</td>
+      <td>Genomics, Software engineering</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7738</td>
+      <td>7931</td>
+      <td>478</td>
+      <td>508</td>
+      <td>8301</td>
+      <td>8301</td>
+      <td>849</td>
+      <td>849</td>
+      <td>1369</td>
+      <td>1369</td>
+      <td>154</td>
+      <td>154</td>
+      <td>17408</td>
+      <td>17601</td>
+      <td>1481</td>
+      <td>1511</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biotradis</td>
+      <td>bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites</td>
+      <td>Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.</td>
+      <td>biotradis</td>
+      <td>biotradis</td>
+      <td></td>
+      <td>biotradis</td>
+      <td>The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.</td>
+      <td>Sequence analysis</td>
+      <td>Mobile genetic elements, Workflows</td>
+      <td>Up-to-date</td>
+      <td>https://www.sanger.ac.uk/science/tools/bio-tradis</td>
+      <td>Genome annotation</td>
+      <td>biotradis</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis</td>
+      <td>1.4.5</td>
+      <td>biotradis</td>
+      <td>1.4.5</td>
+      <td>Sequence analysis</td>
+      <td>Mobile genetic elements, Workflows</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6243</td>
+      <td>6243</td>
+      <td>375</td>
+      <td>375</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6243</td>
+      <td>6243</td>
+      <td>375</td>
+      <td>375</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biotransformer</td>
+      <td>biotransformer</td>
+      <td>BioTransformer is a tool for prediction of small molecule metabolism in mammals.</td>
+      <td>biotransformer</td>
+      <td>biotransformer</td>
+      <td></td>
+      <td>BioTransformer</td>
+      <td>BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.</td>
+      <td>Metabolic pathway prediction, PTM site prediction, Natural product identification</td>
+      <td>Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR</td>
+      <td>Up-to-date</td>
+      <td>https://bitbucket.org/djoumbou/biotransformerjar/src/master/</td>
+      <td>Metabolomics</td>
+      <td>biotransformer</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer</td>
+      <td>3.0.20230403</td>
+      <td>biotransformer</td>
+      <td>3.0.20230403</td>
+      <td>Metabolic pathway prediction, PTM site prediction, Natural product identification</td>
+      <td>Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>biscot</td>
+      <td>biscot</td>
+      <td>Bionano scaffolding correction tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/institut-de-genomique/biscot</td>
+      <td>Assembly</td>
+      <td>biscot</td>
+      <td>iuc</td>
+      <td>https://github.com/bgruening/iuc/tree/master/tools/biscot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot</td>
+      <td>2.3.3</td>
+      <td>biscot</td>
+      <td>2.3.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bismark</td>
+      <td>bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor</td>
+      <td>A tool to map bisulfite converted sequence reads and determine cytosine methylation states</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.bioinformatics.babraham.ac.uk/projects/bismark/</td>
+      <td>Sequence Analysis, Next Gen Mappers</td>
+      <td>bismark</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bismark</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/bismark</td>
+      <td>0.22.1</td>
+      <td>bismark</td>
+      <td>0.24.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>13715</td>
+      <td>14997</td>
+      <td>992</td>
+      <td>1099</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>197</td>
+      <td>197</td>
+      <td>22</td>
+      <td>22</td>
+      <td>13912</td>
+      <td>15194</td>
+      <td>1014</td>
+      <td>1121</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast</td>
+      <td>magicblast</td>
+      <td>Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://ncbi.github.io/magicblast/</td>
+      <td>Next Gen Mappers</td>
+      <td>magicblast</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast</td>
+      <td>1.7.0</td>
+      <td>magicblast</td>
+      <td>1.7.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>738</td>
+      <td>738</td>
+      <td>151</td>
+      <td>151</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>740</td>
+      <td>740</td>
+      <td>152</td>
+      <td>152</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast2go</td>
+      <td>blast2go</td>
+      <td>Maps BLAST results to GO annotation terms</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go</td>
+      <td>Ontology Manipulation, Sequence Analysis</td>
+      <td>blast2go</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go</td>
+      <td>0.0.11</td>
+      <td>b2g4pipe</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1063</td>
+      <td>1237</td>
+      <td>257</td>
+      <td>300</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1063</td>
+      <td>1237</td>
+      <td>257</td>
+      <td>300</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast_parser</td>
+      <td>blast_parser</td>
+      <td>Convert 12- or 24-column BLAST output into 3-column hcluster_sg input</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/</td>
+      <td>Phylogenetics</td>
+      <td>blast_parser</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser</td>
+      <td>0.1.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>417</td>
+      <td>438</td>
+      <td>99</td>
+      <td>104</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>417</td>
+      <td>438</td>
+      <td>99</td>
+      <td>104</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast_plus_remote_blastp</td>
+      <td>blast_plus_remote_blastp</td>
+      <td>NCBI BLAST+ with -remote option</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://blast.ncbi.nlm.nih.gov/</td>
+      <td>Sequence Analysis</td>
+      <td>blast_plus_remote_blastp</td>
+      <td>galaxyp</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp</td>
+      <td>2.6.0</td>
+      <td>blast</td>
+      <td>2.16.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast_rbh</td>
+      <td>blast_reciprocal_best_hits</td>
+      <td>BLAST Reciprocal Best Hits (RBH) from two FASTA files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh</td>
+      <td>Fasta Manipulation, Sequence Analysis</td>
+      <td>blast_rbh</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh</td>
+      <td>0.3.0</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>24916</td>
+      <td>27120</td>
+      <td>283</td>
+      <td>347</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24916</td>
+      <td>27120</td>
+      <td>283</td>
+      <td>347</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast_to_scaffold</td>
+      <td>blast2scaffold</td>
+      <td>Generate DNA scaffold from blastn or tblastx alignments of Contigs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Sequence Analysis, Assembly</td>
+      <td>blast_to_scaffold</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold</td>
+      <td>1.1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blast_unmatched</td>
+      <td>blast_unmatched</td>
+      <td>Extract unmatched query sequences from blast</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Fasta Manipulation</td>
+      <td>blast_unmatched</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched</td>
+      <td>1.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blastparser_and_hits</td>
+      <td>BlastParser_and_hits</td>
+      <td>Parse blast outputs and compile hits</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Assembly, RNA</td>
+      <td>blastparser_and_hits</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits</td>
+      <td>2.7.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blastx_to_scaffold</td>
+      <td>blastx2scaffold</td>
+      <td>Generate DNA scaffold from blastx alignment of Contigs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Sequence Analysis, Assembly</td>
+      <td>blastx_to_scaffold</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold</td>
+      <td>1.1.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blastxml_to_gapped_gff3</td>
+      <td>blastxml_to_gapped_gff3</td>
+      <td>BlastXML to gapped GFF3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3</td>
+      <td>Convert Formats, Sequence Analysis</td>
+      <td>blastxml_to_gapped_gff3</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3</td>
+      <td>1.1</td>
+      <td>bcbiogff</td>
+      <td>0.6.6</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>585</td>
+      <td>585</td>
+      <td>102</td>
+      <td>102</td>
+      <td>172</td>
+      <td>172</td>
+      <td>63</td>
+      <td>63</td>
+      <td>135</td>
+      <td>135</td>
+      <td>16</td>
+      <td>16</td>
+      <td>892</td>
+      <td>892</td>
+      <td>181</td>
+      <td>181</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blastxml_to_top_descr</td>
+      <td>blastxml_to_top_descr</td>
+      <td>Make table of top BLAST match descriptions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr</td>
+      <td>Convert Formats, Sequence Analysis, Text Manipulation</td>
+      <td>blastxml_to_top_descr</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr</td>
+      <td>0.1.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>264392</td>
+      <td>265217</td>
+      <td>483</td>
+      <td>552</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>264392</td>
+      <td>265217</td>
+      <td>483</td>
+      <td>552</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blat_coverage_report</td>
+      <td>generate_coverage_report</td>
+      <td>Polymorphism of the Reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Next Gen Mappers, Sequence Analysis</td>
+      <td>blat_coverage_report</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blat_mapping</td>
+      <td>blat2wig</td>
+      <td>Coverage of the Reads in wiggle format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Next Gen Mappers, Sequence Analysis</td>
+      <td>blat_mapping</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blobtoolkit</td>
+      <td>blobtoolkit</td>
+      <td>Identification and isolation non-target data in draft and publicly available genome assemblies.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://blobtoolkit.genomehubs.org/</td>
+      <td>Sequence Analysis, Assembly</td>
+      <td>blobtoolkit</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit</td>
+      <td>4.0.7</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1527</td>
+      <td>1527</td>
+      <td>79</td>
+      <td>79</td>
+      <td>6</td>
+      <td>6</td>
+      <td>1</td>
+      <td>1</td>
+      <td>317</td>
+      <td>317</td>
+      <td>26</td>
+      <td>26</td>
+      <td>1850</td>
+      <td>1850</td>
+      <td>106</td>
+      <td>106</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blockbuster</td>
+      <td>blockbuster</td>
+      <td>Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>blockbuster</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster</td>
+      <td>0.1.2</td>
+      <td>blockbuster</td>
+      <td>0.0.1.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>768</td>
+      <td>3043</td>
+      <td>97</td>
+      <td>119</td>
+      <td>14</td>
+      <td>14</td>
+      <td>11</td>
+      <td>11</td>
+      <td>276</td>
+      <td>276</td>
+      <td>9</td>
+      <td>9</td>
+      <td>1058</td>
+      <td>3333</td>
+      <td>117</td>
+      <td>139</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>blockclust</td>
+      <td>blockclust</td>
+      <td>BlockClust detects transcripts with similar processing patterns.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust</td>
+      <td>RNA</td>
+      <td>blockclust</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust</td>
+      <td>1.1.1</td>
+      <td>blockclust</td>
+      <td>1.1.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>811</td>
+      <td>1501</td>
+      <td>54</td>
+      <td>79</td>
+      <td>64</td>
+      <td>64</td>
+      <td>29</td>
+      <td>29</td>
+      <td>561</td>
+      <td>561</td>
+      <td>15</td>
+      <td>15</td>
+      <td>1436</td>
+      <td>2126</td>
+      <td>98</td>
+      <td>123</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bowtie2</td>
+      <td>bowtie2</td>
+      <td>Bowtie2: Fast and sensitive read alignment</td>
+      <td>bowtie2</td>
+      <td>bowtie2</td>
+      <td></td>
+      <td>Bowtie 2</td>
+      <td>Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.</td>
+      <td>Read mapping</td>
+      <td>Mapping, Genomics, Mapping</td>
+      <td>To update</td>
+      <td>http://bowtie-bio.sourceforge.net/bowtie2</td>
+      <td>Next Gen Mappers</td>
+      <td>bowtie2</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2</td>
+      <td>2.5.3</td>
+      <td>bowtie2</td>
+      <td>2.5.4</td>
+      <td>Read mapping</td>
+      <td>Mapping, Genomics, Mapping</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>397893</td>
+      <td>427447</td>
+      <td>12133</td>
+      <td>13176</td>
+      <td>577209</td>
+      <td>903193</td>
+      <td>33086</td>
+      <td>52020</td>
+      <td>60105</td>
+      <td>67495</td>
+      <td>3779</td>
+      <td>4271</td>
+      <td>1035207</td>
+      <td>1398135</td>
+      <td>48998</td>
+      <td>69467</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bowtie_wrappers</td>
+      <td>bowtie_wrapper</td>
+      <td>Galaxy wrappers for the Bowtie short read mapping tools.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://bowtie-bio.sourceforge.net/</td>
+      <td>Next Gen Mappers</td>
+      <td>bowtie_wrappers</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers</td>
+      <td>1.2.0</td>
+      <td>bowtie</td>
+      <td>1.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>24164</td>
+      <td>25149</td>
+      <td>1320</td>
+      <td>1480</td>
+      <td>17537</td>
+      <td>203397</td>
+      <td>1330</td>
+      <td>17491</td>
+      <td>15654</td>
+      <td>15992</td>
+      <td>291</td>
+      <td>351</td>
+      <td>57355</td>
+      <td>244538</td>
+      <td>2941</td>
+      <td>19322</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bracken</td>
+      <td>est_abundance</td>
+      <td>Bayesian Reestimation of Abundance with KrakEN</td>
+      <td>bracken</td>
+      <td>bracken</td>
+      <td></td>
+      <td>Bracken</td>
+      <td>Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.</td>
+      <td>Statistical calculation</td>
+      <td>Metagenomics, Microbial ecology</td>
+      <td>Up-to-date</td>
+      <td>https://ccb.jhu.edu/software/bracken/</td>
+      <td>Sequence Analysis, Metagenomics</td>
+      <td>bracken</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken</td>
+      <td>3.0</td>
+      <td>bracken</td>
+      <td>3.0</td>
+      <td>Statistical calculation</td>
+      <td>Metagenomics, Microbial ecology</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>51378</td>
+      <td>51378</td>
+      <td>775</td>
+      <td>775</td>
+      <td>3298</td>
+      <td>3298</td>
+      <td>160</td>
+      <td>160</td>
+      <td>1660</td>
+      <td>1660</td>
+      <td>63</td>
+      <td>63</td>
+      <td>56336</td>
+      <td>56336</td>
+      <td>998</td>
+      <td>998</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>braker</td>
+      <td>braker</td>
+      <td>BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/Gaius-Augustus/BRAKER</td>
+      <td>Genome annotation</td>
+      <td>braker</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/braker</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/braker</td>
+      <td>2.1.6</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>165</td>
+      <td>165</td>
+      <td>48</td>
+      <td>48</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>165</td>
+      <td>165</td>
+      <td>48</td>
+      <td>48</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>braker3</td>
+      <td>braker3</td>
+      <td>BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .</td>
+      <td>braker3</td>
+      <td>braker3</td>
+      <td></td>
+      <td>BRAKER3</td>
+      <td>BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes</td>
+      <td>Genome annotation, Gene prediction</td>
+      <td>RNA-Seq, Genomics, Structure prediction, Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/Gaius-Augustus/BRAKER</td>
+      <td>Genome annotation</td>
+      <td>braker3</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/braker</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/braker3</td>
+      <td>3.0.8</td>
+      <td></td>
+      <td></td>
+      <td>Genome annotation, Gene prediction</td>
+      <td>RNA-Seq, Genomics, Structure prediction, Sequence analysis</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1938</td>
+      <td>1938</td>
+      <td>294</td>
+      <td>294</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>412</td>
+      <td>412</td>
+      <td>71</td>
+      <td>71</td>
+      <td>2350</td>
+      <td>2350</td>
+      <td>365</td>
+      <td>365</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>breseq</td>
+      <td>breseq</td>
+      <td>Predicts mutations in microbial genomes</td>
+      <td>breseq</td>
+      <td>breseq</td>
+      <td></td>
+      <td>breseq</td>
+      <td>Runs Breseq software on a set of fastq files.</td>
+      <td>Polymorphism detection</td>
+      <td>Sequencing, Sequence analysis, DNA mutation</td>
+      <td>To update</td>
+      <td>https://github.com/barricklab/breseq</td>
+      <td>Variant Analysis</td>
+      <td>breseq</td>
+      <td>iuc</td>
+      <td></td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq</td>
+      <td>0.35.5</td>
+      <td>breseq</td>
+      <td>0.39.0</td>
+      <td>Polymorphism detection</td>
+      <td>Sequencing, Sequence analysis, DNA mutation</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2976</td>
+      <td>2976</td>
+      <td>98</td>
+      <td>98</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>884</td>
+      <td>884</td>
+      <td>70</td>
+      <td>70</td>
+      <td>3860</td>
+      <td>3860</td>
+      <td>168</td>
+      <td>168</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>brew3r_r</td>
+      <td>brew3r_r</td>
+      <td>Extend 3' end of a GTF using another GTF as a template</td>
+      <td>brew3r.r</td>
+      <td>brew3r.r</td>
+      <td></td>
+      <td>BREW3R.r</td>
+      <td>This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.</td>
+      <td>Genome annotation</td>
+      <td>Transcriptomics, Genomics</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html</td>
+      <td>Transcriptomics, RNA</td>
+      <td>brew3r_r</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r</td>
+      <td>1.0.2</td>
+      <td></td>
+      <td></td>
+      <td>Genome annotation</td>
+      <td>Transcriptomics</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>6</td>
+      <td>6</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bumbershoot</td>
+      <td>idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://proteowizard.sourceforge.net/</td>
+      <td>Proteomics</td>
+      <td></td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot</td>
+      <td>3.0.21142</td>
+      <td>bumbershoot</td>
+      <td>3_0_21142_0e4f4a4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>1186</td>
+      <td>1356</td>
+      <td>21</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1186</td>
+      <td>1356</td>
+      <td>21</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bundle_collections</td>
+      <td>bundle_collection</td>
+      <td>Tool to bundle up list collection into a single zip to be download</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>bundle_collections</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections</td>
+      <td>1.3.0</td>
+      <td>perl-getopt-long</td>
+      <td>2.58</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1518</td>
+      <td>1526</td>
+      <td>73</td>
+      <td>76</td>
+      <td>1520</td>
+      <td>1528</td>
+      <td>74</td>
+      <td>77</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>busco</td>
+      <td>busco</td>
+      <td>BUSCO assess genome and annotation completeness</td>
+      <td>busco</td>
+      <td>busco</td>
+      <td></td>
+      <td>BUSCO</td>
+      <td>Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.</td>
+      <td>Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly</td>
+      <td>Sequence assembly, Genomics, Transcriptomics, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://gitlab.com/ezlab/busco/-/releases</td>
+      <td>Sequence Analysis</td>
+      <td>busco</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco</td>
+      <td>5.7.1</td>
+      <td>busco</td>
+      <td>5.7.1</td>
+      <td>Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly</td>
+      <td>Sequence assembly, Transcriptomics, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>102717</td>
+      <td>103051</td>
+      <td>3877</td>
+      <td>3926</td>
+      <td>34251</td>
+      <td>34251</td>
+      <td>3506</td>
+      <td>3506</td>
+      <td>33192</td>
+      <td>34369</td>
+      <td>2439</td>
+      <td>2525</td>
+      <td>170160</td>
+      <td>171671</td>
+      <td>9822</td>
+      <td>9957</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bwa</td>
+      <td>bwa_mem, bwa</td>
+      <td>Wrapper for bwa mem, aln, sampe, and samse</td>
+      <td>bwa</td>
+      <td>bwa</td>
+      <td></td>
+      <td>BWA</td>
+      <td>Fast, accurate, memory-efficient aligner for short and long sequencing reads</td>
+      <td>Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment</td>
+      <td>Mapping</td>
+      <td>Up-to-date</td>
+      <td>http://bio-bwa.sourceforge.net/</td>
+      <td>Next Gen Mappers</td>
+      <td>bwa</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa</td>
+      <td>0.7.18</td>
+      <td>bwa</td>
+      <td>0.7.18</td>
+      <td>Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment</td>
+      <td>Mapping</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>976935</td>
+      <td>1017671</td>
+      <td>13526</td>
+      <td>14401</td>
+      <td>474702</td>
+      <td>681286</td>
+      <td>32627</td>
+      <td>47624</td>
+      <td>79802</td>
+      <td>87191</td>
+      <td>4219</td>
+      <td>4954</td>
+      <td>1531439</td>
+      <td>1786148</td>
+      <td>50372</td>
+      <td>66979</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bwa_mem2</td>
+      <td>bwa_mem2</td>
+      <td>Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.</td>
+      <td>bwa-mem2</td>
+      <td>bwa-mem2</td>
+      <td></td>
+      <td>Bwa-mem2</td>
+      <td>Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,  dataset and the running machine.</td>
+      <td>Sequence alignment</td>
+      <td>Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bwa-mem2/bwa-mem2</td>
+      <td>Next Gen Mappers</td>
+      <td>bwa_mem2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2</td>
+      <td>2.2.1</td>
+      <td>bwa-mem2</td>
+      <td>2.2.1</td>
+      <td>Sequence alignment</td>
+      <td>Mapping</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>56619</td>
+      <td>56619</td>
+      <td>2324</td>
+      <td>2324</td>
+      <td>36631</td>
+      <td>36631</td>
+      <td>2808</td>
+      <td>2808</td>
+      <td>18121</td>
+      <td>18121</td>
+      <td>713</td>
+      <td>713</td>
+      <td>111371</td>
+      <td>111371</td>
+      <td>5845</td>
+      <td>5845</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>bwameth</td>
+      <td>bwameth</td>
+      <td>Fast and accurate alignment of BS-seq reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/brentp/bwa-meth</td>
+      <td>Sequence Analysis, Next Gen Mappers</td>
+      <td>bwameth</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth</td>
+      <td>0.2.7</td>
+      <td>bwameth</td>
+      <td>0.2.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7970</td>
+      <td>11724</td>
+      <td>643</td>
+      <td>826</td>
+      <td>5524</td>
+      <td>5524</td>
+      <td>611</td>
+      <td>611</td>
+      <td>1242</td>
+      <td>1242</td>
+      <td>114</td>
+      <td>114</td>
+      <td>14736</td>
+      <td>18490</td>
+      <td>1368</td>
+      <td>1551</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>c3s</td>
+      <td>c3s</td>
+      <td>Copernicus Climate Change Service (C3S)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset</td>
+      <td>Climate Analysis</td>
+      <td>c3s</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s</td>
+      <td>0.3.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>234</td>
+      <td>234</td>
+      <td>11</td>
+      <td>11</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>92</td>
+      <td>92</td>
+      <td>3</td>
+      <td>3</td>
+      <td>330</td>
+      <td>330</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cactus</td>
+      <td>cactus_cactus, cactus_export</td>
+      <td>Cactus is a reference-free whole-genome multiple alignment program</td>
+      <td>cactus</td>
+      <td>cactus</td>
+      <td></td>
+      <td>Cactus</td>
+      <td>Cactus is a reference-free whole-genome multiple alignment program.</td>
+      <td>Multiple sequence alignment, Genome alignment</td>
+      <td>Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics</td>
+      <td>To update</td>
+      <td>https://github.com/ComparativeGenomicsToolkit/cactus</td>
+      <td>Sequence Analysis</td>
+      <td>cactus</td>
+      <td>galaxy-australia</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus</td>
+      <td>2.7.1</td>
+      <td></td>
+      <td></td>
+      <td>Multiple sequence alignment, Genome alignment</td>
+      <td>Genomics, Sequence assembly, Mapping, Phylogenetics</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>299</td>
+      <td>299</td>
+      <td>61</td>
+      <td>61</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1339</td>
+      <td>1339</td>
+      <td>95</td>
+      <td>95</td>
+      <td>1638</td>
+      <td>1638</td>
+      <td>156</td>
+      <td>156</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cads</td>
+      <td>cads</td>
+      <td>Copernicus Atmosphere Data Store (ADS)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://ads.atmosphere.copernicus.eu/#!/home</td>
+      <td>Climate Analysis</td>
+      <td>cads</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads</td>
+      <td>0.1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>52</td>
+      <td>52</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>52</td>
+      <td>52</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>calculate_contrast_threshold</td>
+      <td>calculate_contrast_threshold</td>
+      <td>Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold</td>
+      <td>Visualization, Genomic Interval Operations, SAM</td>
+      <td>calculate_contrast_threshold</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold</td>
+      <td>1.0.0</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>calculate_numeric_param</td>
+      <td>calculate_numeric_param</td>
+      <td>Calculate a numeric parameter value using integer and float values.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>calculate_numeric_param</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1393</td>
+      <td>1393</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1393</td>
+      <td>1393</td>
+      <td>10</td>
+      <td>10</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>calisp</td>
+      <td>calisp</td>
+      <td>Calgary approach to isotopes in proteomics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/kinestetika/Calisp/</td>
+      <td>Proteomics</td>
+      <td>calisp</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp</td>
+      <td>3.0.13</td>
+      <td>calisp</td>
+      <td>3.0.13</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>camera</td>
+      <td>abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Metabolomics</td>
+      <td>camera</td>
+      <td>workflow4metabolomics</td>
+      <td></td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera</td>
+      <td>1.48.0</td>
+      <td>r-snow</td>
+      <td>0.4_1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>677</td>
+      <td>787</td>
+      <td>114</td>
+      <td>120</td>
+      <td>60</td>
+      <td>60</td>
+      <td>30</td>
+      <td>30</td>
+      <td>734</td>
+      <td>746</td>
+      <td>26</td>
+      <td>26</td>
+      <td>1471</td>
+      <td>1593</td>
+      <td>170</td>
+      <td>176</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cami_amber</td>
+      <td>biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert</td>
+      <td>Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/CAMI-challenge/AMBER</td>
+      <td>Metagenomics</td>
+      <td>cami_amber</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber</td>
+      <td>2.0.7</td>
+      <td>cami-amber</td>
+      <td>2.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>195</td>
+      <td>195</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>195</td>
+      <td>195</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>canonical_correlation_analysis</td>
+      <td>cca1</td>
+      <td>Canonical Correlation Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>canonical_correlation_analysis</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis</td>
+      <td>1.0.0</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>66</td>
+      <td>75</td>
+      <td>16</td>
+      <td>18</td>
+      <td>141</td>
+      <td>505</td>
+      <td>31</td>
+      <td>147</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>207</td>
+      <td>580</td>
+      <td>47</td>
+      <td>165</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>canu</td>
+      <td>canu</td>
+      <td>Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).</td>
+      <td>canu</td>
+      <td>canu</td>
+      <td></td>
+      <td>CANU</td>
+      <td>De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.</td>
+      <td>De-novo assembly</td>
+      <td>Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/marbl/canu</td>
+      <td></td>
+      <td>canu</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/canu</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/canu</td>
+      <td>2.2</td>
+      <td>canu</td>
+      <td>2.2</td>
+      <td>De-novo assembly</td>
+      <td>Genomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>13360</td>
+      <td>14618</td>
+      <td>1383</td>
+      <td>1444</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3542</td>
+      <td>3542</td>
+      <td>385</td>
+      <td>385</td>
+      <td>16902</td>
+      <td>18160</td>
+      <td>1768</td>
+      <td>1829</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cap3</td>
+      <td>cap3</td>
+      <td>cap3 wrapper</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Assembly</td>
+      <td>cap3</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3</td>
+      <td>2.0.1</td>
+      <td>cap3</td>
+      <td>10.2011</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9869</td>
+      <td>9869</td>
+      <td>158</td>
+      <td>158</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6886</td>
+      <td>6886</td>
+      <td>146</td>
+      <td>146</td>
+      <td>16755</td>
+      <td>16755</td>
+      <td>304</td>
+      <td>304</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cardinal</td>
+      <td>cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots</td>
+      <td>Statistical and computational tools for analyzing mass spectrometry imaging datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cardinalmsi.org</td>
+      <td>Proteomics, Metabolomics</td>
+      <td></td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal</td>
+      <td>3.4.3</td>
+      <td>bioconductor-cardinal</td>
+      <td>3.4.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>9</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>11</td>
+      <td>9</td>
+      <td>0</td>
+      <td>41875</td>
+      <td>50702</td>
+      <td>663</td>
+      <td>713</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1</td>
+      <td>1</td>
+      <td>7512</td>
+      <td>7512</td>
+      <td>231</td>
+      <td>231</td>
+      <td>49399</td>
+      <td>58226</td>
+      <td>895</td>
+      <td>945</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cat</td>
+      <td>cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise</td>
+      <td>Contig Annotation Tool (CAT)</td>
+      <td>cat_bins</td>
+      <td>cat_bins</td>
+      <td></td>
+      <td>CAT and BAT</td>
+      <td>Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.</td>
+      <td>Taxonomic classification, Sequence assembly, Coding region prediction</td>
+      <td>Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly</td>
+      <td>To update</td>
+      <td>https://github.com/dutilh/CAT</td>
+      <td>Metagenomics</td>
+      <td>contig_annotation_tool</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat</td>
+      <td>5.2.3</td>
+      <td>cat</td>
+      <td>5.3</td>
+      <td>Taxonomic classification, Sequence assembly, Coding region prediction</td>
+      <td>Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly</td>
+      <td>5</td>
+      <td>2</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>2</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>3835</td>
+      <td>3835</td>
+      <td>597</td>
+      <td>597</td>
+      <td>1359</td>
+      <td>1359</td>
+      <td>467</td>
+      <td>467</td>
+      <td>646</td>
+      <td>646</td>
+      <td>98</td>
+      <td>98</td>
+      <td>5840</td>
+      <td>5840</td>
+      <td>1162</td>
+      <td>1162</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>categorize_elements_satisfying_criteria</td>
+      <td>categorize_elements_satisfying_criteria</td>
+      <td>Categorize Elements satisfying criteria.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>categorize_elements_satisfying_criteria</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>37</td>
+      <td>41</td>
+      <td>4</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>168</td>
+      <td>186</td>
+      <td>12</td>
+      <td>14</td>
+      <td>205</td>
+      <td>227</td>
+      <td>16</td>
+      <td>19</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ccat</td>
+      <td>peakcalling_ccat</td>
+      <td>Control-based ChIP-seq Analysis Tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>ChIP-seq</td>
+      <td>ccat</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat</td>
+      <td>0.0.2</td>
+      <td>ccat</td>
+      <td>3.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>88</td>
+      <td>175</td>
+      <td>28</td>
+      <td>39</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>88</td>
+      <td>175</td>
+      <td>28</td>
+      <td>39</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cd_hit_dup</td>
+      <td>cd_hit_dup</td>
+      <td>simple tool for removing duplicates from sequencing reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Metagenomics, Sequence Analysis</td>
+      <td>cd_hit_dup</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup</td>
+      <td>0.0.1</td>
+      <td>cd-hit-auxtools</td>
+      <td>4.8.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5946</td>
+      <td>7379</td>
+      <td>407</td>
+      <td>628</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5946</td>
+      <td>7379</td>
+      <td>407</td>
+      <td>628</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cdhit</td>
+      <td>cd_hit</td>
+      <td>Cluster or compare biological sequence datasets</td>
+      <td>cd-hit</td>
+      <td>cd-hit</td>
+      <td></td>
+      <td>cd-hit</td>
+      <td>Cluster a nucleotide dataset into representative sequences.</td>
+      <td>Sequence clustering</td>
+      <td>Sequencing</td>
+      <td>Up-to-date</td>
+      <td>http://weizhongli-lab.org/cd-hit/</td>
+      <td>Sequence Analysis, Fasta Manipulation</td>
+      <td>cd_hit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit</td>
+      <td>4.8.1</td>
+      <td>cd-hit</td>
+      <td>4.8.1</td>
+      <td>Sequence clustering</td>
+      <td>Sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>10414</td>
+      <td>10414</td>
+      <td>510</td>
+      <td>510</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>10418</td>
+      <td>10418</td>
+      <td>512</td>
+      <td>512</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cdo</td>
+      <td>cdo_info, cdo_operations</td>
+      <td>CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://code.mpimet.mpg.de/projects/cdo/</td>
+      <td>Climate Analysis</td>
+      <td></td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo</td>
+      <td>2.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cell-types-analysis</td>
+      <td>ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals</td>
+      <td>Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>suite_cell_types_analysis</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis</td>
+      <td>1.1.1</td>
+      <td>cell-types-analysis</td>
+      <td>0.1.11</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cellpose</td>
+      <td>cellpose</td>
+      <td>Cellpose is an anatomical segmentation algorithm</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/MouseLand/cellpose</td>
+      <td>Imaging</td>
+      <td>cellpose</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cellpose</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cellpose</td>
+      <td>3.0.10</td>
+      <td>cellpose</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cellprofiler</td>
+      <td>cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects</td>
+      <td>cellProfiler wrapper</td>
+      <td>CellProfiler</td>
+      <td>CellProfiler</td>
+      <td>cellprofiler</td>
+      <td>CellProfiler</td>
+      <td>Tool for quantifying data from biological images, particularly in high-throughput experiments.</td>
+      <td>Quantification, Image analysis, Parsing</td>
+      <td>Imaging, Microarray experiment, Genotype and phenotype</td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>cellprofiler</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Quantification, Image analysis, Parsing</td>
+      <td>Imaging, Microarray experiment, Genotype and phenotype</td>
+      <td>0</td>
+      <td>23</td>
+      <td>23</td>
+      <td>0</td>
+      <td>0</td>
+      <td>23</td>
+      <td>23</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>23</td>
+      <td>19</td>
+      <td>0</td>
+      <td>4773</td>
+      <td>4773</td>
+      <td>749</td>
+      <td>749</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5688</td>
+      <td>5688</td>
+      <td>94</td>
+      <td>94</td>
+      <td>10461</td>
+      <td>10461</td>
+      <td>843</td>
+      <td>843</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cellprofiler_v4</td>
+      <td>cp_cellprofiler4</td>
+      <td>cellProfiler4 wrapper</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/CellProfiler/CellProfiler</td>
+      <td>Imaging</td>
+      <td>cellprofiler4</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4</td>
+      <td>4.2.7</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>55</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>55</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cemitool</td>
+      <td>cemitool</td>
+      <td>Gene co-expression network analysis tool</td>
+      <td>cemitool</td>
+      <td>cemitool</td>
+      <td></td>
+      <td>CEMiTool</td>
+      <td>It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.</td>
+      <td>Enrichment analysis, Pathway or network analysis</td>
+      <td>Gene expression, Transcriptomics, Microarray experiment</td>
+      <td>Up-to-date</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>cemitool</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool</td>
+      <td>1.26.0</td>
+      <td>bioconductor-cemitool</td>
+      <td>1.26.0</td>
+      <td>Enrichment analysis, Pathway or network analysis</td>
+      <td>Transcriptomics, Microarray experiment</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>225</td>
+      <td>225</td>
+      <td>32</td>
+      <td>32</td>
+      <td>271</td>
+      <td>271</td>
+      <td>61</td>
+      <td>61</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>496</td>
+      <td>496</td>
+      <td>93</td>
+      <td>93</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cesm</td>
+      <td>cesm</td>
+      <td>Community Earth System Model (CESM)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://www.cesm.ucar.edu/</td>
+      <td>Climate Analysis</td>
+      <td>cesm</td>
+      <td>climate</td>
+      <td>https://github.com/ESCOMP/CESM</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm</td>
+      <td>2.1.3</td>
+      <td>cesm</td>
+      <td>2.1.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cfm</td>
+      <td>cfmid</td>
+      <td>Competitive Fragmentation Modeling (CFM)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://sourceforge.net/p/cfm-id/</td>
+      <td>Metabolomics</td>
+      <td>cfmid</td>
+      <td>computational-metabolomics</td>
+      <td>https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm</td>
+      <td>https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm</td>
+      <td>33</td>
+      <td>cfm</td>
+      <td>33</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chado</td>
+      <td>analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree</td>
+      <td>Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxy-genome-annotation/python-chado</td>
+      <td>Web Services</td>
+      <td></td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado</td>
+      <td></td>
+      <td>python-chado</td>
+      <td>2.3.9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>champ_blocs</td>
+      <td>cb_dissim, cb_ivr, cb_div</td>
+      <td>Compute indicators for turnover boulders fields</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/Marie59/champ_blocs</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs</td>
+      <td>0.0.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>183</td>
+      <td>183</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>183</td>
+      <td>183</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>change_case</td>
+      <td>ChangeCase</td>
+      <td>Convert column case.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>change_case</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case</td>
+      <td>1.0.1</td>
+      <td>perl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>10606</td>
+      <td>12531</td>
+      <td>2204</td>
+      <td>2547</td>
+      <td>9044</td>
+      <td>17167</td>
+      <td>1748</td>
+      <td>2394</td>
+      <td>923</td>
+      <td>938</td>
+      <td>240</td>
+      <td>245</td>
+      <td>20573</td>
+      <td>30636</td>
+      <td>4192</td>
+      <td>5186</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>charts</td>
+      <td>charts</td>
+      <td>Enables advanced visualization options in Galaxy Charts</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/</td>
+      <td>Visualization</td>
+      <td>charts</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts</td>
+      <td>1.0.1</td>
+      <td>r-getopt</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3383</td>
+      <td>4001</td>
+      <td>1576</td>
+      <td>1822</td>
+      <td>7870</td>
+      <td>13727</td>
+      <td>3823</td>
+      <td>6880</td>
+      <td>249</td>
+      <td>350</td>
+      <td>108</td>
+      <td>145</td>
+      <td>11502</td>
+      <td>18078</td>
+      <td>5507</td>
+      <td>8847</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chatgpt</td>
+      <td>chatgpt_openai_api</td>
+      <td>Using the OpenAI GPT models to generate text based on user input.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt</td>
+      <td>Machine Learning</td>
+      <td>chatgpt_openai_api</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt</td>
+      <td>2024</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>62</td>
+      <td>62</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>62</td>
+      <td>62</td>
+      <td>12</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>checkm</td>
+      <td>checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa</td>
+      <td>Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes</td>
+      <td>checkm</td>
+      <td>checkm</td>
+      <td></td>
+      <td>CheckM</td>
+      <td>CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.</td>
+      <td>Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation</td>
+      <td>Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Ecogenomics/CheckM</td>
+      <td>Metagenomics</td>
+      <td>checkm</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm</td>
+      <td>1.2.3</td>
+      <td>checkm-genome</td>
+      <td>1.2.3</td>
+      <td>Sequence assembly validation, Sequence composition calculation, Statistical calculation</td>
+      <td>Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7500</td>
+      <td>7500</td>
+      <td>930</td>
+      <td>930</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7500</td>
+      <td>7500</td>
+      <td>930</td>
+      <td>930</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>checkv</td>
+      <td>checkv_end_to_end</td>
+      <td>Assess quality of single-contig viral genomes</td>
+      <td>checkv</td>
+      <td>checkv</td>
+      <td></td>
+      <td>CheckV</td>
+      <td>CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.</td>
+      <td>Sequence assembly, Validation, Read mapping</td>
+      <td>Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://bitbucket.org/berkeleylab/checkv/</td>
+      <td>Metagenomics</td>
+      <td>checkv</td>
+      <td>ufz</td>
+      <td>https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv</td>
+      <td>1.0.3</td>
+      <td>checkv</td>
+      <td>1.0.3</td>
+      <td>Sequence assembly, Validation, Read mapping</td>
+      <td>Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cherri</td>
+      <td>cherri_eval, cherri_train</td>
+      <td>Computational Help Evaluating RNA-RNA interactions</td>
+      <td>cherri</td>
+      <td>cherri</td>
+      <td></td>
+      <td>cherri</td>
+      <td>CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.</td>
+      <td></td>
+      <td>Molecular interactions, pathways and networks, Structure analysis, Machine learning</td>
+      <td>To update</td>
+      <td>https://github.com/BackofenLab/Cherri</td>
+      <td>Transcriptomics, RNA</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri</td>
+      <td>0.7</td>
+      <td>cherri</td>
+      <td>0.8</td>
+      <td></td>
+      <td>Molecular interactions, pathways and networks, Structure analysis, Machine learning</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>207</td>
+      <td>207</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>207</td>
+      <td>207</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cherry_pick_fasta</td>
+      <td>cherry_pick_fasta</td>
+      <td>Pick fasta sequence with specific header content</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Fasta Manipulation</td>
+      <td>cherry_pick_fasta</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta</td>
+      <td>4.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chewbbaca</td>
+      <td>chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema</td>
+      <td>BSR-Based Allele Calling Algorithm</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/B-UMMI/chewBBACA/tree/master</td>
+      <td>Variant Analysis</td>
+      <td>chewbbaca</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca</td>
+      <td></td>
+      <td>chewbbaca</td>
+      <td>3.3.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>727</td>
+      <td>727</td>
+      <td>76</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>727</td>
+      <td>727</td>
+      <td>76</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chipseeker</td>
+      <td>chipseeker</td>
+      <td>A tool for ChIP peak annotation and visualization</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html</td>
+      <td>ChIP-seq, Genome annotation</td>
+      <td>chipseeker</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker</td>
+      <td>1.32.0</td>
+      <td>bioconductor-chipseeker</td>
+      <td>1.38.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>16468</td>
+      <td>18344</td>
+      <td>956</td>
+      <td>991</td>
+      <td>33692</td>
+      <td>34453</td>
+      <td>2559</td>
+      <td>2625</td>
+      <td>2948</td>
+      <td>2948</td>
+      <td>104</td>
+      <td>104</td>
+      <td>53108</td>
+      <td>55745</td>
+      <td>3619</td>
+      <td>3720</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chira</td>
+      <td>chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify</td>
+      <td>Chimeric Read Annotator for RNA-RNA interactome data</td>
+      <td>chira</td>
+      <td>chira</td>
+      <td></td>
+      <td>ChiRA</td>
+      <td>ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.</td>
+      <td></td>
+      <td>RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pavanvidem/chira</td>
+      <td>RNA, Transcriptomics, Sequence Analysis</td>
+      <td>chira</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira</td>
+      <td>1.4.3</td>
+      <td>chira</td>
+      <td>1.4.3</td>
+      <td></td>
+      <td>Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>16542</td>
+      <td>16542</td>
+      <td>287</td>
+      <td>287</td>
+      <td>1061</td>
+      <td>1061</td>
+      <td>102</td>
+      <td>102</td>
+      <td>27</td>
+      <td>27</td>
+      <td>5</td>
+      <td>5</td>
+      <td>17630</td>
+      <td>17630</td>
+      <td>394</td>
+      <td>394</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chopin2</td>
+      <td>chopin2</td>
+      <td>Domain-Agnostic Supervised Learning with Hyperdimensional Computing</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/cumbof/chopin2</td>
+      <td>Machine Learning</td>
+      <td>chopin2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2</td>
+      <td>1.0.9.post1</td>
+      <td>chopin2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chromeister</td>
+      <td>chromeister</td>
+      <td>ultra-fast pairwise genome comparisons</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/estebanpw/chromeister</td>
+      <td>Sequence Analysis</td>
+      <td>chromeister</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister</td>
+      <td>1.5.a</td>
+      <td>chromeister</td>
+      <td>1.5.a</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2696</td>
+      <td>2696</td>
+      <td>398</td>
+      <td>398</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1235</td>
+      <td>1235</td>
+      <td>186</td>
+      <td>186</td>
+      <td>3931</td>
+      <td>3931</td>
+      <td>584</td>
+      <td>584</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>chromosome_diagram</td>
+      <td>chromosome_diagram</td>
+      <td>Chromosome Diagrams using Biopython</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Sequence Analysis, Visualization</td>
+      <td>chromosome_diagram</td>
+      <td>peterjc</td>
+      <td></td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram</td>
+      <td>0.0.3</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>circexplorer</td>
+      <td>circexplorer</td>
+      <td>A combined strategy to identify circular RNAs (circRNAs and ciRNAs)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/YangLab/CIRCexplorer</td>
+      <td>Sequence Analysis, RNA</td>
+      <td>circexplorer</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer</td>
+      <td>1.1.9.0</td>
+      <td>circexplorer</td>
+      <td>1.1.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>211</td>
+      <td>263</td>
+      <td>32</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>209</td>
+      <td>209</td>
+      <td>6</td>
+      <td>6</td>
+      <td>420</td>
+      <td>472</td>
+      <td>38</td>
+      <td>46</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>circexplorer2</td>
+      <td>circexplorer2</td>
+      <td>Comprehensive and integrative circular RNA analysis toolset.</td>
+      <td>circexplorer2</td>
+      <td>circexplorer2</td>
+      <td></td>
+      <td>CIRCexplorer2</td>
+      <td>Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.</td>
+      <td></td>
+      <td>RNA splicing, Gene transcripts, Literature and language</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/YangLab/CIRCexplorer2</td>
+      <td>RNA, Assembly</td>
+      <td>circexplorer2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2</td>
+      <td>2.3.8</td>
+      <td>circexplorer2</td>
+      <td>2.3.8</td>
+      <td></td>
+      <td>RNA splicing, Gene transcripts, Literature and language</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>524</td>
+      <td>524</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>524</td>
+      <td>524</td>
+      <td>32</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>circos</td>
+      <td>circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile</td>
+      <td>Build Circos Plots in Galaxy</td>
+      <td>galactic_circos</td>
+      <td>galactic_circos</td>
+      <td></td>
+      <td>Galactic Circos</td>
+      <td>Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.</td>
+      <td>Sequence visualisation</td>
+      <td></td>
+      <td>To update</td>
+      <td>http://circos.ca/</td>
+      <td>Graphics</td>
+      <td>circos</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos</td>
+      <td>0.69.8</td>
+      <td>circos</td>
+      <td>0.69.9</td>
+      <td>Sequence visualisation</td>
+      <td></td>
+      <td>11</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>26265</td>
+      <td>26265</td>
+      <td>2483</td>
+      <td>2483</td>
+      <td>31332</td>
+      <td>31332</td>
+      <td>3535</td>
+      <td>3535</td>
+      <td>26359</td>
+      <td>26359</td>
+      <td>999</td>
+      <td>999</td>
+      <td>83956</td>
+      <td>83956</td>
+      <td>7017</td>
+      <td>7017</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cite_seq_count</td>
+      <td>cite_seq_count</td>
+      <td>Count CMO/HTO</td>
+      <td>CITE-seq-Count</td>
+      <td>CITE-seq-Count</td>
+      <td></td>
+      <td>CITE-seq-Count</td>
+      <td>Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.</td>
+      <td>RNA-Seq quantification</td>
+      <td>Transcriptomics, Immunoproteins and antigens</td>
+      <td>To update</td>
+      <td>https://github.com/Hoohm/CITE-seq-Count</td>
+      <td>Single Cell, Transcriptomics, Proteomics</td>
+      <td>cite_seq_count</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count</td>
+      <td>1.4.4</td>
+      <td>cite-seq-count</td>
+      <td>1.4.5</td>
+      <td>RNA-Seq quantification</td>
+      <td>Transcriptomics, Immunoproteins and antigens</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21</td>
+      <td>21</td>
+      <td>4</td>
+      <td>4</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td>48</td>
+      <td>48</td>
+      <td>10</td>
+      <td>10</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>clair3</td>
+      <td>clair3</td>
+      <td>Symphonizing pileup and full-alignment for high-performance long-read variant calling</td>
+      <td>clair3</td>
+      <td>clair3</td>
+      <td></td>
+      <td>Clair3</td>
+      <td>Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.</td>
+      <td>Variant calling</td>
+      <td>Molecular genetics</td>
+      <td>To update</td>
+      <td>https://github.com/HKU-BAL/Clair3</td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>clair3</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3</td>
+      <td>1.0.8</td>
+      <td>clair3</td>
+      <td>1.0.10</td>
+      <td>Variant calling</td>
+      <td>Molecular genetics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3388</td>
+      <td>3388</td>
+      <td>187</td>
+      <td>187</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>3390</td>
+      <td>3390</td>
+      <td>189</td>
+      <td>189</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>clc_assembly_cell</td>
+      <td>clc_assembler, clc_mapper</td>
+      <td>Galaxy wrapper for the CLC Assembly Cell suite from CLCBio</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell</td>
+      <td>Assembly, Next Gen Mappers, SAM</td>
+      <td>clc_assembly_cell</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell</td>
+      <td>0.0.7</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>climate-stripes</td>
+      <td>climate_stripes</td>
+      <td>Create climate stripes from a tabular input file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.climate-lab-book.ac.uk/2018/warming-stripes/</td>
+      <td>Climate Analysis, Visualization</td>
+      <td>climate_stripes</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes</td>
+      <td>1.0.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>239</td>
+      <td>239</td>
+      <td>35</td>
+      <td>35</td>
+      <td>16</td>
+      <td>16</td>
+      <td>2</td>
+      <td>2</td>
+      <td>182</td>
+      <td>182</td>
+      <td>3</td>
+      <td>3</td>
+      <td>437</td>
+      <td>437</td>
+      <td>40</td>
+      <td>40</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>clinod</td>
+      <td>clinod</td>
+      <td>NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins</td>
+      <td>clinod</td>
+      <td>clinod</td>
+      <td></td>
+      <td>clinod</td>
+      <td>The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.compbio.dundee.ac.uk/www-nod/</td>
+      <td>Sequence Analysis</td>
+      <td>clinod</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod</td>
+      <td>0.1.0</td>
+      <td>clinod</td>
+      <td>1.3</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>548</td>
+      <td>548</td>
+      <td>18</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>548</td>
+      <td>548</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>clustalw</td>
+      <td>clustalw</td>
+      <td>ClustalW multiple sequence alignment program for DNA or proteins</td>
+      <td>clustal2</td>
+      <td>clustal2</td>
+      <td></td>
+      <td>Clustal 2 (Clustal W, Clustal X)</td>
+      <td>Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.</td>
+      <td>Multiple sequence alignment</td>
+      <td>Phylogeny, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://www.clustal.org/clustal2/</td>
+      <td>Phylogenetics, Sequence Analysis</td>
+      <td>clustalw</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw</td>
+      <td>2.1</td>
+      <td>clustalw</td>
+      <td>2.1</td>
+      <td>Multiple sequence alignment</td>
+      <td>Phylogeny, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>79867</td>
+      <td>80817</td>
+      <td>1675</td>
+      <td>1785</td>
+      <td>49493</td>
+      <td>87884</td>
+      <td>3703</td>
+      <td>7380</td>
+      <td>8797</td>
+      <td>9713</td>
+      <td>670</td>
+      <td>728</td>
+      <td>138157</td>
+      <td>178414</td>
+      <td>6048</td>
+      <td>9893</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cluster</td>
+      <td>gops_cluster_1</td>
+      <td>Cluster the intervals of a dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>cluster</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>513</td>
+      <td>813</td>
+      <td>18</td>
+      <td>35</td>
+      <td>2406</td>
+      <td>30579</td>
+      <td>156</td>
+      <td>1547</td>
+      <td>1353</td>
+      <td>1393</td>
+      <td>17</td>
+      <td>20</td>
+      <td>4272</td>
+      <td>32785</td>
+      <td>191</td>
+      <td>1602</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>clustering_from_distmat</td>
+      <td>clustering_from_distmat</td>
+      <td>Distance matrix-based hierarchical clustering using SciPy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/</td>
+      <td>Statistics</td>
+      <td>clustering_from_distmat</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat</td>
+      <td>1.1.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cmsearch_deoverlap</td>
+      <td>cmsearch_deoverlap</td>
+      <td>removes lower scoring overlaps from cmsearch results.</td>
+      <td>cmsearch-deoverlap</td>
+      <td>cmsearch-deoverlap</td>
+      <td></td>
+      <td>cmsearch-deoverlap</td>
+      <td>Removes lower scoring overlaps from cmsearch results.</td>
+      <td>Comparison, Alignment</td>
+      <td>Biology, Medicine</td>
+      <td>To update</td>
+      <td>https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl</td>
+      <td>RNA</td>
+      <td>cmsearch_deoverlap</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap</td>
+      <td>0.08+galaxy2</td>
+      <td>perl</td>
+      <td></td>
+      <td>Comparison, Alignment</td>
+      <td>Biology, Medicine</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2609</td>
+      <td>2609</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2609</td>
+      <td>2609</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cmv</td>
+      <td>cmcv, cmv, hmmcv, hmmv</td>
+      <td>cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/eggzilla/cmv</td>
+      <td>RNA</td>
+      <td>cmv</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv</td>
+      <td>1.0.8</td>
+      <td>cmv</td>
+      <td>1.0.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>90</td>
+      <td>112</td>
+      <td>11</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>90</td>
+      <td>112</td>
+      <td>11</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cnv-phenopacket</td>
+      <td>cnv_phenopacket</td>
+      <td>cnv-phenopacket Converts TSV metadata file to JSON.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pypi.org/project/cnv-phenopacket/</td>
+      <td>Variant Analysis</td>
+      <td>cnv_phenopacket</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket</td>
+      <td>1.0.2</td>
+      <td>cnv-phenopacket</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cnv-vcf2json</td>
+      <td>cnv_vcf2json</td>
+      <td>cnv-vcf2json Converts structural variants VCF file to JSON.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pypi.org/project/cnv-phenopacket/</td>
+      <td>Variant Analysis</td>
+      <td>cnv-vcf2json</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json</td>
+      <td>1.1.0</td>
+      <td>cnv-vcf2json</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cnvkit</td>
+      <td>cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target</td>
+      <td>detecting copy number variants and alterations genome-wide from high-throughput sequencing</td>
+      <td>cnvkit</td>
+      <td>cnvkit</td>
+      <td></td>
+      <td>CNVkit</td>
+      <td>CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.</td>
+      <td>Variant calling</td>
+      <td>DNA structural variation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/etal/cnvkit</td>
+      <td>Variant Analysis</td>
+      <td>cnvkit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit</td>
+      <td>0.9.11</td>
+      <td>cnvkit</td>
+      <td>0.9.11</td>
+      <td>Variant calling</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>618</td>
+      <td>618</td>
+      <td>177</td>
+      <td>177</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>618</td>
+      <td>618</td>
+      <td>177</td>
+      <td>177</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>codeml</td>
+      <td>codeml</td>
+      <td>Detects positive selection</td>
+      <td>paml</td>
+      <td>paml</td>
+      <td></td>
+      <td>PAML</td>
+      <td>Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.</td>
+      <td>Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis</td>
+      <td>Phylogenetics, Sequence analysis</td>
+      <td>To update</td>
+      <td>http://abacus.gene.ucl.ac.uk/software/paml.html</td>
+      <td>Phylogenetics</td>
+      <td>codeml</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml</td>
+      <td>4.9</td>
+      <td>paml</td>
+      <td>4.10.7</td>
+      <td>Probabilistic sequence generation</td>
+      <td>Phylogenetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>61197</td>
+      <td>61220</td>
+      <td>64</td>
+      <td>65</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>61197</td>
+      <td>61220</td>
+      <td>64</td>
+      <td>65</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cofold</td>
+      <td>cofold</td>
+      <td>Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.e-rna.org/cofold/</td>
+      <td>RNA</td>
+      <td>cofold</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold</td>
+      <td>2.0.4.0</td>
+      <td>cofold</td>
+      <td>2.0.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>316</td>
+      <td>355</td>
+      <td>25</td>
+      <td>29</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>316</td>
+      <td>355</td>
+      <td>25</td>
+      <td>29</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cojac</td>
+      <td>cooc_mutbamscan, cooc_pubmut, cooc_tabmut</td>
+      <td>co-occurrence of mutations on amplicons</td>
+      <td>cojac</td>
+      <td>cojac</td>
+      <td></td>
+      <td>COJAC</td>
+      <td>CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.</td>
+      <td></td>
+      <td>Genetic variation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cbg-ethz/cojac</td>
+      <td>Metagenomics, Sequence Analysis</td>
+      <td>cojac</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac</td>
+      <td>0.9.2</td>
+      <td>cojac</td>
+      <td>0.9.2</td>
+      <td></td>
+      <td>Genetic variation</td>
+      <td>2</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2758</td>
+      <td>2758</td>
+      <td>22</td>
+      <td>22</td>
+      <td>20</td>
+      <td>20</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2778</td>
+      <td>2778</td>
+      <td>32</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>colabfold</td>
+      <td>colabfold_alphafold, colabfold_msa</td>
+      <td>Protein prediction based on AlphaFold2</td>
+      <td>Colabfold</td>
+      <td>Colabfold</td>
+      <td></td>
+      <td>ColabFold</td>
+      <td>ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.</td>
+      <td>Database search, Protein structure prediction, Fold recognition</td>
+      <td>Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics</td>
+      <td>To update</td>
+      <td>https://github.com/sokrypton/ColabFold</td>
+      <td>Proteomics, Graphics</td>
+      <td>colabfold</td>
+      <td>iuc</td>
+      <td>https://github.com/sokrypton/ColabFold</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold</td>
+      <td>1.5.5</td>
+      <td></td>
+      <td></td>
+      <td>Database search, Protein structure prediction, Fold recognition</td>
+      <td>Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6771</td>
+      <td>6771</td>
+      <td>50</td>
+      <td>50</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6771</td>
+      <td>6771</td>
+      <td>50</td>
+      <td>50</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>colibread</td>
+      <td>commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak</td>
+      <td>Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://colibread.inria.fr/</td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>colibread</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread</td>
+      <td>24.7.14</td>
+      <td>commet</td>
+      <td>24.7.14</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>273</td>
+      <td>273</td>
+      <td>40</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>273</td>
+      <td>273</td>
+      <td>40</td>
+      <td>40</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>collapse_collection</td>
+      <td>collapse_dataset</td>
+      <td>Collection tool that collapses a list of files into a single datasset in order of appears in collection</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>collapse_collections</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection</td>
+      <td>5.1.0</td>
+      <td>gawk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>39518</td>
+      <td>40471</td>
+      <td>3555</td>
+      <td>3629</td>
+      <td>22007</td>
+      <td>24841</td>
+      <td>3536</td>
+      <td>4045</td>
+      <td>3969</td>
+      <td>4101</td>
+      <td>814</td>
+      <td>835</td>
+      <td>65494</td>
+      <td>69413</td>
+      <td>7905</td>
+      <td>8509</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>collection_column_join</td>
+      <td>collection_column_join</td>
+      <td>Column Join on Collections</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join</td>
+      <td>Text Manipulation</td>
+      <td>collection_column_join</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join</td>
+      <td>0.0.3</td>
+      <td>coreutils</td>
+      <td>8.25</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>23979</td>
+      <td>25337</td>
+      <td>3827</td>
+      <td>4011</td>
+      <td>21671</td>
+      <td>25163</td>
+      <td>4645</td>
+      <td>5045</td>
+      <td>2939</td>
+      <td>3036</td>
+      <td>688</td>
+      <td>701</td>
+      <td>48589</td>
+      <td>53536</td>
+      <td>9160</td>
+      <td>9757</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>collection_element_identifiers</td>
+      <td>collection_element_identifiers</td>
+      <td>Extract element identifiers of a collection</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers</td>
+      <td>Text Manipulation</td>
+      <td>collection_element_identifiers</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers</td>
+      <td>0.0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6905</td>
+      <td>7102</td>
+      <td>1620</td>
+      <td>1630</td>
+      <td>7761</td>
+      <td>7761</td>
+      <td>1897</td>
+      <td>1897</td>
+      <td>1157</td>
+      <td>1157</td>
+      <td>243</td>
+      <td>243</td>
+      <td>15823</td>
+      <td>16020</td>
+      <td>3760</td>
+      <td>3770</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>color_deconvolution</td>
+      <td>ip_color_deconvolution</td>
+      <td>Color-deconvolution methods</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>color_deconvolution</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution</td>
+      <td>0.8-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15</td>
+      <td>16</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>16</td>
+      <td>2</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>colorize_labels</td>
+      <td>colorize_labels</td>
+      <td>Colorize label map</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>colorize_labels</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels</td>
+      <td>3.2.1</td>
+      <td>networkx</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>column_arrange_by_header</td>
+      <td>bg_column_arrange_by_header</td>
+      <td>Column arrange by header name</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>column_arrange_by_header</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header</td>
+      <td>0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5356</td>
+      <td>5636</td>
+      <td>446</td>
+      <td>484</td>
+      <td>2026</td>
+      <td>2026</td>
+      <td>375</td>
+      <td>375</td>
+      <td>1400</td>
+      <td>1531</td>
+      <td>117</td>
+      <td>138</td>
+      <td>8782</td>
+      <td>9193</td>
+      <td>938</td>
+      <td>997</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>column_maker</td>
+      <td>Add_a_column1</td>
+      <td>Compute an expression on every row</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker</td>
+      <td>Text Manipulation</td>
+      <td>column_maker</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker</td>
+      <td>2.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2940752</td>
+      <td>3907183</td>
+      <td>5422</td>
+      <td>6121</td>
+      <td>263254</td>
+      <td>737503</td>
+      <td>6095</td>
+      <td>13728</td>
+      <td>96478</td>
+      <td>97667</td>
+      <td>884</td>
+      <td>974</td>
+      <td>3300484</td>
+      <td>4742353</td>
+      <td>12401</td>
+      <td>20823</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>column_order_header_sort</td>
+      <td>column_order_header_sort</td>
+      <td>Sort Column Order by heading</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort</td>
+      <td>Text Manipulation</td>
+      <td>column_order_header_sort</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort</td>
+      <td>0.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3735</td>
+      <td>3891</td>
+      <td>268</td>
+      <td>297</td>
+      <td>1923</td>
+      <td>1923</td>
+      <td>381</td>
+      <td>381</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5658</td>
+      <td>5814</td>
+      <td>649</td>
+      <td>678</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>column_remove_by_header</td>
+      <td>column_remove_by_header</td>
+      <td>Remove columns by header</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header</td>
+      <td>Text Manipulation</td>
+      <td>column_remove_by_header</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header</td>
+      <td>1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>8331</td>
+      <td>8917</td>
+      <td>613</td>
+      <td>662</td>
+      <td>5206</td>
+      <td>5206</td>
+      <td>716</td>
+      <td>716</td>
+      <td>1976</td>
+      <td>1976</td>
+      <td>27</td>
+      <td>27</td>
+      <td>15513</td>
+      <td>16099</td>
+      <td>1356</td>
+      <td>1405</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>combineJSON</td>
+      <td>combine_json</td>
+      <td>JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>combine_json</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>combine_assembly_stats</td>
+      <td>combine_stats</td>
+      <td>Combine multiple Assemblystats datasets into a single tabular report</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Assembly</td>
+      <td>combine_assemblystats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats</td>
+      <td>1.0</td>
+      <td>perl-getopt-long</td>
+      <td>2.58</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>combine_metaphlan_humann</td>
+      <td>combine_metaphlan_humann</td>
+      <td>Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances</td>
+      <td>combine_metaphlan_and_humann</td>
+      <td>combine_metaphlan_and_humann</td>
+      <td></td>
+      <td>Combine Metaphlan and HUMAnN</td>
+      <td>This tool combine MetaPhlAn outputs and HUMANnN outputs</td>
+      <td>Aggregation</td>
+      <td>Metagenomics, Molecular interactions, pathways and networks</td>
+      <td>To update</td>
+      <td></td>
+      <td>Metagenomics</td>
+      <td>combine_metaphlan2_humann2</td>
+      <td>bebatut</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann</td>
+      <td>0.3.0</td>
+      <td>python</td>
+      <td></td>
+      <td>Aggregation</td>
+      <td>Metagenomics, Molecular interactions, pathways and networks</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>530</td>
+      <td>530</td>
+      <td>65</td>
+      <td>65</td>
+      <td>8</td>
+      <td>8</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>538</td>
+      <td>538</td>
+      <td>71</td>
+      <td>71</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>combine_tabular_collection</td>
+      <td>combine</td>
+      <td>Combine Tabular Collection into a single file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>combine_tabular_collection</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compalignp</td>
+      <td>compalignp</td>
+      <td>Compute fractional identity between trusted alignment and test alignment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td></td>
+      <td>RNA, Sequence Analysis</td>
+      <td>compalignp</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp</td>
+      <td>1.0</td>
+      <td>compalignp</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>39</td>
+      <td>221</td>
+      <td>5</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>221</td>
+      <td>5</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compare_humann2_output</td>
+      <td>compare_humann2_output</td>
+      <td>Compare outputs of HUMAnN2 for several samples and extract similar and specific information</td>
+      <td>compare_humann2_outputs</td>
+      <td>compare_humann2_outputs</td>
+      <td></td>
+      <td>Compare HUMAnN2 outputs</td>
+      <td>This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples</td>
+      <td>Comparison</td>
+      <td>Metagenomics, Gene and protein families</td>
+      <td>To update</td>
+      <td></td>
+      <td>Metagenomics</td>
+      <td>compare_humann2_output</td>
+      <td>bebatut</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td>Comparison</td>
+      <td>Metagenomics, Gene and protein families</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>306</td>
+      <td>332</td>
+      <td>28</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>306</td>
+      <td>332</td>
+      <td>28</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compleasm</td>
+      <td>compleasm</td>
+      <td>Compleasm: a faster and more accurate reimplementation of BUSCO</td>
+      <td>compleasm</td>
+      <td>compleasm</td>
+      <td></td>
+      <td>compleasm</td>
+      <td>"Compleasm: a faster and more accurate reimplementation of BUSCO"</td>
+      <td>Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly</td>
+      <td>Sequence assembly, Genomics, Transcriptomics, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/huangnengCSU/compleasm</td>
+      <td>Sequence Analysis</td>
+      <td>compleasm</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm</td>
+      <td>0.2.6</td>
+      <td>compleasm</td>
+      <td>0.2.6</td>
+      <td>Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly</td>
+      <td>Sequence assembly, Transcriptomics, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>266</td>
+      <td>266</td>
+      <td>39</td>
+      <td>39</td>
+      <td>28</td>
+      <td>28</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>294</td>
+      <td>294</td>
+      <td>54</td>
+      <td>54</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>complement</td>
+      <td>gops_complement_1</td>
+      <td>Complement intervals of a dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>complement</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>187</td>
+      <td>233</td>
+      <td>15</td>
+      <td>20</td>
+      <td>495</td>
+      <td>4810</td>
+      <td>165</td>
+      <td>836</td>
+      <td>405</td>
+      <td>451</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1087</td>
+      <td>5494</td>
+      <td>187</td>
+      <td>863</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compose_text_param</td>
+      <td>compose_text_param</td>
+      <td>Compose a text parameter value using text, integer and float values</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>compose_text_param</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param</td>
+      <td>0.1.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45827</td>
+      <td>45831</td>
+      <td>689</td>
+      <td>691</td>
+      <td>7721</td>
+      <td>7721</td>
+      <td>303</td>
+      <td>303</td>
+      <td>1481</td>
+      <td>1481</td>
+      <td>121</td>
+      <td>121</td>
+      <td>55029</td>
+      <td>55033</td>
+      <td>1113</td>
+      <td>1115</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compress_file</td>
+      <td>compress_file</td>
+      <td>Compress files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file</td>
+      <td>Text Manipulation</td>
+      <td>compress_file</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file</td>
+      <td>0.1.0</td>
+      <td>gzip</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6343</td>
+      <td>6343</td>
+      <td>290</td>
+      <td>290</td>
+      <td>3674</td>
+      <td>3674</td>
+      <td>286</td>
+      <td>286</td>
+      <td>11832</td>
+      <td>11832</td>
+      <td>59</td>
+      <td>59</td>
+      <td>21849</td>
+      <td>21849</td>
+      <td>635</td>
+      <td>635</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compute_motif_frequencies_for_all_motifs</td>
+      <td>compute_motif_frequencies_for_all_motifs</td>
+      <td>Compute Motif Frequencies For All Motifs, motif by motif.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Statistics</td>
+      <td>compute_motif_frequencies_for_all_motifs</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>85</td>
+      <td>96</td>
+      <td>9</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>316</td>
+      <td>334</td>
+      <td>8</td>
+      <td>8</td>
+      <td>401</td>
+      <td>430</td>
+      <td>17</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compute_motifs_frequency</td>
+      <td>compute_motifs_frequency</td>
+      <td>Compute Motif Frequencies in indel flanking regions.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Statistics</td>
+      <td>compute_motifs_frequency</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>55</td>
+      <td>65</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>317</td>
+      <td>335</td>
+      <td>5</td>
+      <td>5</td>
+      <td>372</td>
+      <td>400</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>compute_q_values</td>
+      <td>compute_q_values</td>
+      <td>Compute q-values based on multiple simultaneous tests p-values</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>compute_q_values</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values</td>
+      <td>1.0.1</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>35</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>35</td>
+      <td>0</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>concat</td>
+      <td>gops_concat_1</td>
+      <td>Concatenate two bed files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>concat</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat</td>
+      <td>1.0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>575128</td>
+      <td>575441</td>
+      <td>694</td>
+      <td>783</td>
+      <td>43420</td>
+      <td>85345</td>
+      <td>629</td>
+      <td>3508</td>
+      <td>19330</td>
+      <td>19418</td>
+      <td>104</td>
+      <td>117</td>
+      <td>637878</td>
+      <td>680204</td>
+      <td>1427</td>
+      <td>4408</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>concat_channels</td>
+      <td>ip_concat_channels</td>
+      <td>Concatenate images</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>concat_channels</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels</td>
+      <td>0.3-1</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>76</td>
+      <td>82</td>
+      <td>11</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>76</td>
+      <td>82</td>
+      <td>11</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>concat_multi_datasets</td>
+      <td>cat_multi_datasets</td>
+      <td>Concatenate multiple datasets tail-to-head, including collection datasets.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Text Manipulation</td>
+      <td>concatenate_multiple_datasets</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets</td>
+      <td>1.4.3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4822</td>
+      <td>4824</td>
+      <td>613</td>
+      <td>614</td>
+      <td>1317</td>
+      <td>1317</td>
+      <td>204</td>
+      <td>204</td>
+      <td>3088</td>
+      <td>3795</td>
+      <td>252</td>
+      <td>289</td>
+      <td>9227</td>
+      <td>9936</td>
+      <td>1069</td>
+      <td>1107</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>concat_paired</td>
+      <td>concat_fastqs</td>
+      <td>Concatenate paired datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/concat</td>
+      <td>Text Manipulation</td>
+      <td>concat_paired</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/concat</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired</td>
+      <td>0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>concoct</td>
+      <td>concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering</td>
+      <td>CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.</td>
+      <td>concoct</td>
+      <td>concoct</td>
+      <td></td>
+      <td>CONCOCT</td>
+      <td>A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.</td>
+      <td>Sequence clustering, Read binning</td>
+      <td>Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BinPro/CONCOCT</td>
+      <td>Metagenomics</td>
+      <td>concoct</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct</td>
+      <td>1.1.0</td>
+      <td>concoct</td>
+      <td>1.1.0</td>
+      <td>Sequence clustering, Read binning</td>
+      <td>Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2105</td>
+      <td>2105</td>
+      <td>155</td>
+      <td>155</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2105</td>
+      <td>2105</td>
+      <td>155</td>
+      <td>155</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>condense_characters</td>
+      <td>Condense characters1</td>
+      <td>Condense consecutive characters.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>condense_characters</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>47</td>
+      <td>2173</td>
+      <td>28</td>
+      <td>368</td>
+      <td>195</td>
+      <td>205</td>
+      <td>8</td>
+      <td>8</td>
+      <td>242</td>
+      <td>2378</td>
+      <td>36</td>
+      <td>376</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>consensus_from_alignments</td>
+      <td>aligned_to_consensus</td>
+      <td>Tool to compute a consensus sequence from several aligned fasta sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>consalign</td>
+      <td>ecology</td>
+      <td>https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments</td>
+      <td>1.0.0</td>
+      <td>r-bioseq</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1184</td>
+      <td>1184</td>
+      <td>154</td>
+      <td>154</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1184</td>
+      <td>1184</td>
+      <td>154</td>
+      <td>154</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>consolidate_vcfs</td>
+      <td>consolidate_vcfs</td>
+      <td>Combines freebayes and mpileup files for use by vcf2snvalignment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>consolidate_vcfs</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>convert_characters</td>
+      <td>Convert characters1</td>
+      <td>Convert delimiters to tab.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>convert_characters</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters</td>
+      <td>1.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>23589</td>
+      <td>28986</td>
+      <td>1061</td>
+      <td>1200</td>
+      <td>23507</td>
+      <td>160693</td>
+      <td>2302</td>
+      <td>8699</td>
+      <td>5413</td>
+      <td>6446</td>
+      <td>251</td>
+      <td>329</td>
+      <td>52509</td>
+      <td>196125</td>
+      <td>3614</td>
+      <td>10228</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>convert_solid_color2nuc</td>
+      <td>color2nuc</td>
+      <td>Convert Color Space to Nucleotides</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation</td>
+      <td>convert_solid_color2nuc</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cooler</td>
+      <td>cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify</td>
+      <td>cooler different tools to process Hi-C from mirnylab</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/open2c/cooler</td>
+      <td>Epigenetics</td>
+      <td>cooler</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler</td>
+      <td>0.9.3</td>
+      <td>htslib</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>170</td>
+      <td>170</td>
+      <td>26</td>
+      <td>26</td>
+      <td>195</td>
+      <td>195</td>
+      <td>39</td>
+      <td>39</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>365</td>
+      <td>365</td>
+      <td>65</td>
+      <td>65</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>coordinates_of_roi</td>
+      <td>ip_coordinates_of_roi</td>
+      <td>Coordinates of ROI</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>coordinates_of_roi</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi</td>
+      <td>0.0.4-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>16077</td>
+      <td>16547</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16077</td>
+      <td>16547</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>coprarna</td>
+      <td>coprarna</td>
+      <td>Target prediction for prokaryotic trans-acting small RNAs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/PatrickRWright/CopraRNA</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>coprarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/PatrickRWright/CopraRNA</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna</td>
+      <td>2.1.1</td>
+      <td>coprarna</td>
+      <td>2.1.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>correlation</td>
+      <td>cor2</td>
+      <td>Correlation for numeric columns</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>correlation</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation</td>
+      <td>1.0.0</td>
+      <td>rpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>398</td>
+      <td>876</td>
+      <td>106</td>
+      <td>134</td>
+      <td>412</td>
+      <td>5568</td>
+      <td>105</td>
+      <td>755</td>
+      <td>192</td>
+      <td>239</td>
+      <td>21</td>
+      <td>27</td>
+      <td>1002</td>
+      <td>6683</td>
+      <td>232</td>
+      <td>916</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>correlation_analysis</td>
+      <td>correlation_analysis</td>
+      <td>[Metabolomics][W4M] Metabolites Correlation Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>correlation_analysis</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis</td>
+      <td>1.0.1+galaxy0</td>
+      <td>r-batch</td>
+      <td>1.1_4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cosg</td>
+      <td>cosg</td>
+      <td>Marker gene identification for single-cell sequencing data using COSG.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/genecell/COSG</td>
+      <td>Transcriptomics, Sequence Analysis, Single Cell</td>
+      <td>cosg</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg</td>
+      <td>1.0.1</td>
+      <td>cosg</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>count_gff_features</td>
+      <td>count_gff_features</td>
+      <td>Count GFF Features</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>count_gff_features</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features</td>
+      <td>0.2</td>
+      <td>galaxy-ops</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>280</td>
+      <td>307</td>
+      <td>110</td>
+      <td>124</td>
+      <td>712</td>
+      <td>1277</td>
+      <td>332</td>
+      <td>628</td>
+      <td>476</td>
+      <td>541</td>
+      <td>55</td>
+      <td>79</td>
+      <td>1468</td>
+      <td>2125</td>
+      <td>497</td>
+      <td>831</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>count_objects</td>
+      <td>ip_count_objects</td>
+      <td>Count Objects</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>count_objects</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects</td>
+      <td>0.0.5-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>314</td>
+      <td>326</td>
+      <td>73</td>
+      <td>75</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>129</td>
+      <td>129</td>
+      <td>6</td>
+      <td>6</td>
+      <td>443</td>
+      <td>455</td>
+      <td>79</td>
+      <td>81</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>count_roi_variants</td>
+      <td>count_roi_variants</td>
+      <td>Count sequence variants in region of interest in BAM file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants</td>
+      <td>Assembly, SAM</td>
+      <td>count_roi_variants</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants</td>
+      <td>0.0.6</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>coverage</td>
+      <td>gops_coverage_1</td>
+      <td>Coverage of a set of intervals on second set of intervals</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>coverage</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1560</td>
+      <td>1725</td>
+      <td>43</td>
+      <td>58</td>
+      <td>4328</td>
+      <td>44209</td>
+      <td>193</td>
+      <td>2113</td>
+      <td>283</td>
+      <td>316</td>
+      <td>16</td>
+      <td>18</td>
+      <td>6171</td>
+      <td>46250</td>
+      <td>252</td>
+      <td>2189</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>coverage_report</td>
+      <td>CoverageReport2</td>
+      <td>Generate Detailed Coverage Report from BAM file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc</td>
+      <td>Sequence Analysis</td>
+      <td>coverage_report</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report</td>
+      <td>0.0.4</td>
+      <td>perl-number-format</td>
+      <td>1.76</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>coverage_stats</td>
+      <td>coverage_stats</td>
+      <td>BAM coverage statistics using samtools idxstats and depth</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats</td>
+      <td>Assembly, SAM</td>
+      <td>coverage_stats</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats</td>
+      <td>0.1.0</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>coverm</td>
+      <td>coverm_contig, coverm_genome</td>
+      <td>CoverM genome and contig wrappers</td>
+      <td>coverm</td>
+      <td>coverm</td>
+      <td></td>
+      <td>CoverM</td>
+      <td>Read coverage calculator for metagenomics</td>
+      <td>Local alignment</td>
+      <td>Bioinformatics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/wwood/CoverM</td>
+      <td>Sequence Analysis</td>
+      <td>coverm</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tools/coverm</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm</td>
+      <td>0.7.0</td>
+      <td>coverm</td>
+      <td>0.7.0</td>
+      <td>Local alignment</td>
+      <td>Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1081</td>
+      <td>1081</td>
+      <td>151</td>
+      <td>151</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1081</td>
+      <td>1081</td>
+      <td>151</td>
+      <td>151</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cpat</td>
+      <td>cpat</td>
+      <td>Coding-potential assessment tool using an alignment-free logistic regression model.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/liguowang/cpat</td>
+      <td>Transcriptomics</td>
+      <td>cpat</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cpat</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/cpat</td>
+      <td>3.0.5</td>
+      <td>cpat</td>
+      <td>3.0.5</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>204</td>
+      <td>204</td>
+      <td>47</td>
+      <td>47</td>
+      <td>165</td>
+      <td>165</td>
+      <td>40</td>
+      <td>40</td>
+      <td>125</td>
+      <td>125</td>
+      <td>7</td>
+      <td>7</td>
+      <td>494</td>
+      <td>494</td>
+      <td>94</td>
+      <td>94</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cpm_tpm_rpk</td>
+      <td>cpm_tpm_rpk</td>
+      <td>Generate CPM,TPM or RPK from raw counts</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>cpm_tpm_rpk</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk</td>
+      <td>0.6.0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>crispr_studio</td>
+      <td>crispr_studio</td>
+      <td>CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.</td>
+      <td>crisprstudio</td>
+      <td>crisprstudio</td>
+      <td></td>
+      <td>CRISPRStudio</td>
+      <td>CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.</td>
+      <td>Visualisation</td>
+      <td>Sequence analysis, Genomics, Data visualisation</td>
+      <td>To update</td>
+      <td>https://github.com/moineaulab/CRISPRStudio</td>
+      <td>Sequence Analysis</td>
+      <td>crispr_studio</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio</td>
+      <td>1+galaxy0</td>
+      <td>crispr_studio</td>
+      <td>1</td>
+      <td>Visualisation</td>
+      <td>Sequence analysis, Genomics, Data visualisation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1052</td>
+      <td>1053</td>
+      <td>75</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1052</td>
+      <td>1053</td>
+      <td>75</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>crosscontamination_barcode_filter</td>
+      <td>crosscontamination_barcode_filter</td>
+      <td>Barcode contamination discovery tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, Visualization</td>
+      <td>crosscontamination_barcode_filter</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter</td>
+      <td>0.3</td>
+      <td>r-ggplot2</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>276</td>
+      <td>390</td>
+      <td>61</td>
+      <td>76</td>
+      <td>131</td>
+      <td>131</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>407</td>
+      <td>521</td>
+      <td>103</td>
+      <td>118</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>crossmap</td>
+      <td>crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig</td>
+      <td>CrossMap converts genome coordinates or annotation files between genome assemblies</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://crossmap.sourceforge.net/</td>
+      <td>Convert Formats, Genomic Interval Operations</td>
+      <td>crossmap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap</td>
+      <td>0.7.0</td>
+      <td>crossmap</td>
+      <td>0.7.0</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>6</td>
+      <td>5</td>
+      <td>0</td>
+      <td>2182</td>
+      <td>2182</td>
+      <td>331</td>
+      <td>331</td>
+      <td>5251</td>
+      <td>5251</td>
+      <td>903</td>
+      <td>903</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7433</td>
+      <td>7433</td>
+      <td>1234</td>
+      <td>1234</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>crt</td>
+      <td>crispr_recognition_tool</td>
+      <td>CRISPR Recognition Tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>crispr_recognition_tool</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/crt</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/crt</td>
+      <td>1.2.0</td>
+      <td>crisper_recognition_tool</td>
+      <td>1.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4066</td>
+      <td>4139</td>
+      <td>166</td>
+      <td>180</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4066</td>
+      <td>4139</td>
+      <td>166</td>
+      <td>180</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cryptogenotyper</td>
+      <td>CryptoGenotyper</td>
+      <td>CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/CryptoGenotyper</td>
+      <td>Sequence Analysis</td>
+      <td>cryptogenotyper</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/CryptoGenotyper</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper</td>
+      <td>1.0</td>
+      <td>cryptogenotyper</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9942</td>
+      <td>9942</td>
+      <td>26</td>
+      <td>26</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9942</td>
+      <td>9942</td>
+      <td>26</td>
+      <td>26</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>csvtk</td>
+      <td>csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq</td>
+      <td>Rapid data investigation and manipulation of csv/tsv files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bioinf.shenwei.me/csvtk/</td>
+      <td>Text Manipulation</td>
+      <td>csvtk</td>
+      <td>nml</td>
+      <td>https://github.com/shenwei356/csvtk</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk</td>
+      <td>0.20.0</td>
+      <td>csvtk</td>
+      <td>0.30.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cta</td>
+      <td>cta_astro_tool</td>
+      <td>Basic simulation of CTA telescope observations using gammapy package</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Astronomy</td>
+      <td>cta_astro_tool</td>
+      <td>astroteam</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta</td>
+      <td>0.0.1+galaxy0</td>
+      <td>unzip</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ctd_batch</td>
+      <td>ctdBatch_1</td>
+      <td>CTD analysis of chemicals, diseases, or genes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>ctd_batch</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>196</td>
+      <td>211</td>
+      <td>41</td>
+      <td>48</td>
+      <td>1</td>
+      <td>447</td>
+      <td>1</td>
+      <td>161</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>197</td>
+      <td>658</td>
+      <td>42</td>
+      <td>209</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cuffcompare</td>
+      <td>cuffcompare</td>
+      <td>Galaxy wrappers for the Cuffcompare tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
+      <td>Transcriptomics</td>
+      <td>cuffcompare</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare</td>
+      <td>2.2.1</td>
+      <td>cufflinks</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>768</td>
+      <td>1199</td>
+      <td>171</td>
+      <td>300</td>
+      <td>2205</td>
+      <td>24981</td>
+      <td>754</td>
+      <td>5750</td>
+      <td>251</td>
+      <td>493</td>
+      <td>46</td>
+      <td>98</td>
+      <td>3224</td>
+      <td>26673</td>
+      <td>971</td>
+      <td>6148</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cuffdiff</td>
+      <td>cuffdiff</td>
+      <td>Galaxy wrappers for the Cuffdiff tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
+      <td>Transcriptomics</td>
+      <td>cuffdiff</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff</td>
+      <td>2.2.1</td>
+      <td>cufflinks</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4176</td>
+      <td>6065</td>
+      <td>564</td>
+      <td>725</td>
+      <td>24284</td>
+      <td>117007</td>
+      <td>4952</td>
+      <td>20249</td>
+      <td>971</td>
+      <td>4231</td>
+      <td>193</td>
+      <td>616</td>
+      <td>29431</td>
+      <td>127303</td>
+      <td>5709</td>
+      <td>21590</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cufflinks</td>
+      <td>cufflinks</td>
+      <td>Galaxy wrappers for the Cufflinks tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
+      <td>Transcriptomics</td>
+      <td>cufflinks</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks</td>
+      <td>2.2.1</td>
+      <td>cufflinks</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>26122</td>
+      <td>33320</td>
+      <td>870</td>
+      <td>1213</td>
+      <td>70653</td>
+      <td>349091</td>
+      <td>6984</td>
+      <td>27076</td>
+      <td>3963</td>
+      <td>10315</td>
+      <td>440</td>
+      <td>836</td>
+      <td>100738</td>
+      <td>392726</td>
+      <td>8294</td>
+      <td>29125</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cuffmerge</td>
+      <td>cuffmerge</td>
+      <td>Galaxy wrappers for the Cuffmerge tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
+      <td>Transcriptomics</td>
+      <td>cuffmerge</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge</td>
+      <td>2.2.1</td>
+      <td>cufflinks</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2406</td>
+      <td>3448</td>
+      <td>351</td>
+      <td>637</td>
+      <td>20978</td>
+      <td>67769</td>
+      <td>3641</td>
+      <td>13764</td>
+      <td>1209</td>
+      <td>3057</td>
+      <td>227</td>
+      <td>573</td>
+      <td>24593</td>
+      <td>74274</td>
+      <td>4219</td>
+      <td>14974</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cuffnorm</td>
+      <td>cuffnorm</td>
+      <td>The Cuffnorm tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
+      <td>Transcriptomics</td>
+      <td>cuffnorm</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm</td>
+      <td>2.2.1</td>
+      <td>cufflinks</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>374</td>
+      <td>701</td>
+      <td>81</td>
+      <td>114</td>
+      <td>1032</td>
+      <td>13499</td>
+      <td>273</td>
+      <td>1166</td>
+      <td>262</td>
+      <td>322</td>
+      <td>53</td>
+      <td>70</td>
+      <td>1668</td>
+      <td>14522</td>
+      <td>407</td>
+      <td>1350</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cuffquant</td>
+      <td>cuffquant</td>
+      <td>The Cuffquant tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://cole-trapnell-lab.github.io/cufflinks/</td>
+      <td>Transcriptomics</td>
+      <td>cuffquant</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant</td>
+      <td>2.2.1</td>
+      <td>cufflinks</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>408</td>
+      <td>732</td>
+      <td>54</td>
+      <td>71</td>
+      <td>1964</td>
+      <td>15883</td>
+      <td>267</td>
+      <td>1310</td>
+      <td>308</td>
+      <td>422</td>
+      <td>26</td>
+      <td>46</td>
+      <td>2680</td>
+      <td>17037</td>
+      <td>347</td>
+      <td>1427</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cummerbund</td>
+      <td>cummeRbund</td>
+      <td>Wrapper for the Bioconductor cummeRbund library</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/cummeRbund.html</td>
+      <td>RNA, Visualization</td>
+      <td>cummerbund</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund</td>
+      <td>2.16.0</td>
+      <td>fonts-conda-ecosystem</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1251</td>
+      <td>1803</td>
+      <td>98</td>
+      <td>166</td>
+      <td>3461</td>
+      <td>15159</td>
+      <td>486</td>
+      <td>2044</td>
+      <td>2425</td>
+      <td>3338</td>
+      <td>57</td>
+      <td>159</td>
+      <td>7137</td>
+      <td>20300</td>
+      <td>641</td>
+      <td>2369</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cummerbund_to_tabular</td>
+      <td>cummerbund_to_cuffdiff</td>
+      <td>Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats, Next Gen Mappers</td>
+      <td>cummerbund_to_tabular</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>888</td>
+      <td>1208</td>
+      <td>43</td>
+      <td>97</td>
+      <td>1334</td>
+      <td>2683</td>
+      <td>101</td>
+      <td>479</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2222</td>
+      <td>3891</td>
+      <td>144</td>
+      <td>576</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>curve_fitting</td>
+      <td>ip_curve_fitting</td>
+      <td>Polynomial curve fitting to data points</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis</td>
+      <td>Imaging</td>
+      <td>curve_fitting</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting</td>
+      <td>0.0.3-2</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>custom_pro_db</td>
+      <td>custom_pro_db</td>
+      <td>CustomProDB</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/customProDB.html</td>
+      <td>Proteomics</td>
+      <td>custom_pro_db</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db</td>
+      <td>1.22.0</td>
+      <td>bioconductor-rgalaxy</td>
+      <td>1.37.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1729</td>
+      <td>1744</td>
+      <td>144</td>
+      <td>146</td>
+      <td>450</td>
+      <td>450</td>
+      <td>72</td>
+      <td>72</td>
+      <td>361</td>
+      <td>361</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2540</td>
+      <td>2555</td>
+      <td>228</td>
+      <td>230</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>custom_pro_db_annotation_data_manager</td>
+      <td></td>
+      <td>CustomProDB Annotation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/customProDB.html</td>
+      <td>Proteomics</td>
+      <td>custom_pro_db_annotation_data_manager</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cut_columns</td>
+      <td>Cut1</td>
+      <td>Select columns from a dataset.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>cut_columns</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns</td>
+      <td>1.0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1973168</td>
+      <td>2034965</td>
+      <td>11939</td>
+      <td>12833</td>
+      <td>352364</td>
+      <td>803522</td>
+      <td>12967</td>
+      <td>30199</td>
+      <td>128777</td>
+      <td>133584</td>
+      <td>2341</td>
+      <td>2572</td>
+      <td>2454309</td>
+      <td>2972071</td>
+      <td>27247</td>
+      <td>45604</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cutadapt</td>
+      <td>cutadapt</td>
+      <td>Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).</td>
+      <td>cutadapt</td>
+      <td>cutadapt</td>
+      <td></td>
+      <td>Cutadapt</td>
+      <td>Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.</td>
+      <td>Sequence trimming, Primer removal, Read pre-processing</td>
+      <td>Genomics, Probes and primers, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://cutadapt.readthedocs.org/en/stable/</td>
+      <td>Fasta Manipulation, Fastq Manipulation, Sequence Analysis</td>
+      <td>cutadapt</td>
+      <td>lparsons</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt</td>
+      <td>4.9</td>
+      <td>cutadapt</td>
+      <td>4.9</td>
+      <td>Sequence trimming, Primer removal, Read pre-processing</td>
+      <td>Genomics, Probes and primers, Sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>259754</td>
+      <td>272370</td>
+      <td>11716</td>
+      <td>12601</td>
+      <td>334550</td>
+      <td>362356</td>
+      <td>18618</td>
+      <td>20162</td>
+      <td>64377</td>
+      <td>65986</td>
+      <td>3507</td>
+      <td>3627</td>
+      <td>658681</td>
+      <td>700712</td>
+      <td>33841</td>
+      <td>36390</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cutesv</td>
+      <td>cutesv</td>
+      <td>Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.</td>
+      <td>cuteSV</td>
+      <td>cuteSV</td>
+      <td></td>
+      <td>cuteSV</td>
+      <td>Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis</td>
+      <td>Split read mapping, Genotyping, Structural variation detection</td>
+      <td>DNA structural variation, Sequencing, Computer science</td>
+      <td>To update</td>
+      <td>https://github.com/tjiangHIT/cuteSV</td>
+      <td>Variant Analysis</td>
+      <td>cutesv</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv</td>
+      <td>1.0.8</td>
+      <td>cutesv</td>
+      <td>2.1.1</td>
+      <td>Split read mapping, Genotyping, Structural variation detection</td>
+      <td>Sequencing, Computer science</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>260</td>
+      <td>260</td>
+      <td>43</td>
+      <td>43</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>119</td>
+      <td>8</td>
+      <td>8</td>
+      <td>379</td>
+      <td>379</td>
+      <td>51</td>
+      <td>51</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>cwpair2</td>
+      <td>cwpair2</td>
+      <td>Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>ChIP-seq</td>
+      <td>cwpair2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2</td>
+      <td>1.1.1</td>
+      <td>matplotlib</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>173</td>
+      <td>280</td>
+      <td>41</td>
+      <td>83</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>173</td>
+      <td>280</td>
+      <td>41</td>
+      <td>83</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dada2</td>
+      <td>dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts</td>
+      <td>DADA2 wrappers</td>
+      <td>dada2</td>
+      <td>dada2</td>
+      <td></td>
+      <td>dada2</td>
+      <td>This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.</td>
+      <td>Variant calling, DNA barcoding</td>
+      <td>Sequencing, Genetic variation, Microbial ecology, Metagenomics</td>
+      <td>To update</td>
+      <td>https://benjjneb.github.io/dada2/index.html</td>
+      <td>Metagenomics</td>
+      <td>dada2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2</td>
+      <td></td>
+      <td>bioconductor-dada2</td>
+      <td>1.30.0</td>
+      <td>Variant calling, DNA barcoding</td>
+      <td>Sequencing, Genetic variation, Microbial ecology, Metagenomics</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>92240</td>
+      <td>92240</td>
+      <td>2716</td>
+      <td>2716</td>
+      <td>179176</td>
+      <td>179176</td>
+      <td>5317</td>
+      <td>5317</td>
+      <td>12478</td>
+      <td>12478</td>
+      <td>394</td>
+      <td>394</td>
+      <td>283894</td>
+      <td>283894</td>
+      <td>8427</td>
+      <td>8427</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>das_tool</td>
+      <td>Fasta_to_Contig2Bin, das_tool</td>
+      <td>DAS Tool for genome resolved metagenomics</td>
+      <td>dastool</td>
+      <td>dastool</td>
+      <td></td>
+      <td>dastool</td>
+      <td>DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.</td>
+      <td>Read binning</td>
+      <td>Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cmks/DAS_Tool</td>
+      <td>Metagenomics</td>
+      <td>das_tool</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool</td>
+      <td>1.1.7</td>
+      <td>das_tool</td>
+      <td>1.1.7</td>
+      <td>Read binning</td>
+      <td>Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1323</td>
+      <td>1323</td>
+      <td>47</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1323</td>
+      <td>1323</td>
+      <td>47</td>
+      <td>47</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>data-hca</td>
+      <td>hca_matrix_downloader</td>
+      <td>Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, Sequence Analysis</td>
+      <td>suite_human_cell_atlas_tools</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca</td>
+      <td>v0.0.4+galaxy0</td>
+      <td>hca-matrix-downloader</td>
+      <td>0.0.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>441</td>
+      <td>451</td>
+      <td>83</td>
+      <td>87</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>444</td>
+      <td>454</td>
+      <td>85</td>
+      <td>89</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>data-scxa</td>
+      <td>retrieve_scxa</td>
+      <td>Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, Sequence Analysis</td>
+      <td>suite_ebi_expression_atlas</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa</td>
+      <td>v0.0.2+galaxy2</td>
+      <td>wget</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>867</td>
+      <td>877</td>
+      <td>213</td>
+      <td>216</td>
+      <td>339</td>
+      <td>339</td>
+      <td>94</td>
+      <td>94</td>
+      <td>64</td>
+      <td>64</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1270</td>
+      <td>1280</td>
+      <td>312</td>
+      <td>315</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>data_exploration</td>
+      <td>tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs</td>
+      <td>Explore data through multiple statistical tools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/Marie59/Data_explo_tools</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration</td>
+      <td>0.0.0</td>
+      <td>r-tangles</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>967</td>
+      <td>967</td>
+      <td>308</td>
+      <td>308</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>967</td>
+      <td>967</td>
+      <td>308</td>
+      <td>308</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>data_manager_eggnog_mapper</td>
+      <td></td>
+      <td>downloads eggnog data for eggnog-mapper</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>data_manager_eggnog_mapper</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>data_manager_eggnog_mapper_abspath</td>
+      <td></td>
+      <td>download eggnog data for eggnog-mapper</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>data_manager_eggnog_mapper_abspath</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>data_source_iris_tcga</td>
+      <td>data_source_iris_tcga</td>
+      <td>IRIS-TCGA Data source tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Data Source</td>
+      <td>data_source_iris_tcga</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga</td>
+      <td>1.0.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>datamash</td>
+      <td>datamash_ops, datamash_reverse, datamash_transpose</td>
+      <td>GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.gnu.org/software/datamash/</td>
+      <td>Text Manipulation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash</td>
+      <td>1.8</td>
+      <td>datamash</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>748586</td>
+      <td>760943</td>
+      <td>7066</td>
+      <td>7307</td>
+      <td>98089</td>
+      <td>112831</td>
+      <td>5306</td>
+      <td>6131</td>
+      <td>16235</td>
+      <td>16317</td>
+      <td>2161</td>
+      <td>2171</td>
+      <td>862910</td>
+      <td>890091</td>
+      <td>14533</td>
+      <td>15609</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dbbuilder</td>
+      <td>dbbuilder</td>
+      <td>Protein Database Downloader</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder</td>
+      <td>Proteomics</td>
+      <td>dbbuilder</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder</td>
+      <td>0.3.4</td>
+      <td>wget</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4813</td>
+      <td>5555</td>
+      <td>687</td>
+      <td>805</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>961</td>
+      <td>961</td>
+      <td>87</td>
+      <td>87</td>
+      <td>5774</td>
+      <td>6516</td>
+      <td>774</td>
+      <td>892</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>decontaminator</td>
+      <td>decontaminator</td>
+      <td>Deep Learning method for novel virus detection in sequencing data</td>
+      <td>decontaminator</td>
+      <td>decontaminator</td>
+      <td></td>
+      <td>decontaminator</td>
+      <td>Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.</td>
+      <td>Filtering</td>
+      <td>Metagenomics</td>
+      <td>To update</td>
+      <td>https://github.com/cbib/decontaminator</td>
+      <td>Machine Learning</td>
+      <td>decontaminator</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator</td>
+      <td>1.0.0</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Filtering</td>
+      <td>Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>decoupler</td>
+      <td>score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk</td>
+      <td>decoupler - Ensemble of methods to infer biological activities</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://decoupler-py.readthedocs.io/en/latest/</td>
+      <td>Transcriptomics</td>
+      <td>suite_decoupler</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler</td>
+      <td>1.4.0+galaxy3</td>
+      <td>decoupler</td>
+      <td>1.5.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>decoyfasta</td>
+      <td></td>
+      <td>Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>decoyfasta</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>deepmicro</td>
+      <td>deepmicro</td>
+      <td>Representation learning and classification framework</td>
+      <td>DeepMicro</td>
+      <td>DeepMicro</td>
+      <td></td>
+      <td>DeepMicro</td>
+      <td>Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.</td>
+      <td>Essential dynamics, Splitting, Community profiling</td>
+      <td>Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/paulzierep/DeepMicro</td>
+      <td>Machine Learning</td>
+      <td>deepmicro</td>
+      <td>iuc</td>
+      <td>https://github.com/paulzierep/DeepMicro</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro</td>
+      <td>1.4</td>
+      <td>deepmicro</td>
+      <td>1.4</td>
+      <td>Essential dynamics, Splitting</td>
+      <td>Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>558</td>
+      <td>558</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>558</td>
+      <td>558</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>deepsig</td>
+      <td>deepsig</td>
+      <td>Predictor of signal peptides in proteins based on deep learning</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BolognaBiocomp/deepsig</td>
+      <td>Genome annotation</td>
+      <td>deepsig</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig</td>
+      <td>1.2.5</td>
+      <td>deepsig</td>
+      <td>1.2.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>37</td>
+      <td>37</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>deepvariant</td>
+      <td>deepvariant</td>
+      <td>DeepVariant is a deep learning-based variant caller</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/google/deepvariant</td>
+      <td>Variant Analysis</td>
+      <td>deepvariant</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant</td>
+      <td>1.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2561</td>
+      <td>2561</td>
+      <td>325</td>
+      <td>325</td>
+      <td>2916</td>
+      <td>2916</td>
+      <td>460</td>
+      <td>460</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5477</td>
+      <td>5477</td>
+      <td>785</td>
+      <td>785</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>deg_annotate</td>
+      <td>deg_annotate</td>
+      <td>Annotate DESeq2/DEXSeq output tables</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate</td>
+      <td>Transcriptomics</td>
+      <td>deg_annotate</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate</td>
+      <td>1.1.0</td>
+      <td>bedtools</td>
+      <td>2.31.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>22774</td>
+      <td>23146</td>
+      <td>4084</td>
+      <td>4155</td>
+      <td>33972</td>
+      <td>33972</td>
+      <td>5372</td>
+      <td>5372</td>
+      <td>4236</td>
+      <td>4236</td>
+      <td>846</td>
+      <td>846</td>
+      <td>60982</td>
+      <td>61354</td>
+      <td>10302</td>
+      <td>10373</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>delete_overlapping_indels</td>
+      <td>delete_overlapping_indels</td>
+      <td>Delete Overlapping Indels from a chromosome indels file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>delete_overlapping_indels</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>33</td>
+      <td>40</td>
+      <td>6</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>33</td>
+      <td>40</td>
+      <td>6</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>delly</td>
+      <td>delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge</td>
+      <td>Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.</td>
+      <td>delly2</td>
+      <td>delly2</td>
+      <td></td>
+      <td>Delly2</td>
+      <td>Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.</td>
+      <td>Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis</td>
+      <td>DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases</td>
+      <td>To update</td>
+      <td>https://github.com/dellytools/delly</td>
+      <td>Variant Analysis</td>
+      <td>delly</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly</td>
+      <td>0.9.1</td>
+      <td>delly</td>
+      <td>1.2.9</td>
+      <td>Indel detection, Structural variation detection, Genotyping</td>
+      <td>Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1451</td>
+      <td>1451</td>
+      <td>288</td>
+      <td>288</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1451</td>
+      <td>1451</td>
+      <td>288</td>
+      <td>288</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>deseq2</td>
+      <td>deseq2</td>
+      <td>Differential gene expression analysis based on the negative binomial distribution</td>
+      <td>DESeq2</td>
+      <td>DESeq2</td>
+      <td></td>
+      <td>DESeq2</td>
+      <td>R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.</td>
+      <td>Differential gene expression analysis, RNA-Seq analysis</td>
+      <td>RNA-Seq</td>
+      <td>To update</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>deseq2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2</td>
+      <td>2.11.40.8</td>
+      <td>bioconductor-deseq2</td>
+      <td>1.42.0</td>
+      <td>Differential gene expression analysis, RNA-Seq analysis</td>
+      <td>RNA-Seq</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>97434</td>
+      <td>109474</td>
+      <td>11355</td>
+      <td>12514</td>
+      <td>183905</td>
+      <td>246475</td>
+      <td>24951</td>
+      <td>31957</td>
+      <td>18551</td>
+      <td>20166</td>
+      <td>2647</td>
+      <td>2905</td>
+      <td>299890</td>
+      <td>376115</td>
+      <td>38953</td>
+      <td>47376</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>deseq2_normalization</td>
+      <td>deseq2_normalization</td>
+      <td>Normalizes gene hitlists</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Transcriptomics, Sequence Analysis, Statistics</td>
+      <td>deseq2_normalization</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization</td>
+      <td>1.40.2+galaxy0</td>
+      <td>bioconductor-deseq2</td>
+      <td>1.42.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>detection_viz</td>
+      <td>ip_detection_viz</td>
+      <td>Detection Visualization</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>detection_viz</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz</td>
+      <td>0.3-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>43</td>
+      <td>48</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>48</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dewseq</td>
+      <td>dewseq</td>
+      <td>DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers</td>
+      <td>Sequence Analysis, RNA, CLIP-seq</td>
+      <td>dewseq</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq</td>
+      <td>0.1.0+galaxy0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>89</td>
+      <td>89</td>
+      <td>18</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>89</td>
+      <td>89</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dexseq</td>
+      <td>dexseq, dexseq_count, plotdexseq</td>
+      <td>Inference of differential exon usage in RNA-Seq</td>
+      <td>dexseq</td>
+      <td>dexseq</td>
+      <td></td>
+      <td>DEXSeq</td>
+      <td>The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.</td>
+      <td>Enrichment analysis, Exonic splicing enhancer prediction</td>
+      <td>RNA-Seq</td>
+      <td>Up-to-date</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>dexseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq</td>
+      <td>1.48.0</td>
+      <td>bioconductor-dexseq</td>
+      <td>1.48.0</td>
+      <td>Enrichment analysis, Exonic splicing enhancer prediction</td>
+      <td>RNA-Seq</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>14874</td>
+      <td>16927</td>
+      <td>533</td>
+      <td>837</td>
+      <td>18475</td>
+      <td>28854</td>
+      <td>1403</td>
+      <td>2568</td>
+      <td>3854</td>
+      <td>4271</td>
+      <td>141</td>
+      <td>163</td>
+      <td>37203</td>
+      <td>50052</td>
+      <td>2077</td>
+      <td>3568</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dgidb_annotator</td>
+      <td>dgidb_annotate</td>
+      <td>Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Systems Biology, Variant Analysis</td>
+      <td>dgidb_annotator</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>59</td>
+      <td>69</td>
+      <td>26</td>
+      <td>30</td>
+      <td>0</td>
+      <td>304</td>
+      <td>0</td>
+      <td>133</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59</td>
+      <td>373</td>
+      <td>26</td>
+      <td>163</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dia_umpire</td>
+      <td>dia_umpire_se</td>
+      <td>DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://diaumpire.sourceforge.net/</td>
+      <td>Proteomics</td>
+      <td>dia_umpire</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire</td>
+      <td>2.1.3</td>
+      <td>dia_umpire</td>
+      <td>2.1.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>28</td>
+      <td>33</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>134</td>
+      <td>134</td>
+      <td>4</td>
+      <td>4</td>
+      <td>162</td>
+      <td>167</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dialignr</td>
+      <td>dialignr</td>
+      <td>DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/shubham1637/DIAlignR</td>
+      <td>Proteomics</td>
+      <td>dialignr</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr</td>
+      <td>1.2.0</td>
+      <td>bioconductor-dialignr</td>
+      <td>2.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diamond</td>
+      <td>bg_diamond, bg_diamond_makedb, bg_diamond_view</td>
+      <td>DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.</td>
+      <td>diamond</td>
+      <td>diamond</td>
+      <td></td>
+      <td>Diamond</td>
+      <td>Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.</td>
+      <td>Sequence alignment analysis</td>
+      <td>Sequence analysis, Proteins</td>
+      <td>To update</td>
+      <td>https://github.com/bbuchfink/diamond</td>
+      <td>Sequence Analysis</td>
+      <td>diamond</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond</td>
+      <td>2.0.15</td>
+      <td>diamond</td>
+      <td>2.1.9</td>
+      <td>Sequence alignment analysis</td>
+      <td>Sequence analysis, Proteins</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>61376</td>
+      <td>61746</td>
+      <td>1847</td>
+      <td>1895</td>
+      <td>23164</td>
+      <td>28729</td>
+      <td>1140</td>
+      <td>1556</td>
+      <td>63034</td>
+      <td>63034</td>
+      <td>522</td>
+      <td>522</td>
+      <td>147574</td>
+      <td>153509</td>
+      <td>3509</td>
+      <td>3973</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diann</td>
+      <td>diann</td>
+      <td>DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/vdemichev/DiaNN</td>
+      <td>Proteomics</td>
+      <td>diann</td>
+      <td>galaxyp</td>
+      <td>https://github.com/vdemichev/DiaNN</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann</td>
+      <td>1.8.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>72</td>
+      <td>72</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>171</td>
+      <td>171</td>
+      <td>14</td>
+      <td>14</td>
+      <td>243</td>
+      <td>243</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diapysef</td>
+      <td>diapysef</td>
+      <td>diapysef is a convenience package for working with DIA-PASEF data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pypi.org/project/diapysef/</td>
+      <td>Proteomics</td>
+      <td>diapysef</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef</td>
+      <td>0.3.5.0</td>
+      <td>diapysef</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>262</td>
+      <td>262</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>256</td>
+      <td>256</td>
+      <td>6</td>
+      <td>6</td>
+      <td>518</td>
+      <td>518</td>
+      <td>44</td>
+      <td>44</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diff</td>
+      <td>diff</td>
+      <td>GNU diff tool that calculates the differences between two files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.gnu.org/software/diffutils/</td>
+      <td>Text Manipulation</td>
+      <td>diff</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/diff</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/diff</td>
+      <td>3.7</td>
+      <td>diffutils</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>362</td>
+      <td>362</td>
+      <td>99</td>
+      <td>99</td>
+      <td>23</td>
+      <td>23</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>385</td>
+      <td>385</td>
+      <td>116</td>
+      <td>116</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diffacto</td>
+      <td>diffacto</td>
+      <td>Diffacto comparative protein abundance estimation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/statisticalbiotechnology/diffacto</td>
+      <td>Proteomics</td>
+      <td>diffacto</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto</td>
+      <td>1.0.6</td>
+      <td>diffacto</td>
+      <td>1.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diffbind</td>
+      <td>diffbind</td>
+      <td>Diffbind provides functions for  processing  ChIP-Seq  data.</td>
+      <td>diffbind</td>
+      <td>diffbind</td>
+      <td></td>
+      <td>DiffBind</td>
+      <td>Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.</td>
+      <td>Differential binding analysis</td>
+      <td>ChIP-seq</td>
+      <td>Up-to-date</td>
+      <td>http://bioconductor.org/packages/release/bioc/html/DiffBind.html</td>
+      <td>ChIP-seq</td>
+      <td>diffbind</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind</td>
+      <td>3.12.0</td>
+      <td>bioconductor-diffbind</td>
+      <td>3.12.0</td>
+      <td>Differential binding analysis</td>
+      <td>ChIP-seq</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7092</td>
+      <td>7663</td>
+      <td>606</td>
+      <td>652</td>
+      <td>14367</td>
+      <td>18624</td>
+      <td>1360</td>
+      <td>1916</td>
+      <td>1477</td>
+      <td>1640</td>
+      <td>69</td>
+      <td>84</td>
+      <td>22936</td>
+      <td>27927</td>
+      <td>2035</td>
+      <td>2652</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>diffbind</td>
+      <td></td>
+      <td>Diffbind provides functions for  processing  ChIP-Seq  data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://bioconductor.org/packages/release/bioc/html/DiffBind.html</td>
+      <td>ChIP-seq</td>
+      <td>diffbind</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/diffbind</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/diffbind</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>digestdb</td>
+      <td>digestdb</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>digestdb</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb</td>
+      <td>0.1.0</td>
+      <td>trans_proteomic_pipeline</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dimet</td>
+      <td>dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@</td>
+      <td>DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cbib/DIMet</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet</td>
+      <td>0.2.4</td>
+      <td>dimet</td>
+      <td>0.2.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>directag_and_tagrecon</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>directag_and_tagrecon</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>disco</td>
+      <td>disco</td>
+      <td>DISCO is a overlap-layout-consensus (OLC) metagenome assembler</td>
+      <td>disco</td>
+      <td>disco</td>
+      <td></td>
+      <td>DISCO</td>
+      <td>DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.</td>
+      <td>Protein sequence analysis</td>
+      <td>Structure determination</td>
+      <td>To update</td>
+      <td>http://disco.omicsbio.org/</td>
+      <td>Metagenomics, Assembly</td>
+      <td>disco</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco</td>
+      <td></td>
+      <td>disco</td>
+      <td>1.2</td>
+      <td>Protein sequence analysis</td>
+      <td>Structure determination</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>358</td>
+      <td>406</td>
+      <td>124</td>
+      <td>139</td>
+      <td>1361</td>
+      <td>1361</td>
+      <td>384</td>
+      <td>384</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1719</td>
+      <td>1767</td>
+      <td>508</td>
+      <td>523</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>divide_pg_snp</td>
+      <td>dividePgSnp</td>
+      <td>Separate pgSnp alleles into columns</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>divide_pg_snp</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>26</td>
+      <td>32</td>
+      <td>8</td>
+      <td>9</td>
+      <td>86</td>
+      <td>172</td>
+      <td>20</td>
+      <td>53</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>112</td>
+      <td>204</td>
+      <td>28</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dnabot</td>
+      <td>dnabot</td>
+      <td>DNA assembly using BASIC on OpenTrons</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT</td>
+      <td>Synthetic Biology</td>
+      <td>dnabot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot</td>
+      <td>3.1.0</td>
+      <td>dnabot</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dnaweaver</td>
+      <td>dnaweaver</td>
+      <td>Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Edinburgh-Genome-Foundry/DnaWeaver</td>
+      <td>Synthetic Biology</td>
+      <td>dnaweaver</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver</td>
+      <td>1.0.2</td>
+      <td>dnaweaver_synbiocad</td>
+      <td>1.0.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dorina</td>
+      <td>dorina_search</td>
+      <td>data source for RNA interactions in post-transcriptional regulation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA, Data Source</td>
+      <td>dorina</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>921</td>
+      <td>1626</td>
+      <td>4</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>921</td>
+      <td>1626</td>
+      <td>4</td>
+      <td>31</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dose_responses</td>
+      <td>dr_curve</td>
+      <td>A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools</td>
+      <td>Ecology</td>
+      <td>dose_response_analysis_tool</td>
+      <td>ufz</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses</td>
+      <td>3.0_1</td>
+      <td>r-drc</td>
+      <td>3.0_1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dot2ct</td>
+      <td>rnastructure_dot2ct</td>
+      <td>Dot-Bracket to Connect Table (CT)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, RNA</td>
+      <td>dot2ct</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct</td>
+      <td>5.7.a</td>
+      <td>rnastructure</td>
+      <td>6.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dotknot</td>
+      <td>dotknot</td>
+      <td>DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://dotknot.csse.uwa.edu.au/</td>
+      <td>RNA, Proteomics</td>
+      <td>dotknot</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot</td>
+      <td>1.3.1</td>
+      <td>vienna_rna</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>74</td>
+      <td>88</td>
+      <td>12</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>74</td>
+      <td>88</td>
+      <td>12</td>
+      <td>15</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dram</td>
+      <td>dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer</td>
+      <td>DRAM for distilling microbial metabolism to automate the curation of microbiome function</td>
+      <td>dram</td>
+      <td>dram</td>
+      <td></td>
+      <td>DRAM</td>
+      <td>Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes</td>
+      <td>Gene functional annotation</td>
+      <td>Metagenomics, Biological databases, Molecular genetics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/WrightonLabCSU/DRAM</td>
+      <td>Metagenomics</td>
+      <td>dram</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram</td>
+      <td>1.5.0</td>
+      <td>dram</td>
+      <td>1.5.0</td>
+      <td>Gene functional annotation</td>
+      <td>Metagenomics, Biological databases, Molecular genetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7358</td>
+      <td>7358</td>
+      <td>88</td>
+      <td>88</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7358</td>
+      <td>7358</td>
+      <td>88</td>
+      <td>88</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>draw_stacked_barplots</td>
+      <td>draw_stacked_barplots</td>
+      <td>Draw Stacked Bar Plots for different categories and different criteria</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Statistics</td>
+      <td>draw_stacked_barplots</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots</td>
+      <td>1.0.0</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>189</td>
+      <td>216</td>
+      <td>47</td>
+      <td>52</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>183</td>
+      <td>213</td>
+      <td>22</td>
+      <td>31</td>
+      <td>372</td>
+      <td>429</td>
+      <td>69</td>
+      <td>83</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>drep</td>
+      <td>drep_compare, drep_dereplicate</td>
+      <td>dRep compares and dereplicates genome sets</td>
+      <td>drep</td>
+      <td>drep</td>
+      <td></td>
+      <td>dRep</td>
+      <td>Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.</td>
+      <td>Genome comparison</td>
+      <td>Metagenomics, Genomics, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/MrOlm/drep</td>
+      <td>Metagenomics</td>
+      <td>drep</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep</td>
+      <td>3.5.0</td>
+      <td>drep</td>
+      <td>3.5.0</td>
+      <td>Genome comparison</td>
+      <td>Metagenomics, Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>916</td>
+      <td>916</td>
+      <td>113</td>
+      <td>113</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>916</td>
+      <td>916</td>
+      <td>113</td>
+      <td>113</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>droplet-barcode-plot</td>
+      <td>_dropletBarcodePlot</td>
+      <td>Make a cell barcode plot for droplet single-cell RNA-seq QC</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary</td>
+      <td>Sequence Analysis</td>
+      <td>droplet_barcode_plot</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot</td>
+      <td>1.6.1+galaxy2</td>
+      <td>scxa-plots</td>
+      <td>0.0.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1151</td>
+      <td>1151</td>
+      <td>184</td>
+      <td>184</td>
+      <td>356</td>
+      <td>356</td>
+      <td>77</td>
+      <td>77</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1510</td>
+      <td>1510</td>
+      <td>262</td>
+      <td>262</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dropletutils</td>
+      <td>dropletutils_empty_drops, dropletutils_read_10x</td>
+      <td>De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_dropletutils</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils</td>
+      <td>1.0.4</td>
+      <td>dropletutils-scripts</td>
+      <td>0.0.5</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1900</td>
+      <td>1901</td>
+      <td>412</td>
+      <td>413</td>
+      <td>609</td>
+      <td>609</td>
+      <td>131</td>
+      <td>131</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2509</td>
+      <td>2510</td>
+      <td>543</td>
+      <td>544</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dropletutils</td>
+      <td>dropletutils</td>
+      <td>DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data</td>
+      <td>dropletutils</td>
+      <td>dropletutils</td>
+      <td></td>
+      <td>DropletUtils</td>
+      <td>Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.</td>
+      <td>Loading, Community profiling</td>
+      <td>Gene expression, RNA-seq, Sequencing, Transcriptomics</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html</td>
+      <td>Single Cell, Sequence Analysis</td>
+      <td>dropletutils</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils</td>
+      <td>1.10.0</td>
+      <td>bioconductor-dropletutils</td>
+      <td>1.22.0</td>
+      <td></td>
+      <td>Sequencing, Transcriptomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4413</td>
+      <td>4442</td>
+      <td>430</td>
+      <td>431</td>
+      <td>4403</td>
+      <td>4403</td>
+      <td>255</td>
+      <td>255</td>
+      <td>1816</td>
+      <td>1816</td>
+      <td>33</td>
+      <td>33</td>
+      <td>10632</td>
+      <td>10661</td>
+      <td>718</td>
+      <td>719</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dwt_cor_ava_perclass</td>
+      <td>compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom</td>
+      <td>Compute P-values and Correlation Coefficients for Feature Occurrences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>dwt_cor_ava_perclass</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass</td>
+      <td>1.0.1</td>
+      <td>r-waveslim</td>
+      <td>1.7.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>136</td>
+      <td>141</td>
+      <td>8</td>
+      <td>11</td>
+      <td>136</td>
+      <td>141</td>
+      <td>8</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dwt_cor_avb_all</td>
+      <td>compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom</td>
+      <td>Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>dwt_cor_avb_all</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all</td>
+      <td>1.0.1</td>
+      <td>r-waveslim</td>
+      <td>1.7.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>124</td>
+      <td>124</td>
+      <td>7</td>
+      <td>7</td>
+      <td>124</td>
+      <td>124</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dwt_ivc_all</td>
+      <td>compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom</td>
+      <td>Compute P-values and Second Moments for Feature Occurrences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>dwt_ivc_all</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all</td>
+      <td>1.0.1</td>
+      <td>r-waveslim</td>
+      <td>1.7.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>123</td>
+      <td>5</td>
+      <td>7</td>
+      <td>121</td>
+      <td>123</td>
+      <td>5</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dwt_var_perclass</td>
+      <td>compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom</td>
+      <td>Compute P-values and Max Variances for Feature Occurrences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>dwt_var_perclass</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass</td>
+      <td>1.0.1</td>
+      <td>r-waveslim</td>
+      <td>1.7.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>131</td>
+      <td>132</td>
+      <td>7</td>
+      <td>8</td>
+      <td>131</td>
+      <td>132</td>
+      <td>7</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>dwt_var_perfeature</td>
+      <td>dwt_var1</td>
+      <td>Wavelet variance using Discrete Wavelet Transfoms</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>dwt_var_perfeature</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature</td>
+      <td>1.0.2</td>
+      <td>r-bitops</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>30</td>
+      <td>36</td>
+      <td>2</td>
+      <td>4</td>
+      <td>11</td>
+      <td>11</td>
+      <td>4</td>
+      <td>4</td>
+      <td>206</td>
+      <td>220</td>
+      <td>6</td>
+      <td>7</td>
+      <td>247</td>
+      <td>267</td>
+      <td>12</td>
+      <td>15</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ear</td>
+      <td>make_ear</td>
+      <td>A tool to compile assembly reports and stastics from assembly pipeline</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ERGA-consortium/EARs/tree/main</td>
+      <td>Sequence Analysis, Assembly</td>
+      <td>erga_ear</td>
+      <td>bgruening</td>
+      <td>https://github.com/ERGA-consortium/EARs/tree/main</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/ear</td>
+      <td>24.08.26</td>
+      <td>reportlab</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>28</td>
+      <td>28</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>28</td>
+      <td>28</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ebi_tools</td>
+      <td>ebi_search_rest_results</td>
+      <td>Tools to query and download data from several EMBL-EBI databases</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.ebi.ac.uk/services/all</td>
+      <td>Web Services, Data Source</td>
+      <td>ebi_tools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools</td>
+      <td>0.1.1</td>
+      <td>six</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>276</td>
+      <td>406</td>
+      <td>133</td>
+      <td>163</td>
+      <td>1421</td>
+      <td>1421</td>
+      <td>547</td>
+      <td>547</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1697</td>
+      <td>1827</td>
+      <td>680</td>
+      <td>710</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ectyper</td>
+      <td>ectyper</td>
+      <td>EC-Typer - in silico serotyping of Escherichia coli species</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/ecoli_serotyping</td>
+      <td>Sequence Analysis</td>
+      <td>ectyper</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/ecoli_serotyping</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper</td>
+      <td>1.0.0</td>
+      <td>ectyper</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12996</td>
+      <td>12996</td>
+      <td>137</td>
+      <td>137</td>
+      <td>10</td>
+      <td>10</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13006</td>
+      <td>13006</td>
+      <td>138</td>
+      <td>138</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>edger</td>
+      <td>edger</td>
+      <td>Perform RNA-Seq differential expression analysis using edgeR pipeline</td>
+      <td>edger</td>
+      <td>edger</td>
+      <td></td>
+      <td>edgeR</td>
+      <td>Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.</td>
+      <td>Differential gene expression analysis</td>
+      <td>Genetics, RNA-Seq, ChIP-seq</td>
+      <td>To update</td>
+      <td>http://bioconductor.org/packages/release/bioc/html/edgeR.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>edger</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger</td>
+      <td>3.36.0</td>
+      <td>bioconductor-edger</td>
+      <td>4.0.16</td>
+      <td>Differential gene expression analysis</td>
+      <td>Genetics, RNA-Seq, ChIP-seq</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>19294</td>
+      <td>20905</td>
+      <td>2423</td>
+      <td>2618</td>
+      <td>48876</td>
+      <td>58723</td>
+      <td>6341</td>
+      <td>7527</td>
+      <td>8010</td>
+      <td>8705</td>
+      <td>846</td>
+      <td>892</td>
+      <td>76180</td>
+      <td>88333</td>
+      <td>9610</td>
+      <td>11037</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>edta</td>
+      <td>edta</td>
+      <td>The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations.</td>
+      <td>edta</td>
+      <td>edta</td>
+      <td></td>
+      <td>The Extensive de novo TE Annotator (EDTA)</td>
+      <td>The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.</td>
+      <td>De-novo assembly, Deisotoping, Genome annotation</td>
+      <td>Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms</td>
+      <td>To update</td>
+      <td>https://github.com/oushujun/EDTA</td>
+      <td>Variant Analysis</td>
+      <td>edta</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/edta</td>
+      <td></td>
+      <td>edta</td>
+      <td>2.2.0</td>
+      <td>De-novo assembly, Deisotoping, Genome annotation</td>
+      <td>Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4495</td>
+      <td>4495</td>
+      <td>111</td>
+      <td>111</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4495</td>
+      <td>4495</td>
+      <td>111</td>
+      <td>111</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>effectiveT3</td>
+      <td>effectiveT3</td>
+      <td>Find bacterial type III effectors in protein sequences</td>
+      <td>effectivet3</td>
+      <td>effectivet3</td>
+      <td></td>
+      <td>EffectiveT3</td>
+      <td>Prediction of putative Type-III secreted proteins.</td>
+      <td>Sequence classification</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>http://effectors.org</td>
+      <td>Sequence Analysis</td>
+      <td>effectivet3</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3</td>
+      <td>0.0.21</td>
+      <td>effectiveT3</td>
+      <td>1.0.1</td>
+      <td>Sequence classification</td>
+      <td>Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>eggnog_mapper</td>
+      <td>eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search</td>
+      <td>eggnog-mapper fast functional annotation of novel sequences</td>
+      <td>eggnog-mapper-v2</td>
+      <td>eggnog-mapper-v2</td>
+      <td></td>
+      <td>eggNOG-mapper v2</td>
+      <td>EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.</td>
+      <td>Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval</td>
+      <td>Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis</td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>eggnog_mapper</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper</td>
+      <td>2.1.8</td>
+      <td>eggnog-mapper</td>
+      <td>2.1.12</td>
+      <td>Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval</td>
+      <td>Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1</td>
+      <td>3</td>
+      <td>1</td>
+      <td>0</td>
+      <td>34432</td>
+      <td>34437</td>
+      <td>1149</td>
+      <td>1152</td>
+      <td>42</td>
+      <td>42</td>
+      <td>2</td>
+      <td>2</td>
+      <td>21027</td>
+      <td>21027</td>
+      <td>413</td>
+      <td>413</td>
+      <td>55501</td>
+      <td>55506</td>
+      <td>1564</td>
+      <td>1567</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>egsea</td>
+      <td>egsea</td>
+      <td>This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing</td>
+      <td>egsea</td>
+      <td>egsea</td>
+      <td></td>
+      <td>EGSEA</td>
+      <td>This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.</td>
+      <td>Gene set testing</td>
+      <td>Systems biology</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/EGSEA.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>egsea</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea</td>
+      <td>1.20.0</td>
+      <td>bioconductor-egsea</td>
+      <td>1.28.0</td>
+      <td>Gene set testing</td>
+      <td>Systems biology</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2809</td>
+      <td>3060</td>
+      <td>371</td>
+      <td>402</td>
+      <td>5179</td>
+      <td>5179</td>
+      <td>759</td>
+      <td>759</td>
+      <td>1931</td>
+      <td>1931</td>
+      <td>226</td>
+      <td>226</td>
+      <td>9919</td>
+      <td>10170</td>
+      <td>1356</td>
+      <td>1387</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>embl2fa</td>
+      <td>embl2fa</td>
+      <td>Converts EMBL flat format to fasta format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Text Manipulation</td>
+      <td>embl2fa</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa</td>
+      <td>0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>emboss_5</td>
+      <td>EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110</td>
+      <td>Galaxy wrappers for EMBOSS version 5.0.0 tools</td>
+      <td>emboss</td>
+      <td>emboss</td>
+      <td></td>
+      <td>EMBOSS</td>
+      <td>Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.</td>
+      <td>Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment</td>
+      <td>Molecular biology, Sequence analysis, Biology</td>
+      <td>To update</td>
+      <td>http://emboss.open-bio.org/</td>
+      <td>Sequence Analysis, Fasta Manipulation</td>
+      <td>emboss_5</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5</td>
+      <td>5.0.0</td>
+      <td>emboss</td>
+      <td>6.6.0</td>
+      <td>Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment</td>
+      <td>Molecular biology, Sequence analysis</td>
+      <td>107</td>
+      <td>107</td>
+      <td>107</td>
+      <td>0</td>
+      <td>107</td>
+      <td>107</td>
+      <td>107</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>107</td>
+      <td>0</td>
+      <td>0</td>
+      <td>107</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>107</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>107</td>
+      <td>107</td>
+      <td>107</td>
+      <td>0</td>
+      <td>143762</td>
+      <td>148864</td>
+      <td>4481</td>
+      <td>5039</td>
+      <td>151989</td>
+      <td>296028</td>
+      <td>13224</td>
+      <td>31140</td>
+      <td>24955</td>
+      <td>27001</td>
+      <td>2397</td>
+      <td>2705</td>
+      <td>320706</td>
+      <td>471893</td>
+      <td>20102</td>
+      <td>38884</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ena_upload</td>
+      <td>ena_upload</td>
+      <td>Submits experimental data and respective metadata to the European Nucleotide Archive (ENA).</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/usegalaxy-eu/ena-upload-cli</td>
+      <td>Data Export</td>
+      <td>ena_upload</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload</td>
+      <td>0.7.3</td>
+      <td>ena-upload-cli</td>
+      <td>0.7.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>366</td>
+      <td>366</td>
+      <td>41</td>
+      <td>41</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1302</td>
+      <td>1302</td>
+      <td>14</td>
+      <td>14</td>
+      <td>1668</td>
+      <td>1668</td>
+      <td>55</td>
+      <td>55</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>enasearch</td>
+      <td>enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data</td>
+      <td>A Python library for interacting with ENA's API</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bebatut/enasearch</td>
+      <td>Data Source</td>
+      <td>enasearch</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch</td>
+      <td></td>
+      <td>enasearch</td>
+      <td>0.2.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>1989</td>
+      <td>2302</td>
+      <td>367</td>
+      <td>453</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1989</td>
+      <td>2302</td>
+      <td>367</td>
+      <td>453</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>encyclopedia</td>
+      <td>encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut</td>
+      <td>Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/searleb/encyclopedia/wiki/Home</td>
+      <td>Proteomics</td>
+      <td>encyclopedia</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia</td>
+      <td>1.12.34</td>
+      <td>encyclopedia</td>
+      <td>2.12.30</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>4</td>
+      <td>7</td>
+      <td>0</td>
+      <td>2</td>
+      <td>4</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>738</td>
+      <td>738</td>
+      <td>98</td>
+      <td>98</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>42</td>
+      <td>42</td>
+      <td>4</td>
+      <td>4</td>
+      <td>781</td>
+      <td>781</td>
+      <td>103</td>
+      <td>103</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ensembl_vep</td>
+      <td>ensembl_vep</td>
+      <td>Ensembl VEP: Annotate VCFs with variant effect predictions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Ensembl/ensembl-vep</td>
+      <td>Variant Analysis</td>
+      <td>ensembl_vep</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep</td>
+      <td>112.0</td>
+      <td>ensembl-vep</td>
+      <td>112.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>171</td>
+      <td>171</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>171</td>
+      <td>171</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>eodie</td>
+      <td>eodie</td>
+      <td>Earth Observation Data Information Extractor</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://eodie.readthedocs.io/</td>
+      <td>Climate Analysis</td>
+      <td>eodie</td>
+      <td>climate</td>
+      <td>https://gitlab.com/eetun-tiimi/EODIE</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie</td>
+      <td>1.0.2</td>
+      <td>eodie</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45</td>
+      <td>45</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>45</td>
+      <td>45</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>epicseg</td>
+      <td>epicseg_segment</td>
+      <td>EpiCSeg is a tool for conducting chromatin segmentation.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/lamortenera/epicseg</td>
+      <td>Epigenetics</td>
+      <td>epicseg</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/epicseg</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/epicseg</td>
+      <td>@VERSION_STRING@</td>
+      <td>epicseg</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>160</td>
+      <td>252</td>
+      <td>17</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>160</td>
+      <td>252</td>
+      <td>17</td>
+      <td>21</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>episcanpy</td>
+      <td>episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess</td>
+      <td>EpiScanpy – Epigenomics single cell analysis in python</td>
+      <td>episcanpy</td>
+      <td>episcanpy</td>
+      <td></td>
+      <td>epiScanpy</td>
+      <td>Epigenomics Single Cell Analysis in Python.</td>
+      <td>Enrichment analysis, Imputation</td>
+      <td>Epigenomics, Cell biology, DNA</td>
+      <td>To update</td>
+      <td>https://github.com/colomemaria/epiScanpy</td>
+      <td>Single Cell, Epigenetics</td>
+      <td>episcanpy</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy</td>
+      <td>0.3.2</td>
+      <td>episcanpy</td>
+      <td>0.4.0</td>
+      <td>Enrichment analysis, Imputation</td>
+      <td>Epigenomics, Cell biology, DNA</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>880</td>
+      <td>880</td>
+      <td>80</td>
+      <td>80</td>
+      <td>221</td>
+      <td>221</td>
+      <td>37</td>
+      <td>37</td>
+      <td>49</td>
+      <td>49</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1150</td>
+      <td>1150</td>
+      <td>120</td>
+      <td>120</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>essential_climate_variables</td>
+      <td>cds_essential_variability</td>
+      <td>Get Copernicus Essential Climate Variables for assessing climate variability</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview</td>
+      <td>Climate Analysis, Data Source</td>
+      <td>cds_essential_variability</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables</td>
+      <td>0.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>232</td>
+      <td>336</td>
+      <td>39</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>232</td>
+      <td>336</td>
+      <td>39</td>
+      <td>40</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ete</td>
+      <td>ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator</td>
+      <td>Analyse phylogenetic trees using the ETE Toolkit</td>
+      <td>ete</td>
+      <td>ete</td>
+      <td></td>
+      <td>ete</td>
+      <td>The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org</td>
+      <td>Phylogenetic analysis, Phylogenetic tree editing</td>
+      <td>Phylogenetics</td>
+      <td>To update</td>
+      <td>http://etetoolkit.org/</td>
+      <td>Phylogenetics</td>
+      <td>ete</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete</td>
+      <td>3.1.2</td>
+      <td>ete3</td>
+      <td>3.1.1</td>
+      <td>Phylogenetic tree editing</td>
+      <td>Phylogenetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>820</td>
+      <td>966</td>
+      <td>89</td>
+      <td>106</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>820</td>
+      <td>966</td>
+      <td>89</td>
+      <td>106</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>evidencemodeler</td>
+      <td>evidencemodeler</td>
+      <td>EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.</td>
+      <td>EvidenceModeler</td>
+      <td>EvidenceModeler</td>
+      <td></td>
+      <td>EvidenceModeler</td>
+      <td>The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.</td>
+      <td>Gene prediction</td>
+      <td>Gene expression, Gene structure</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file</td>
+      <td>Genome annotation</td>
+      <td>evidencemodeler</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler</td>
+      <td>2.1.0</td>
+      <td>evidencemodeler</td>
+      <td>2.1.0</td>
+      <td>Gene prediction</td>
+      <td>Gene expression, Gene structure</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>exomedepth</td>
+      <td>exomedepth</td>
+      <td>ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data</td>
+      <td>exomedepth</td>
+      <td>exomedepth</td>
+      <td></td>
+      <td>ExomeDepth</td>
+      <td>Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.</td>
+      <td>Sequence analysis, Variant calling, Genotyping, Copy number estimation</td>
+      <td>Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases</td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/package=ExomeDepth</td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>exomedepth</td>
+      <td>crs4</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth</td>
+      <td>1.1.0</td>
+      <td>r-exomedepth</td>
+      <td>1.1.16</td>
+      <td>Sequence analysis, Variant calling, Genotyping, Copy number estimation</td>
+      <td>Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>517</td>
+      <td>517</td>
+      <td>61</td>
+      <td>61</td>
+      <td>2995</td>
+      <td>2995</td>
+      <td>184</td>
+      <td>184</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3512</td>
+      <td>3512</td>
+      <td>245</td>
+      <td>245</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>exonerate</td>
+      <td>exonerate</td>
+      <td>Exonerate is a generic tool for pairwise sequence comparison.</td>
+      <td>exonerate</td>
+      <td>exonerate</td>
+      <td></td>
+      <td>Exonerate</td>
+      <td>A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.</td>
+      <td>Pairwise sequence alignment, Protein threading, Genome alignment</td>
+      <td>Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks</td>
+      <td>Up-to-date</td>
+      <td>https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate</td>
+      <td>Sequence Analysis</td>
+      <td>exonerate</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate</td>
+      <td>2.4.0</td>
+      <td>exonerate</td>
+      <td>2.4.0</td>
+      <td>Pairwise sequence alignment, Protein threading, Genome alignment</td>
+      <td>Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1030</td>
+      <td>1072</td>
+      <td>185</td>
+      <td>188</td>
+      <td>1058</td>
+      <td>1058</td>
+      <td>189</td>
+      <td>189</td>
+      <td>922</td>
+      <td>922</td>
+      <td>35</td>
+      <td>35</td>
+      <td>3010</td>
+      <td>3052</td>
+      <td>409</td>
+      <td>412</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>exparna</td>
+      <td>exparna</td>
+      <td>ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp</td>
+      <td>RNA</td>
+      <td>exparna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna</td>
+      <td>1.0.1</td>
+      <td>exparna</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>export2graphlan</td>
+      <td>export2graphlan</td>
+      <td>export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn</td>
+      <td>export2graphlan</td>
+      <td>export2graphlan</td>
+      <td></td>
+      <td>export2graphlan</td>
+      <td>export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.</td>
+      <td>Conversion</td>
+      <td>Taxonomy, Metabolomics, Biomarkers</td>
+      <td>To update</td>
+      <td>https://bitbucket.org/CibioCM/export2graphlan/overview</td>
+      <td>Metagenomics</td>
+      <td>export2graphlan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan</td>
+      <td>0.20</td>
+      <td>export2graphlan</td>
+      <td>0.22</td>
+      <td>Conversion</td>
+      <td>Taxonomy, Metabolomics, Biomarkers</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5396</td>
+      <td>5938</td>
+      <td>580</td>
+      <td>607</td>
+      <td>628</td>
+      <td>628</td>
+      <td>168</td>
+      <td>168</td>
+      <td>519</td>
+      <td>519</td>
+      <td>107</td>
+      <td>107</td>
+      <td>6543</td>
+      <td>7085</td>
+      <td>855</td>
+      <td>882</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>export_to_cluster</td>
+      <td>export_to_cluster</td>
+      <td>Export datasets to cluster</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/</td>
+      <td>Data Export</td>
+      <td>export_to_cluster</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster</td>
+      <td>0.0.2</td>
+      <td>EXPORT_DIR_PREFIX</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>express</td>
+      <td>express</td>
+      <td>Quantify the abundances of a set of target sequences from sampled subsequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>express</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/express</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/express</td>
+      <td>1.1.1</td>
+      <td>eXpress</td>
+      <td>1.5.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>278</td>
+      <td>337</td>
+      <td>34</td>
+      <td>45</td>
+      <td>0</td>
+      <td>1184</td>
+      <td>0</td>
+      <td>117</td>
+      <td>2402</td>
+      <td>2844</td>
+      <td>23</td>
+      <td>60</td>
+      <td>2680</td>
+      <td>4365</td>
+      <td>57</td>
+      <td>222</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>extract_genomic_dna</td>
+      <td>Extract genomic DNA 1</td>
+      <td>Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Genomic Interval Operations</td>
+      <td>extract_genomic_dna</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna</td>
+      <td>3.0.3+galaxy2</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9409</td>
+      <td>12735</td>
+      <td>813</td>
+      <td>923</td>
+      <td>20180</td>
+      <td>259099</td>
+      <td>2072</td>
+      <td>11791</td>
+      <td>168</td>
+      <td>611</td>
+      <td>20</td>
+      <td>63</td>
+      <td>29757</td>
+      <td>272445</td>
+      <td>2905</td>
+      <td>12777</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ez_histograms</td>
+      <td>ez_histograms</td>
+      <td>ggplot2 histograms and density plots</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/tidyverse/ggplot2</td>
+      <td>Visualization, Statistics</td>
+      <td>ez_histograms</td>
+      <td>artbio</td>
+      <td>https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms</td>
+      <td>3.4.4</td>
+      <td>r-ggplot2</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>falco</td>
+      <td>falco</td>
+      <td>A high throughput sequence QC analysis tool</td>
+      <td>falco</td>
+      <td>falco</td>
+      <td></td>
+      <td>Falco</td>
+      <td>A high-speed FastQC emulation for quality control of sequencing data.</td>
+      <td>Sequencing quality control, Visualisation, Read mapping</td>
+      <td>Workflows, Mapping, Imaging</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/smithlabcode/falco/</td>
+      <td>Sequence Analysis</td>
+      <td>falco</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco</td>
+      <td>1.2.4</td>
+      <td>falco</td>
+      <td>1.2.4</td>
+      <td>Sequencing quality control, Visualisation, Read mapping</td>
+      <td>Workflows, Mapping, Imaging</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4298</td>
+      <td>4298</td>
+      <td>34</td>
+      <td>34</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4298</td>
+      <td>4298</td>
+      <td>34</td>
+      <td>34</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fargene</td>
+      <td>fargene</td>
+      <td>fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )</td>
+      <td>fargene</td>
+      <td>fargene</td>
+      <td></td>
+      <td>fARGene</td>
+      <td>fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Metagenomics, Microbiology, Public health and epidemiology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/fannyhb/fargene</td>
+      <td>Sequence Analysis</td>
+      <td>fargene</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene</td>
+      <td>0.1</td>
+      <td>fargene</td>
+      <td>0.1</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Metagenomics, Microbiology, Public health and epidemiology</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>601</td>
+      <td>601</td>
+      <td>128</td>
+      <td>128</td>
+      <td>1165</td>
+      <td>1165</td>
+      <td>232</td>
+      <td>232</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1766</td>
+      <td>1766</td>
+      <td>360</td>
+      <td>360</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasplit</td>
+      <td>fasplit</td>
+      <td>faSplit is a tool to split a single FASTA file into several files</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Fasta Manipulation</td>
+      <td>ucsc_fasplit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit</td>
+      <td>469</td>
+      <td>ucsc-fasplit</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3278</td>
+      <td>3361</td>
+      <td>460</td>
+      <td>478</td>
+      <td>6144</td>
+      <td>6144</td>
+      <td>595</td>
+      <td>595</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>183</td>
+      <td>183</td>
+      <td>10561</td>
+      <td>10644</td>
+      <td>1238</td>
+      <td>1256</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta2bed</td>
+      <td>fasta2bed</td>
+      <td>Convert multiple fasta file into tabular bed file format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Sequence Analysis</td>
+      <td>fasta2bed</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed</td>
+      <td>1.0.0</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_clipping_histogram</td>
+      <td>cshl_fasta_clipping_histogram</td>
+      <td>Length Distribution chart</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Graphics, Statistics</td>
+      <td>fasta_clipping_histogram</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5191</td>
+      <td>5367</td>
+      <td>104</td>
+      <td>130</td>
+      <td>5191</td>
+      <td>5367</td>
+      <td>104</td>
+      <td>130</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_compute_length</td>
+      <td>fasta_compute_length</td>
+      <td>Compute sequence length</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length</td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_compute_length</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length</td>
+      <td>1.0.4</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>8547</td>
+      <td>9136</td>
+      <td>978</td>
+      <td>1129</td>
+      <td>17748</td>
+      <td>51150</td>
+      <td>1404</td>
+      <td>5670</td>
+      <td>4239</td>
+      <td>4404</td>
+      <td>162</td>
+      <td>190</td>
+      <td>30534</td>
+      <td>64690</td>
+      <td>2544</td>
+      <td>6989</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_concatenate_by_species</td>
+      <td>fasta_concatenate0</td>
+      <td>Concatenate FASTA alignment by species</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_concatenate_by_species</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species</td>
+      <td>0.0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>39695</td>
+      <td>39742</td>
+      <td>242</td>
+      <td>255</td>
+      <td>13660</td>
+      <td>19007</td>
+      <td>600</td>
+      <td>1398</td>
+      <td>1521</td>
+      <td>1603</td>
+      <td>92</td>
+      <td>112</td>
+      <td>54876</td>
+      <td>60352</td>
+      <td>934</td>
+      <td>1765</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_extract</td>
+      <td>fa-extract-sequence</td>
+      <td>extract single fasta from multiple fasta file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract</td>
+      <td>Sequence Analysis</td>
+      <td>fasta_extract</td>
+      <td>nml</td>
+      <td>https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract</td>
+      <td>1.1.0</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1286</td>
+      <td>1827</td>
+      <td>144</td>
+      <td>181</td>
+      <td>1296</td>
+      <td>1837</td>
+      <td>145</td>
+      <td>182</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_filter_by_id</td>
+      <td>fasta_filter_by_id</td>
+      <td>Filter FASTA sequences by ID (DEPRECATED)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id</td>
+      <td>Fasta Manipulation, Sequence Analysis, Text Manipulation</td>
+      <td>fasta_filter_by_id</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id</td>
+      <td>0.0.7</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_filter_by_length</td>
+      <td>fasta_filter_by_length</td>
+      <td>Filter sequences by length</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_filter_by_length</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length</td>
+      <td>1.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>47494</td>
+      <td>51924</td>
+      <td>889</td>
+      <td>997</td>
+      <td>50663</td>
+      <td>101663</td>
+      <td>1488</td>
+      <td>3742</td>
+      <td>3919</td>
+      <td>5601</td>
+      <td>241</td>
+      <td>276</td>
+      <td>102076</td>
+      <td>159188</td>
+      <td>2618</td>
+      <td>5015</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_formatter</td>
+      <td>cshl_fasta_formatter</td>
+      <td>FASTA Width formatter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_formatter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>5235</td>
+      <td>5486</td>
+      <td>237</td>
+      <td>288</td>
+      <td>4060</td>
+      <td>25609</td>
+      <td>480</td>
+      <td>2039</td>
+      <td>816</td>
+      <td>1093</td>
+      <td>73</td>
+      <td>89</td>
+      <td>10111</td>
+      <td>32188</td>
+      <td>790</td>
+      <td>2416</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_merge_files_and_filter_unique_sequences</td>
+      <td>fasta_merge_files_and_filter_unique_sequences</td>
+      <td>Concatenate FASTA database files together</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/</td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_merge_files_and_filter_unique_sequences</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences</td>
+      <td>1.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>30917</td>
+      <td>32191</td>
+      <td>1142</td>
+      <td>1257</td>
+      <td>36869</td>
+      <td>36869</td>
+      <td>1346</td>
+      <td>1346</td>
+      <td>5236</td>
+      <td>5236</td>
+      <td>230</td>
+      <td>230</td>
+      <td>73022</td>
+      <td>74296</td>
+      <td>2718</td>
+      <td>2833</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_nucleotide_changer</td>
+      <td>cshl_fasta_nucleotides_changer</td>
+      <td>RNA/DNA converter.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_nucleotide_changer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>497</td>
+      <td>808</td>
+      <td>71</td>
+      <td>108</td>
+      <td>2249</td>
+      <td>5479</td>
+      <td>216</td>
+      <td>703</td>
+      <td>415</td>
+      <td>437</td>
+      <td>18</td>
+      <td>20</td>
+      <td>3161</td>
+      <td>6724</td>
+      <td>305</td>
+      <td>831</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_nucleotide_color_plot</td>
+      <td>fasta_nucleotide_color_plot</td>
+      <td>Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot</td>
+      <td>Visualization</td>
+      <td>fasta_nucleotide_color_plot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot</td>
+      <td>1.0.1</td>
+      <td>openjdk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>164</td>
+      <td>179</td>
+      <td>42</td>
+      <td>47</td>
+      <td>758</td>
+      <td>905</td>
+      <td>128</td>
+      <td>170</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>922</td>
+      <td>1084</td>
+      <td>170</td>
+      <td>217</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_stats</td>
+      <td>fasta-stats</td>
+      <td>Display summary statistics for a fasta file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/</td>
+      <td>Sequence Analysis</td>
+      <td>fasta_stats</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats</td>
+      <td>2.0</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>43726</td>
+      <td>44512</td>
+      <td>3104</td>
+      <td>3259</td>
+      <td>19941</td>
+      <td>19941</td>
+      <td>3693</td>
+      <td>3693</td>
+      <td>16788</td>
+      <td>18589</td>
+      <td>2467</td>
+      <td>2650</td>
+      <td>80455</td>
+      <td>83042</td>
+      <td>9264</td>
+      <td>9602</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasta_to_tabular</td>
+      <td>fasta2tab</td>
+      <td>FASTA-to-Tabular converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation</td>
+      <td>fasta_to_tabular</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular</td>
+      <td>1.1.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>108876</td>
+      <td>113638</td>
+      <td>1572</td>
+      <td>1793</td>
+      <td>82527</td>
+      <td>192112</td>
+      <td>2209</td>
+      <td>8565</td>
+      <td>5711</td>
+      <td>7649</td>
+      <td>275</td>
+      <td>334</td>
+      <td>197114</td>
+      <td>313399</td>
+      <td>4056</td>
+      <td>10692</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastani</td>
+      <td>fastani</td>
+      <td>Fast alignment-free computation of whole-genome Average Nucleotide Identity</td>
+      <td>fastani</td>
+      <td>fastani</td>
+      <td></td>
+      <td>FastANI</td>
+      <td>FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.</td>
+      <td>Genome alignment, Sequence similarity search</td>
+      <td>Microbiology, Genetic variation</td>
+      <td>To update</td>
+      <td>https://github.com/ParBLiSS/FastANI</td>
+      <td>Sequence Analysis</td>
+      <td>fastani</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani</td>
+      <td>1.3</td>
+      <td>fastani</td>
+      <td>1.34</td>
+      <td>Genome alignment, Sequence similarity search</td>
+      <td>Microbiology, Genetic variation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6685</td>
+      <td>6685</td>
+      <td>603</td>
+      <td>603</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6685</td>
+      <td>6685</td>
+      <td>603</td>
+      <td>603</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastg2protlib</td>
+      <td>fastg2protlib-peptides, fastg2protlib-validate</td>
+      <td>Generate FASTA from FASTG</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/fastg2protlib.git</td>
+      <td>Proteomics</td>
+      <td>fastg2protlib</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib</td>
+      <td>1.0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastk</td>
+      <td>fastk_fastk</td>
+      <td>FastK: A K-mer counter (for HQ assembly data sets)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/thegenemyers/FASTK</td>
+      <td>Assembly</td>
+      <td>fastk</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk</td>
+      <td>1.0.0</td>
+      <td>fastk</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>136</td>
+      <td>136</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>136</td>
+      <td>136</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastp</td>
+      <td>fastp</td>
+      <td>Fast all-in-one preprocessing for FASTQ files</td>
+      <td>fastp</td>
+      <td>fastp</td>
+      <td></td>
+      <td>fastp</td>
+      <td>A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.</td>
+      <td>Sequencing quality control, Sequence contamination filtering</td>
+      <td>Sequence analysis, Probes and primers</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/OpenGene/fastp</td>
+      <td>Sequence Analysis</td>
+      <td>fastp</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp</td>
+      <td>0.23.4</td>
+      <td>fastp</td>
+      <td>0.23.4</td>
+      <td>Sequence contamination filtering</td>
+      <td>Probes and primers</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1126086</td>
+      <td>1127111</td>
+      <td>6847</td>
+      <td>6909</td>
+      <td>422259</td>
+      <td>422259</td>
+      <td>10722</td>
+      <td>10722</td>
+      <td>76462</td>
+      <td>76462</td>
+      <td>2242</td>
+      <td>2242</td>
+      <td>1624807</td>
+      <td>1625832</td>
+      <td>19811</td>
+      <td>19873</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_combiner</td>
+      <td>fastq_combiner</td>
+      <td>Combine FASTA and QUAL into FASTQ</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation, Fasta Manipulation</td>
+      <td>fastq_combiner</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>8604</td>
+      <td>8799</td>
+      <td>215</td>
+      <td>240</td>
+      <td>54200</td>
+      <td>75329</td>
+      <td>919</td>
+      <td>2957</td>
+      <td>1562</td>
+      <td>1680</td>
+      <td>76</td>
+      <td>85</td>
+      <td>64366</td>
+      <td>85808</td>
+      <td>1210</td>
+      <td>3282</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_filter</td>
+      <td>fastq_filter</td>
+      <td>Filter FASTQ reads by quality score and length</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15582</td>
+      <td>18350</td>
+      <td>690</td>
+      <td>771</td>
+      <td>40489</td>
+      <td>121585</td>
+      <td>2715</td>
+      <td>9239</td>
+      <td>4657</td>
+      <td>5793</td>
+      <td>214</td>
+      <td>287</td>
+      <td>60728</td>
+      <td>145728</td>
+      <td>3619</td>
+      <td>10297</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_filter_by_id</td>
+      <td>fastq_filter_by_id</td>
+      <td>Filter FASTQ sequences by ID (DEPRECATED)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id</td>
+      <td>Fastq Manipulation, Sequence Analysis, Text Manipulation</td>
+      <td>fastq_filter_by_id</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id</td>
+      <td>0.0.7</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_groomer</td>
+      <td>fastq_groomer</td>
+      <td>Convert between various FASTQ quality formats.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_groomer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>92594</td>
+      <td>102535</td>
+      <td>2576</td>
+      <td>2995</td>
+      <td>179461</td>
+      <td>897457</td>
+      <td>9437</td>
+      <td>44701</td>
+      <td>15434</td>
+      <td>25533</td>
+      <td>664</td>
+      <td>1073</td>
+      <td>287489</td>
+      <td>1025525</td>
+      <td>12677</td>
+      <td>48769</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_info</td>
+      <td>fastq_info</td>
+      <td>FASTQ info allows to validate single or paired fastq files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/nunofonseca/fastq_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_info</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info</td>
+      <td>0.25.1</td>
+      <td>fastq_utils</td>
+      <td>0.25.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7560</td>
+      <td>7560</td>
+      <td>1266</td>
+      <td>1266</td>
+      <td>6539</td>
+      <td>6539</td>
+      <td>1581</td>
+      <td>1581</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14099</td>
+      <td>14099</td>
+      <td>2847</td>
+      <td>2847</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_manipulation</td>
+      <td>fastq_manipulation</td>
+      <td>Manipulate FASTQ reads on various attributes.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_manipulation</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2488</td>
+      <td>3132</td>
+      <td>215</td>
+      <td>267</td>
+      <td>6241</td>
+      <td>14508</td>
+      <td>834</td>
+      <td>2121</td>
+      <td>4121</td>
+      <td>4592</td>
+      <td>131</td>
+      <td>158</td>
+      <td>12850</td>
+      <td>22232</td>
+      <td>1180</td>
+      <td>2546</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_masker_by_quality</td>
+      <td>fastq_masker_by_quality</td>
+      <td>FASTQ Masker by quality score</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_masker_by_quality</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>234</td>
+      <td>249</td>
+      <td>43</td>
+      <td>44</td>
+      <td>2648</td>
+      <td>8092</td>
+      <td>288</td>
+      <td>983</td>
+      <td>442</td>
+      <td>466</td>
+      <td>12</td>
+      <td>17</td>
+      <td>3324</td>
+      <td>8807</td>
+      <td>343</td>
+      <td>1044</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_pair</td>
+      <td>fastq_pair</td>
+      <td>Paired-end fastq pairer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/linsalrob/fastq-pair</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_pair</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair</td>
+      <td>1.0+galaxy0</td>
+      <td>fastq-pair</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_pair_names</td>
+      <td>fastq_pair_names</td>
+      <td>Extract FASTQ paired read names</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names</td>
+      <td>Sequence Analysis</td>
+      <td>fastq_pair_names</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names</td>
+      <td>0.0.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_paired_end_deinterlacer</td>
+      <td>fastq_paired_end_deinterlacer</td>
+      <td>FASTQ de-interlacer on paired end reads.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_paired_end_deinterlacer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5873</td>
+      <td>8936</td>
+      <td>532</td>
+      <td>657</td>
+      <td>14738</td>
+      <td>20229</td>
+      <td>1889</td>
+      <td>2366</td>
+      <td>2316</td>
+      <td>2711</td>
+      <td>225</td>
+      <td>261</td>
+      <td>22927</td>
+      <td>31876</td>
+      <td>2646</td>
+      <td>3284</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_paired_end_interlacer</td>
+      <td>fastq_paired_end_interlacer</td>
+      <td>FASTQ interlacer on paired end reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_paired_end_interlacer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>18216</td>
+      <td>19573</td>
+      <td>2348</td>
+      <td>2492</td>
+      <td>23484</td>
+      <td>25936</td>
+      <td>3482</td>
+      <td>3851</td>
+      <td>6207</td>
+      <td>6551</td>
+      <td>1402</td>
+      <td>1442</td>
+      <td>47907</td>
+      <td>52060</td>
+      <td>7232</td>
+      <td>7785</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_paired_end_joiner</td>
+      <td>fastq_paired_end_joiner</td>
+      <td>FASTQ joiner on paired end reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_paired_end_joiner</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15628</td>
+      <td>17130</td>
+      <td>536</td>
+      <td>679</td>
+      <td>24157</td>
+      <td>58368</td>
+      <td>1954</td>
+      <td>5716</td>
+      <td>1941</td>
+      <td>2266</td>
+      <td>172</td>
+      <td>214</td>
+      <td>41726</td>
+      <td>77764</td>
+      <td>2662</td>
+      <td>6609</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_paired_end_splitter</td>
+      <td>fastq_paired_end_splitter</td>
+      <td>FASTQ splitter on joined paired end reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_paired_end_splitter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3169</td>
+      <td>3521</td>
+      <td>459</td>
+      <td>535</td>
+      <td>19309</td>
+      <td>30747</td>
+      <td>1410</td>
+      <td>3441</td>
+      <td>807</td>
+      <td>1023</td>
+      <td>219</td>
+      <td>247</td>
+      <td>23285</td>
+      <td>35291</td>
+      <td>2088</td>
+      <td>4223</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_paired_unpaired</td>
+      <td>fastq_paired_unpaired</td>
+      <td>Divide FASTQ file into paired and unpaired reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired</td>
+      <td>Sequence Analysis, Text Manipulation</td>
+      <td>fastq_paired_unpaired</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired</td>
+      <td>0.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_provider</td>
+      <td>fastq_provider</td>
+      <td>Retrieval and download of FASTQ files from ENA and other repositories such as HCA.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ebi-gene-expression-group/atlas-fastq-provider</td>
+      <td>Data Source, RNA, Transcriptomics</td>
+      <td>atlas_fastq_provider</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider</td>
+      <td>0.4.4</td>
+      <td>atlas-fastq-provider</td>
+      <td>0.4.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_quality_boxplot</td>
+      <td>cshl_fastq_quality_boxplot</td>
+      <td>Draw quality score boxplot</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fastq Manipulation, Graphics, Statistics</td>
+      <td>fastq_quality_boxplot</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1271</td>
+      <td>1393</td>
+      <td>131</td>
+      <td>176</td>
+      <td>12763</td>
+      <td>58819</td>
+      <td>2073</td>
+      <td>8850</td>
+      <td>430</td>
+      <td>479</td>
+      <td>32</td>
+      <td>51</td>
+      <td>14464</td>
+      <td>60691</td>
+      <td>2236</td>
+      <td>9077</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_quality_converter</td>
+      <td>cshl_fastq_quality_converter</td>
+      <td>Quality format converter (ASCII-Numeric)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_quality_converter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>335</td>
+      <td>352</td>
+      <td>44</td>
+      <td>47</td>
+      <td>1583</td>
+      <td>9696</td>
+      <td>269</td>
+      <td>2229</td>
+      <td>1131</td>
+      <td>1254</td>
+      <td>15</td>
+      <td>27</td>
+      <td>3049</td>
+      <td>11302</td>
+      <td>328</td>
+      <td>2303</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_quality_filter</td>
+      <td>cshl_fastq_quality_filter</td>
+      <td>Filter by quality</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_quality_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>17279</td>
+      <td>18386</td>
+      <td>3826</td>
+      <td>4062</td>
+      <td>55268</td>
+      <td>136888</td>
+      <td>6055</td>
+      <td>12590</td>
+      <td>7685</td>
+      <td>9356</td>
+      <td>1854</td>
+      <td>2043</td>
+      <td>80232</td>
+      <td>164630</td>
+      <td>11735</td>
+      <td>18695</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_quality_trimmer</td>
+      <td>cshl_fastq_quality_trimmer</td>
+      <td>FASTQ trimmer based on quality</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/agordon/fastx_toolkit</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_quality_trimmer</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer</td>
+      <td>0.0.14+galaxy0</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_stats</td>
+      <td>fastq_stats</td>
+      <td>FASTQ Summary Statistics by column</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_stats</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3858</td>
+      <td>4595</td>
+      <td>680</td>
+      <td>815</td>
+      <td>15213</td>
+      <td>81513</td>
+      <td>3159</td>
+      <td>14109</td>
+      <td>3855</td>
+      <td>4163</td>
+      <td>184</td>
+      <td>256</td>
+      <td>22926</td>
+      <td>90271</td>
+      <td>4023</td>
+      <td>15180</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_to_fasta</td>
+      <td>cshl_fastq_to_fasta</td>
+      <td>FASTQ to FASTA converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Convert Formats</td>
+      <td>fastq_to_fasta</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>36069</td>
+      <td>37805</td>
+      <td>1151</td>
+      <td>1234</td>
+      <td>45213</td>
+      <td>99852</td>
+      <td>2691</td>
+      <td>6370</td>
+      <td>8457</td>
+      <td>13335</td>
+      <td>408</td>
+      <td>609</td>
+      <td>89739</td>
+      <td>150992</td>
+      <td>4250</td>
+      <td>8213</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_to_tabular</td>
+      <td>fastq_to_tabular</td>
+      <td>FASTQ to Tabular converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_to_tabular</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>12895</td>
+      <td>14110</td>
+      <td>269</td>
+      <td>297</td>
+      <td>13315</td>
+      <td>30673</td>
+      <td>612</td>
+      <td>1810</td>
+      <td>5125</td>
+      <td>5373</td>
+      <td>64</td>
+      <td>87</td>
+      <td>31335</td>
+      <td>50156</td>
+      <td>945</td>
+      <td>2194</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_trimmer</td>
+      <td>fastq_trimmer</td>
+      <td>FASTQ Trimmer by quality</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_trimmer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>10114</td>
+      <td>11383</td>
+      <td>582</td>
+      <td>665</td>
+      <td>23906</td>
+      <td>92351</td>
+      <td>1986</td>
+      <td>8818</td>
+      <td>1588</td>
+      <td>2607</td>
+      <td>108</td>
+      <td>212</td>
+      <td>35608</td>
+      <td>106341</td>
+      <td>2676</td>
+      <td>9695</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_trimmer_by_quality</td>
+      <td>fastq_quality_trimmer</td>
+      <td>FASTQ Quality Trimmer by sliding window</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fastq Manipulation</td>
+      <td>fastq_trimmer_by_quality</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4881</td>
+      <td>6165</td>
+      <td>859</td>
+      <td>967</td>
+      <td>29458</td>
+      <td>99179</td>
+      <td>3455</td>
+      <td>11369</td>
+      <td>2171</td>
+      <td>2678</td>
+      <td>259</td>
+      <td>338</td>
+      <td>36510</td>
+      <td>108022</td>
+      <td>4573</td>
+      <td>12674</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastq_utils</td>
+      <td>fastq_filter_n, fastq_trim_poly_at</td>
+      <td>Set of tools for handling fastq files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/nunofonseca/fastq_utils</td>
+      <td>Transcriptomics, RNA</td>
+      <td>fastq_utils</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils</td>
+      <td>0.25.1+galaxy0</td>
+      <td>fastq_utils</td>
+      <td>0.25.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastqc</td>
+      <td>fastqc</td>
+      <td>Read QC reports using FastQC</td>
+      <td>fastqc</td>
+      <td>fastqc</td>
+      <td></td>
+      <td>FastQC</td>
+      <td>This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.</td>
+      <td>Sequence composition calculation, Sequencing quality control, Statistical calculation</td>
+      <td>Sequencing, Data quality management, Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.bioinformatics.babraham.ac.uk/projects/fastqc/</td>
+      <td>Fastq Manipulation</td>
+      <td>fastqc</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc</td>
+      <td>0.74+galaxy1</td>
+      <td>fastqc</td>
+      <td>0.12.1</td>
+      <td>Sequence composition calculation, Sequencing quality control, Statistical calculation</td>
+      <td>Sequencing, Data quality management, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1784056</td>
+      <td>1913280</td>
+      <td>41344</td>
+      <td>43940</td>
+      <td>2269843</td>
+      <td>3195869</td>
+      <td>90828</td>
+      <td>140008</td>
+      <td>410004</td>
+      <td>445555</td>
+      <td>14195</td>
+      <td>16026</td>
+      <td>4463903</td>
+      <td>5554704</td>
+      <td>146367</td>
+      <td>199974</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastqc_stats</td>
+      <td>FastQC_Summary</td>
+      <td>Summary multiple FastQC into a single tabular line report</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Sequence Analysis</td>
+      <td>fastqc_stats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats</td>
+      <td>1.2</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastqe</td>
+      <td>fastqe</td>
+      <td>FASTQE</td>
+      <td>fastqe</td>
+      <td>fastqe</td>
+      <td></td>
+      <td>FASTQE</td>
+      <td>Compute quality stats for FASTQ files and print those stats as emoji... for some reason.</td>
+      <td>Sequencing quality control</td>
+      <td>Sequence analysis, Sequencing</td>
+      <td>To update</td>
+      <td>https://fastqe.com/</td>
+      <td>Sequence Analysis</td>
+      <td>fastqe</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe</td>
+      <td>0.3.1+galaxy0</td>
+      <td>fastqe</td>
+      <td>0.3.1</td>
+      <td>Sequencing quality control</td>
+      <td>Sequence analysis, Sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5162</td>
+      <td>5162</td>
+      <td>2350</td>
+      <td>2350</td>
+      <td>10176</td>
+      <td>10176</td>
+      <td>4714</td>
+      <td>4714</td>
+      <td>2610</td>
+      <td>2610</td>
+      <td>991</td>
+      <td>991</td>
+      <td>17948</td>
+      <td>17948</td>
+      <td>8055</td>
+      <td>8055</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastqsolexa_to_fasta_qual</td>
+      <td>fastqsolexa_to_fasta_qual</td>
+      <td>FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats, Fastq Manipulation</td>
+      <td>fastqsolexa_to_fasta_qual</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastqtofasta</td>
+      <td>fastq_to_fasta_python</td>
+      <td>FASTQ to FASTA converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>fastqtofasta</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>208349</td>
+      <td>217568</td>
+      <td>3421</td>
+      <td>3732</td>
+      <td>131388</td>
+      <td>245005</td>
+      <td>5108</td>
+      <td>13227</td>
+      <td>18655</td>
+      <td>18655</td>
+      <td>679</td>
+      <td>679</td>
+      <td>358392</td>
+      <td>481228</td>
+      <td>9208</td>
+      <td>17638</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fasttree</td>
+      <td>fasttree</td>
+      <td>FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL</td>
+      <td>fasttree</td>
+      <td>fasttree</td>
+      <td></td>
+      <td>FastTree</td>
+      <td>Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.</td>
+      <td>Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)</td>
+      <td>Phylogenetics, Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.microbesonline.org/fasttree/</td>
+      <td>Phylogenetics</td>
+      <td>fasttree</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree</td>
+      <td>2.1.10</td>
+      <td>fasttree</td>
+      <td>2.1.11</td>
+      <td></td>
+      <td>Phylogenetics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>65542</td>
+      <td>65631</td>
+      <td>1049</td>
+      <td>1071</td>
+      <td>25992</td>
+      <td>25992</td>
+      <td>2147</td>
+      <td>2147</td>
+      <td>6733</td>
+      <td>7339</td>
+      <td>649</td>
+      <td>745</td>
+      <td>98267</td>
+      <td>98962</td>
+      <td>3845</td>
+      <td>3963</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_artifacts_filter</td>
+      <td>cshl_fastx_artifacts_filter</td>
+      <td>Remove sequencing artifacts</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td>fastx_artifacts_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1769</td>
+      <td>2020</td>
+      <td>88</td>
+      <td>101</td>
+      <td>6948</td>
+      <td>24960</td>
+      <td>358</td>
+      <td>2424</td>
+      <td>623</td>
+      <td>998</td>
+      <td>32</td>
+      <td>50</td>
+      <td>9340</td>
+      <td>27978</td>
+      <td>478</td>
+      <td>2575</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_barcode_splitter</td>
+      <td>cshl_fastx_barcode_splitter</td>
+      <td>Barcode Splitter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td>fastx_barcode_splitter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>16957</td>
+      <td>18124</td>
+      <td>225</td>
+      <td>260</td>
+      <td>37001</td>
+      <td>89126</td>
+      <td>919</td>
+      <td>2720</td>
+      <td>863</td>
+      <td>989</td>
+      <td>56</td>
+      <td>68</td>
+      <td>54821</td>
+      <td>108239</td>
+      <td>1200</td>
+      <td>3048</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_clipper</td>
+      <td>cshl_fastx_clipper</td>
+      <td>Clip adapter sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td>fastx_clipper</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3140</td>
+      <td>3520</td>
+      <td>178</td>
+      <td>212</td>
+      <td>13975</td>
+      <td>117900</td>
+      <td>1198</td>
+      <td>6006</td>
+      <td>409</td>
+      <td>712</td>
+      <td>36</td>
+      <td>55</td>
+      <td>17524</td>
+      <td>122132</td>
+      <td>1412</td>
+      <td>6273</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_collapser</td>
+      <td>cshl_fastx_collapser</td>
+      <td>Collapse sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation</td>
+      <td>fastx_collapser</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>64187</td>
+      <td>67981</td>
+      <td>326</td>
+      <td>349</td>
+      <td>87477</td>
+      <td>185555</td>
+      <td>781</td>
+      <td>3067</td>
+      <td>16563</td>
+      <td>17125</td>
+      <td>58</td>
+      <td>78</td>
+      <td>168227</td>
+      <td>270661</td>
+      <td>1165</td>
+      <td>3494</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_nucleotides_distribution</td>
+      <td>cshl_fastx_nucleotides_distribution</td>
+      <td>Draw nucleotides distribution chart</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fastq Manipulation, Graphics</td>
+      <td>fastx_nucleotides_distribution</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>174</td>
+      <td>272</td>
+      <td>61</td>
+      <td>92</td>
+      <td>4295</td>
+      <td>25068</td>
+      <td>1056</td>
+      <td>4180</td>
+      <td>1127</td>
+      <td>1171</td>
+      <td>70</td>
+      <td>89</td>
+      <td>5596</td>
+      <td>26511</td>
+      <td>1187</td>
+      <td>4361</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_quality_statistics</td>
+      <td>cshl_fastx_quality_statistics</td>
+      <td>Compute quality statistics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fastq Manipulation, Statistics</td>
+      <td>fastx_quality_statistics</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2218</td>
+      <td>2344</td>
+      <td>168</td>
+      <td>206</td>
+      <td>20551</td>
+      <td>60032</td>
+      <td>3784</td>
+      <td>9866</td>
+      <td>2347</td>
+      <td>2460</td>
+      <td>234</td>
+      <td>256</td>
+      <td>25116</td>
+      <td>64836</td>
+      <td>4186</td>
+      <td>10328</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_renamer</td>
+      <td>cshl_fastx_renamer</td>
+      <td>Rename sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td>fastx_renamer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2364</td>
+      <td>2526</td>
+      <td>180</td>
+      <td>214</td>
+      <td>6572</td>
+      <td>11745</td>
+      <td>303</td>
+      <td>1024</td>
+      <td>462</td>
+      <td>696</td>
+      <td>49</td>
+      <td>64</td>
+      <td>9398</td>
+      <td>14967</td>
+      <td>532</td>
+      <td>1302</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_reverse_complement</td>
+      <td>cshl_fastx_reverse_complement</td>
+      <td>Reverse-Complement</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fastq Manipulation, Fasta Manipulation</td>
+      <td>fastx_reverse_complement</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>10707</td>
+      <td>12597</td>
+      <td>356</td>
+      <td>415</td>
+      <td>21568</td>
+      <td>67304</td>
+      <td>574</td>
+      <td>1527</td>
+      <td>719</td>
+      <td>861</td>
+      <td>61</td>
+      <td>78</td>
+      <td>32994</td>
+      <td>80762</td>
+      <td>991</td>
+      <td>2020</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fastx_trimmer</td>
+      <td>cshl_fastx_trimmer</td>
+      <td>Trim sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hannonlab.cshl.edu/fastx_toolkit/</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td>fastx_trimmer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer</td>
+      <td>0.0.14</td>
+      <td>fastx_toolkit</td>
+      <td>0.0.14</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>13584</td>
+      <td>14557</td>
+      <td>550</td>
+      <td>641</td>
+      <td>123676</td>
+      <td>206733</td>
+      <td>2034</td>
+      <td>8390</td>
+      <td>2819</td>
+      <td>4757</td>
+      <td>229</td>
+      <td>267</td>
+      <td>140079</td>
+      <td>226047</td>
+      <td>2813</td>
+      <td>9298</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fates-emerald</td>
+      <td>ctsm_fates</td>
+      <td>EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api</td>
+      <td>Climate Analysis</td>
+      <td>ctsm_fates</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald</td>
+      <td>2.0</td>
+      <td>fates-emerald</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>264</td>
+      <td>264</td>
+      <td>69</td>
+      <td>69</td>
+      <td>34</td>
+      <td>34</td>
+      <td>11</td>
+      <td>11</td>
+      <td>103</td>
+      <td>103</td>
+      <td>1</td>
+      <td>1</td>
+      <td>401</td>
+      <td>401</td>
+      <td>81</td>
+      <td>81</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fatovcf</td>
+      <td>fatovcf</td>
+      <td>Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Convert Formats</td>
+      <td>ucsc_fatovcf</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf</td>
+      <td>448</td>
+      <td>ucsc-fatovcf</td>
+      <td>448</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>385</td>
+      <td>385</td>
+      <td>46</td>
+      <td>46</td>
+      <td>587</td>
+      <td>587</td>
+      <td>107</td>
+      <td>107</td>
+      <td>58</td>
+      <td>58</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1030</td>
+      <td>1030</td>
+      <td>158</td>
+      <td>158</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>feature_alignment</td>
+      <td>feature_alignment</td>
+      <td>TRIC integrates information from all available runs via a graph-based alignment strategy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>feature_alignment</td>
+      <td>galaxyp</td>
+      <td>https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment</td>
+      <td>0.11.0</td>
+      <td>msproteomicstools</td>
+      <td>0.11.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>featurecounter</td>
+      <td>featureCoverage1</td>
+      <td>Feature coverage</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>featurecounter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter</td>
+      <td>2.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>22308</td>
+      <td>22388</td>
+      <td>16</td>
+      <td>19</td>
+      <td>350</td>
+      <td>13711</td>
+      <td>54</td>
+      <td>349</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22658</td>
+      <td>36099</td>
+      <td>70</td>
+      <td>368</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>featurecounts</td>
+      <td>featurecounts</td>
+      <td>featureCounts counts the number of reads aligned to defined masked regions in a reference genome</td>
+      <td>featurecounts</td>
+      <td>featurecounts</td>
+      <td></td>
+      <td>FeatureCounts</td>
+      <td>featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.</td>
+      <td>Read summarisation, RNA-Seq quantification</td>
+      <td>RNA-Seq</td>
+      <td>To update</td>
+      <td>http://bioinf.wehi.edu.au/featureCounts</td>
+      <td>RNA, Transcriptomics, Sequence Analysis</td>
+      <td>featurecounts</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts</td>
+      <td>2.0.3</td>
+      <td>subread</td>
+      <td>2.0.6</td>
+      <td>Read summarisation, RNA-Seq quantification</td>
+      <td>RNA-Seq</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>740719</td>
+      <td>770524</td>
+      <td>11699</td>
+      <td>12547</td>
+      <td>643892</td>
+      <td>784396</td>
+      <td>23272</td>
+      <td>27598</td>
+      <td>66108</td>
+      <td>68867</td>
+      <td>2348</td>
+      <td>2463</td>
+      <td>1450719</td>
+      <td>1623787</td>
+      <td>37319</td>
+      <td>42608</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>feelnc</td>
+      <td>feelnc</td>
+      <td>Galaxy wrapper for FEELnc</td>
+      <td>feelnc</td>
+      <td>feelnc</td>
+      <td></td>
+      <td>FEELnc</td>
+      <td>A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.</td>
+      <td>Annotation, Classification</td>
+      <td>RNA-seq, Functional, regulatory and non-coding RNA</td>
+      <td>To update</td>
+      <td>https://github.com/tderrien/FEELnc</td>
+      <td>Sequence Analysis</td>
+      <td>feelnc</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc</td>
+      <td>0.2.1</td>
+      <td>feelnc</td>
+      <td>0.2</td>
+      <td>Annotation, Classification</td>
+      <td>Functional, regulatory and non-coding RNA</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1375</td>
+      <td>1500</td>
+      <td>95</td>
+      <td>99</td>
+      <td>797</td>
+      <td>797</td>
+      <td>116</td>
+      <td>116</td>
+      <td>59</td>
+      <td>59</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2231</td>
+      <td>2356</td>
+      <td>214</td>
+      <td>218</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>feelnc2asko</td>
+      <td>feelnc2asko</td>
+      <td>Convert FeelNC GTF to GFF3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/tderrien/FEELnc</td>
+      <td>Convert Formats</td>
+      <td>feelnc2asko</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko</td>
+      <td>0.1</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>feht</td>
+      <td>feht</td>
+      <td>Automatically identify makers predictive of groups.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Sequence Analysis</td>
+      <td>feht</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht</td>
+      <td>0.1.0</td>
+      <td>feht</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fermikit</td>
+      <td>fermi2, fermikit_variants</td>
+      <td>FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lh3/fermikit</td>
+      <td>Assembly, Variant Analysis</td>
+      <td>fermikit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit</td>
+      <td>r193</td>
+      <td>fermi2</td>
+      <td>r193</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fetch_fasta_from_ncbi</td>
+      <td>retrieve_fasta_from_NCBI</td>
+      <td>Fetch fasta sequences from NCBI using eutils wrappers</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Fasta Manipulation, Data Source</td>
+      <td>fetch_fasta_from_ncbi</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi</td>
+      <td>3.1.0</td>
+      <td>urllib3</td>
+      <td>1.12</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fgsea</td>
+      <td>fgsea</td>
+      <td>Perform gene set testing using fgsea</td>
+      <td>fgsea</td>
+      <td>fgsea</td>
+      <td></td>
+      <td>fgsea</td>
+      <td>The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.</td>
+      <td>Gene-set enrichment analysis</td>
+      <td>Genetics</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/fgsea.html</td>
+      <td>Visualization, Transcriptomics, Statistics</td>
+      <td>fgsea</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea</td>
+      <td>1.8.0+galaxy1</td>
+      <td>bioconductor-fgsea</td>
+      <td>1.28.0</td>
+      <td>Gene-set enrichment analysis</td>
+      <td>Genetics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5618</td>
+      <td>5820</td>
+      <td>582</td>
+      <td>607</td>
+      <td>21673</td>
+      <td>21673</td>
+      <td>938</td>
+      <td>938</td>
+      <td>869</td>
+      <td>869</td>
+      <td>110</td>
+      <td>110</td>
+      <td>28160</td>
+      <td>28362</td>
+      <td>1630</td>
+      <td>1655</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>file_manipulation</td>
+      <td>bg_uniq</td>
+      <td>This tool returns all unique lines from a tab-separated file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation</td>
+      <td>Text Manipulation</td>
+      <td>unique</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation</td>
+      <td>0.4</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6690</td>
+      <td>8818</td>
+      <td>554</td>
+      <td>612</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6690</td>
+      <td>8818</td>
+      <td>554</td>
+      <td>612</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_by_fasta_ids</td>
+      <td>filter_by_fasta_ids</td>
+      <td>Filter FASTA on the headers and/or the sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation, Proteomics</td>
+      <td>filter_by_fasta_ids</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids</td>
+      <td>2.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>26717</td>
+      <td>29932</td>
+      <td>1026</td>
+      <td>1072</td>
+      <td>42990</td>
+      <td>42990</td>
+      <td>1176</td>
+      <td>1176</td>
+      <td>9619</td>
+      <td>9619</td>
+      <td>230</td>
+      <td>230</td>
+      <td>79326</td>
+      <td>82541</td>
+      <td>2432</td>
+      <td>2478</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_compounds</td>
+      <td>filter_orgmet_anorg</td>
+      <td>Tool for filtering organometallics/anorganic compounds from a list of compounds.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools/</td>
+      <td>Metabolomics</td>
+      <td>filter_compounds</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds</td>
+      <td>3.1.1</td>
+      <td>openbabel</td>
+      <td>2.3.90dev7d621d9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_density</td>
+      <td>filterdensity</td>
+      <td>Filter out position based on distance between SNVs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>filter_density</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_spades_repeats</td>
+      <td>filter_spades_repeat</td>
+      <td>Remove short and repeat contigs/scaffolds</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools/</td>
+      <td>Assembly</td>
+      <td>filter_spades_repeats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools/</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats</td>
+      <td>1.0.1</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_stats</td>
+      <td>filterstat</td>
+      <td>SNVPhyl filter_stats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>filter_stats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_transcripts_via_tracking</td>
+      <td>filter_combined_via_tracking</td>
+      <td>Filter Combined Transcripts</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>filter_transcripts_via_tracking</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>23</td>
+      <td>24</td>
+      <td>9</td>
+      <td>10</td>
+      <td>62</td>
+      <td>635</td>
+      <td>26</td>
+      <td>241</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>87</td>
+      <td>661</td>
+      <td>37</td>
+      <td>253</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filter_vcf</td>
+      <td>filtervcf</td>
+      <td>SNVPhyl filter_vcf</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>filter_vcf</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>filtlong</td>
+      <td>filtlong</td>
+      <td>Filtlong - Filtering long reads by quality</td>
+      <td>filtlong</td>
+      <td>filtlong</td>
+      <td></td>
+      <td>Filtlong</td>
+      <td>Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.</td>
+      <td>Filtering, Sequencing quality control</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/rrwick/Filtlong</td>
+      <td>Fastq Manipulation, Sequence Analysis</td>
+      <td>filtlong</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong</td>
+      <td>0.2.1</td>
+      <td>filtlong</td>
+      <td>0.2.1</td>
+      <td>Filtering, Sequencing quality control</td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>53310</td>
+      <td>53944</td>
+      <td>1499</td>
+      <td>1575</td>
+      <td>25043</td>
+      <td>25043</td>
+      <td>726</td>
+      <td>726</td>
+      <td>10824</td>
+      <td>10824</td>
+      <td>593</td>
+      <td>593</td>
+      <td>89177</td>
+      <td>89811</td>
+      <td>2818</td>
+      <td>2894</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>find_diag_hits</td>
+      <td>find_diag_hits</td>
+      <td>Find diagnostic hits</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Metagenomics</td>
+      <td>find_diag_hits</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits</td>
+      <td>1.0.0</td>
+      <td>taxonomy</td>
+      <td>0.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>62</td>
+      <td>70</td>
+      <td>10</td>
+      <td>12</td>
+      <td>3</td>
+      <td>1787</td>
+      <td>1</td>
+      <td>204</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>1857</td>
+      <td>11</td>
+      <td>216</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>find_repeats</td>
+      <td>findrepeat</td>
+      <td>Find repetitive regions on a reference genome using MUMMer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>find_repeats</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>find_subsequences</td>
+      <td>bg_find_subsequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>find_subsequences</td>
+      <td>bgruening</td>
+      <td></td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences</td>
+      <td>0.3</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>554</td>
+      <td>784</td>
+      <td>69</td>
+      <td>79</td>
+      <td>2820</td>
+      <td>3047</td>
+      <td>323</td>
+      <td>361</td>
+      <td>20</td>
+      <td>20</td>
+      <td>1</td>
+      <td>1</td>
+      <td>3394</td>
+      <td>3851</td>
+      <td>393</td>
+      <td>441</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fisher_test</td>
+      <td>fishertest</td>
+      <td>Fisher's exact test on two-column hit lists.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Statistics</td>
+      <td>fishertest</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test</td>
+      <td>2.32.0+galaxy0</td>
+      <td>bioconductor-qvalue</td>
+      <td>2.34.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>flair</td>
+      <td>flair_collapse, flair_correct</td>
+      <td>FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/BrooksLabUCSC/flair</td>
+      <td>Nanopore</td>
+      <td>flair</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair</td>
+      <td>1.5</td>
+      <td>flair</td>
+      <td>2.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1985</td>
+      <td>1985</td>
+      <td>41</td>
+      <td>41</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1985</td>
+      <td>1985</td>
+      <td>41</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>flanking_features</td>
+      <td>flanking_features_1</td>
+      <td>Fetch closest non-overlapping feature for every interval</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>flanking_features</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features</td>
+      <td>4.0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>589</td>
+      <td>731</td>
+      <td>51</td>
+      <td>63</td>
+      <td>2445</td>
+      <td>32847</td>
+      <td>304</td>
+      <td>2549</td>
+      <td>1214</td>
+      <td>1294</td>
+      <td>15</td>
+      <td>22</td>
+      <td>4248</td>
+      <td>34872</td>
+      <td>370</td>
+      <td>2634</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>flash</td>
+      <td>flash</td>
+      <td>Fast Length Adjustment of SHort reads</td>
+      <td>flash</td>
+      <td>flash</td>
+      <td></td>
+      <td>FLASH</td>
+      <td>Identifies paired-end reads which overlap in the middle, converting them to single long reads</td>
+      <td>Read pre-processing, Sequence merging, Sequence assembly</td>
+      <td>Sequencing, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://ccb.jhu.edu/software/FLASH/</td>
+      <td>Assembly, Fastq Manipulation</td>
+      <td>flash</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash</td>
+      <td>1.2.11</td>
+      <td>flash</td>
+      <td>1.2.11</td>
+      <td>Read pre-processing, Sequence merging, Sequence assembly</td>
+      <td>Sequencing, Sequence assembly</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>22017</td>
+      <td>22304</td>
+      <td>239</td>
+      <td>255</td>
+      <td>9399</td>
+      <td>14886</td>
+      <td>462</td>
+      <td>709</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>31420</td>
+      <td>37194</td>
+      <td>702</td>
+      <td>965</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>flashlfq</td>
+      <td>flashlfq</td>
+      <td>FlashLFQ mass-spectrometry proteomics label-free quantification</td>
+      <td>flashlfq</td>
+      <td>flashlfq</td>
+      <td></td>
+      <td>FlashLFQ</td>
+      <td>FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.</td>
+      <td>Label-free quantification</td>
+      <td>Proteomics experiment, Proteomics</td>
+      <td>To update</td>
+      <td>https://github.com/smith-chem-wisc/FlashLFQ</td>
+      <td>Proteomics</td>
+      <td>flashlfq</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq</td>
+      <td>1.0.3.1</td>
+      <td>flashlfq</td>
+      <td>1.2.6</td>
+      <td>Label-free quantification</td>
+      <td>Proteomics experiment, Proteomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>661</td>
+      <td>715</td>
+      <td>52</td>
+      <td>54</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>167</td>
+      <td>167</td>
+      <td>15</td>
+      <td>15</td>
+      <td>828</td>
+      <td>882</td>
+      <td>67</td>
+      <td>69</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>flexynesis</td>
+      <td>flexynesis</td>
+      <td>This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BIMSBbioinfo/flexynesis/tree/main</td>
+      <td>Machine Learning, Statistics, Systems Biology</td>
+      <td>flexynesis</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis</td>
+      <td>0.2.10</td>
+      <td>flexynesis</td>
+      <td>0.2.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>flye</td>
+      <td>flye</td>
+      <td>Assembly of long and error-prone reads.</td>
+      <td>Flye</td>
+      <td>Flye</td>
+      <td></td>
+      <td>Flye</td>
+      <td>Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.</td>
+      <td>Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly</td>
+      <td>Sequence assembly, Metagenomics, Whole genome sequencing, Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/fenderglass/Flye/</td>
+      <td>Assembly</td>
+      <td>flye</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/flye</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/flye</td>
+      <td>2.9.5</td>
+      <td>flye</td>
+      <td>2.9.5</td>
+      <td>Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly</td>
+      <td>Sequence assembly, Metagenomics, Whole genome sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>32514</td>
+      <td>32675</td>
+      <td>3379</td>
+      <td>3422</td>
+      <td>19434</td>
+      <td>19434</td>
+      <td>2537</td>
+      <td>2537</td>
+      <td>9843</td>
+      <td>9843</td>
+      <td>1624</td>
+      <td>1624</td>
+      <td>61791</td>
+      <td>61952</td>
+      <td>7540</td>
+      <td>7583</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>footprint</td>
+      <td>footprint</td>
+      <td>Find transcription factor footprints</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/</td>
+      <td>Epigenetics</td>
+      <td>footprint</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/footprint</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/footprint</td>
+      <td>1.0.0</td>
+      <td>footprint</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>format_cd_hit_output</td>
+      <td>format_cd_hit_output</td>
+      <td>Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation</td>
+      <td>format_cd_hit_output</td>
+      <td>bebatut</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output</td>
+      <td>1.0.0+galaxy1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>189</td>
+      <td>203</td>
+      <td>57</td>
+      <td>60</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>189</td>
+      <td>203</td>
+      <td>57</td>
+      <td>60</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>format_metaphlan2_output</td>
+      <td>format_metaphlan2_output</td>
+      <td>Format MetaPhlAn2 output to extract abundance at different taxonomic levels</td>
+      <td>format_metaphlan2_output</td>
+      <td>format_metaphlan2_output</td>
+      <td></td>
+      <td>Format metaphlan2 output</td>
+      <td>This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).</td>
+      <td>Formatting</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>To update</td>
+      <td></td>
+      <td>Metagenomics</td>
+      <td>format_metaphlan2_output</td>
+      <td>bebatut</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td>Formatting</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5940</td>
+      <td>6474</td>
+      <td>558</td>
+      <td>608</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5940</td>
+      <td>6474</td>
+      <td>558</td>
+      <td>608</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fraggenescan</td>
+      <td>fraggenescan</td>
+      <td>Tool for finding (fragmented) genes in short read</td>
+      <td>fraggenescan</td>
+      <td>fraggenescan</td>
+      <td></td>
+      <td>FragGeneScan</td>
+      <td>Application for finding (fragmented) genes in short reads</td>
+      <td>Gene prediction</td>
+      <td>Genetics, Sequence analysis</td>
+      <td>To update</td>
+      <td>https://sourceforge.net/projects/fraggenescan/</td>
+      <td>Sequence Analysis</td>
+      <td>fraggenescan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan</td>
+      <td></td>
+      <td>fraggenescan</td>
+      <td>1.31</td>
+      <td>Gene prediction</td>
+      <td>Genetics, Sequence analysis</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1257</td>
+      <td>1450</td>
+      <td>150</td>
+      <td>162</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1052</td>
+      <td>1052</td>
+      <td>45</td>
+      <td>45</td>
+      <td>2309</td>
+      <td>2502</td>
+      <td>195</td>
+      <td>207</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fragpipe</td>
+      <td>fragpipe</td>
+      <td>Data analysis for mass spectrometry-based proteomics.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://fragpipe.nesvilab.org/</td>
+      <td>Proteomics</td>
+      <td>fragpipe</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe</td>
+      <td>20.0</td>
+      <td>fragpipe</td>
+      <td>20.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>64</td>
+      <td>64</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>64</td>
+      <td>64</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>free_energy</td>
+      <td></td>
+      <td>Free energy tools of BRIDGE.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>freeenergy</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>freebayes</td>
+      <td>freebayes, bamleftalign</td>
+      <td>Galaxy Freebayes Bayesian genetic variant detector tool</td>
+      <td>freebayes</td>
+      <td>freebayes</td>
+      <td></td>
+      <td>FreeBayes</td>
+      <td>Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.</td>
+      <td>Variant calling, Statistical calculation</td>
+      <td>Genomics, Genetic variation, Rare diseases</td>
+      <td>To update</td>
+      <td>https://github.com/ekg/freebayes</td>
+      <td>Variant Analysis</td>
+      <td>freebayes</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes</td>
+      <td>1.3.6</td>
+      <td>freebayes</td>
+      <td>1.3.8</td>
+      <td>Variant calling, Statistical calculation</td>
+      <td>Genomics, Genetic variation, Rare diseases</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>149715</td>
+      <td>171093</td>
+      <td>8158</td>
+      <td>8794</td>
+      <td>144708</td>
+      <td>256315</td>
+      <td>15996</td>
+      <td>25107</td>
+      <td>19156</td>
+      <td>21936</td>
+      <td>2251</td>
+      <td>2571</td>
+      <td>313579</td>
+      <td>449344</td>
+      <td>26405</td>
+      <td>36472</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>freec</td>
+      <td>control_freec</td>
+      <td>Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.</td>
+      <td>freec</td>
+      <td>freec</td>
+      <td></td>
+      <td>FREEC</td>
+      <td>A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.</td>
+      <td>Copy number estimation, Variant calling, Genome alignment</td>
+      <td>DNA structural variation, Oncology, Human genetics, Data mining</td>
+      <td>To update</td>
+      <td>http://boevalab.inf.ethz.ch/FREEC/</td>
+      <td>Variant Analysis</td>
+      <td>control_freec</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec</td>
+      <td>11.6</td>
+      <td>gawk</td>
+      <td></td>
+      <td>Copy number estimation, Variant calling, Genome alignment</td>
+      <td>Oncology, Human genetics, Data mining</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>748</td>
+      <td>748</td>
+      <td>91</td>
+      <td>91</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1</td>
+      <td>1</td>
+      <td>760</td>
+      <td>760</td>
+      <td>92</td>
+      <td>92</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>freyja</td>
+      <td>freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants</td>
+      <td>lineage abundances estimation</td>
+      <td>freyja</td>
+      <td>freyja</td>
+      <td></td>
+      <td>Freyja</td>
+      <td>Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset</td>
+      <td>RNA-Seq quantification</td>
+      <td>Metagenomics</td>
+      <td>To update</td>
+      <td>https://github.com/andersen-lab/Freyja</td>
+      <td>Metagenomics, Sequence Analysis</td>
+      <td>freyja</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja</td>
+      <td>1.4.4</td>
+      <td>freyja</td>
+      <td>1.5.1</td>
+      <td>RNA-Seq quantification</td>
+      <td>Metagenomics</td>
+      <td>2</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21757</td>
+      <td>21757</td>
+      <td>101</td>
+      <td>101</td>
+      <td>217</td>
+      <td>217</td>
+      <td>21</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21974</td>
+      <td>21974</td>
+      <td>122</td>
+      <td>122</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>frogs</td>
+      <td>FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom</td>
+      <td>Suite for metabarcoding analysis</td>
+      <td>frogs</td>
+      <td>frogs</td>
+      <td></td>
+      <td>FROGS</td>
+      <td>The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing</td>
+      <td>To update</td>
+      <td>http://frogs.toulouse.inrae.fr/</td>
+      <td>Metagenomics</td>
+      <td>frogs</td>
+      <td>frogs</td>
+      <td>https://github.com/geraldinepascal/FROGS-wrappers/</td>
+      <td>https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs</td>
+      <td>4.1.0</td>
+      <td>frogs</td>
+      <td>5.0.0</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fromHicupToJuicebox</td>
+      <td>fromHicupToJuicebox</td>
+      <td>Convert the output of hicup (as sam or bam) to the input of juicebox.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Epigenetics</td>
+      <td>from_hicup_to_juicebox</td>
+      <td>lldelisle</td>
+      <td></td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox</td>
+      <td>0.0.2</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fromgtfTobed12</td>
+      <td>fromgtfTobed12</td>
+      <td>Convert GTF files to BED12 format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pythonhosted.org/gffutils/contents.html</td>
+      <td>Convert Formats</td>
+      <td>fromgtftobed12</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12</td>
+      <td>0.11.1+galaxy1</td>
+      <td>gffutils</td>
+      <td>0.13</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>fsd</td>
+      <td>fsd, fsd_beforevsafter, fsd_regions, td</td>
+      <td>Tool that plots a histogram of sizes of read families</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics</td>
+      <td>duplex_family_size_distribution</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd</td>
+      <td>1.0.2</td>
+      <td>matplotlib</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>578</td>
+      <td>578</td>
+      <td>34</td>
+      <td>34</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>578</td>
+      <td>578</td>
+      <td>34</td>
+      <td>34</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>funannotate</td>
+      <td>funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort</td>
+      <td>Funannotate is a genome prediction, annotation, and comparison software package.</td>
+      <td>funannotate</td>
+      <td>funannotate</td>
+      <td></td>
+      <td>funannotate</td>
+      <td>funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).</td>
+      <td>Genome annotation</td>
+      <td>Genomics</td>
+      <td>To update</td>
+      <td>https://funannotate.readthedocs.io</td>
+      <td>Genome annotation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate</td>
+      <td>1.8.15</td>
+      <td></td>
+      <td></td>
+      <td>Genome annotation</td>
+      <td>Genomics</td>
+      <td>3</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>3</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8648</td>
+      <td>8648</td>
+      <td>1408</td>
+      <td>1408</td>
+      <td>32</td>
+      <td>32</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6406</td>
+      <td>6406</td>
+      <td>597</td>
+      <td>597</td>
+      <td>15086</td>
+      <td>15086</td>
+      <td>2011</td>
+      <td>2011</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>garnett</td>
+      <td>garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file</td>
+      <td>De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_garnett</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett</td>
+      <td>0.2.8</td>
+      <td>garnett-cli</td>
+      <td>0.0.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gatk4</td>
+      <td>filtermutectcalls, mergemutectstats, mutect2</td>
+      <td>Find somatic variations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>gatk4</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4</td>
+      <td>4.1.7.0</td>
+      <td>gatk4</td>
+      <td>4.5.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gatk4</td>
+      <td>gatk4_mutect2</td>
+      <td>A Galaxy wrapper for Mutect2 from GATK</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://software.broadinstitute.org/gatk/gatk4</td>
+      <td>Variant Analysis</td>
+      <td>gatk4_mutect2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4</td>
+      <td>4.1.7.0</td>
+      <td>gatk4</td>
+      <td>4.5.0.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3463</td>
+      <td>3463</td>
+      <td>452</td>
+      <td>452</td>
+      <td>9040</td>
+      <td>9040</td>
+      <td>1639</td>
+      <td>1639</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12503</td>
+      <td>12503</td>
+      <td>2091</td>
+      <td>2091</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gblocks</td>
+      <td>gblocks</td>
+      <td>Gblocks</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://molevol.cmima.csic.es/castresana/Gblocks.html</td>
+      <td>Sequence Analysis</td>
+      <td>gblocks</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks</td>
+      <td>0.91b</td>
+      <td>gblocks</td>
+      <td>0.91b</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>466</td>
+      <td>466</td>
+      <td>62</td>
+      <td>62</td>
+      <td>466</td>
+      <td>466</td>
+      <td>62</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gc_derivatization</td>
+      <td>gc_derivatization</td>
+      <td>In silico derivatization for GC.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/gc-meox-tms</td>
+      <td>Metabolomics</td>
+      <td>gc_derivatization</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization</td>
+      <td>1.0.1</td>
+      <td>gc-meox-tms</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gcms2isocor</td>
+      <td>gcms2isocor</td>
+      <td>Conversion from GCMS PostRun Analysis to Isocor</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Metabolomics</td>
+      <td>gcms2isocor</td>
+      <td>genouest</td>
+      <td></td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor</td>
+      <td>0.1.0</td>
+      <td>openjdk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gcms2isocor</td>
+      <td>gcms2isocor</td>
+      <td>Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/p2m2/p2m2tools</td>
+      <td>Metabolomics</td>
+      <td>gcms2isocor</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor</td>
+      <td>0.2.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gdal</td>
+      <td>gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo</td>
+      <td>Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.gdal.org</td>
+      <td>Ecology</td>
+      <td>gdal</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal</td>
+      <td>3.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>1409</td>
+      <td>1498</td>
+      <td>39</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1409</td>
+      <td>1498</td>
+      <td>39</td>
+      <td>42</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gdcwebapp</td>
+      <td>data_source_gdcwebapp</td>
+      <td>GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://bioinf.iasi.cnr.it/gdcwebapp/</td>
+      <td>Data Source, Convert Formats</td>
+      <td>gdcwebapp</td>
+      <td>iuc</td>
+      <td>https://github.com/fabio-cumbo/GDCWebApp4Galaxy</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp</td>
+      <td>1.0.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gecko</td>
+      <td>gecko</td>
+      <td>Ungapped genome comparison</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/otorreno/gecko</td>
+      <td>Sequence Analysis</td>
+      <td>gecko</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko</td>
+      <td>1.2</td>
+      <td>gecko</td>
+      <td>1.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>723</td>
+      <td>723</td>
+      <td>235</td>
+      <td>235</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>786</td>
+      <td>786</td>
+      <td>95</td>
+      <td>95</td>
+      <td>1509</td>
+      <td>1509</td>
+      <td>330</td>
+      <td>330</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gemini</td>
+      <td>gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@</td>
+      <td>GEMINI: a flexible framework for exploring genome variation</td>
+      <td>gemini</td>
+      <td>gemini</td>
+      <td></td>
+      <td>GEMINI</td>
+      <td>GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.</td>
+      <td>Sequence analysis, Genetic variation analysis</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/arq5x/gemini</td>
+      <td>Sequence Analysis, Next Gen Mappers</td>
+      <td>gemini</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini</td>
+      <td>0.20.1</td>
+      <td>gemini</td>
+      <td>0.30.2</td>
+      <td>Sequence analysis, Genetic variation analysis</td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>4967</td>
+      <td>5475</td>
+      <td>1863</td>
+      <td>1992</td>
+      <td>992</td>
+      <td>1118</td>
+      <td>279</td>
+      <td>370</td>
+      <td>3756</td>
+      <td>3811</td>
+      <td>423</td>
+      <td>425</td>
+      <td>9715</td>
+      <td>10404</td>
+      <td>2565</td>
+      <td>2787</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genebed_maf_to_fasta</td>
+      <td>GeneBed_Maf_Fasta2</td>
+      <td>Stitch gene blocks given a set of coding exon intervals</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/</td>
+      <td>Genomic Interval Operations</td>
+      <td>genebed_maf_to_fasta</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta</td>
+      <td>1.0.1+galaxy0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>2</td>
+      <td>2</td>
+      <td>221</td>
+      <td>2905</td>
+      <td>23</td>
+      <td>279</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>225</td>
+      <td>2909</td>
+      <td>25</td>
+      <td>281</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genehunter_modscore</td>
+      <td>genehunter_modscore</td>
+      <td>Maximised LOD score pedigree analysis utility</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1</td>
+      <td>Variant Analysis</td>
+      <td>genehunter_modscore</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore</td>
+      <td>3.0.0</td>
+      <td>ghm</td>
+      <td>3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>geneiobio</td>
+      <td>gene_iobio_display_generation_iframe</td>
+      <td>Gene.iobio is an interactive tool for variant and trio analysis.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/iobio/gene.iobio</td>
+      <td>Sequence Analysis</td>
+      <td>geneiobio</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio</td>
+      <td>4.7.1+galaxy1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>101</td>
+      <td>101</td>
+      <td>25</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59</td>
+      <td>59</td>
+      <td>6</td>
+      <td>6</td>
+      <td>160</td>
+      <td>160</td>
+      <td>31</td>
+      <td>31</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genenotebook</td>
+      <td>genenotebook_build</td>
+      <td>Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://genenotebook.github.io</td>
+      <td>Web Services</td>
+      <td></td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook</td>
+      <td>0.4.16</td>
+      <td>genoboo</td>
+      <td>0.4.16</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>generate_pc_lda_matrix</td>
+      <td>generate_matrix_for_pca_and_lda1</td>
+      <td>Generate a Matrix for using PC and LDA</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>generate_pc_lda_matrix</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>115</td>
+      <td>124</td>
+      <td>29</td>
+      <td>30</td>
+      <td>518</td>
+      <td>1029</td>
+      <td>102</td>
+      <td>261</td>
+      <td>184</td>
+      <td>198</td>
+      <td>14</td>
+      <td>17</td>
+      <td>817</td>
+      <td>1351</td>
+      <td>145</td>
+      <td>308</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genetrack</td>
+      <td>genetrack</td>
+      <td>Contains a tool that separately identifies peaks on the forward "+” (W) and reverse “-” (C) strand.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>ChIP-seq</td>
+      <td>genetrack</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack</td>
+      <td></td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>445</td>
+      <td>660</td>
+      <td>104</td>
+      <td>197</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>445</td>
+      <td>660</td>
+      <td>104</td>
+      <td>197</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genform</td>
+      <td>genform</td>
+      <td>genform: generation of molecular formulas by high-resolution MS and MS/MS data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://sourceforge.net/projects/genform/</td>
+      <td>Metabolomics</td>
+      <td>genform</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform</td>
+      <td></td>
+      <td>genform</td>
+      <td>r8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>68</td>
+      <td>68</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>68</td>
+      <td>68</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genomad</td>
+      <td>genomad_end_to_end</td>
+      <td>Identify virus and plasmid genomes from nucleotide sequences</td>
+      <td>genomad</td>
+      <td>genomad</td>
+      <td></td>
+      <td>geNomad</td>
+      <td>geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.</td>
+      <td>Sequence annotation, Taxonomic classification</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/apcamargo/genomad/</td>
+      <td>Metagenomics</td>
+      <td>genomad</td>
+      <td>ufz</td>
+      <td>https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad</td>
+      <td>1.8.0</td>
+      <td>genomad</td>
+      <td>1.8.1</td>
+      <td>Sequence annotation, Taxonomic classification</td>
+      <td>Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genomescope</td>
+      <td>genomescope</td>
+      <td>Analyze unassembled short reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tbenavi1/genomescope2.0</td>
+      <td>Statistics</td>
+      <td>genomescope</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope</td>
+      <td>2.0.1</td>
+      <td>genomescope2</td>
+      <td>2.0.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3181</td>
+      <td>3181</td>
+      <td>665</td>
+      <td>665</td>
+      <td>2112</td>
+      <td>2112</td>
+      <td>435</td>
+      <td>435</td>
+      <td>1622</td>
+      <td>1622</td>
+      <td>148</td>
+      <td>148</td>
+      <td>6915</td>
+      <td>6915</td>
+      <td>1248</td>
+      <td>1248</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genomic_super_signature</td>
+      <td>genomic_super_signature</td>
+      <td>Interpretation of RNAseq experiments through robust, efficient comparison to public databases</td>
+      <td>genomicsupersignature</td>
+      <td>genomicsupersignature</td>
+      <td></td>
+      <td>GenomicSuperSignature</td>
+      <td>GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.</td>
+      <td>Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction</td>
+      <td>RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment</td>
+      <td>To update</td>
+      <td>https://github.com/shbrief/GenomicSuperSignature</td>
+      <td>Sequence Analysis, RNA, Transcriptomics</td>
+      <td>genomic_super_signature</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature</td>
+      <td>1.2.0</td>
+      <td>bioconductor-genomicsupersignature</td>
+      <td>1.10.0</td>
+      <td>Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction</td>
+      <td>RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>47</td>
+      <td>47</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>47</td>
+      <td>47</td>
+      <td>13</td>
+      <td>13</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>genrich</td>
+      <td>genrich</td>
+      <td>Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/jsh58/Genrich</td>
+      <td>ChIP-seq</td>
+      <td>genrich</td>
+      <td>iuc</td>
+      <td>https://github.com/jsh58/Genrich</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich</td>
+      <td>0.5+galaxy2</td>
+      <td>genrich</td>
+      <td>0.6.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3534</td>
+      <td>3577</td>
+      <td>402</td>
+      <td>405</td>
+      <td>2840</td>
+      <td>2840</td>
+      <td>419</td>
+      <td>419</td>
+      <td>571</td>
+      <td>571</td>
+      <td>31</td>
+      <td>31</td>
+      <td>6945</td>
+      <td>6988</td>
+      <td>852</td>
+      <td>855</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>getTn5ExtendedCoverage</td>
+      <td>getTn5ExtendedCoverage</td>
+      <td>Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Epigenetics</td>
+      <td>gettn5extendedcoverage</td>
+      <td>lldelisle</td>
+      <td></td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage</td>
+      <td>0.0.2</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>get_flanks</td>
+      <td>get_flanks1</td>
+      <td>Get flanks returns flanking region/s for every gene</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>get_flanks</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3768</td>
+      <td>325011</td>
+      <td>1462</td>
+      <td>2044</td>
+      <td>9350</td>
+      <td>242043</td>
+      <td>2201</td>
+      <td>6583</td>
+      <td>787</td>
+      <td>1070</td>
+      <td>119</td>
+      <td>146</td>
+      <td>13905</td>
+      <td>568124</td>
+      <td>3782</td>
+      <td>8773</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>get_hrun</td>
+      <td>get_hrun</td>
+      <td>Annotate indel variants with homopolymer context</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun</td>
+      <td>Variant Analysis</td>
+      <td>get_hrun</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun</td>
+      <td>0.5.9.2</td>
+      <td>pyfaidx</td>
+      <td>0.8.1.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>get_orfs_or_cdss</td>
+      <td>get_orfs_or_cdss</td>
+      <td>Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss</td>
+      <td>Sequence Analysis</td>
+      <td>get_orfs_or_cdss</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss</td>
+      <td>0.2.3</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>746</td>
+      <td>746</td>
+      <td>136</td>
+      <td>136</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1504</td>
+      <td>1504</td>
+      <td>244</td>
+      <td>244</td>
+      <td>2250</td>
+      <td>2250</td>
+      <td>380</td>
+      <td>380</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>get_pairs</td>
+      <td>get_pairs</td>
+      <td>Separate paired and unpaired reads from two fastq files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fastq Manipulation</td>
+      <td>get_pairs</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs</td>
+      <td>0.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>get_reference_fasta</td>
+      <td>get_fasta_reference</td>
+      <td>Obtain reference genome sequence.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Data Source, Fasta Manipulation</td>
+      <td>get_reference_fasta</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta</td>
+      <td>0.3.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>getindelrates_3way</td>
+      <td>indelRates_3way</td>
+      <td>Estimate Indel Rates for 3-way alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>getindelrates_3way</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>290</td>
+      <td>20</td>
+      <td>86</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>290</td>
+      <td>20</td>
+      <td>86</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>getindels_2way</td>
+      <td>getIndels_2way</td>
+      <td>Fetch Indels from pairwise alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>getindels_2way</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way</td>
+      <td>1.0.0</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>74</td>
+      <td>237</td>
+      <td>24</td>
+      <td>61</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>74</td>
+      <td>237</td>
+      <td>24</td>
+      <td>61</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>getmlst</td>
+      <td>getmlst</td>
+      <td>Download MLST datasets by species from pubmlst.org</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>getmlst</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst</td>
+      <td>0.1.4.1</td>
+      <td>srst2</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>getorganelle</td>
+      <td>get_annotated_regions_from_gb, get_organelle_from_reads</td>
+      <td>GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.</td>
+      <td>getorganelle</td>
+      <td>getorganelle</td>
+      <td></td>
+      <td>GetOrganelle</td>
+      <td>A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.</td>
+      <td>De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming</td>
+      <td>Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Kinggerm/GetOrganelle</td>
+      <td>Assembly</td>
+      <td>getorganelle</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle</td>
+      <td>1.7.7.1</td>
+      <td>getorganelle</td>
+      <td>1.7.7.1</td>
+      <td>De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming</td>
+      <td>Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1542</td>
+      <td>1542</td>
+      <td>159</td>
+      <td>159</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>587</td>
+      <td>587</td>
+      <td>64</td>
+      <td>64</td>
+      <td>2129</td>
+      <td>2129</td>
+      <td>223</td>
+      <td>223</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gfa_to_fa</td>
+      <td>gfa_to_fa</td>
+      <td>gfa_to_fa - Converting GFA format to Fasta format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://gfa-spec.github.io/GFA-spec/</td>
+      <td>Convert Formats</td>
+      <td>gfa_to_fa</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa</td>
+      <td>0.1.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9664</td>
+      <td>9775</td>
+      <td>763</td>
+      <td>765</td>
+      <td>5623</td>
+      <td>5623</td>
+      <td>493</td>
+      <td>493</td>
+      <td>1000</td>
+      <td>1000</td>
+      <td>135</td>
+      <td>135</td>
+      <td>16287</td>
+      <td>16398</td>
+      <td>1391</td>
+      <td>1393</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gfastats</td>
+      <td>gfastats</td>
+      <td>Tool for generating sequence statistics and simultaneous genome assembly file manipulation.</td>
+      <td>gfastats</td>
+      <td>gfastats</td>
+      <td></td>
+      <td>gfastats</td>
+      <td>gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.</td>
+      <td>Data handling</td>
+      <td>Computational biology</td>
+      <td>To update</td>
+      <td>https://github.com/vgl-hub/gfastats</td>
+      <td>Sequence Analysis</td>
+      <td>gfastats</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/gfastats</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/gfastats</td>
+      <td>1.3.6</td>
+      <td>gfastats</td>
+      <td>1.3.7</td>
+      <td>Data handling</td>
+      <td>Computational biology</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11748</td>
+      <td>11748</td>
+      <td>767</td>
+      <td>767</td>
+      <td>6560</td>
+      <td>6560</td>
+      <td>397</td>
+      <td>397</td>
+      <td>2556</td>
+      <td>2556</td>
+      <td>106</td>
+      <td>106</td>
+      <td>20864</td>
+      <td>20864</td>
+      <td>1270</td>
+      <td>1270</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gff3_rebase</td>
+      <td>gff3.rebase</td>
+      <td>Rebase a GFF against a parent GFF (e.g. an original genome)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase</td>
+      <td>Sequence Analysis</td>
+      <td>gff3_rebase</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase</td>
+      <td>1.2</td>
+      <td>bcbiogff</td>
+      <td>0.6.6</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>806</td>
+      <td>812</td>
+      <td>68</td>
+      <td>68</td>
+      <td>197</td>
+      <td>197</td>
+      <td>37</td>
+      <td>37</td>
+      <td>132</td>
+      <td>132</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1135</td>
+      <td>1141</td>
+      <td>117</td>
+      <td>117</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gffcompare</td>
+      <td>gffcompare</td>
+      <td>Galaxy wrappers for Geo Pertea's GffCompare package.</td>
+      <td>gffcompare</td>
+      <td>gffcompare</td>
+      <td></td>
+      <td>gffcompare</td>
+      <td>Program for comparing, annotating, merging and tracking transcripts in GFF files.</td>
+      <td>Sequence annotation</td>
+      <td>Nucleic acids, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/gpertea/gffcompare/</td>
+      <td>Transcriptomics</td>
+      <td>gffcompare</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare</td>
+      <td>0.12.6</td>
+      <td>gffcompare</td>
+      <td>0.12.6</td>
+      <td>Sequence annotation</td>
+      <td>Nucleic acids, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3560</td>
+      <td>3980</td>
+      <td>916</td>
+      <td>999</td>
+      <td>5281</td>
+      <td>8000</td>
+      <td>1713</td>
+      <td>2521</td>
+      <td>1468</td>
+      <td>1642</td>
+      <td>208</td>
+      <td>225</td>
+      <td>10309</td>
+      <td>13622</td>
+      <td>2837</td>
+      <td>3745</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gffcompare_to_bed</td>
+      <td>gffcompare_to_bed</td>
+      <td>Filter and convert a gffCompare GTF to BED</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/gpertea/gffcompare/</td>
+      <td>Convert Formats</td>
+      <td>gffcompare_to_bed</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed</td>
+      <td>0.2.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1375</td>
+      <td>2230</td>
+      <td>329</td>
+      <td>347</td>
+      <td>1071</td>
+      <td>1071</td>
+      <td>362</td>
+      <td>362</td>
+      <td>492</td>
+      <td>492</td>
+      <td>64</td>
+      <td>64</td>
+      <td>2938</td>
+      <td>3793</td>
+      <td>755</td>
+      <td>773</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gffread</td>
+      <td>gffread</td>
+      <td>gffread filters and/or converts GFF3/GTF2 records</td>
+      <td>gffread</td>
+      <td>gffread</td>
+      <td></td>
+      <td>gffread</td>
+      <td>program for filtering, converting and manipulating GFF files</td>
+      <td>Sequence annotation</td>
+      <td>Nucleic acids, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/</td>
+      <td>Sequence Analysis</td>
+      <td>gffread</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread</td>
+      <td>0.12.7</td>
+      <td>gffread</td>
+      <td>0.12.7</td>
+      <td>Sequence annotation</td>
+      <td>Nucleic acids, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>12828</td>
+      <td>13716</td>
+      <td>1740</td>
+      <td>1829</td>
+      <td>15217</td>
+      <td>23818</td>
+      <td>2588</td>
+      <td>3486</td>
+      <td>4423</td>
+      <td>4423</td>
+      <td>732</td>
+      <td>732</td>
+      <td>32468</td>
+      <td>41957</td>
+      <td>5060</td>
+      <td>6047</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ggplot2</td>
+      <td>ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin</td>
+      <td>ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.</td>
+      <td>ggplot2</td>
+      <td>ggplot2</td>
+      <td></td>
+      <td>ggplot2</td>
+      <td>Plotting system for R, based on the grammar of graphics.</td>
+      <td>Visualisation</td>
+      <td>Data visualisation</td>
+      <td>To update</td>
+      <td>https://github.com/tidyverse/ggplot2</td>
+      <td>Visualization</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2</td>
+      <td>3.4.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td>Visualisation</td>
+      <td>Data visualisation</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>24606</td>
+      <td>25662</td>
+      <td>3463</td>
+      <td>3630</td>
+      <td>26805</td>
+      <td>26808</td>
+      <td>5143</td>
+      <td>5144</td>
+      <td>8174</td>
+      <td>8237</td>
+      <td>1259</td>
+      <td>1279</td>
+      <td>59585</td>
+      <td>60707</td>
+      <td>9865</td>
+      <td>10053</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ggupset</td>
+      <td>emc-ggupset</td>
+      <td>Create Upset Plots with ggupset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/const-ae/ggupset</td>
+      <td>Graphics</td>
+      <td>ggupset</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset</td>
+      <td>1.0</td>
+      <td>r-ggupset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gi2taxonomy</td>
+      <td>Fetch Taxonomic Ranks</td>
+      <td>Fetch taxonomic representation</td>
+      <td>gi2taxonomy</td>
+      <td>gi2taxonomy</td>
+      <td></td>
+      <td>gi2taxonomy</td>
+      <td>The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).</td>
+      <td>Database search, ID mapping</td>
+      <td>Taxonomy</td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Metagenomics</td>
+      <td>gi2taxonomy</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy</td>
+      <td>1.1.1</td>
+      <td>taxonomy</td>
+      <td>0.10.0</td>
+      <td>Database search, ID mapping</td>
+      <td>Taxonomy</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>490</td>
+      <td>682</td>
+      <td>74</td>
+      <td>109</td>
+      <td>127</td>
+      <td>14058</td>
+      <td>20</td>
+      <td>1798</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>617</td>
+      <td>14740</td>
+      <td>94</td>
+      <td>1907</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>glimmer</td>
+      <td>glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based</td>
+      <td>Glimmer makes gene predictions.</td>
+      <td>gemini</td>
+      <td>gemini</td>
+      <td></td>
+      <td>GEMINI</td>
+      <td>GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.</td>
+      <td>Sequence analysis, Genetic variation analysis</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://ccb.jhu.edu/software/glimmer/</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer</td>
+      <td></td>
+      <td>glimmer</td>
+      <td>3.02</td>
+      <td>Sequence analysis, Genetic variation analysis</td>
+      <td>Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4343</td>
+      <td>4343</td>
+      <td>407</td>
+      <td>407</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4343</td>
+      <td>4343</td>
+      <td>407</td>
+      <td>407</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>glimmer_hmm</td>
+      <td></td>
+      <td>GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://ccb.jhu.edu/software/glimmerhmm/</td>
+      <td>Sequence Analysis</td>
+      <td>glimmer_hmm</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gmaj</td>
+      <td>gmaj_1</td>
+      <td>GMAJ Multiple Alignment Viewer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Visualization</td>
+      <td>gmaj</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj</td>
+      <td>2.0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>6</td>
+      <td>6</td>
+      <td>85</td>
+      <td>984</td>
+      <td>29</td>
+      <td>230</td>
+      <td>10</td>
+      <td>11</td>
+      <td>7</td>
+      <td>8</td>
+      <td>106</td>
+      <td>1006</td>
+      <td>42</td>
+      <td>244</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gnali</td>
+      <td>gnali</td>
+      <td>A tool to find nonessential, loss-of-function gene variants</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/gnali/</td>
+      <td>Variant Analysis</td>
+      <td>gnali</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/gnali/</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali</td>
+      <td>1.1.0</td>
+      <td>gnali</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>goenrichment</td>
+      <td>goenrichment, goslimmer</td>
+      <td>Performs GO Enrichment analysis.</td>
+      <td>goenrichment</td>
+      <td>goenrichment</td>
+      <td></td>
+      <td>GOEnrichment</td>
+      <td>GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.</td>
+      <td>Gene-set enrichment analysis</td>
+      <td>Transcriptomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/DanFaria/GOEnrichment</td>
+      <td>Genome annotation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment</td>
+      <td>2.0.1</td>
+      <td>goenrichment</td>
+      <td>2.0.1</td>
+      <td>Gene-set enrichment analysis</td>
+      <td>Transcriptomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>5800</td>
+      <td>6212</td>
+      <td>826</td>
+      <td>871</td>
+      <td>7756</td>
+      <td>7756</td>
+      <td>1048</td>
+      <td>1048</td>
+      <td>1149</td>
+      <td>1149</td>
+      <td>215</td>
+      <td>215</td>
+      <td>14705</td>
+      <td>15117</td>
+      <td>2089</td>
+      <td>2134</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>goseq</td>
+      <td>goseq</td>
+      <td>goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data</td>
+      <td>goseq</td>
+      <td>goseq</td>
+      <td></td>
+      <td>GOseq</td>
+      <td>Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.</td>
+      <td>Gene functional annotation</td>
+      <td>RNA-Seq</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/goseq.html</td>
+      <td>Statistics, RNA, Micro-array Analysis</td>
+      <td>goseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq</td>
+      <td>1.50.0</td>
+      <td>bioconductor-goseq</td>
+      <td>1.54.0</td>
+      <td>Gene functional annotation</td>
+      <td>RNA-Seq</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20207</td>
+      <td>21960</td>
+      <td>2807</td>
+      <td>3139</td>
+      <td>24488</td>
+      <td>26198</td>
+      <td>3066</td>
+      <td>3321</td>
+      <td>4155</td>
+      <td>4155</td>
+      <td>545</td>
+      <td>545</td>
+      <td>48850</td>
+      <td>52313</td>
+      <td>6418</td>
+      <td>7005</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gotohscan</td>
+      <td>rbc_gotohscan</td>
+      <td>Find subsequences in db</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>gotohscan</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan</td>
+      <td>1.3.0</td>
+      <td>gotohscan</td>
+      <td>1.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>34</td>
+      <td>72</td>
+      <td>5</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>72</td>
+      <td>5</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gprofiler</td>
+      <td>gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense</td>
+      <td>functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://biit.cs.ut.ee/gprofiler</td>
+      <td>Statistics, Web Services</td>
+      <td>gprofiler</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler</td>
+      <td>@TOOL_VERSION@+galaxy11</td>
+      <td>r-gprofiler2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>4001</td>
+      <td>4001</td>
+      <td>614</td>
+      <td>614</td>
+      <td>7882</td>
+      <td>7882</td>
+      <td>1238</td>
+      <td>1238</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11883</td>
+      <td>11883</td>
+      <td>1852</td>
+      <td>1852</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graph_converter</td>
+      <td>graph_converter</td>
+      <td>Convert between different graph formats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats</td>
+      <td>graph_converter</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graphclust</td>
+      <td>graphclust</td>
+      <td>GraphClust can be used for structural clustering of RNA sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.bioinf.uni-freiburg.de/Software/GraphClust/</td>
+      <td>RNA</td>
+      <td>graphclust</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/graphclust</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/graphclust</td>
+      <td>0.1</td>
+      <td>GraphClust</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graphembed</td>
+      <td>graphembed</td>
+      <td>Compute a 2D embedding of a data matrix given supervised class information</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/fabriziocosta/GraphEmbed</td>
+      <td>Statistics, Graphics</td>
+      <td>graphembed</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed</td>
+      <td>2.4</td>
+      <td>graph_embed</td>
+      <td>2.4</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>78</td>
+      <td>78</td>
+      <td>6</td>
+      <td>6</td>
+      <td>120</td>
+      <td>120</td>
+      <td>43</td>
+      <td>43</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>198</td>
+      <td>198</td>
+      <td>49</td>
+      <td>49</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graphicsmagick</td>
+      <td>graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage</td>
+      <td>Contains tools based on GraphicsMagick</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.graphicsmagick.org</td>
+      <td>Imaging</td>
+      <td>graphicsmagick</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick</td>
+      <td>1.3.45</td>
+      <td>graphicsmagick</td>
+      <td>1.3.26</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1725</td>
+      <td>2708</td>
+      <td>97</td>
+      <td>99</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1727</td>
+      <td>2710</td>
+      <td>99</td>
+      <td>101</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graphlan</td>
+      <td>graphlan, graphlan_annotate</td>
+      <td>GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees</td>
+      <td>graphlan</td>
+      <td>graphlan</td>
+      <td></td>
+      <td>GraPhlAn</td>
+      <td>GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.</td>
+      <td>Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification</td>
+      <td>Metagenomics, Phylogenetics, Phylogenomics, Cladistics</td>
+      <td>To update</td>
+      <td>https://github.com/biobakery/graphlan</td>
+      <td>Metagenomics, Graphics, Phylogenetics</td>
+      <td>graphlan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan</td>
+      <td></td>
+      <td>graphlan</td>
+      <td>1.1.3</td>
+      <td>Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification</td>
+      <td>Metagenomics, Phylogenetics, Phylogenomics, Cladistics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>9816</td>
+      <td>10927</td>
+      <td>1285</td>
+      <td>1350</td>
+      <td>1273</td>
+      <td>1273</td>
+      <td>368</td>
+      <td>368</td>
+      <td>1104</td>
+      <td>1104</td>
+      <td>242</td>
+      <td>242</td>
+      <td>12193</td>
+      <td>13304</td>
+      <td>1895</td>
+      <td>1960</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graphmap</td>
+      <td>graphmap_align, graphmap_overlap</td>
+      <td>Mapper for long, error-prone reads.</td>
+      <td>graphmap</td>
+      <td>graphmap</td>
+      <td></td>
+      <td>graphmap</td>
+      <td>Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1</td>
+      <td>Sequence trimming, EST assembly, Read mapping</td>
+      <td>Gene transcripts, RNA-Seq, RNA splicing</td>
+      <td>To update</td>
+      <td>https://github.com/isovic/graphmap/</td>
+      <td>Assembly</td>
+      <td>graphmap</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/graphmap</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/graphmap</td>
+      <td>0.5.2</td>
+      <td>graphmap</td>
+      <td>0.6.4</td>
+      <td>Sequence trimming, EST assembly, Read mapping</td>
+      <td>Gene transcripts, RNA-Seq, RNA splicing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>7012</td>
+      <td>7344</td>
+      <td>323</td>
+      <td>338</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7012</td>
+      <td>7344</td>
+      <td>323</td>
+      <td>338</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>graphprot</td>
+      <td>graphprot_predict_profile</td>
+      <td>GraphProt models binding preferences of RNA-binding proteins.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/dmaticzka/GraphProt</td>
+      <td>Sequence Analysis, RNA, CLIP-seq</td>
+      <td>graphprot</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot</td>
+      <td>1.1.7+galaxy2</td>
+      <td>graphprot</td>
+      <td>1.1.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>463</td>
+      <td>484</td>
+      <td>18</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>463</td>
+      <td>484</td>
+      <td>18</td>
+      <td>19</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gromacs</td>
+      <td>gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj</td>
+      <td>GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/gromacs</td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>gromacs</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs</td>
+      <td>2022</td>
+      <td>gromacs</td>
+      <td>2021.3</td>
+      <td></td>
+      <td></td>
+      <td>14</td>
+      <td>8</td>
+      <td>15</td>
+      <td>0</td>
+      <td>14</td>
+      <td>8</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>15</td>
+      <td>9</td>
+      <td>0</td>
+      <td>184067</td>
+      <td>184203</td>
+      <td>3441</td>
+      <td>3451</td>
+      <td>9382</td>
+      <td>9382</td>
+      <td>1438</td>
+      <td>1438</td>
+      <td>10325</td>
+      <td>10325</td>
+      <td>648</td>
+      <td>648</td>
+      <td>203774</td>
+      <td>203910</td>
+      <td>5527</td>
+      <td>5537</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_center_scale</td>
+      <td>center_scale</td>
+      <td>Center or scale (standardize) data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Statistics</td>
+      <td>gsc_center_scale</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale</td>
+      <td>4.3.1+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_filter_cells</td>
+      <td>filter_cells</td>
+      <td>Filter single cell RNAseq data on libray depth and number of detected genes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>gsc_filter_cells</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells</td>
+      <td>4.3.1+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_filter_genes</td>
+      <td>filter_genes</td>
+      <td>Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>gsc_filter_genes</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes</td>
+      <td>4.3.1+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_gene_expression_correlations</td>
+      <td>single_cell_gene_expression_correlations</td>
+      <td>Compute single-cell paire-wise gene expressions correlations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>gsc_gene_expression_correlations</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations</td>
+      <td>4.3.1+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_high_dimensions_visualisation</td>
+      <td>high_dimensions_visualisation</td>
+      <td>Generates PCA, t-SNE and HCPC visualisation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics, Visualization</td>
+      <td>gsc_high_dimensions_visualisation</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation</td>
+      <td>4.3+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_mannwhitney_de</td>
+      <td>mannwhitney_de</td>
+      <td>Perform a mann-whitney differential testing between two sets of gene expression data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>gsc_mannwhitney_de</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de</td>
+      <td>4.1.3+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_scran_normalize</td>
+      <td>scran_normalize</td>
+      <td>Normalize raw counts using scran</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>gsc_scran_normalize</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize</td>
+      <td>1.28.1+galaxy0</td>
+      <td>bioconductor-scran</td>
+      <td>1.30.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>89</td>
+      <td>89</td>
+      <td>24</td>
+      <td>24</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>10</td>
+      <td>10</td>
+      <td>2</td>
+      <td>2</td>
+      <td>102</td>
+      <td>102</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gsc_signature_score</td>
+      <td>signature_score</td>
+      <td>Compute signature scores from single cell RNAseq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Transcriptomics</td>
+      <td>gsc_signature_score</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score</td>
+      <td>2.3.9+galaxy0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gstf_preparation</td>
+      <td>gstf_preparation</td>
+      <td>GeneSeqToFamily preparation converts data for the workflow</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/</td>
+      <td>Convert Formats</td>
+      <td>gstf_preparation</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation</td>
+      <td>0.4.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>377</td>
+      <td>400</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>377</td>
+      <td>400</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gtdb_to_taxdump</td>
+      <td>gtdb_to_taxdump</td>
+      <td>Convert GTDB taxonomy to NCBI taxdump format</td>
+      <td>gtdb_to_taxdump</td>
+      <td>gtdb_to_taxdump</td>
+      <td></td>
+      <td>gtdb_to_taxdump</td>
+      <td>Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.</td>
+      <td>Data handling, Mapping, Generation</td>
+      <td>Computational biology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/nick-youngblut/gtdb_to_taxdump</td>
+      <td>Metagenomics</td>
+      <td>gtdb_to_taxdump</td>
+      <td>iuc</td>
+      <td>https://github.com/nick-youngblut/gtdb_to_taxdump</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump</td>
+      <td>0.1.9</td>
+      <td>gtdb_to_taxdump</td>
+      <td>0.1.9</td>
+      <td>Data handling, Mapping, Generation</td>
+      <td>Computational biology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gtdbtk</td>
+      <td>gtdbtk_classify_wf</td>
+      <td>GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes.</td>
+      <td>GTDB-Tk</td>
+      <td>GTDB-Tk</td>
+      <td></td>
+      <td>GTDB-Tk</td>
+      <td>a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).</td>
+      <td>Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval</td>
+      <td>Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Ecogenomics/GTDBTk</td>
+      <td>Metagenomics</td>
+      <td>gtdbtk</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk</td>
+      <td>2.4.0</td>
+      <td>gtdbtk</td>
+      <td>2.4.0</td>
+      <td>Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval</td>
+      <td>Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>476</td>
+      <td>476</td>
+      <td>87</td>
+      <td>87</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>588</td>
+      <td>588</td>
+      <td>74</td>
+      <td>74</td>
+      <td>1064</td>
+      <td>1064</td>
+      <td>161</td>
+      <td>161</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gtf-2-gene-list</td>
+      <td>_ensembl_gtf2gene_list</td>
+      <td>Utility to extract annotations from Ensembl GTF files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary</td>
+      <td>Sequence Analysis</td>
+      <td>gtf2gene_list</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list</td>
+      <td>1.52.0+galaxy0</td>
+      <td>atlas-gene-annotation-manipulation</td>
+      <td>1.1.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1982</td>
+      <td>1983</td>
+      <td>323</td>
+      <td>324</td>
+      <td>1040</td>
+      <td>1040</td>
+      <td>343</td>
+      <td>343</td>
+      <td>205</td>
+      <td>205</td>
+      <td>38</td>
+      <td>38</td>
+      <td>3227</td>
+      <td>3228</td>
+      <td>704</td>
+      <td>705</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gtfToBed12</td>
+      <td>gtftobed12</td>
+      <td>Convert GTF files to BED12 format</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README</td>
+      <td>Convert Formats</td>
+      <td>gtftobed12</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12</td>
+      <td>357</td>
+      <td>ucsc-gtftogenepred</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>8329</td>
+      <td>9363</td>
+      <td>3336</td>
+      <td>3828</td>
+      <td>8009</td>
+      <td>8009</td>
+      <td>3130</td>
+      <td>3130</td>
+      <td>1577</td>
+      <td>1577</td>
+      <td>344</td>
+      <td>344</td>
+      <td>17915</td>
+      <td>18949</td>
+      <td>6810</td>
+      <td>7302</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gubbins</td>
+      <td>gubbins</td>
+      <td>Gubbins - bacterial recombination detection</td>
+      <td>gubbins</td>
+      <td>gubbins</td>
+      <td></td>
+      <td>Gubbins</td>
+      <td>Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.</td>
+      <td>Genotyping, Phylogenetic inference, Ancestral reconstruction</td>
+      <td>Phylogeny, Genotype and phenotype, Whole genome sequencing</td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>gubbins</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins</td>
+      <td>3.2.1</td>
+      <td>gubbins</td>
+      <td>3.3.5</td>
+      <td>Genotyping, Phylogenetic inference, Ancestral reconstruction</td>
+      <td>Phylogeny, Genotype and phenotype, Whole genome sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3690</td>
+      <td>3811</td>
+      <td>326</td>
+      <td>336</td>
+      <td>3323</td>
+      <td>3323</td>
+      <td>235</td>
+      <td>235</td>
+      <td>1895</td>
+      <td>2429</td>
+      <td>234</td>
+      <td>258</td>
+      <td>8908</td>
+      <td>9563</td>
+      <td>795</td>
+      <td>829</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>guppy</td>
+      <td>guppy-basecaller</td>
+      <td>A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Nanopore</td>
+      <td>guppy_basecaller</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy</td>
+      <td>6.5.7+galaxy0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1</td>
+      <td>1</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gvcftools</td>
+      <td>gvcftools_extract_variants</td>
+      <td>gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/sequencing/gvcftools</td>
+      <td>Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools</td>
+      <td>0.1</td>
+      <td>gvcftools</td>
+      <td>0.17.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>gwastools</td>
+      <td>gwastools_manhattan_plot</td>
+      <td></td>
+      <td>gwastools</td>
+      <td>gwastools</td>
+      <td></td>
+      <td>GWASTools</td>
+      <td>Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.</td>
+      <td>Deposition, Analysis, Annotation</td>
+      <td>GWAS study</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/GWASTools.html</td>
+      <td>Visualization, Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td></td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools</td>
+      <td>0.1.0</td>
+      <td>bioconductor-gwastools</td>
+      <td>1.48.0</td>
+      <td>Deposition, Analysis, Annotation</td>
+      <td>GWAS study</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hamronization</td>
+      <td>hamronize_summarize, hamronize_tool</td>
+      <td>Convert AMR gene detection tool output to hAMRonization specification format.</td>
+      <td>hamronization</td>
+      <td>hamronization</td>
+      <td></td>
+      <td>hAMRonization</td>
+      <td>Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure</td>
+      <td>Data handling, Antimicrobial resistance prediction, Parsing</td>
+      <td>Public health and epidemiology, Microbiology, Bioinformatics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pha4ge/hAMRonization</td>
+      <td>Sequence Analysis</td>
+      <td>hamronization</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization</td>
+      <td>1.1.4</td>
+      <td>hamronization</td>
+      <td>1.1.4</td>
+      <td>Antimicrobial resistance prediction, Parsing</td>
+      <td>Public health and epidemiology, Microbiology, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7303</td>
+      <td>7303</td>
+      <td>222</td>
+      <td>222</td>
+      <td>20</td>
+      <td>20</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7323</td>
+      <td>7323</td>
+      <td>224</td>
+      <td>224</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hansel</td>
+      <td>bio_hansel</td>
+      <td>Heidelberg and Enteritidis SNP Elucidation</td>
+      <td>Biohansel</td>
+      <td>Biohansel</td>
+      <td></td>
+      <td>BioHansel</td>
+      <td>BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.</td>
+      <td>Genotyping, SNP detection, Genome assembly</td>
+      <td>Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/bio_hansel</td>
+      <td>Sequence Analysis</td>
+      <td>bio_hansel</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel</td>
+      <td>2.6.1</td>
+      <td>bio_hansel</td>
+      <td>2.6.1</td>
+      <td>Genotyping, SNP detection, Genome assembly</td>
+      <td>Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>349</td>
+      <td>359</td>
+      <td>32</td>
+      <td>33</td>
+      <td>364</td>
+      <td>364</td>
+      <td>53</td>
+      <td>53</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>713</td>
+      <td>723</td>
+      <td>85</td>
+      <td>86</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hapcut2</td>
+      <td>hapcut2</td>
+      <td>Robust and accurate haplotype assembly for diverse sequencing technologies</td>
+      <td>hapcut2</td>
+      <td>hapcut2</td>
+      <td></td>
+      <td>HapCUT2</td>
+      <td>HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md</td>
+      <td>Haplotype mapping, Variant classification</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/vibansal/HapCUT2</td>
+      <td>Assembly</td>
+      <td>hapcut2</td>
+      <td>galaxy-australia</td>
+      <td>https://github.com/galaxyproject/tools-iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2</td>
+      <td>1.3.4</td>
+      <td>hapcut2</td>
+      <td>1.3.4</td>
+      <td>Haplotype mapping, Variant classification</td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>103</td>
+      <td>103</td>
+      <td>4</td>
+      <td>4</td>
+      <td>103</td>
+      <td>103</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hapog</td>
+      <td>hapog</td>
+      <td>Hapo-G - Haplotype-Aware Polishing of Genomes</td>
+      <td>hapog</td>
+      <td>hapog</td>
+      <td></td>
+      <td>Hapo-G</td>
+      <td>Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.</td>
+      <td>Genome assembly, Optimisation and refinement</td>
+      <td>Sequence assembly, Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/institut-de-genomique/HAPO-G</td>
+      <td>Assembly</td>
+      <td>hapog</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog</td>
+      <td>1.3.8</td>
+      <td>hapog</td>
+      <td>1.3.8</td>
+      <td>Genome assembly, Optimisation and refinement</td>
+      <td>Sequence assembly, Genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>502</td>
+      <td>502</td>
+      <td>66</td>
+      <td>66</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>502</td>
+      <td>502</td>
+      <td>66</td>
+      <td>66</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>happy</td>
+      <td>som.py</td>
+      <td>A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.</td>
+      <td>hap.py</td>
+      <td>hap.py</td>
+      <td></td>
+      <td>hap.py</td>
+      <td>This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.</td>
+      <td>Variant calling, Sequence analysis, Genotyping</td>
+      <td>Genomics, DNA polymorphism</td>
+      <td>To update</td>
+      <td>https://github.com/Illumina/hap.py</td>
+      <td>Variant Analysis</td>
+      <td>happy</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy</td>
+      <td>0.3.14</td>
+      <td>hap.py</td>
+      <td>0.3.15</td>
+      <td>Variant calling, Sequence analysis, Genotyping</td>
+      <td>Genomics, DNA polymorphism</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hardklor</td>
+      <td>hardklor, kronik</td>
+      <td>Hardklör</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>hardklor</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor</td>
+      <td>2.30.1+galaxy1</td>
+      <td>hardklor</td>
+      <td>2.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>98</td>
+      <td>111</td>
+      <td>5</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>111</td>
+      <td>5</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hclust2</td>
+      <td>hclust2</td>
+      <td>Plots heatmaps</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/nsegata/hclust2/</td>
+      <td>Data Visualization</td>
+      <td>hclust2</td>
+      <td>rnateam</td>
+      <td>https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hclust2</td>
+      <td>0.99</td>
+      <td>hclust2</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hcluster_sg</td>
+      <td>hcluster_sg</td>
+      <td>Hierarchically clustering on a sparse graph</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/douglasgscofield/hcluster</td>
+      <td>Phylogenetics</td>
+      <td>hcluster_sg</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg</td>
+      <td>0.5.1.1</td>
+      <td>hcluster_sg</td>
+      <td>0.5.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>243</td>
+      <td>263</td>
+      <td>54</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>243</td>
+      <td>263</td>
+      <td>54</td>
+      <td>57</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hcluster_sg_parser</td>
+      <td>hcluster_sg_parser</td>
+      <td>Converts hcluster_sg 3-column output into lists of ids</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/</td>
+      <td>Phylogenetics</td>
+      <td>hcluster_sg_parser</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser</td>
+      <td>0.2.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>266</td>
+      <td>293</td>
+      <td>22</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>266</td>
+      <td>293</td>
+      <td>22</td>
+      <td>25</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>heatmap2</td>
+      <td>ggplot2_heatmap2</td>
+      <td>heatmap.2 function from the R gplots package</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/cran/gplots</td>
+      <td>Visualization</td>
+      <td>ggplot2_heatmap2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2</td>
+      <td>3.1.3.1</td>
+      <td>r-gplots</td>
+      <td>2.17.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>46700</td>
+      <td>50808</td>
+      <td>4645</td>
+      <td>5114</td>
+      <td>64214</td>
+      <td>70429</td>
+      <td>5799</td>
+      <td>6830</td>
+      <td>7783</td>
+      <td>7912</td>
+      <td>704</td>
+      <td>724</td>
+      <td>118697</td>
+      <td>129149</td>
+      <td>11148</td>
+      <td>12668</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>heinz</td>
+      <td>heinz_bum, heinz, heinz_scoring, heinz_visualization</td>
+      <td>An algorithm for identification of the optimal scoring subnetwork.</td>
+      <td>heinz</td>
+      <td>bionet, heinz</td>
+      <td></td>
+      <td>Heinz</td>
+      <td>Tool for single-species active module discovery.</td>
+      <td>Pathway or network analysis</td>
+      <td>Genetics, Gene expression, Molecular interactions, pathways and networks</td>
+      <td>To update</td>
+      <td>https://github.com/ls-cwi/heinz</td>
+      <td>Transcriptomics, Visualization, Statistics</td>
+      <td>heinz</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz</td>
+      <td>1.0</td>
+      <td>bioconductor-bionet</td>
+      <td>1.62.0</td>
+      <td>Pathway or network analysis</td>
+      <td>Genetics, Gene expression, Molecular interactions, pathways and networks</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>1281</td>
+      <td>1434</td>
+      <td>367</td>
+      <td>442</td>
+      <td>1559</td>
+      <td>1559</td>
+      <td>636</td>
+      <td>636</td>
+      <td>678</td>
+      <td>678</td>
+      <td>52</td>
+      <td>52</td>
+      <td>3518</td>
+      <td>3671</td>
+      <td>1055</td>
+      <td>1130</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>helixer</td>
+      <td>helixer</td>
+      <td>Gene calling with Deep Neural Networks</td>
+      <td>helixer</td>
+      <td>helixer</td>
+      <td></td>
+      <td>Helixer</td>
+      <td>Deep Learning to predict gene annotations</td>
+      <td>Gene prediction, Genome annotation</td>
+      <td>Sequence analysis, Gene transcripts</td>
+      <td>To update</td>
+      <td>https://github.com/weberlab-hhu/Helixer</td>
+      <td>Genome annotation</td>
+      <td>helixer</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/helixer</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/helixer</td>
+      <td>0.3.3</td>
+      <td></td>
+      <td></td>
+      <td>Gene prediction, Genome annotation</td>
+      <td>Sequence analysis, Gene transcripts</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>267</td>
+      <td>267</td>
+      <td>39</td>
+      <td>39</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>80</td>
+      <td>80</td>
+      <td>7</td>
+      <td>7</td>
+      <td>347</td>
+      <td>347</td>
+      <td>46</td>
+      <td>46</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hess</td>
+      <td>hess_astro_tool</td>
+      <td>Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Astronomy</td>
+      <td>hess_astro_tool</td>
+      <td>astroteam</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess</td>
+      <td>0.0.2+galaxy0</td>
+      <td>ipython</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hgv_fundo</td>
+      <td>hgv_funDo</td>
+      <td>FunDO human genes associated with disease terms</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>hgv_fundo</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>145</td>
+      <td>1794</td>
+      <td>33</td>
+      <td>397</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>145</td>
+      <td>1794</td>
+      <td>33</td>
+      <td>397</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hgv_hilbertvis</td>
+      <td>hgv_hilbertvis</td>
+      <td>HVIS visualization of genomic data with the Hilbert curve</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.ebi.ac.uk/huber-srv/hilbert/</td>
+      <td>Graphics, Visualization</td>
+      <td>hgv_hilbertvis</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis</td>
+      <td>1.0.0</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>265</td>
+      <td>16</td>
+      <td>60</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119</td>
+      <td>265</td>
+      <td>16</td>
+      <td>60</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hgvsparser</td>
+      <td>hgvsparser</td>
+      <td>Parsing and building variant descriptor strings compliant with the HGVS standard</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/VariantEffect/hgvsParseR/tree/master</td>
+      <td>Variant Analysis</td>
+      <td>hgvsparser</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser</td>
+      <td>0.1.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6346</td>
+      <td>6346</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6346</td>
+      <td>6346</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hicexplorer</td>
+      <td>hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations</td>
+      <td>HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/deeptools/HiCExplorer</td>
+      <td>Sequence Analysis, Visualization</td>
+      <td>hicexplorer</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer</td>
+      <td>3.7.5</td>
+      <td>hicexplorer</td>
+      <td>3.7.5</td>
+      <td></td>
+      <td></td>
+      <td>38</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>38</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>33</td>
+      <td>36</td>
+      <td>33</td>
+      <td>0</td>
+      <td>44449</td>
+      <td>68602</td>
+      <td>3236</td>
+      <td>4177</td>
+      <td>46</td>
+      <td>46</td>
+      <td>21</td>
+      <td>21</td>
+      <td>1328</td>
+      <td>1328</td>
+      <td>67</td>
+      <td>67</td>
+      <td>45823</td>
+      <td>69976</td>
+      <td>3324</td>
+      <td>4265</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hicstuff</td>
+      <td>hicstuff_pipeline</td>
+      <td>A toolkit to generate and manipulate Hi-C matrices</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/koszullab/hicstuff</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff</td>
+      <td>3.1.5</td>
+      <td>hicstuff</td>
+      <td>3.2.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hictk</td>
+      <td>hictk</td>
+      <td>Convert cooler to juicebox_hic</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/paulsengroup/hictk</td>
+      <td>Convert Formats, Epigenetics</td>
+      <td>hictk</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hictk</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hictk</td>
+      <td>1.0.0</td>
+      <td>hictk</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hicup</td>
+      <td>hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater</td>
+      <td>The HiCUP-Pipeline from the Bioinformatics Babraham Institute.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html</td>
+      <td>Epigenetics</td>
+      <td>hicup</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hicup</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hicup</td>
+      <td>0.9.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>7</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>6</td>
+      <td>0</td>
+      <td>901</td>
+      <td>1020</td>
+      <td>160</td>
+      <td>184</td>
+      <td>440</td>
+      <td>440</td>
+      <td>111</td>
+      <td>111</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1341</td>
+      <td>1460</td>
+      <td>271</td>
+      <td>295</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hifiasm</td>
+      <td>hifiasm</td>
+      <td>A fast haplotype-resolved de novo assembler</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/chhylp123/hifiasm</td>
+      <td>Assembly</td>
+      <td>hifiasm</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm</td>
+      <td>0.19.9</td>
+      <td>hifiasm</td>
+      <td>0.19.9</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1819</td>
+      <td>1819</td>
+      <td>539</td>
+      <td>539</td>
+      <td>1334</td>
+      <td>1334</td>
+      <td>389</td>
+      <td>389</td>
+      <td>2472</td>
+      <td>2472</td>
+      <td>137</td>
+      <td>137</td>
+      <td>5625</td>
+      <td>5625</td>
+      <td>1065</td>
+      <td>1065</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hifiasm_meta</td>
+      <td>hifiasm_meta</td>
+      <td>A hifiasm fork for metagenome assembly using Hifi reads.</td>
+      <td>hifiasm-meta</td>
+      <td>hifiasm-meta</td>
+      <td></td>
+      <td>Hifiasm-meta</td>
+      <td>Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly, Metagenomics</td>
+      <td>To update</td>
+      <td>https://github.com/xfengnefx/hifiasm-meta</td>
+      <td>Metagenomics</td>
+      <td>hifiasm_meta</td>
+      <td>galaxy-australia</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta</td>
+      <td>0.3.1</td>
+      <td>hifiasm_meta</td>
+      <td>hamtv0.3.1</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly, Metagenomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>156</td>
+      <td>156</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>220</td>
+      <td>220</td>
+      <td>11</td>
+      <td>11</td>
+      <td>376</td>
+      <td>376</td>
+      <td>31</td>
+      <td>31</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>high_dim_heatmap</td>
+      <td>high_dim_heatmap</td>
+      <td>gplot heatmap.2 function adapted for plotting large heatmaps</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/cran/gplots</td>
+      <td>Visualization</td>
+      <td>high_dim_heatmap</td>
+      <td>artbio</td>
+      <td>https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap</td>
+      <td>3.1.3+galaxy0</td>
+      <td>r-gplots</td>
+      <td>2.17.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hirondelle_crim_ogc_api_processes</td>
+      <td>hirondelle_crim</td>
+      <td>This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AquaINFRA/galaxy</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes</td>
+      <td>0.2.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hisat</td>
+      <td>hisat</td>
+      <td>HISAT is a fast and sensitive spliced alignment program.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://ccb.jhu.edu/software/hisat/index.shtml</td>
+      <td>Assembly</td>
+      <td>hisat</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat</td>
+      <td>1.0.3</td>
+      <td>hisat</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>228</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>228</td>
+      <td>0</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hisat2</td>
+      <td>hisat2</td>
+      <td>HISAT2 is a fast and sensitive spliced alignment program.</td>
+      <td>hisat2</td>
+      <td>hisat2</td>
+      <td></td>
+      <td>HISAT2</td>
+      <td>Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).</td>
+      <td>Sequence alignment</td>
+      <td>RNA-seq</td>
+      <td>Up-to-date</td>
+      <td>http://ccb.jhu.edu/software/hisat2/</td>
+      <td>Assembly</td>
+      <td>hisat2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2</td>
+      <td>2.2.1</td>
+      <td>hisat2</td>
+      <td>2.2.1</td>
+      <td>Sequence alignment</td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>337151</td>
+      <td>353499</td>
+      <td>10046</td>
+      <td>10719</td>
+      <td>699868</td>
+      <td>896164</td>
+      <td>26656</td>
+      <td>34018</td>
+      <td>87016</td>
+      <td>94859</td>
+      <td>5302</td>
+      <td>5695</td>
+      <td>1124035</td>
+      <td>1344522</td>
+      <td>42004</td>
+      <td>50432</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>histogram</td>
+      <td>histogram_rpy</td>
+      <td>Histogram of a numeric column</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Statistics</td>
+      <td>histogram</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram</td>
+      <td>1.0.4</td>
+      <td>rpy2</td>
+      <td>2.7.8</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3748</td>
+      <td>4661</td>
+      <td>866</td>
+      <td>1002</td>
+      <td>5993</td>
+      <td>48272</td>
+      <td>1507</td>
+      <td>7101</td>
+      <td>549</td>
+      <td>746</td>
+      <td>152</td>
+      <td>253</td>
+      <td>10290</td>
+      <td>53679</td>
+      <td>2525</td>
+      <td>8356</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hivclustering</td>
+      <td>hivclustering</td>
+      <td>Infers transmission networks from pairwise distances inferred by tn93</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pypi.org/project/hivclustering/</td>
+      <td>Next Gen Mappers</td>
+      <td>hivclustering</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering</td>
+      <td>1.3.1</td>
+      <td>python-hivclustering</td>
+      <td>1.8.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hivtrace</td>
+      <td>hivtrace</td>
+      <td>An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>hivtrace</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace</td>
+      <td>1.0.1</td>
+      <td>hivtrace</td>
+      <td>1.5.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hmmer3</td>
+      <td>hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer</td>
+      <td>HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).</td>
+      <td>hmmer3</td>
+      <td>hmmer3</td>
+      <td></td>
+      <td>HMMER3</td>
+      <td>This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.</td>
+      <td>Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search</td>
+      <td>Sequence analysis, Sequence sites, features and motifs, Gene and protein families</td>
+      <td>Up-to-date</td>
+      <td>http://hmmer.org/</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3</td>
+      <td>3.4</td>
+      <td>hmmer</td>
+      <td>3.4</td>
+      <td>Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search</td>
+      <td>Sequence analysis, Sequence sites, features and motifs, Gene and protein families</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>35919</td>
+      <td>36952</td>
+      <td>1283</td>
+      <td>1321</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3023</td>
+      <td>3023</td>
+      <td>180</td>
+      <td>180</td>
+      <td>38942</td>
+      <td>39975</td>
+      <td>1463</td>
+      <td>1501</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>homer</td>
+      <td></td>
+      <td>Software for motif discovery and next generation sequencing analysis.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://homer.salk.edu/homer/</td>
+      <td>Sequence Analysis</td>
+      <td>homer</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/homer</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/homer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>homer</td>
+      <td>homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide</td>
+      <td>HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.</td>
+      <td>homer</td>
+      <td>homer</td>
+      <td></td>
+      <td>homer</td>
+      <td>HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.</td>
+      <td>Sequence motif discovery</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://homer.ucsd.edu/homer/index.html</td>
+      <td>Sequence Analysis</td>
+      <td>data_manager_homer_preparse</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer</td>
+      <td>4.11</td>
+      <td>homer</td>
+      <td>4.11</td>
+      <td>Sequence motif discovery</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8531</td>
+      <td>8531</td>
+      <td>633</td>
+      <td>633</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8531</td>
+      <td>8531</td>
+      <td>633</td>
+      <td>633</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>htseq-clip</td>
+      <td>htseq_clip</td>
+      <td>htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/EMBL-Hentze-group/htseq-clip</td>
+      <td>Sequence Analysis, RNA, CLIP-seq</td>
+      <td>htseq_clip</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip</td>
+      <td>0.1.0+galaxy0</td>
+      <td>htseq-clip</td>
+      <td>2.19.0b0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>98</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>98</td>
+      <td>19</td>
+      <td>19</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>htseq_count</td>
+      <td>htseq_count</td>
+      <td>Count aligned reads (SAM/BAM) that overlap genomic features (GFF)</td>
+      <td>htseq</td>
+      <td>htseq</td>
+      <td></td>
+      <td>HTSeq</td>
+      <td>Python framework to process and analyse high-throughput sequencing (HTS) data</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://readthedocs.org/projects/htseq/</td>
+      <td>Genomic Interval Operations, SAM, Sequence Analysis, RNA</td>
+      <td>htseq_count</td>
+      <td>lparsons</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count</td>
+      <td>2.0.5</td>
+      <td>htseq</td>
+      <td>2.0.5</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>144907</td>
+      <td>168824</td>
+      <td>3703</td>
+      <td>4366</td>
+      <td>213407</td>
+      <td>346792</td>
+      <td>10798</td>
+      <td>16485</td>
+      <td>27209</td>
+      <td>33124</td>
+      <td>2613</td>
+      <td>2854</td>
+      <td>385523</td>
+      <td>548740</td>
+      <td>17114</td>
+      <td>23705</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>humann</td>
+      <td>humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways</td>
+      <td>HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution</td>
+      <td>humann</td>
+      <td>humann</td>
+      <td></td>
+      <td>humann</td>
+      <td>HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”</td>
+      <td>Species frequency estimation, Taxonomic classification, Phylogenetic analysis</td>
+      <td>Metagenomics, Phylogenomics</td>
+      <td>Up-to-date</td>
+      <td>http://huttenhower.sph.harvard.edu/humann</td>
+      <td>Metagenomics</td>
+      <td>humann</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann</td>
+      <td>3.9</td>
+      <td>humann</td>
+      <td>3.9</td>
+      <td>Species frequency estimation, Taxonomic classification, Phylogenetic analysis</td>
+      <td>Metagenomics, Phylogenomics</td>
+      <td>6</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>6</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>26659</td>
+      <td>26659</td>
+      <td>2067</td>
+      <td>2067</td>
+      <td>865</td>
+      <td>865</td>
+      <td>174</td>
+      <td>174</td>
+      <td>3238</td>
+      <td>3238</td>
+      <td>351</td>
+      <td>351</td>
+      <td>30762</td>
+      <td>30762</td>
+      <td>2592</td>
+      <td>2592</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hybpiper</td>
+      <td>hybpiper</td>
+      <td>Analyse targeted sequence capture data</td>
+      <td>HybPiper</td>
+      <td>HybPiper</td>
+      <td></td>
+      <td>HybPiper</td>
+      <td>Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.</td>
+      <td>Sequence trimming, Sequence assembly, Read mapping</td>
+      <td>Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics</td>
+      <td>To update</td>
+      <td>https://github.com/mossmatters/HybPiper</td>
+      <td>Sequence Analysis, Phylogenetics</td>
+      <td>hybpiper</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper</td>
+      <td>2.1.6</td>
+      <td>hybpiper</td>
+      <td>2.3.0</td>
+      <td>Sequence trimming, Sequence assembly, Read mapping</td>
+      <td>Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1571</td>
+      <td>1571</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>144</td>
+      <td>144</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1715</td>
+      <td>1715</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hyperstack_to_bleach_corrected_movie</td>
+      <td>hyperstack_to_bleach_corrected_movie</td>
+      <td>Generate blach corrected movie from hyperstack</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>hyperstack_to_bleach_corrected_movie</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie</td>
+      <td>20230328</td>
+      <td>Fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hyphy</td>
+      <td>hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary</td>
+      <td>Hypothesis Testing using Phylogenies</td>
+      <td>HyPhy</td>
+      <td>HyPhy</td>
+      <td></td>
+      <td>HyPhy</td>
+      <td>Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.</td>
+      <td>Statistical calculation</td>
+      <td>Phylogeny, Small molecules, Molecular interactions, pathways and networks</td>
+      <td>To update</td>
+      <td>http://www.hyphy.org</td>
+      <td>Phylogenetics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy</td>
+      <td>2.5.47</td>
+      <td>hyphy</td>
+      <td>2.5.62</td>
+      <td>Statistical calculation</td>
+      <td>Phylogeny, Small molecules, Molecular interactions, pathways and networks</td>
+      <td>17</td>
+      <td>2</td>
+      <td>17</td>
+      <td>0</td>
+      <td>17</td>
+      <td>2</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>17</td>
+      <td>12</td>
+      <td>0</td>
+      <td>11429</td>
+      <td>11429</td>
+      <td>428</td>
+      <td>428</td>
+      <td>7751</td>
+      <td>7751</td>
+      <td>676</td>
+      <td>676</td>
+      <td>715</td>
+      <td>715</td>
+      <td>58</td>
+      <td>58</td>
+      <td>19895</td>
+      <td>19895</td>
+      <td>1162</td>
+      <td>1162</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>hypo</td>
+      <td>hypo</td>
+      <td>Super Fast &amp; Accurate Polisher for Long Read Genome Assemblies</td>
+      <td>HyPo</td>
+      <td>HyPo</td>
+      <td></td>
+      <td>HyPo</td>
+      <td>HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.</td>
+      <td>Optimisation and refinement, Genome assembly</td>
+      <td>Sequence assembly, Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/kensung-lab/hypo</td>
+      <td>Assembly</td>
+      <td>hypo</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo</td>
+      <td>1.0.3</td>
+      <td>hypo</td>
+      <td>1.0.3</td>
+      <td>Optimisation and refinement, Genome assembly</td>
+      <td>Sequence assembly, Genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>473</td>
+      <td>93</td>
+      <td>93</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>473</td>
+      <td>93</td>
+      <td>93</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>icescreen</td>
+      <td>icescreen</td>
+      <td>ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.</td>
+      <td>icescreen</td>
+      <td>icescreen</td>
+      <td></td>
+      <td>ICEscreen</td>
+      <td>A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.</td>
+      <td>Database search, Protein feature detection</td>
+      <td>Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation</td>
+      <td>To update</td>
+      <td>https://icescreen.migale.inrae.fr/</td>
+      <td>Genome annotation</td>
+      <td>icescreen</td>
+      <td>iuc</td>
+      <td>https://forgemia.inra.fr/ices_imes_analysis/icescreen</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen</td>
+      <td>1.3.1</td>
+      <td>icescreen</td>
+      <td>1.3.2</td>
+      <td>Database search, Protein feature detection</td>
+      <td>Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>idba_ud</td>
+      <td>idba_hybrid, idba_tran, idba_ud</td>
+      <td>Wrappers for the idba assembler variants.</td>
+      <td>idba</td>
+      <td>idba</td>
+      <td></td>
+      <td>IDBA</td>
+      <td>A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly</td>
+      <td>To update</td>
+      <td>https://i.cs.hku.hk/~alse/hkubrg/projects/index.html</td>
+      <td>Assembly</td>
+      <td>idba</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud</td>
+      <td></td>
+      <td>idba</td>
+      <td>1.1.3</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1200</td>
+      <td>1220</td>
+      <td>187</td>
+      <td>195</td>
+      <td>1588</td>
+      <td>1588</td>
+      <td>267</td>
+      <td>267</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2788</td>
+      <td>2808</td>
+      <td>454</td>
+      <td>462</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>idconvert</td>
+      <td>idconvert</td>
+      <td>Convert mass spectrometry identification files on linux or MacOSX</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>idconvert</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert</td>
+      <td></td>
+      <td>proteowizard</td>
+      <td>3_0_9992</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>241</td>
+      <td>276</td>
+      <td>24</td>
+      <td>33</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>241</td>
+      <td>276</td>
+      <td>24</td>
+      <td>33</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>idr</td>
+      <td>idr</td>
+      <td>Galaxy wrappers for the IDR package from Nathan Boleu</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/nboley/idr</td>
+      <td>Sequence Analysis</td>
+      <td>idr</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr</td>
+      <td>2.0.3</td>
+      <td>idr</td>
+      <td>2.0.4.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2953</td>
+      <td>3027</td>
+      <td>109</td>
+      <td>114</td>
+      <td>1710</td>
+      <td>1710</td>
+      <td>199</td>
+      <td>199</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4663</td>
+      <td>4737</td>
+      <td>308</td>
+      <td>313</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>idr_download</td>
+      <td>idr_download_by_ids</td>
+      <td>Image Data Resource downloading tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://idr.openmicroscopy.org</td>
+      <td>Data Source</td>
+      <td>idr_download_by_ids</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download</td>
+      <td>0.45</td>
+      <td>omero-py</td>
+      <td>5.11.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>404</td>
+      <td>404</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>24</td>
+      <td>1</td>
+      <td>1</td>
+      <td>428</td>
+      <td>428</td>
+      <td>38</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>iedb_api</td>
+      <td>iedb_api</td>
+      <td>Get epitope binding predictions from IEDB-API</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://tools.immuneepitope.org/main/tools-api/</td>
+      <td>Data Source, Sequence Analysis</td>
+      <td>iedb_api</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api</td>
+      <td>2.15.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1539</td>
+      <td>1539</td>
+      <td>35</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1539</td>
+      <td>1539</td>
+      <td>35</td>
+      <td>35</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>illumina_methylation_analyser</td>
+      <td>illumina_methylation_analyser</td>
+      <td>Methylation analyzer for Illumina 450k DNA emthylation microarrays</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser</td>
+      <td>Sequence Analysis</td>
+      <td>illumina_methylation_analyser</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser</td>
+      <td>0.1</td>
+      <td>Rscript</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>image_info</td>
+      <td>ip_imageinfo</td>
+      <td>Extracts image metadata</td>
+      <td></td>
+      <td></td>
+      <td>python-bioformats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>image_info</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info</td>
+      <td>5.7.1</td>
+      <td>bftools</td>
+      <td>6.7.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>273</td>
+      <td>659</td>
+      <td>101</td>
+      <td>102</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>153</td>
+      <td>153</td>
+      <td>15</td>
+      <td>15</td>
+      <td>426</td>
+      <td>812</td>
+      <td>116</td>
+      <td>117</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>image_math</td>
+      <td>image_math</td>
+      <td>Process images using arithmetic expressions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>image_math</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math</td>
+      <td>1.26.4</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>image_registration_affine</td>
+      <td>ip_image_registration</td>
+      <td>Intensity-based Image Registration</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>image_registration_affine</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine</td>
+      <td>0.0.3-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>imagecoordinates_flipaxis</td>
+      <td>imagecoordinates_flipaxis</td>
+      <td>Flip coordinate axes</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>imagecoordinates_flipaxis</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis</td>
+      <td>0.1-2</td>
+      <td>pandas</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>21409</td>
+      <td>21849</td>
+      <td>10</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21409</td>
+      <td>21849</td>
+      <td>10</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>imagej2</td>
+      <td>imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary</td>
+      <td>ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.</td>
+      <td>imagej</td>
+      <td>imagej</td>
+      <td>imagej2</td>
+      <td>ImageJ2</td>
+      <td>It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.</td>
+      <td>Image analysis, Image annotation, Visualisation</td>
+      <td>Imaging</td>
+      <td>To update</td>
+      <td>http://fiji.sc</td>
+      <td>Imaging</td>
+      <td>imagej2</td>
+      <td>imgteam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>Image analysis, Image annotation, Visualisation</td>
+      <td>Imaging</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>0</td>
+      <td>1731</td>
+      <td>1731</td>
+      <td>109</td>
+      <td>109</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1731</td>
+      <td>1731</td>
+      <td>109</td>
+      <td>109</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>improviser</td>
+      <td>proteomics_improviser</td>
+      <td>Visualisation of PepXML files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.improviser.uni-freiburg.de/</td>
+      <td>Proteomics</td>
+      <td>proteomics_improviser</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser</td>
+      <td>1.1.0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>incucyte_stack_and_upload_omero</td>
+      <td>incucyte_stack_and_upload_omero</td>
+      <td>Combine images to stack and upload to the omero server</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>incucyte_stack_and_upload_omero</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero</td>
+      <td>20231221</td>
+      <td>Fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>indels_3way</td>
+      <td>indels_3way</td>
+      <td>Fetch Indels from 3-way alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>indels_3way</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way</td>
+      <td>1.0.3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>18</td>
+      <td>22</td>
+      <td>1</td>
+      <td>1</td>
+      <td>44</td>
+      <td>292</td>
+      <td>3</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>62</td>
+      <td>314</td>
+      <td>4</td>
+      <td>22</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>infercnv</td>
+      <td>infercnv</td>
+      <td>Infer Copy Number Variation from Single-Cell RNA-Seq Data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/broadinstitute/infercnv</td>
+      <td>Transcriptomics, Variant Analysis</td>
+      <td>infercnv</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv</td>
+      <td>1.20.0</td>
+      <td>bioconductor-infercnv</td>
+      <td>1.20.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>infernal</td>
+      <td>infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat</td>
+      <td>Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.</td>
+      <td>infernal</td>
+      <td>infernal</td>
+      <td></td>
+      <td>Infernal</td>
+      <td>Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.</td>
+      <td>Nucleic acid feature detection</td>
+      <td>Sequence sites, features and motifs, Structural genomics</td>
+      <td>To update</td>
+      <td>http://infernal.janelia.org/</td>
+      <td>RNA</td>
+      <td>infernal</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/infernal</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal</td>
+      <td>1.1.4</td>
+      <td>infernal</td>
+      <td>1.1.5</td>
+      <td>Nucleic acid feature detection</td>
+      <td>Sequence sites, features and motifs, Structural genomics</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>59700</td>
+      <td>112582</td>
+      <td>223</td>
+      <td>282</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1157</td>
+      <td>1221</td>
+      <td>34</td>
+      <td>35</td>
+      <td>60857</td>
+      <td>113803</td>
+      <td>257</td>
+      <td>317</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>influx_data_manager</td>
+      <td>influx_data_manager</td>
+      <td>Handling influx_si data inputs in Galaxy workflows</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/</td>
+      <td>Metabolomics</td>
+      <td>influx_si_data_manager</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager</td>
+      <td>1.0.2</td>
+      <td>influx-si-data-manager</td>
+      <td>1.0.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>influx_si</td>
+      <td>influx_si</td>
+      <td>metabolic flux estimation based on [in]stationary labeling</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/sgsokol/influx</td>
+      <td>Metabolomics</td>
+      <td>influx_si</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si</td>
+      <td>7.0.1</td>
+      <td>influx_si</td>
+      <td>7.0.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>inforna</td>
+      <td></td>
+      <td>INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp</td>
+      <td>RNA</td>
+      <td>inforna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>instagraal</td>
+      <td>instagraal</td>
+      <td>Large genome reassembly based on Hi-C data</td>
+      <td>instagraal</td>
+      <td>instagraal</td>
+      <td></td>
+      <td>instaGRAAL</td>
+      <td>Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)</td>
+      <td>Genome assembly, Mapping assembly, Genetic mapping, Scaffolding</td>
+      <td>Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites</td>
+      <td>To update</td>
+      <td>https://github.com/koszullab/instaGRAAL</td>
+      <td>Assembly</td>
+      <td>instagraal</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/instagraal</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/instagraal</td>
+      <td>0.1.6</td>
+      <td></td>
+      <td></td>
+      <td>Genome assembly, Mapping assembly, Genetic mapping, Scaffolding</td>
+      <td>Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>157</td>
+      <td>157</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>157</td>
+      <td>157</td>
+      <td>14</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>instrain</td>
+      <td>instrain_compare, instrain_profile</td>
+      <td>InStrain is a tool for analysis of co-occurring genome populations from metagenomes</td>
+      <td>instrain</td>
+      <td>instrain</td>
+      <td></td>
+      <td>InStrain</td>
+      <td>InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification</td>
+      <td>SNP detection, Genome comparison</td>
+      <td>Mapping, Metagenomics</td>
+      <td>To update</td>
+      <td>https://instrain.readthedocs.io/en/latest/#</td>
+      <td>Metagenomics</td>
+      <td>instrain</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain</td>
+      <td>1.5.3</td>
+      <td>instrain</td>
+      <td>1.9.0</td>
+      <td>SNP detection, Genome comparison</td>
+      <td>Mapping, Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>102</td>
+      <td>102</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>102</td>
+      <td>102</td>
+      <td>16</td>
+      <td>16</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>intarna</td>
+      <td>intarna</td>
+      <td>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BackofenLab/IntaRNA</td>
+      <td>RNA</td>
+      <td>intarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna</td>
+      <td>3.4.1</td>
+      <td>intarna</td>
+      <td>3.4.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3071</td>
+      <td>7652</td>
+      <td>41</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3071</td>
+      <td>7652</td>
+      <td>41</td>
+      <td>47</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>integron_finder</td>
+      <td>integron_finder</td>
+      <td>"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"</td>
+      <td>integron_finder</td>
+      <td>integron_finder</td>
+      <td></td>
+      <td>Integron Finder</td>
+      <td>A tool to detect Integron in DNA sequences.</td>
+      <td>Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation</td>
+      <td>Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/gem-pasteur/Integron_Finder</td>
+      <td>Sequence Analysis</td>
+      <td>integronfinder</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder</td>
+      <td>2.0.5</td>
+      <td>integron_finder</td>
+      <td>2.0.5</td>
+      <td>Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation</td>
+      <td>Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55149</td>
+      <td>55149</td>
+      <td>161</td>
+      <td>161</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6085</td>
+      <td>6085</td>
+      <td>73</td>
+      <td>73</td>
+      <td>61234</td>
+      <td>61234</td>
+      <td>234</td>
+      <td>234</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>intermine_galaxy_exchange</td>
+      <td>galaxy_intermine_exchange</td>
+      <td>InterMine Exporter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/intermine</td>
+      <td>Convert Formats</td>
+      <td>intermine_galaxy_exchange</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange</td>
+      <td>0.0.1</td>
+      <td>coreutils</td>
+      <td>8.25</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>37</td>
+      <td>46</td>
+      <td>6</td>
+      <td>12</td>
+      <td>72</td>
+      <td>87</td>
+      <td>13</td>
+      <td>15</td>
+      <td>108</td>
+      <td>108</td>
+      <td>1</td>
+      <td>1</td>
+      <td>217</td>
+      <td>241</td>
+      <td>20</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>interpolation</td>
+      <td>interpolation_run_idw_interpolation</td>
+      <td>Run IDW interpolation based on a .csv and .geojson file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AquaINFRA/galaxy</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation</td>
+      <td>1.0</td>
+      <td>r-getopt</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>interproscan</td>
+      <td>interproscan</td>
+      <td>Interproscan queries the interpro database and provides annotations.</td>
+      <td>interproscan_ebi</td>
+      <td>interproscan_ebi</td>
+      <td></td>
+      <td>InterProScan (EBI)</td>
+      <td>Scan sequences against the InterPro protein signature databases.</td>
+      <td>Sequence motif recognition, Protein feature detection</td>
+      <td>Gene and protein families, Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.ebi.ac.uk/Tools/pfa/iprscan5/</td>
+      <td>Sequence Analysis</td>
+      <td>interproscan</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan</td>
+      <td>5.59-91.0</td>
+      <td>interproscan</td>
+      <td>5.59_91.0</td>
+      <td>Sequence motif recognition, Protein feature detection</td>
+      <td>Gene and protein families, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>34689</td>
+      <td>55189</td>
+      <td>1634</td>
+      <td>1713</td>
+      <td>65</td>
+      <td>65</td>
+      <td>15</td>
+      <td>15</td>
+      <td>10897</td>
+      <td>10897</td>
+      <td>607</td>
+      <td>607</td>
+      <td>45651</td>
+      <td>66151</td>
+      <td>2256</td>
+      <td>2335</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>intersect</td>
+      <td>gops_intersect_1</td>
+      <td>Intersect the intervals of two datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>intersect</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20472</td>
+      <td>349984</td>
+      <td>2351</td>
+      <td>3007</td>
+      <td>45587</td>
+      <td>778988</td>
+      <td>4359</td>
+      <td>14116</td>
+      <td>6087</td>
+      <td>7417</td>
+      <td>484</td>
+      <td>561</td>
+      <td>72146</td>
+      <td>1136389</td>
+      <td>7194</td>
+      <td>17684</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>interval2maf</td>
+      <td>Interval2Maf1</td>
+      <td>Extract MAF blocks given a set of intervals</td>
+      <td>bx-python</td>
+      <td>bx-python</td>
+      <td></td>
+      <td>bx-python</td>
+      <td>Tools for manipulating biological data, particularly multiple sequence alignments.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/</td>
+      <td>Genomic Interval Operations</td>
+      <td>interval2maf</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf</td>
+      <td>1.0.1+galaxy1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>32</td>
+      <td>107</td>
+      <td>7</td>
+      <td>10</td>
+      <td>758</td>
+      <td>19538</td>
+      <td>87</td>
+      <td>1246</td>
+      <td>16</td>
+      <td>24</td>
+      <td>2</td>
+      <td>2</td>
+      <td>806</td>
+      <td>19669</td>
+      <td>96</td>
+      <td>1258</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>intervene</td>
+      <td>intervene_pairwise, intervene_upset</td>
+      <td>Create pairwise and upset plots</td>
+      <td>intervene</td>
+      <td>intervene</td>
+      <td></td>
+      <td>Intervene</td>
+      <td>Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.</td>
+      <td>Sequence comparison, Sequence visualisation</td>
+      <td>Computational biology</td>
+      <td>Up-to-date</td>
+      <td>https://intervene.readthedocs.io</td>
+      <td>Statistics</td>
+      <td>intervene</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene</td>
+      <td>0.6.5</td>
+      <td>intervene</td>
+      <td>0.6.5</td>
+      <td>Sequence comparison, Sequence visualisation</td>
+      <td>Computational biology</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1557</td>
+      <td>1607</td>
+      <td>278</td>
+      <td>292</td>
+      <td>4458</td>
+      <td>4458</td>
+      <td>458</td>
+      <td>458</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6015</td>
+      <td>6065</td>
+      <td>736</td>
+      <td>750</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ipo</td>
+      <td>ipo4retgroup, ipo4xcmsSet</td>
+      <td>[W4M][LC-MS] IPO</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/rietho/IPO</td>
+      <td>Metabolomics</td>
+      <td>ipo</td>
+      <td>lecorguille</td>
+      <td>https://github.com/rietho/IPO</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo</td>
+      <td>1.10.0</td>
+      <td>bioconductor-ipo</td>
+      <td>1.28.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>iprscan5</td>
+      <td></td>
+      <td>Interproscan queries the interpro database and provides annotations.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.ebi.ac.uk/Tools/pfa/iprscan5/</td>
+      <td>Sequence Analysis</td>
+      <td>iprscan5</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>iqtree</td>
+      <td>iqtree</td>
+      <td>Efficient phylogenomic software by maximum likelihood</td>
+      <td>iqtree</td>
+      <td>iqtree</td>
+      <td></td>
+      <td>iqtree</td>
+      <td>A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time</td>
+      <td>Phylogenetic analysis, Sequence analysis</td>
+      <td>Phylogenetics</td>
+      <td>Up-to-date</td>
+      <td>http://www.iqtree.org/</td>
+      <td>Phylogenetics</td>
+      <td>iqtree</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree</td>
+      <td>2.3.6</td>
+      <td>iqtree</td>
+      <td>2.3.6</td>
+      <td>Phylogenetic analysis, Sequence analysis</td>
+      <td>Phylogenetics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>28279</td>
+      <td>28481</td>
+      <td>1623</td>
+      <td>1646</td>
+      <td>24662</td>
+      <td>24662</td>
+      <td>2093</td>
+      <td>2093</td>
+      <td>9780</td>
+      <td>10086</td>
+      <td>979</td>
+      <td>992</td>
+      <td>62721</td>
+      <td>63229</td>
+      <td>4695</td>
+      <td>4731</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>irissv</td>
+      <td>irissv</td>
+      <td>Refine insertion sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/mkirsche/Iris</td>
+      <td>Variant Analysis</td>
+      <td>irissv</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tools/irissv/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv</td>
+      <td>1.0.5</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>isescan</td>
+      <td>isescan</td>
+      <td>"ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."</td>
+      <td>ISEScan</td>
+      <td>ISEScan</td>
+      <td></td>
+      <td>ISEScan</td>
+      <td>Automated identification of insertion sequence elements in prokaryotic genomes.</td>
+      <td>Structural variation detection</td>
+      <td>Genomics, DNA structural variation, Sequence analysis, Genetic variation</td>
+      <td>To update</td>
+      <td>https://github.com/xiezhq/ISEScan</td>
+      <td>Sequence Analysis</td>
+      <td>ISEScan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan</td>
+      <td>1.7.2.3</td>
+      <td>isescan</td>
+      <td>1.7.2.1</td>
+      <td>Structural variation detection</td>
+      <td>Genomics, Sequence analysis, Genetic variation</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59386</td>
+      <td>59386</td>
+      <td>151</td>
+      <td>151</td>
+      <td>56</td>
+      <td>56</td>
+      <td>1</td>
+      <td>1</td>
+      <td>4741</td>
+      <td>4741</td>
+      <td>59</td>
+      <td>59</td>
+      <td>64183</td>
+      <td>64183</td>
+      <td>211</td>
+      <td>211</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>isoformswitchanalyzer</td>
+      <td>isoformswitchanalyzer</td>
+      <td>Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.</td>
+      <td>IsoformSwitchAnalyzeR</td>
+      <td>IsoformSwitchAnalyzeR</td>
+      <td></td>
+      <td>IsoformSwitchAnalyzeR</td>
+      <td>Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.</td>
+      <td>Sequence comparison, Sequence analysis</td>
+      <td>Computational biology, Gene transcripts</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>isoformswitchanalyzer</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer</td>
+      <td>1.20.0</td>
+      <td>bioconductor-isoformswitchanalyzer</td>
+      <td>2.2.0</td>
+      <td>Sequence comparison, Sequence analysis</td>
+      <td>Computational biology, Gene transcripts</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1301</td>
+      <td>1301</td>
+      <td>59</td>
+      <td>59</td>
+      <td>1331</td>
+      <td>1331</td>
+      <td>60</td>
+      <td>60</td>
+      <td>507</td>
+      <td>507</td>
+      <td>9</td>
+      <td>9</td>
+      <td>3139</td>
+      <td>3139</td>
+      <td>128</td>
+      <td>128</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>isolib</td>
+      <td>isolib</td>
+      <td>Create an isotopic pattern library for given compounds and adducts.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools/</td>
+      <td>Metabolomics</td>
+      <td>isolib</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/isolib</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/isolib</td>
+      <td>1.0.1+galaxy0</td>
+      <td>bioconductor-metabocoreutils</td>
+      <td>1.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>isoplot</td>
+      <td>isoplot</td>
+      <td>Isoplot is a software for the visualisation of MS data from C13 labelling experiments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Metabolomics, Visualization</td>
+      <td>isoplot</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/llegregam/Isoplot/tree/main</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot</td>
+      <td>1.3.0+galaxy1</td>
+      <td>isoplot</td>
+      <td>1.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>itsx</td>
+      <td>itsx</td>
+      <td>ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.</td>
+      <td>ITSx</td>
+      <td>ITSx</td>
+      <td></td>
+      <td>ITSx</td>
+      <td>TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.</td>
+      <td>Sequence feature detection</td>
+      <td>Functional, regulatory and non-coding RNA, Microbiology</td>
+      <td>Up-to-date</td>
+      <td>https://microbiology.se/software/itsx/</td>
+      <td>Metagenomics</td>
+      <td>itsx</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/itsx</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/itsx</td>
+      <td>1.1.3</td>
+      <td>itsx</td>
+      <td>1.1.3</td>
+      <td>Sequence feature detection</td>
+      <td>Functional, regulatory and non-coding RNA, Microbiology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1426</td>
+      <td>1426</td>
+      <td>71</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1426</td>
+      <td>1426</td>
+      <td>71</td>
+      <td>71</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ivar</td>
+      <td>ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants</td>
+      <td>iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/andersen-lab/ivar</td>
+      <td>Sequence Analysis</td>
+      <td>ivar</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar</td>
+      <td>1.4.3</td>
+      <td>ivar</td>
+      <td>1.4.3</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>1252220</td>
+      <td>1252220</td>
+      <td>2366</td>
+      <td>2366</td>
+      <td>126027</td>
+      <td>126027</td>
+      <td>2496</td>
+      <td>2496</td>
+      <td>41901</td>
+      <td>41901</td>
+      <td>993</td>
+      <td>993</td>
+      <td>1420148</td>
+      <td>1420148</td>
+      <td>5855</td>
+      <td>5855</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>iwtomics</td>
+      <td>iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot</td>
+      <td>Interval-Wise Testing for Omics Data</td>
+      <td>iwtomics</td>
+      <td>iwtomics</td>
+      <td></td>
+      <td>IWTomics</td>
+      <td>Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.</td>
+      <td>Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison</td>
+      <td>Statistics and probability</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/IWTomics.html</td>
+      <td>Statistics</td>
+      <td>iwtomics</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics</td>
+      <td>1.0.0</td>
+      <td>bioconductor-iwtomics</td>
+      <td>1.26.0</td>
+      <td>Differential gene expression analysis, Peak calling, Genome annotation, Comparison</td>
+      <td>Statistics and probability</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>675</td>
+      <td>690</td>
+      <td>27</td>
+      <td>28</td>
+      <td>159</td>
+      <td>251</td>
+      <td>29</td>
+      <td>49</td>
+      <td>383</td>
+      <td>383</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1217</td>
+      <td>1324</td>
+      <td>68</td>
+      <td>89</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jasminesv</td>
+      <td>jasminesv</td>
+      <td>Merge structural variants across samples</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/mkirsche/Jasmine/</td>
+      <td>Variant Analysis</td>
+      <td>jasminesv</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/jasminesv/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv</td>
+      <td>1.0.11</td>
+      <td>jasminesv</td>
+      <td>1.1.5</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>32</td>
+      <td>32</td>
+      <td>9</td>
+      <td>9</td>
+      <td>53</td>
+      <td>53</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>85</td>
+      <td>85</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jbrowse</td>
+      <td>jbrowse_to_standalone, jbrowse</td>
+      <td>JBrowse Genome Browser integrated as a Galaxy Tool</td>
+      <td>jbrowse</td>
+      <td>jbrowse</td>
+      <td></td>
+      <td>JBrowse</td>
+      <td>Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.</td>
+      <td>Genome visualisation</td>
+      <td>Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://jbrowse.org</td>
+      <td>Sequence Analysis</td>
+      <td>jbrowse</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse</td>
+      <td>1.16.11</td>
+      <td>jbrowse</td>
+      <td>1.16.11</td>
+      <td>Genome visualisation</td>
+      <td>Genomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>21153</td>
+      <td>22174</td>
+      <td>5514</td>
+      <td>5779</td>
+      <td>17428</td>
+      <td>17428</td>
+      <td>6458</td>
+      <td>6458</td>
+      <td>15673</td>
+      <td>17267</td>
+      <td>3248</td>
+      <td>3786</td>
+      <td>54254</td>
+      <td>56869</td>
+      <td>15220</td>
+      <td>16023</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jbrowse</td>
+      <td>jbrowse_to_container</td>
+      <td>A tool allowing to export a JBrowse dataset into a JBrowse docker container</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://jbrowse.org</td>
+      <td>Web Services</td>
+      <td>jbrowse_to_container</td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse</td>
+      <td></td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jbrowse2</td>
+      <td>jbrowse2</td>
+      <td>JBrowse2 Genome Browser integrated as a Galaxy Tool</td>
+      <td>jbrowse_2</td>
+      <td>jbrowse_2</td>
+      <td></td>
+      <td>JBrowse 2</td>
+      <td>Modular genome browser with views of synteny and structural variation.</td>
+      <td>Genome visualisation, Structure visualisation, Pathway visualisation</td>
+      <td>Mapping, Structural variation, Genomics, Gene structure, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://jbrowse.org</td>
+      <td>Sequence Analysis</td>
+      <td>jbrowse2</td>
+      <td>fubar</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2</td>
+      <td>2.15.4</td>
+      <td>jbrowse2</td>
+      <td>2.15.4</td>
+      <td>Genome visualisation, Structure visualisation, Pathway visualisation</td>
+      <td>Mapping, Structural variation, Genomics, Gene structure, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1312</td>
+      <td>1312</td>
+      <td>219</td>
+      <td>219</td>
+      <td>116</td>
+      <td>116</td>
+      <td>58</td>
+      <td>58</td>
+      <td>37</td>
+      <td>37</td>
+      <td>6</td>
+      <td>6</td>
+      <td>1465</td>
+      <td>1465</td>
+      <td>283</td>
+      <td>283</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jcvi_gff_stats</td>
+      <td>jcvi_gff_stats</td>
+      <td>Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/tanghaibao/jcvi</td>
+      <td>Sequence Analysis</td>
+      <td>jcvi_gff_stats</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats</td>
+      <td>0.8.4</td>
+      <td>jcvi</td>
+      <td>1.4.16</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2747</td>
+      <td>2926</td>
+      <td>596</td>
+      <td>637</td>
+      <td>2311</td>
+      <td>2311</td>
+      <td>741</td>
+      <td>741</td>
+      <td>1145</td>
+      <td>1145</td>
+      <td>469</td>
+      <td>469</td>
+      <td>6203</td>
+      <td>6382</td>
+      <td>1806</td>
+      <td>1847</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jellyfish</td>
+      <td>jellyfish</td>
+      <td>Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA</td>
+      <td>Jellyfish</td>
+      <td>Jellyfish</td>
+      <td></td>
+      <td>Jellyfish</td>
+      <td>A command-line algorithm for counting k-mers in DNA sequence.</td>
+      <td>k-mer counting</td>
+      <td>Sequence analysis, Genomics</td>
+      <td>To update</td>
+      <td>https://github.com/gmarcais/Jellyfish</td>
+      <td>Assembly</td>
+      <td>jellyfish</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish</td>
+      <td></td>
+      <td>kmer-jellyfish</td>
+      <td>2.3.1</td>
+      <td>k-mer counting</td>
+      <td>Sequence analysis, Genomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1825</td>
+      <td>1825</td>
+      <td>237</td>
+      <td>237</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>971</td>
+      <td>971</td>
+      <td>56</td>
+      <td>56</td>
+      <td>2796</td>
+      <td>2796</td>
+      <td>293</td>
+      <td>293</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>join</td>
+      <td>gops_join_1</td>
+      <td>Join the intervals of two datasets side-by-side</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>join</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15624</td>
+      <td>330820</td>
+      <td>1864</td>
+      <td>2438</td>
+      <td>52317</td>
+      <td>513688</td>
+      <td>10198</td>
+      <td>39421</td>
+      <td>1329</td>
+      <td>1645</td>
+      <td>213</td>
+      <td>289</td>
+      <td>69270</td>
+      <td>846153</td>
+      <td>12275</td>
+      <td>42148</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>join_files_by_id</td>
+      <td>join_files_by_id</td>
+      <td>This tool will join datasets according to a column with identifier</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id</td>
+      <td>Text Manipulation</td>
+      <td>join_files_by_id</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id</td>
+      <td>1.0</td>
+      <td>r-data.table</td>
+      <td>1.11.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>join_files_on_column_fuzzy</td>
+      <td>join_files_on_column_fuzzy</td>
+      <td>Join two files on a common column, allowing a certain difference.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>join_files_on_column_fuzzy</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy</td>
+      <td>1.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1980</td>
+      <td>2697</td>
+      <td>345</td>
+      <td>410</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1081</td>
+      <td>1081</td>
+      <td>44</td>
+      <td>44</td>
+      <td>3061</td>
+      <td>3778</td>
+      <td>389</td>
+      <td>454</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jq</td>
+      <td>jq</td>
+      <td>JQ is a lightweight and flexible command-line JSON processor</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://stedolan.github.io/jq/</td>
+      <td>Text Manipulation</td>
+      <td>jq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq</td>
+      <td>1.0</td>
+      <td>jq</td>
+      <td>1.5</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>660</td>
+      <td>2374</td>
+      <td>61</td>
+      <td>63</td>
+      <td>336</td>
+      <td>336</td>
+      <td>82</td>
+      <td>82</td>
+      <td>281</td>
+      <td>281</td>
+      <td>11</td>
+      <td>11</td>
+      <td>1277</td>
+      <td>2991</td>
+      <td>154</td>
+      <td>156</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jupyter_job</td>
+      <td>run_jupyter_job</td>
+      <td>Run jupyter notebook script in Galaxy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Machine Learning</td>
+      <td>run_jupyter_job</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job</td>
+      <td>0.0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>30</td>
+      <td>30</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>30</td>
+      <td>30</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>justdiff</td>
+      <td>justdiff</td>
+      <td>Unix diff</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Text Manipulation</td>
+      <td>justdiff</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff</td>
+      <td>3.10+galaxy0</td>
+      <td>diffutils</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>justgzip</td>
+      <td>justgzip</td>
+      <td>Compress fastq sequence files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Convert Formats</td>
+      <td>justgzip</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip</td>
+      <td>2.8+galaxy0</td>
+      <td>pigz</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>jvarkit</td>
+      <td>jvarkit_wgscoverageplotter</td>
+      <td>Jvarkit : Java utilities for Bioinformatics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://lindenb.github.io/jvarkit/</td>
+      <td>SAM</td>
+      <td>jvarkit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit</td>
+      <td>20201223</td>
+      <td>jvarkit-wgscoverageplotter</td>
+      <td>20201223</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7179</td>
+      <td>7179</td>
+      <td>509</td>
+      <td>509</td>
+      <td>11138</td>
+      <td>11138</td>
+      <td>1145</td>
+      <td>1145</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18317</td>
+      <td>18317</td>
+      <td>1654</td>
+      <td>1654</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kallisto</td>
+      <td>kallisto_pseudo, kallisto_quant</td>
+      <td>kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.</td>
+      <td>kallisto</td>
+      <td>kallisto</td>
+      <td></td>
+      <td>kallisto</td>
+      <td>A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.</td>
+      <td>Gene expression profiling</td>
+      <td>Transcriptomics, RNA-seq, Gene expression</td>
+      <td>To update</td>
+      <td>https://pachterlab.github.io/kallisto/</td>
+      <td>Transcriptomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto</td>
+      <td>0.48.0</td>
+      <td>kallisto</td>
+      <td>0.51.1</td>
+      <td>Gene expression profiling</td>
+      <td>Transcriptomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>28398</td>
+      <td>29031</td>
+      <td>932</td>
+      <td>965</td>
+      <td>73705</td>
+      <td>80087</td>
+      <td>2603</td>
+      <td>3025</td>
+      <td>5333</td>
+      <td>5567</td>
+      <td>218</td>
+      <td>230</td>
+      <td>107436</td>
+      <td>114685</td>
+      <td>3753</td>
+      <td>4220</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kaptive</td>
+      <td>kaptive</td>
+      <td>Kaptive reports information about capsular (K) loci found in genome assemblies.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>kaptive</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive</td>
+      <td>0.3.0</td>
+      <td>kaptive</td>
+      <td>3.0.0b5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kat_filter</td>
+      <td>kat_@EXECUTABLE@</td>
+      <td>Filtering kmers or reads from a database of kmers hashes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>kat_filter</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter</td>
+      <td>2.3</td>
+      <td>kat</td>
+      <td>2.4.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kat_sect</td>
+      <td>kat_@EXECUTABLE@</td>
+      <td>SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>kat_sect</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect</td>
+      <td>2.3</td>
+      <td>kat</td>
+      <td>2.4.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kc-align</td>
+      <td>kc-align</td>
+      <td>Kc-Align custom tool</td>
+      <td>kc-align</td>
+      <td>kc-align</td>
+      <td></td>
+      <td>kc-align</td>
+      <td>A fast and accurate tool for performing codon-aware multiple sequence alignments</td>
+      <td>Multiple sequence alignment</td>
+      <td>Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/davebx/kc-align</td>
+      <td>Sequence Analysis</td>
+      <td>kc_align</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align</td>
+      <td>1.0.2</td>
+      <td>kcalign</td>
+      <td>1.0.2</td>
+      <td>Multiple sequence alignment</td>
+      <td>Mapping</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>379</td>
+      <td>379</td>
+      <td>53</td>
+      <td>53</td>
+      <td>8259</td>
+      <td>8259</td>
+      <td>271</td>
+      <td>271</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8638</td>
+      <td>8638</td>
+      <td>324</td>
+      <td>324</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kegalign</td>
+      <td>kegalign</td>
+      <td>A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/galaxyproject/KegAlign</td>
+      <td>Next Gen Mappers</td>
+      <td>kegalign</td>
+      <td>richard-burhans</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign</td>
+      <td>0.1.2.7</td>
+      <td>kegalign-full</td>
+      <td>0.1.2.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kernel_canonical_correlation_analysis</td>
+      <td>kcca1</td>
+      <td>Kernel Canonical Correlation Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>kernel_canonical_correlation_analysis</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis</td>
+      <td>1.0.0</td>
+      <td>rpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>62</td>
+      <td>70</td>
+      <td>4</td>
+      <td>4</td>
+      <td>207</td>
+      <td>334</td>
+      <td>27</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>269</td>
+      <td>404</td>
+      <td>31</td>
+      <td>75</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kernel_principal_component_analysis</td>
+      <td>kpca1</td>
+      <td>Kernel Principal Component Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>kernel_principal_component_analysis</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis</td>
+      <td>1.0.0</td>
+      <td>rpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>144</td>
+      <td>157</td>
+      <td>26</td>
+      <td>30</td>
+      <td>268</td>
+      <td>707</td>
+      <td>83</td>
+      <td>248</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>412</td>
+      <td>864</td>
+      <td>109</td>
+      <td>278</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>khmer</td>
+      <td>khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median</td>
+      <td>In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more</td>
+      <td>khmer</td>
+      <td>khmer</td>
+      <td></td>
+      <td>khmer</td>
+      <td>khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.</td>
+      <td>Standardisation and normalisation, De-novo assembly</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://khmer.readthedocs.org/</td>
+      <td>Assembly, Next Gen Mappers</td>
+      <td>khmer</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer</td>
+      <td>3.0.0a3</td>
+      <td>khmer</td>
+      <td>3.0.0a3</td>
+      <td>Standardisation and normalisation, De-novo assembly</td>
+      <td>Sequence assembly</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>1995</td>
+      <td>2091</td>
+      <td>174</td>
+      <td>193</td>
+      <td>1430</td>
+      <td>1430</td>
+      <td>389</td>
+      <td>389</td>
+      <td>1580</td>
+      <td>1580</td>
+      <td>56</td>
+      <td>56</td>
+      <td>5005</td>
+      <td>5101</td>
+      <td>619</td>
+      <td>638</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>king</td>
+      <td>king</td>
+      <td>Kinship-based INference for Gwas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://people.virginia.edu/~wc9c/KING/</td>
+      <td>Variant Analysis</td>
+      <td>king</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/king</td>
+      <td>2.2.7</td>
+      <td>king</td>
+      <td>2.2.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kinwalker</td>
+      <td></td>
+      <td>Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.bioinf.uni-leipzig.de/Software/Kinwalker/</td>
+      <td>RNA</td>
+      <td>kinwalker</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kleborate</td>
+      <td>kleborate</td>
+      <td>Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)</td>
+      <td>kleborate</td>
+      <td>kleborate</td>
+      <td></td>
+      <td>Kleborate</td>
+      <td>Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).</td>
+      <td>Multilocus sequence typing, Genome assembly, Virulence prediction</td>
+      <td>Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing</td>
+      <td>To update</td>
+      <td>https://github.com/katholt/Kleborate/wiki</td>
+      <td>Metagenomics</td>
+      <td>kleborate</td>
+      <td>iuc</td>
+      <td>https://github.com/katholt/Kleborate</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate</td>
+      <td>2.3.2</td>
+      <td>kleborate</td>
+      <td>3.1.0</td>
+      <td>Multilocus sequence typing, Genome assembly, Virulence prediction</td>
+      <td>Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>503</td>
+      <td>503</td>
+      <td>58</td>
+      <td>58</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>503</td>
+      <td>503</td>
+      <td>58</td>
+      <td>58</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kma</td>
+      <td>kma_map</td>
+      <td>Map with KMA</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/genomicepidemiology/kma</td>
+      <td>Next Gen Mappers</td>
+      <td>kma</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma</td>
+      <td>1.4.14</td>
+      <td>kma</td>
+      <td>1.4.15</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kmd_hmdb_data_plot</td>
+      <td>kmd_hmdb_data_plot</td>
+      <td>retrieves data from KMD HMDB API and produce plot and csv file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics</td>
+      <td>Metabolomics</td>
+      <td>kmd_hmdb_data_plot</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot</td>
+      <td>1.0.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kofamscan</td>
+      <td>kofamscan</td>
+      <td>Gene function annotation tool based on KEGG Orthology and hidden Markov model</td>
+      <td>kofamscan</td>
+      <td>kofamscan</td>
+      <td></td>
+      <td>kofamscan</td>
+      <td>KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.</td>
+      <td>Sequence analysis, Gene functional annotation</td>
+      <td>Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/takaram/kofam_scan</td>
+      <td>Sequence Analysis</td>
+      <td>kofamscan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan</td>
+      <td>1.3.0</td>
+      <td>kofamscan</td>
+      <td>1.3.0</td>
+      <td>Sequence analysis, Gene functional annotation</td>
+      <td>Genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1342</td>
+      <td>1342</td>
+      <td>63</td>
+      <td>63</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1342</td>
+      <td>1342</td>
+      <td>63</td>
+      <td>63</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kraken</td>
+      <td>kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken</td>
+      <td>Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.</td>
+      <td>kraken</td>
+      <td>kraken</td>
+      <td></td>
+      <td>Kraken</td>
+      <td>System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.</td>
+      <td>Taxonomic classification</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>To update</td>
+      <td>http://ccb.jhu.edu/software/kraken/</td>
+      <td>Metagenomics</td>
+      <td>kraken</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken</td>
+      <td></td>
+      <td>kraken</td>
+      <td>1.1.1</td>
+      <td>Taxonomic classification</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>48136</td>
+      <td>48164</td>
+      <td>2754</td>
+      <td>2760</td>
+      <td>59952</td>
+      <td>130398</td>
+      <td>5869</td>
+      <td>8654</td>
+      <td>29008</td>
+      <td>31148</td>
+      <td>1936</td>
+      <td>2200</td>
+      <td>137096</td>
+      <td>209710</td>
+      <td>10559</td>
+      <td>13614</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kraken2</td>
+      <td>kraken2</td>
+      <td>Kraken2 for taxonomic designation.</td>
+      <td>kraken2</td>
+      <td>kraken2</td>
+      <td></td>
+      <td>kraken2</td>
+      <td>Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.</td>
+      <td>Taxonomic classification</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>http://ccb.jhu.edu/software/kraken/</td>
+      <td>Metagenomics</td>
+      <td>kraken2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2</td>
+      <td>2.1.3</td>
+      <td>kraken2</td>
+      <td>2.1.3</td>
+      <td>Taxonomic classification</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>271367</td>
+      <td>271786</td>
+      <td>6384</td>
+      <td>6409</td>
+      <td>101752</td>
+      <td>101752</td>
+      <td>4662</td>
+      <td>4662</td>
+      <td>53562</td>
+      <td>53562</td>
+      <td>1663</td>
+      <td>1663</td>
+      <td>426681</td>
+      <td>427100</td>
+      <td>12709</td>
+      <td>12734</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kraken2tax</td>
+      <td>Kraken2Tax</td>
+      <td>Convert Kraken output to Galaxy taxonomy data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Metagenomics</td>
+      <td>kraken2tax</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax</td>
+      <td>1.2+galaxy0</td>
+      <td>gawk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>23008</td>
+      <td>23014</td>
+      <td>1060</td>
+      <td>1061</td>
+      <td>16194</td>
+      <td>24490</td>
+      <td>1719</td>
+      <td>2168</td>
+      <td>14898</td>
+      <td>14898</td>
+      <td>436</td>
+      <td>436</td>
+      <td>54100</td>
+      <td>62402</td>
+      <td>3215</td>
+      <td>3665</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kraken_biom</td>
+      <td>kraken_biom</td>
+      <td>Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/smdabdoub/kraken-biom</td>
+      <td>Metagenomics</td>
+      <td>kraken_biom</td>
+      <td>iuc</td>
+      <td>https://github.com/smdabdoub/kraken-biom</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom</td>
+      <td>1.2.0</td>
+      <td>kraken-biom</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3185</td>
+      <td>3185</td>
+      <td>495</td>
+      <td>495</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>385</td>
+      <td>385</td>
+      <td>48</td>
+      <td>48</td>
+      <td>3570</td>
+      <td>3570</td>
+      <td>543</td>
+      <td>543</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>kraken_taxonomy_report</td>
+      <td>kraken_taxonomy_report</td>
+      <td>Kraken taxonomy report</td>
+      <td>Kraken-Taxonomy-Report</td>
+      <td>Kraken-Taxonomy-Report</td>
+      <td></td>
+      <td>Kraken-Taxonomy-Report</td>
+      <td>view report of classification for multiple samples</td>
+      <td>Visualisation, Classification</td>
+      <td>Metagenomics, Taxonomy</td>
+      <td>To update</td>
+      <td>https://github.com/blankenberg/Kraken-Taxonomy-Report</td>
+      <td>Metagenomics</td>
+      <td>kraken_taxonomy_report</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report</td>
+      <td>0.0.3</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td>Visualisation, Classification</td>
+      <td>Metagenomics, Taxonomy</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3981</td>
+      <td>3986</td>
+      <td>769</td>
+      <td>771</td>
+      <td>4087</td>
+      <td>5610</td>
+      <td>991</td>
+      <td>1284</td>
+      <td>88</td>
+      <td>88</td>
+      <td>41</td>
+      <td>41</td>
+      <td>8156</td>
+      <td>9684</td>
+      <td>1801</td>
+      <td>2096</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>krakentools</td>
+      <td>krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa</td>
+      <td>KrakenTools is a suite of scripts to be used alongside the Kraken</td>
+      <td>krakentools</td>
+      <td>krakentools</td>
+      <td></td>
+      <td>KrakenTools</td>
+      <td>KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files</td>
+      <td>Visualisation, Aggregation</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/jenniferlu717/KrakenTools</td>
+      <td>Metagenomics</td>
+      <td>krakentools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools</td>
+      <td>1.2</td>
+      <td>krakentools</td>
+      <td>1.2</td>
+      <td>Visualisation, Aggregation</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48516</td>
+      <td>48516</td>
+      <td>2373</td>
+      <td>2373</td>
+      <td>8787</td>
+      <td>8787</td>
+      <td>943</td>
+      <td>943</td>
+      <td>4369</td>
+      <td>4369</td>
+      <td>393</td>
+      <td>393</td>
+      <td>61672</td>
+      <td>61672</td>
+      <td>3709</td>
+      <td>3709</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>krocus</td>
+      <td>krocus</td>
+      <td>Predict MLST directly from uncorrected long reads</td>
+      <td>krocus</td>
+      <td>krocus</td>
+      <td></td>
+      <td>krocus</td>
+      <td>Predict MLST directly from uncorrected long reads</td>
+      <td>Multilocus sequence typing, k-mer counting</td>
+      <td>Public health and epidemiology</td>
+      <td>To update</td>
+      <td>https://github.com/quadram-institute-bioscience/krocus</td>
+      <td>Sequence Analysis</td>
+      <td>krocus</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus</td>
+      <td>1.0.1</td>
+      <td>krocus</td>
+      <td>1.0.3</td>
+      <td>Multilocus sequence typing, k-mer counting</td>
+      <td>Public health and epidemiology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>label_to_binary</td>
+      <td>label_to_binary</td>
+      <td>Convert label map to binary image</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>label_to_binary</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary</td>
+      <td>1.26.4</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>labelimage2points</td>
+      <td>ip_labelimage_to_points</td>
+      <td>Label Image to Points</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>labelimage2points</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points</td>
+      <td>0.2-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>34</td>
+      <td>38</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>38</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>labels</td>
+      <td>bg_labels</td>
+      <td>remaps and annotates alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/labels</td>
+      <td>Sequence Analysis</td>
+      <td>labels</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/labels</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/labels</td>
+      <td>1.0.5.0</td>
+      <td>labels</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>landmark_registration</td>
+      <td>ip_landmark_registration</td>
+      <td>Landmark Registration</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>landmark_registration</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration</td>
+      <td>0.1.0-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>887</td>
+      <td>927</td>
+      <td>13</td>
+      <td>15</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>891</td>
+      <td>931</td>
+      <td>16</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>last</td>
+      <td>last_al, last_db, last_split, last_train, last_maf_convert</td>
+      <td>LAST finds similar regions between sequences.</td>
+      <td>last</td>
+      <td>last</td>
+      <td></td>
+      <td>LAST</td>
+      <td>Short read alignment program incorporating quality scores</td>
+      <td>Sequence alignment</td>
+      <td>Genomics, Comparative genomics</td>
+      <td>To update</td>
+      <td>http://last.cbrc.jp/</td>
+      <td>Sequence Analysis</td>
+      <td>last</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/last</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/last</td>
+      <td>1205</td>
+      <td>last</td>
+      <td>1584</td>
+      <td>Sequence alignment</td>
+      <td>Comparative genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>329</td>
+      <td>329</td>
+      <td>94</td>
+      <td>94</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>329</td>
+      <td>329</td>
+      <td>94</td>
+      <td>94</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lastz</td>
+      <td>lastz_wrapper_2, lastz_d_wrapper</td>
+      <td>Galaxy wrappers for the Lastz and Lastz_d</td>
+      <td>lastz</td>
+      <td>lastz</td>
+      <td></td>
+      <td>LASTZ</td>
+      <td>A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.</td>
+      <td>Sequence alignment, Read mapping</td>
+      <td>Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lastz/lastz</td>
+      <td>Next Gen Mappers</td>
+      <td>lastz</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz</td>
+      <td>1.04.22</td>
+      <td>lastz</td>
+      <td>1.04.22</td>
+      <td>Sequence alignment, Read mapping</td>
+      <td>Genomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>77409</td>
+      <td>84356</td>
+      <td>447</td>
+      <td>475</td>
+      <td>156658</td>
+      <td>193590</td>
+      <td>870</td>
+      <td>3511</td>
+      <td>38579</td>
+      <td>38780</td>
+      <td>173</td>
+      <td>203</td>
+      <td>272646</td>
+      <td>316726</td>
+      <td>1490</td>
+      <td>4189</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lastz_paired_reads</td>
+      <td>lastz_paired_reads_wrapper</td>
+      <td>Galaxy wrapper for the Lastz alignment tool on paired reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Next Gen Mappers</td>
+      <td>lastz_paired_reads</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads</td>
+      <td>1.1.1</td>
+      <td>lastz</td>
+      <td>1.04.22</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7</td>
+      <td>9</td>
+      <td>3</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>10</td>
+      <td>5</td>
+      <td>5</td>
+      <td>15</td>
+      <td>19</td>
+      <td>8</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lca_wrapper</td>
+      <td>lca1</td>
+      <td>Find lowest diagnostic rank</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Metagenomics</td>
+      <td>lca_wrapper</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper</td>
+      <td>1.0.1</td>
+      <td>taxonomy</td>
+      <td>0.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>89</td>
+      <td>137</td>
+      <td>4</td>
+      <td>20</td>
+      <td>118</td>
+      <td>6136</td>
+      <td>15</td>
+      <td>1112</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>207</td>
+      <td>6273</td>
+      <td>19</td>
+      <td>1132</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lcrgenie</td>
+      <td>lcrgenie</td>
+      <td>Ligase Chain Reaction Genie</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/neilswainston/LCRGenie</td>
+      <td>Synthetic Biology</td>
+      <td>lcrgenie</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie</td>
+      <td>1.0.2</td>
+      <td>lcr_genie</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lda_analysis</td>
+      <td>lda_analy1</td>
+      <td>Perform Linear Discriminant Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Statistics</td>
+      <td>lda_analysis</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis</td>
+      <td>1.0.1</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>147</td>
+      <td>159</td>
+      <td>46</td>
+      <td>48</td>
+      <td>793</td>
+      <td>1538</td>
+      <td>101</td>
+      <td>314</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>3</td>
+      <td>940</td>
+      <td>1701</td>
+      <td>147</td>
+      <td>365</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>legsta</td>
+      <td>legsta</td>
+      <td>Performs in silico Legionella pneumophila sequence based typing.</td>
+      <td>legsta</td>
+      <td>legsta</td>
+      <td></td>
+      <td>legsta</td>
+      <td>Performs in silico Legionella pneumophila sequence based typing</td>
+      <td>Sequence analysis</td>
+      <td>Public health and epidemiology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tseemann/legsta</td>
+      <td>Sequence Analysis</td>
+      <td>legsta</td>
+      <td>iuc</td>
+      <td>https://github.com/tseemann/legsta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta</td>
+      <td>0.5.1</td>
+      <td>legsta</td>
+      <td>0.5.1</td>
+      <td>Sequence analysis</td>
+      <td>Public health and epidemiology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>92</td>
+      <td>92</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>92</td>
+      <td>92</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>length_and_gc_content</td>
+      <td>length_and_gc_content</td>
+      <td>Gets gene length and gc content from a fasta and a GTF file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content</td>
+      <td>Fasta Manipulation, Statistics, RNA, Micro-array Analysis</td>
+      <td>length_and_gc_content</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content</td>
+      <td>0.1.2</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4349</td>
+      <td>4466</td>
+      <td>666</td>
+      <td>698</td>
+      <td>2093</td>
+      <td>2286</td>
+      <td>928</td>
+      <td>998</td>
+      <td>201</td>
+      <td>201</td>
+      <td>77</td>
+      <td>77</td>
+      <td>6643</td>
+      <td>6953</td>
+      <td>1671</td>
+      <td>1773</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lfq_protein_quant</td>
+      <td>lfq_protein_quant</td>
+      <td>Enable protein summarisation and quantitation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/compomics/LFQ_galaxy_p</td>
+      <td>Proteomics</td>
+      <td>lfq_protein_quant</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant</td>
+      <td>1.0</td>
+      <td>bioconductor-msnbase</td>
+      <td>2.28.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>78</td>
+      <td>116</td>
+      <td>12</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>78</td>
+      <td>116</td>
+      <td>12</td>
+      <td>19</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lighter</td>
+      <td>lighter</td>
+      <td>Lighter is a kmer-based error correction method for whole genome sequencing data</td>
+      <td>lighter</td>
+      <td>lighter</td>
+      <td></td>
+      <td>Lighter</td>
+      <td>Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.</td>
+      <td>k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection</td>
+      <td>Sequencing, Whole genome sequencing, DNA, Genomics</td>
+      <td>To update</td>
+      <td>https://github.com/mourisl/Lighter</td>
+      <td>Sequence Analysis, Fasta Manipulation</td>
+      <td>lighter</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/lighter</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/lighter</td>
+      <td>1.0</td>
+      <td>lighter</td>
+      <td>1.1.3</td>
+      <td>k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection</td>
+      <td>Whole genome sequencing, DNA, Genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>149</td>
+      <td>171</td>
+      <td>27</td>
+      <td>30</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>149</td>
+      <td>171</td>
+      <td>27</td>
+      <td>30</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>limma_voom</td>
+      <td>limma_voom</td>
+      <td>Perform RNA-Seq differential expression analysis using limma voom pipeline</td>
+      <td>limma</td>
+      <td>limma</td>
+      <td></td>
+      <td>limma</td>
+      <td>Data analysis, linear models and differential expression for microarray data.</td>
+      <td>RNA-Seq analysis</td>
+      <td>Molecular biology, Genetics</td>
+      <td>Up-to-date</td>
+      <td>http://bioconductor.org/packages/release/bioc/html/limma.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>limma_voom</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom</td>
+      <td>3.58.1</td>
+      <td>bioconductor-limma</td>
+      <td>3.58.1</td>
+      <td>RNA-Seq analysis</td>
+      <td>Molecular biology, Genetics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>23442</td>
+      <td>24466</td>
+      <td>2379</td>
+      <td>2475</td>
+      <td>45734</td>
+      <td>49342</td>
+      <td>4565</td>
+      <td>5032</td>
+      <td>9327</td>
+      <td>9517</td>
+      <td>835</td>
+      <td>842</td>
+      <td>78503</td>
+      <td>83325</td>
+      <td>7779</td>
+      <td>8349</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lineagespot</td>
+      <td>lineagespot</td>
+      <td>Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)</td>
+      <td>lineagespot</td>
+      <td>lineagespot</td>
+      <td></td>
+      <td>lineagespot</td>
+      <td>Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).</td>
+      <td>Variant calling</td>
+      <td>Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation</td>
+      <td>To update</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html</td>
+      <td>Metagenomics, Sequence Analysis</td>
+      <td>lineagespot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot</td>
+      <td>1.6.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td>Variant calling</td>
+      <td>Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>39</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>39</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>linear_regression</td>
+      <td>LinearRegression1</td>
+      <td>Perform Linear Regression</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>linear_regression</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression</td>
+      <td>1.0.1</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>146</td>
+      <td>1103</td>
+      <td>31</td>
+      <td>271</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>146</td>
+      <td>1103</td>
+      <td>31</td>
+      <td>271</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>links</td>
+      <td>links</td>
+      <td>Scaffold genome assemblies with long reads.</td>
+      <td>links</td>
+      <td>links</td>
+      <td></td>
+      <td>LINKS</td>
+      <td>LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.</td>
+      <td>Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming</td>
+      <td>Sequence assembly, Mapping, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bcgsc/LINKS</td>
+      <td>Assembly</td>
+      <td>links</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/links</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/links</td>
+      <td>2.0.1</td>
+      <td>links</td>
+      <td>2.0.1</td>
+      <td>Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming</td>
+      <td>Sequence assembly, Mapping, Sequencing</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>512</td>
+      <td>512</td>
+      <td>126</td>
+      <td>126</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>480</td>
+      <td>480</td>
+      <td>65</td>
+      <td>65</td>
+      <td>992</td>
+      <td>992</td>
+      <td>191</td>
+      <td>191</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>locarna</td>
+      <td>locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile</td>
+      <td>LocARNA - A suite for multiple alignment and folding of RNAs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://www.bioinf.uni-freiburg.de/Software/LocARNA/</td>
+      <td>RNA</td>
+      <td>locarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna</td>
+      <td>2.0.1</td>
+      <td>locarna</td>
+      <td>2.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>314</td>
+      <td>350</td>
+      <td>36</td>
+      <td>46</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>314</td>
+      <td>350</td>
+      <td>36</td>
+      <td>46</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lofreq</td>
+      <td>lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi</td>
+      <td>LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://csb5.github.io/lofreq/</td>
+      <td>Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq</td>
+      <td>2.1.5</td>
+      <td>lofreq</td>
+      <td>2.1.5</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>4176367</td>
+      <td>4176367</td>
+      <td>4301</td>
+      <td>4301</td>
+      <td>509615</td>
+      <td>509615</td>
+      <td>8213</td>
+      <td>8213</td>
+      <td>106342</td>
+      <td>106342</td>
+      <td>1815</td>
+      <td>1815</td>
+      <td>4792324</td>
+      <td>4792324</td>
+      <td>14329</td>
+      <td>14329</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>logistic_regression_vif</td>
+      <td>LogisticRegression</td>
+      <td>Perform Logistic Regression with vif</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis, Statistics</td>
+      <td>logistic_regression_vif</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif</td>
+      <td>1.0.1</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>64</td>
+      <td>173</td>
+      <td>12</td>
+      <td>48</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>64</td>
+      <td>173</td>
+      <td>12</td>
+      <td>48</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>logol</td>
+      <td>logol_wrapper</td>
+      <td>Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://logol.genouest.org/web/app.php/logol</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/logol</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/logol</td>
+      <td>1.7.8</td>
+      <td>logol</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>longorf</td>
+      <td>longORF</td>
+      <td>obtain longest ORF in six-frame translations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>longorf</td>
+      <td>mbernt</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf</td>
+      <td>0.3.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lorikeet</td>
+      <td>lorikeet_spoligotype</td>
+      <td>Tools for M. tuberculosis DNA fingerprinting (spoligotyping)</td>
+      <td>lorikeet</td>
+      <td>lorikeet</td>
+      <td></td>
+      <td>lorikeet</td>
+      <td>Tools for M. tuberculosis DNA fingerprinting (spoligotyping)</td>
+      <td>Sequence analysis, Genotyping</td>
+      <td>Genotype and phenotype</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/AbeelLab/lorikeet</td>
+      <td>Sequence Analysis</td>
+      <td>lorikeet_spoligotype</td>
+      <td>iuc</td>
+      <td>https://github.com/AbeelLab/lorikeet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet</td>
+      <td>20</td>
+      <td>lorikeet</td>
+      <td>20</td>
+      <td>Sequence analysis, Genotyping</td>
+      <td>Genotype and phenotype</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>822</td>
+      <td>822</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>822</td>
+      <td>822</td>
+      <td>14</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lotus2</td>
+      <td>lotus2</td>
+      <td>LotuS2 OTU processing pipeline</td>
+      <td>lotus2</td>
+      <td>lotus2</td>
+      <td></td>
+      <td>lotus2</td>
+      <td>LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.</td>
+      <td>Sequence feature detection, DNA barcoding</td>
+      <td>Metagenomics, Taxonomy, Microbial ecology</td>
+      <td>To update</td>
+      <td>http://lotus2.earlham.ac.uk/</td>
+      <td>Metagenomics</td>
+      <td>lotus2</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2</td>
+      <td>2.32</td>
+      <td>lotus2</td>
+      <td>2.34.1</td>
+      <td>Sequence feature detection, DNA barcoding</td>
+      <td>Metagenomics, Taxonomy, Microbial ecology</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1219</td>
+      <td>1219</td>
+      <td>182</td>
+      <td>182</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>37</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1256</td>
+      <td>1256</td>
+      <td>186</td>
+      <td>186</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ltq_iquant_cli</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>ltq_iquant_cli</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lumpy_smoove</td>
+      <td>lumpy_smoove, vcf2hrdetect</td>
+      <td>Galaxy wrapper of the lumpy-using smoove workflow</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>lumpy_smoove</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove</td>
+      <td>0.2.8+galaxy1</td>
+      <td>svtyper</td>
+      <td>0.7.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lumpy_sv</td>
+      <td>lumpy_prep, lumpy_sv</td>
+      <td>LUMPY - a general probabilistic framework for structural variant discovery</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://layerlab.org/software/</td>
+      <td>Variant Analysis</td>
+      <td>lumpy_sv</td>
+      <td>iuc</td>
+      <td>https://github.com/arq5x/lumpy-sv</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv</td>
+      <td>0.3.1</td>
+      <td>lumpy-sv</td>
+      <td>0.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1534</td>
+      <td>1534</td>
+      <td>199</td>
+      <td>199</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1534</td>
+      <td>1534</td>
+      <td>199</td>
+      <td>199</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>lumpy_sv</td>
+      <td>lumpy</td>
+      <td>Find structural variations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>lumpy_sv</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv</td>
+      <td>1.3</td>
+      <td>lumpy-sv</td>
+      <td>0.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>m6anet</td>
+      <td>m6anet</td>
+      <td>m6anet to detect m6A RNA modifications from nanopore data</td>
+      <td>m6Anet</td>
+      <td>m6Anet</td>
+      <td></td>
+      <td>m6Anet</td>
+      <td>Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.</td>
+      <td>Quantification, Imputation, Gene expression profiling</td>
+      <td>RNA-Seq, Transcriptomics, RNA, Machine learning</td>
+      <td>Up-to-date</td>
+      <td>https://m6anet.readthedocs.io/en/latest</td>
+      <td>Sequence Analysis</td>
+      <td>m6anet</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet</td>
+      <td>2.1.0</td>
+      <td>m6anet</td>
+      <td>2.1.0</td>
+      <td>Quantification, Imputation, Gene expression profiling</td>
+      <td>RNA-Seq, Transcriptomics, RNA, Machine learning</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>44</td>
+      <td>44</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>44</td>
+      <td>44</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maaslin2</td>
+      <td>maaslin2</td>
+      <td>MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.</td>
+      <td>maaslin2</td>
+      <td>maaslin2</td>
+      <td></td>
+      <td>MaAsLin2</td>
+      <td>MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.</td>
+      <td>Filtering, Statistical calculation, Standardisation and normalisation, Visualisation</td>
+      <td>Metagenomics, Statistics and probability</td>
+      <td>Up-to-date</td>
+      <td>http://huttenhower.sph.harvard.edu/maaslin</td>
+      <td>Metagenomics</td>
+      <td>maaslin2</td>
+      <td>iuc</td>
+      <td>https://github.com/biobakery/Maaslin2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2</td>
+      <td>1.18.0</td>
+      <td>bioconductor-maaslin2</td>
+      <td>1.18.0</td>
+      <td>Filtering, Standardisation and normalisation, Visualisation</td>
+      <td>Metagenomics, Statistics and probability</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2835</td>
+      <td>2835</td>
+      <td>59</td>
+      <td>59</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2835</td>
+      <td>2835</td>
+      <td>59</td>
+      <td>59</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>macs2</td>
+      <td>macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak</td>
+      <td>MACS - Model-based Analysis of ChIP-Seq</td>
+      <td>macs</td>
+      <td>macs</td>
+      <td></td>
+      <td>MACS</td>
+      <td>Model-based Analysis of ChIP-seq data.</td>
+      <td>Peak calling, Enrichment analysis, Gene regulatory network analysis</td>
+      <td>ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/taoliu/MACS</td>
+      <td>Sequence Analysis, Statistics</td>
+      <td>macs2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2</td>
+      <td>2.2.9.1</td>
+      <td>macs2</td>
+      <td>2.2.9.1</td>
+      <td>Peak calling, Enrichment analysis, Gene regulatory network analysis</td>
+      <td>ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites</td>
+      <td>9</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>87810</td>
+      <td>96069</td>
+      <td>4980</td>
+      <td>5629</td>
+      <td>153500</td>
+      <td>227569</td>
+      <td>12946</td>
+      <td>18825</td>
+      <td>10988</td>
+      <td>12301</td>
+      <td>692</td>
+      <td>807</td>
+      <td>252298</td>
+      <td>335939</td>
+      <td>18618</td>
+      <td>25261</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maf_cpg_filter</td>
+      <td>cpgFilter</td>
+      <td>Mask CpG/non-CpG sites from MAF file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>maf_cpg_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>85</td>
+      <td>356</td>
+      <td>6</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>85</td>
+      <td>356</td>
+      <td>6</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maf_stats</td>
+      <td>maf_stats1</td>
+      <td>MAF Coverage statistics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/</td>
+      <td>Genomic Interval Operations</td>
+      <td>maf_stats</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats</td>
+      <td>1.0.2+galaxy0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15</td>
+      <td>21</td>
+      <td>7</td>
+      <td>9</td>
+      <td>227</td>
+      <td>2470</td>
+      <td>52</td>
+      <td>464</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>243</td>
+      <td>2492</td>
+      <td>60</td>
+      <td>474</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mafft</td>
+      <td>rbc_mafft_add, rbc_mafft</td>
+      <td>Multiple alignment program for amino acid or nucleotide sequences</td>
+      <td>MAFFT</td>
+      <td>MAFFT</td>
+      <td></td>
+      <td>MAFFT</td>
+      <td>MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.</td>
+      <td>Multiple sequence alignment</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://mafft.cbrc.jp/alignment/software/</td>
+      <td>RNA</td>
+      <td>mafft</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mafft</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mafft</td>
+      <td>7.526</td>
+      <td>mafft</td>
+      <td>7.525</td>
+      <td>Multiple sequence alignment</td>
+      <td>Sequence analysis</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>172433</td>
+      <td>174456</td>
+      <td>1865</td>
+      <td>1951</td>
+      <td>108640</td>
+      <td>122790</td>
+      <td>4266</td>
+      <td>5521</td>
+      <td>20027</td>
+      <td>20027</td>
+      <td>1172</td>
+      <td>1172</td>
+      <td>301100</td>
+      <td>317273</td>
+      <td>7303</td>
+      <td>8644</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maftoaxt</td>
+      <td>maftoaxt</td>
+      <td>Convert dataset from MAF to axt format</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Convert Formats</td>
+      <td>ucsc_maftoaxt</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt</td>
+      <td>469</td>
+      <td>ucsc-maftoaxt</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mageck</td>
+      <td>mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test</td>
+      <td>Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.</td>
+      <td>mageck</td>
+      <td>mageck</td>
+      <td></td>
+      <td>MAGeCK</td>
+      <td>Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.</td>
+      <td>Genetic variation analysis</td>
+      <td>Genetics, Genetic variation, Genomics</td>
+      <td>To update</td>
+      <td>https://sourceforge.net/projects/mageck/</td>
+      <td>Genome editing</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck</td>
+      <td>0.5.9.2</td>
+      <td>mageck</td>
+      <td>0.5.9.5</td>
+      <td>Genetic variation analysis</td>
+      <td>Genetics, Genetic variation, Genomics</td>
+      <td>3</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>3</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>11761</td>
+      <td>12093</td>
+      <td>873</td>
+      <td>889</td>
+      <td>5762</td>
+      <td>5762</td>
+      <td>473</td>
+      <td>473</td>
+      <td>5610</td>
+      <td>5610</td>
+      <td>343</td>
+      <td>343</td>
+      <td>23133</td>
+      <td>23465</td>
+      <td>1689</td>
+      <td>1705</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mahotas_features</td>
+      <td>ip_mahotas_features</td>
+      <td>Compute image features using mahotas.</td>
+      <td></td>
+      <td></td>
+      <td>mahotas-feature-computation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/luispedro/mahotas</td>
+      <td>Imaging</td>
+      <td>mahotas_features</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features</td>
+      <td>0.7-2</td>
+      <td>mahotas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>39</td>
+      <td>44</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>44</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>make_nr</td>
+      <td>make_nr</td>
+      <td>Make a FASTA file non-redundant</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr</td>
+      <td>Fasta Manipulation, Sequence Analysis</td>
+      <td>make_nr</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr</td>
+      <td>0.0.3</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maker</td>
+      <td>maker, maker_map_ids</td>
+      <td>MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.</td>
+      <td>maker</td>
+      <td>maker</td>
+      <td></td>
+      <td>MAKER</td>
+      <td>Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.</td>
+      <td>Genome annotation</td>
+      <td>Genomics, DNA, Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.yandell-lab.org/software/maker.html</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker</td>
+      <td>2.31.11</td>
+      <td>maker</td>
+      <td>3.01.03</td>
+      <td>Genome annotation</td>
+      <td>Genomics, DNA, Sequence analysis</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>6417</td>
+      <td>6861</td>
+      <td>1315</td>
+      <td>1366</td>
+      <td>7235</td>
+      <td>7235</td>
+      <td>1858</td>
+      <td>1858</td>
+      <td>4112</td>
+      <td>4112</td>
+      <td>902</td>
+      <td>902</td>
+      <td>17764</td>
+      <td>18208</td>
+      <td>4075</td>
+      <td>4126</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maldiquant</td>
+      <td>maldi_quant_peak_detection, maldi_quant_preprocessing</td>
+      <td>MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://strimmerlab.org/software/maldiquant/</td>
+      <td>Proteomics</td>
+      <td>MALDIquant</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant</td>
+      <td>1.22.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1452</td>
+      <td>3822</td>
+      <td>61</td>
+      <td>68</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1065</td>
+      <td>1065</td>
+      <td>39</td>
+      <td>39</td>
+      <td>2517</td>
+      <td>4887</td>
+      <td>100</td>
+      <td>107</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>malt</td>
+      <td>malt_run</td>
+      <td>Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/husonlab/malt</td>
+      <td>Next Gen Mappers</td>
+      <td>malt_run</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt</td>
+      <td>0.5.3</td>
+      <td>malt</td>
+      <td>0.62</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>24</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>24</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>manta</td>
+      <td>manta</td>
+      <td>Structural variant and indel caller for mapped sequencing data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>manta</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/manta</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/manta</td>
+      <td>1.6</td>
+      <td>manta</td>
+      <td>1.6.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>34</td>
+      <td>34</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>218</td>
+      <td>218</td>
+      <td>34</td>
+      <td>34</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>map_param_value</td>
+      <td>map_param_value</td>
+      <td>Map a parameter value to another value</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>map_param_value</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3780</td>
+      <td>3780</td>
+      <td>67</td>
+      <td>67</td>
+      <td>1012</td>
+      <td>1012</td>
+      <td>57</td>
+      <td>57</td>
+      <td>105</td>
+      <td>105</td>
+      <td>3</td>
+      <td>3</td>
+      <td>4897</td>
+      <td>4897</td>
+      <td>127</td>
+      <td>127</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>map_peptides_to_bed</td>
+      <td>map_peptides_to_bed</td>
+      <td>Map peptides to a reference genome for display by a genome browser</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>map_peptides_to_bed</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed</td>
+      <td>0.2</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>38</td>
+      <td>44</td>
+      <td>6</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>38</td>
+      <td>44</td>
+      <td>6</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mapping_quality_stats</td>
+      <td>mapqstatistics</td>
+      <td>Collects and shows the distribution of MAPQ values in a BAM alignment file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Sequence Analysis, Statistics</td>
+      <td>mapping_quality_stats</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats</td>
+      <td>0.22.0</td>
+      <td>r-optparse</td>
+      <td>1.3.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mapping_to_ucsc</td>
+      <td>mapToUCSC</td>
+      <td>Format mapping data as UCSC custom track</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Visualization, Convert Formats, Next Gen Mappers</td>
+      <td>mapping_to_ucsc</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mapseq</td>
+      <td>mapseq</td>
+      <td>fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.</td>
+      <td>mapseq</td>
+      <td>mapseq</td>
+      <td></td>
+      <td>MAPseq</td>
+      <td>Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .</td>
+      <td>k-mer counting</td>
+      <td>Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs</td>
+      <td>To update</td>
+      <td>https://github.com/jfmrod/MAPseq</td>
+      <td>Metagenomics</td>
+      <td>mapseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq</td>
+      <td>2.1.1</td>
+      <td>perl</td>
+      <td></td>
+      <td>k-mer counting</td>
+      <td>Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7871</td>
+      <td>7871</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7871</td>
+      <td>7871</td>
+      <td>32</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>marine_omics</td>
+      <td>sanntis_marine</td>
+      <td>The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic &amp; metagenomic data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Finn-Lab/SanntiS</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics</td>
+      <td>0.9.3.5</td>
+      <td>sanntis</td>
+      <td>0.9.3.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>51</td>
+      <td>51</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>51</td>
+      <td>51</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mash</td>
+      <td>mash_screen, mash_sketch</td>
+      <td>Fast genome and metagenome distance estimation using MinHash</td>
+      <td>mash</td>
+      <td>mash</td>
+      <td></td>
+      <td>Mash</td>
+      <td>Fast genome and metagenome distance estimation using MinHash.</td>
+      <td>Sequence distance matrix generation</td>
+      <td>Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/marbl/Mash</td>
+      <td>Metagenomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash</td>
+      <td>2.3</td>
+      <td>mash</td>
+      <td>2.3</td>
+      <td>Sequence distance matrix generation</td>
+      <td>Metagenomics, Statistics and probability, Sequence analysis, DNA mutation</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>10119</td>
+      <td>10119</td>
+      <td>61</td>
+      <td>61</td>
+      <td>19</td>
+      <td>19</td>
+      <td>9</td>
+      <td>9</td>
+      <td>647</td>
+      <td>647</td>
+      <td>7</td>
+      <td>7</td>
+      <td>10785</td>
+      <td>10785</td>
+      <td>77</td>
+      <td>77</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mashmap</td>
+      <td>mashmap</td>
+      <td>Fast local alignment boundaries</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap</td>
+      <td>Sequence Analysis</td>
+      <td>mashmap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap</td>
+      <td>3.1.3</td>
+      <td>mashmap</td>
+      <td>3.1.3</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>894</td>
+      <td>894</td>
+      <td>12</td>
+      <td>12</td>
+      <td>81</td>
+      <td>81</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>975</td>
+      <td>975</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>masigpro</td>
+      <td>masigpro</td>
+      <td>Identify significantly differential expression profiles in time-course microarray experiments</td>
+      <td>masigpro</td>
+      <td>masigpro</td>
+      <td></td>
+      <td>maSigPro</td>
+      <td>Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.</td>
+      <td>Regression analysis</td>
+      <td>Gene expression, Molecular genetics, Microarray experiment, RNA-Seq</td>
+      <td>To update</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>masigpro</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro</td>
+      <td>1.49.3</td>
+      <td>coreutils</td>
+      <td>8.25</td>
+      <td>Regression analysis</td>
+      <td>Gene expression, Microarray experiment, RNA-Seq</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>471</td>
+      <td>582</td>
+      <td>35</td>
+      <td>40</td>
+      <td>589</td>
+      <td>589</td>
+      <td>80</td>
+      <td>80</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1060</td>
+      <td>1171</td>
+      <td>115</td>
+      <td>120</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>matchms</td>
+      <td>matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting</td>
+      <td>Searching, filtering and converting mass spectral libraries.</td>
+      <td>matchms</td>
+      <td>matchms</td>
+      <td></td>
+      <td>Matchms</td>
+      <td>Tool to import, process, clean, and compare mass spectrometry data.</td>
+      <td>Spectral library search, Format validation, Filtering</td>
+      <td>Metabolomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/matchms/matchms</td>
+      <td>Metabolomics</td>
+      <td>matchms</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/matchms</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/matchms</td>
+      <td>0.27.0</td>
+      <td>matchms</td>
+      <td>0.27.0</td>
+      <td>Spectral library search, Format validation, Filtering</td>
+      <td>Metabolomics</td>
+      <td>2</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>2</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1620</td>
+      <td>1620</td>
+      <td>70</td>
+      <td>70</td>
+      <td>27</td>
+      <td>27</td>
+      <td>8</td>
+      <td>8</td>
+      <td>1685</td>
+      <td>1685</td>
+      <td>12</td>
+      <td>12</td>
+      <td>3332</td>
+      <td>3332</td>
+      <td>90</td>
+      <td>90</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mauve_contig_mover</td>
+      <td>mauve_contig_mover</td>
+      <td>Order a draft genome relative to a related reference genome</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/mauve_contig_mover</td>
+      <td>Sequence Analysis</td>
+      <td>mauve_contig_mover</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/mauve_contig_mover</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover</td>
+      <td>1.0.10</td>
+      <td>mauve</td>
+      <td>2.4.0.r4736</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mavedb</td>
+      <td>mavedb_importer</td>
+      <td>data source for MaveDB</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Data Source</td>
+      <td>mavedb_importer</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb</td>
+      <td>0.9</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maxbin2</td>
+      <td>maxbin2</td>
+      <td>clusters metagenomic contigs into bins</td>
+      <td>maxbin</td>
+      <td>maxbin</td>
+      <td></td>
+      <td>MaxBin</td>
+      <td>Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.</td>
+      <td>Sequence assembly</td>
+      <td>Metagenomics, Sequence assembly, Microbiology</td>
+      <td>To update</td>
+      <td>https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html</td>
+      <td>Metagenomics</td>
+      <td>maxbin2</td>
+      <td>mbernt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2</td>
+      <td></td>
+      <td>maxbin2</td>
+      <td>2.2.7</td>
+      <td>Sequence assembly</td>
+      <td>Metagenomics, Sequence assembly, Microbiology</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2798</td>
+      <td>2798</td>
+      <td>314</td>
+      <td>314</td>
+      <td>2452</td>
+      <td>2452</td>
+      <td>508</td>
+      <td>508</td>
+      <td>914</td>
+      <td>914</td>
+      <td>89</td>
+      <td>89</td>
+      <td>6164</td>
+      <td>6164</td>
+      <td>911</td>
+      <td>911</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>maxquant</td>
+      <td>maxquant, maxquant_mqpar</td>
+      <td>wrapper for MaxQuant</td>
+      <td>maxquant</td>
+      <td>maxquant</td>
+      <td></td>
+      <td>MaxQuant</td>
+      <td>Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.</td>
+      <td>Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting</td>
+      <td>Proteomics experiment, Proteomics, Statistics and probability</td>
+      <td>Up-to-date</td>
+      <td>https://www.maxquant.org/</td>
+      <td>Proteomics</td>
+      <td>maxquant</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant</td>
+      <td>2.0.3.0</td>
+      <td>maxquant</td>
+      <td>2.0.3.0</td>
+      <td>Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering</td>
+      <td>Proteomics experiment, Proteomics, Statistics and probability</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>6863</td>
+      <td>7021</td>
+      <td>1251</td>
+      <td>1264</td>
+      <td>2798</td>
+      <td>2798</td>
+      <td>543</td>
+      <td>543</td>
+      <td>3189</td>
+      <td>3189</td>
+      <td>352</td>
+      <td>352</td>
+      <td>12850</td>
+      <td>13008</td>
+      <td>2146</td>
+      <td>2159</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mcl</td>
+      <td>mcl</td>
+      <td>The Markov Cluster Algorithm, a cluster algorithm for graphs</td>
+      <td>mcl</td>
+      <td>mcl</td>
+      <td></td>
+      <td>MCL</td>
+      <td>MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.</td>
+      <td>Clustering, Network analysis, Gene regulatory network analysis</td>
+      <td>Molecular interactions, pathways and networks</td>
+      <td>Up-to-date</td>
+      <td>https://micans.org/mcl/man/mcl.html</td>
+      <td>Sequence Analysis</td>
+      <td>mcl</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/mcl</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl</td>
+      <td>22.282</td>
+      <td>mcl</td>
+      <td>22.282</td>
+      <td>Clustering, Gene regulatory network analysis</td>
+      <td>Molecular interactions, pathways and networks</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>35</td>
+      <td>35</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>35</td>
+      <td>35</td>
+      <td>13</td>
+      <td>13</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mdanalysis</td>
+      <td>mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf</td>
+      <td>MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/MDAnalysis/mdanalysis</td>
+      <td>Computational chemistry</td>
+      <td>mdanalysis</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis</td>
+      <td>1.0.0</td>
+      <td>mdanalysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>10</td>
+      <td>5</td>
+      <td>10</td>
+      <td>0</td>
+      <td>10</td>
+      <td>5</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>3209</td>
+      <td>3268</td>
+      <td>318</td>
+      <td>326</td>
+      <td>182</td>
+      <td>182</td>
+      <td>51</td>
+      <td>51</td>
+      <td>397</td>
+      <td>397</td>
+      <td>39</td>
+      <td>39</td>
+      <td>3788</td>
+      <td>3847</td>
+      <td>408</td>
+      <td>416</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mdfileconverter</td>
+      <td>md_converter</td>
+      <td>A tool for interconverting between different MD structure and trajectory file formats.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>md_converter</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter</td>
+      <td>1.9.7</td>
+      <td>mdtraj</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>26720</td>
+      <td>26762</td>
+      <td>251</td>
+      <td>253</td>
+      <td>784</td>
+      <td>784</td>
+      <td>54</td>
+      <td>54</td>
+      <td>977</td>
+      <td>977</td>
+      <td>53</td>
+      <td>53</td>
+      <td>28481</td>
+      <td>28523</td>
+      <td>358</td>
+      <td>360</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mdslicer</td>
+      <td>md_slicer</td>
+      <td>A tool for slicing trajectory files using MDTraj.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>md_converter</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer</td>
+      <td>1.9.9</td>
+      <td>mdtraj</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>174</td>
+      <td>174</td>
+      <td>19</td>
+      <td>19</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td>441</td>
+      <td>441</td>
+      <td>7</td>
+      <td>7</td>
+      <td>621</td>
+      <td>621</td>
+      <td>30</td>
+      <td>30</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mdtraj</td>
+      <td>traj_selections_and_merge</td>
+      <td>MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/mdtraj/mdtraj</td>
+      <td>Computational chemistry</td>
+      <td>mdtraj</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj</td>
+      <td>1.9.7</td>
+      <td>mdtraj</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>36</td>
+      <td>36</td>
+      <td>8</td>
+      <td>8</td>
+      <td>63</td>
+      <td>63</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>99</td>
+      <td>99</td>
+      <td>12</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mea</td>
+      <td>mea</td>
+      <td>Maximum expected accuracy prediction</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.bioinf.uni-leipzig.de/Software/mea</td>
+      <td>RNA</td>
+      <td>mea</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea</td>
+      <td>0.6.4.1</td>
+      <td>mea</td>
+      <td>0.6.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>73</td>
+      <td>86</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>73</td>
+      <td>86</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mean-per-zone</td>
+      <td>mean_per_zone</td>
+      <td>Creates a png image showing statistic over areas as defined in the vector file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/</td>
+      <td>Visualization, GIS, Climate Analysis</td>
+      <td>mean_per_zone</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone</td>
+      <td>0.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20</td>
+      <td>25</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>25</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>measure_gastruloids</td>
+      <td>measureGastruloids</td>
+      <td>Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>measure_gastruloids</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids</td>
+      <td>20221216</td>
+      <td>fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>medaka</td>
+      <td>medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant</td>
+      <td>Sequence correction provided by ONT Research</td>
+      <td>medaka</td>
+      <td>medaka</td>
+      <td></td>
+      <td>Medaka</td>
+      <td>medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.</td>
+      <td>Base-calling, Variant calling, Sequence assembly</td>
+      <td>Sequence assembly, Machine learning</td>
+      <td>To update</td>
+      <td>https://github.com/nanoporetech/medaka</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka</td>
+      <td>1.7.2</td>
+      <td>medaka</td>
+      <td>2.0.0</td>
+      <td>Base-calling, Variant calling, Sequence assembly</td>
+      <td>Sequence assembly, Machine learning</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>117975</td>
+      <td>117975</td>
+      <td>1693</td>
+      <td>1693</td>
+      <td>55063</td>
+      <td>55063</td>
+      <td>796</td>
+      <td>796</td>
+      <td>9325</td>
+      <td>9325</td>
+      <td>639</td>
+      <td>639</td>
+      <td>182363</td>
+      <td>182363</td>
+      <td>3128</td>
+      <td>3128</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>medenv</td>
+      <td>iabiodiv_smartbiodiv_med_environ</td>
+      <td>Retrieve environmental data from etopo, cmems and woa</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/jeremyfix/medenv</td>
+      <td>Ecology, Data Source</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/jeremyfix/medenv</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv</td>
+      <td>0.1.0</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>megablast_xml_parser</td>
+      <td>megablast_xml_parser</td>
+      <td>Parse blast XML output</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Next Gen Mappers, Convert Formats</td>
+      <td>megablast_xml_parser</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser</td>
+      <td>1.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>743</td>
+      <td>816</td>
+      <td>103</td>
+      <td>141</td>
+      <td>292</td>
+      <td>2868</td>
+      <td>82</td>
+      <td>459</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1035</td>
+      <td>3684</td>
+      <td>185</td>
+      <td>600</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>megahit</td>
+      <td>megahit</td>
+      <td>An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.</td>
+      <td>megahit</td>
+      <td>megahit</td>
+      <td></td>
+      <td>MEGAHIT</td>
+      <td>Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.</td>
+      <td>Genome assembly</td>
+      <td>Metagenomics, Sequencing, Ecology, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/voutcn/megahit</td>
+      <td>Sequence Analysis, Assembly, Metagenomics</td>
+      <td>megahit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit</td>
+      <td>1.2.9</td>
+      <td>megahit</td>
+      <td>1.2.9</td>
+      <td>Genome assembly</td>
+      <td>Metagenomics, Sequencing, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>12692</td>
+      <td>13292</td>
+      <td>1349</td>
+      <td>1400</td>
+      <td>16645</td>
+      <td>16645</td>
+      <td>2140</td>
+      <td>2140</td>
+      <td>6214</td>
+      <td>6214</td>
+      <td>431</td>
+      <td>431</td>
+      <td>35551</td>
+      <td>36151</td>
+      <td>3920</td>
+      <td>3971</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>megahit_contig2fastg</td>
+      <td>megahit_contig2fastg</td>
+      <td>A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)</td>
+      <td>megahit</td>
+      <td>megahit</td>
+      <td></td>
+      <td>MEGAHIT</td>
+      <td>Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.</td>
+      <td>Genome assembly</td>
+      <td>Metagenomics, Sequencing, Ecology, Sequence assembly</td>
+      <td>To update</td>
+      <td>https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp</td>
+      <td>Sequence Analysis, Assembly, Metagenomics</td>
+      <td>megahit_contig2fastg</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg</td>
+      <td>1.1.3</td>
+      <td>megahit</td>
+      <td>1.2.9</td>
+      <td>Genome assembly</td>
+      <td>Metagenomics, Sequencing, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>513</td>
+      <td>557</td>
+      <td>152</td>
+      <td>155</td>
+      <td>74</td>
+      <td>74</td>
+      <td>35</td>
+      <td>35</td>
+      <td>10</td>
+      <td>10</td>
+      <td>4</td>
+      <td>4</td>
+      <td>597</td>
+      <td>641</td>
+      <td>191</td>
+      <td>194</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>megan</td>
+      <td>megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma</td>
+      <td>MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).</td>
+      <td>megan</td>
+      <td>megan</td>
+      <td></td>
+      <td>MEGAN</td>
+      <td>Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.</td>
+      <td>Sequence analysis, Taxonomic classification</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/husonlab/megan-ce</td>
+      <td>Sequence Analysis</td>
+      <td>megan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan</td>
+      <td>6.21.7</td>
+      <td>megan</td>
+      <td>6.25.9</td>
+      <td>Sequence analysis, Taxonomic classification</td>
+      <td>Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4130</td>
+      <td>4130</td>
+      <td>447</td>
+      <td>447</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4130</td>
+      <td>4130</td>
+      <td>447</td>
+      <td>447</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>meme</td>
+      <td>meme_dreme, meme_fimo, meme_meme, meme_psp_gen</td>
+      <td>The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.</td>
+      <td>meme_meme</td>
+      <td>meme_fimo, meme_meme</td>
+      <td></td>
+      <td>meme_meme</td>
+      <td>An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.</td>
+      <td>Nucleic acid feature detection, Protein feature detection, Statistical calculation</td>
+      <td>Data mining, Sequence analysis, Genetic variation, Statistics and probability</td>
+      <td>To update</td>
+      <td>http://meme-suite.org/</td>
+      <td>ChIP-seq</td>
+      <td>meme</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme</td>
+      <td>5.5.6</td>
+      <td>meme</td>
+      <td>5.5.7</td>
+      <td>Nucleic acid feature detection, Protein feature detection, Statistical calculation</td>
+      <td>Data mining, Sequence analysis, Genetic variation, Statistics and probability</td>
+      <td>3</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>20990</td>
+      <td>22979</td>
+      <td>762</td>
+      <td>892</td>
+      <td>10975</td>
+      <td>25929</td>
+      <td>1551</td>
+      <td>3249</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31965</td>
+      <td>48908</td>
+      <td>2313</td>
+      <td>4141</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>meme_chip</td>
+      <td>meme_chip</td>
+      <td>Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://meme-suite.org/</td>
+      <td>ChIP-seq</td>
+      <td>meme_chip</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip</td>
+      <td>4.11.2</td>
+      <td>graphicsmagick</td>
+      <td>1.3.26</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6413</td>
+      <td>7000</td>
+      <td>705</td>
+      <td>743</td>
+      <td>7260</td>
+      <td>7260</td>
+      <td>1171</td>
+      <td>1171</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13673</td>
+      <td>14260</td>
+      <td>1876</td>
+      <td>1914</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>meneco</td>
+      <td>meneco</td>
+      <td>Meneco computes minimal completions to your draft network with reactions from a repair network</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://bioasp.github.io/meneco/</td>
+      <td>Systems Biology</td>
+      <td>meneco</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/meneco</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/meneco</td>
+      <td>1.5.2</td>
+      <td>meneco</td>
+      <td>1.5.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>meningotype</td>
+      <td>meningotype</td>
+      <td>Assign sequence type to N. meningitidis genome assemblies</td>
+      <td>meningotype</td>
+      <td>meningotype</td>
+      <td></td>
+      <td>meningotype</td>
+      <td>In silico typing of Neisseria meningitidis contigs.</td>
+      <td>Genotyping, Multilocus sequence typing</td>
+      <td>Microbiology, Genotype and phenotype</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/MDU-PHL/meningotype</td>
+      <td>Sequence Analysis</td>
+      <td>meningotype</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype</td>
+      <td>0.8.5</td>
+      <td>meningotype</td>
+      <td>0.8.5</td>
+      <td>Multilocus sequence typing</td>
+      <td>Microbiology, Genotype and phenotype</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>merge</td>
+      <td>gops_merge_1</td>
+      <td>Merge the overlapping intervals of a dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>merge</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>565922</td>
+      <td>566630</td>
+      <td>418</td>
+      <td>441</td>
+      <td>45844</td>
+      <td>107523</td>
+      <td>671</td>
+      <td>4353</td>
+      <td>19828</td>
+      <td>19994</td>
+      <td>100</td>
+      <td>137</td>
+      <td>631594</td>
+      <td>694147</td>
+      <td>1189</td>
+      <td>4931</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>merge_cols</td>
+      <td>mergeCols1</td>
+      <td>Merge columns together.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>merge_cols</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols</td>
+      <td>1.0.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>20905</td>
+      <td>31051</td>
+      <td>1906</td>
+      <td>2128</td>
+      <td>21780</td>
+      <td>132833</td>
+      <td>885</td>
+      <td>3172</td>
+      <td>1524</td>
+      <td>1925</td>
+      <td>122</td>
+      <td>152</td>
+      <td>44209</td>
+      <td>165809</td>
+      <td>2913</td>
+      <td>5452</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mergeneighboursinlabelimage</td>
+      <td>ip_merge_neighbours_in_label</td>
+      <td>Merge Neighbours in Label Image</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>mergeneighboursinlabelimage</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage</td>
+      <td>0.3-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>18</td>
+      <td>25</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>25</td>
+      <td>2</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>merlin</td>
+      <td>merlin</td>
+      <td>Pedigree Analysis package</td>
+      <td>merlin</td>
+      <td>merlin</td>
+      <td></td>
+      <td>Merlin</td>
+      <td>Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation</td>
+      <td>Haplotype mapping, Genetic mapping</td>
+      <td>GWAS study, Mapping</td>
+      <td>Up-to-date</td>
+      <td>http://csg.sph.umich.edu/abecasis/Merlin/</td>
+      <td>Variant Analysis</td>
+      <td>merlin</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin</td>
+      <td>1.1.2</td>
+      <td>merlin</td>
+      <td>1.1.2</td>
+      <td>Haplotype mapping</td>
+      <td>GWAS study, Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>merqury</td>
+      <td>merqury, merquryplot</td>
+      <td>Merqury is a tool for evaluating genomes assemblies based of k-mer operations.</td>
+      <td>merqury</td>
+      <td>merqury</td>
+      <td></td>
+      <td>Merqury</td>
+      <td>Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.</td>
+      <td>Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly</td>
+      <td>Sequence assembly, Whole genome sequencing, Plant biology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/marbl/merqury</td>
+      <td>Assembly</td>
+      <td>merqury</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury</td>
+      <td>1.3</td>
+      <td>merqury</td>
+      <td>1.3</td>
+      <td>Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly</td>
+      <td>Sequence assembly, Whole genome sequencing, Plant biology</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3150</td>
+      <td>3150</td>
+      <td>477</td>
+      <td>477</td>
+      <td>730</td>
+      <td>730</td>
+      <td>196</td>
+      <td>196</td>
+      <td>1183</td>
+      <td>1183</td>
+      <td>151</td>
+      <td>151</td>
+      <td>5063</td>
+      <td>5063</td>
+      <td>824</td>
+      <td>824</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>meryl</td>
+      <td>meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode</td>
+      <td>Meryl a k-mer counter.</td>
+      <td>meryl</td>
+      <td>meryl</td>
+      <td></td>
+      <td>Meryl</td>
+      <td>Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.</td>
+      <td>k-mer counting</td>
+      <td>Whole genome sequencing, Genomics, Sequence analysis, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/marbl/meryl</td>
+      <td>Assembly</td>
+      <td>meryl</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl</td>
+      <td>1.3</td>
+      <td>merqury</td>
+      <td>1.3</td>
+      <td>k-mer counting</td>
+      <td>Whole genome sequencing, Genomics, Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>meta_proteome_analyzer</td>
+      <td>meta_proteome_analyzer</td>
+      <td>MetaProteomeAnalyzer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/compomics/meta-proteome-analyzer/</td>
+      <td>Proteomics</td>
+      <td>meta_proteome_analyzer</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer</td>
+      <td>2.0.0</td>
+      <td>mpa-portable</td>
+      <td>2.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>126</td>
+      <td>126</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>126</td>
+      <td>126</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metabat2</td>
+      <td>metabat2_jgi_summarize_bam_contig_depths, metabat2</td>
+      <td>MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.</td>
+      <td>MetaBAT_2</td>
+      <td>MetaBAT_2</td>
+      <td></td>
+      <td>MetaBAT 2</td>
+      <td>an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning</td>
+      <td>Read binning, Sequence assembly, Genome annotation</td>
+      <td>Metagenomics, Sequence assembly, Metagenomic sequencing</td>
+      <td>To update</td>
+      <td>https://bitbucket.org/berkeleylab/metabat/src/master/</td>
+      <td>Metagenomics</td>
+      <td>metabat2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2</td>
+      <td>2.15</td>
+      <td>metabat2</td>
+      <td>2.17</td>
+      <td>Read binning, Sequence assembly, Genome annotation</td>
+      <td>Metagenomics, Sequence assembly, Metagenomic sequencing</td>
+      <td>2</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6135</td>
+      <td>6135</td>
+      <td>382</td>
+      <td>382</td>
+      <td>881</td>
+      <td>881</td>
+      <td>151</td>
+      <td>151</td>
+      <td>1094</td>
+      <td>1094</td>
+      <td>104</td>
+      <td>104</td>
+      <td>8110</td>
+      <td>8110</td>
+      <td>637</td>
+      <td>637</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metabuli</td>
+      <td>metabuli_classify</td>
+      <td>Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences</td>
+      <td>metabuli</td>
+      <td>metabuli</td>
+      <td></td>
+      <td>metabuli</td>
+      <td>Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid</td>
+      <td>Taxonomic classification</td>
+      <td>Taxonomy</td>
+      <td>To update</td>
+      <td>https://github.com/steineggerlab/Metabuli</td>
+      <td>Sequence Analysis, Metagenomics</td>
+      <td>metabuli</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli</td>
+      <td>1.0.5</td>
+      <td>metabuli</td>
+      <td>1.0.8</td>
+      <td>Taxonomic classification</td>
+      <td>Taxonomy</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metaeuk</td>
+      <td>metaeuk_easy_predict</td>
+      <td>MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand.</td>
+      <td>MetaEuk</td>
+      <td>MetaEuk</td>
+      <td></td>
+      <td>MetaEuk</td>
+      <td>MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics</td>
+      <td>Homology-based gene prediction</td>
+      <td>Metagenomics, Gene and protein families</td>
+      <td>To update</td>
+      <td>https://github.com/soedinglab/metaeuk</td>
+      <td>Sequence Analysis, Genome annotation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk</td>
+      <td>7.bba0d80</td>
+      <td>metaeuk</td>
+      <td>6.a5d39d9</td>
+      <td>Homology-based gene prediction</td>
+      <td>Metagenomics, Gene and protein families</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>312</td>
+      <td>312</td>
+      <td>40</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>312</td>
+      <td>312</td>
+      <td>40</td>
+      <td>40</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metagene_annotator</td>
+      <td>metagene_annotator</td>
+      <td>MetaGeneAnnotator gene-finding program for prokaryote and phage</td>
+      <td>metageneannotator</td>
+      <td>metageneannotator</td>
+      <td></td>
+      <td>MetaGeneAnnotator</td>
+      <td>Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.</td>
+      <td>Sequence annotation</td>
+      <td>Genomics, Model organisms, Data submission, annotation and curation</td>
+      <td>Up-to-date</td>
+      <td>http://metagene.nig.ac.jp/</td>
+      <td>Sequence Analysis</td>
+      <td>metagene_annotator</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator</td>
+      <td>1.0</td>
+      <td>metagene_annotator</td>
+      <td>1.0</td>
+      <td>Sequence annotation</td>
+      <td>Genomics, Model organisms, Data submission, annotation and curation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>980</td>
+      <td>980</td>
+      <td>323</td>
+      <td>323</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>980</td>
+      <td>980</td>
+      <td>323</td>
+      <td>323</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metagenomeseq</td>
+      <td>metagenomeseq_normalizaton</td>
+      <td>metagenomeSeq Normalization</td>
+      <td>metagenomeseq</td>
+      <td>metagenomeseq</td>
+      <td></td>
+      <td>metagenomeSeq</td>
+      <td>Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.</td>
+      <td>Sequence visualisation, Statistical calculation</td>
+      <td>Metagenomics, Sequencing</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html</td>
+      <td>Metagenomics</td>
+      <td>metagenomeseq_normalization</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq</td>
+      <td>1.16.0-0.0.1</td>
+      <td>bioconductor-metagenomeseq</td>
+      <td>1.43.0</td>
+      <td>Sequence visualisation, Statistical calculation</td>
+      <td>Metagenomics, Sequencing</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>556</td>
+      <td>756</td>
+      <td>17</td>
+      <td>21</td>
+      <td>310</td>
+      <td>514</td>
+      <td>35</td>
+      <td>55</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>866</td>
+      <td>1270</td>
+      <td>52</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metanovo</td>
+      <td>metanovo</td>
+      <td>Produce targeted databases for mass spectrometry analysis.</td>
+      <td>metanovo</td>
+      <td>metanovo</td>
+      <td></td>
+      <td>MetaNovo</td>
+      <td>An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.</td>
+      <td>Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis</td>
+      <td>Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/uct-cbio/proteomics-pipelines</td>
+      <td>Proteomics</td>
+      <td>metanovo</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo</td>
+      <td>1.9.4</td>
+      <td>metanovo</td>
+      <td>1.9.4</td>
+      <td>Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis</td>
+      <td>Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4471</td>
+      <td>4471</td>
+      <td>29</td>
+      <td>29</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4471</td>
+      <td>4471</td>
+      <td>29</td>
+      <td>29</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metaphlan</td>
+      <td>customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan</td>
+      <td>MetaPhlAn for Metagenomic Phylogenetic Analysis</td>
+      <td>metaphlan</td>
+      <td>metaphlan</td>
+      <td></td>
+      <td>MetaPhlAn</td>
+      <td>Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.</td>
+      <td>Nucleic acid sequence analysis, Phylogenetic tree analysis</td>
+      <td>Metagenomics, Phylogenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/biobakery/MetaPhlAn</td>
+      <td>Metagenomics</td>
+      <td>metaphlan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan</td>
+      <td>4.1.1</td>
+      <td>metaphlan</td>
+      <td>4.1.1</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Metagenomics, Phylogenomics</td>
+      <td>1</td>
+      <td>2</td>
+      <td>4</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>16629</td>
+      <td>16648</td>
+      <td>1183</td>
+      <td>1187</td>
+      <td>3983</td>
+      <td>3983</td>
+      <td>572</td>
+      <td>572</td>
+      <td>4747</td>
+      <td>4747</td>
+      <td>278</td>
+      <td>278</td>
+      <td>25359</td>
+      <td>25378</td>
+      <td>2033</td>
+      <td>2037</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metaquantome</td>
+      <td>metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz</td>
+      <td>quantitative analysis of microbiome taxonomy and function</td>
+      <td>metaQuantome</td>
+      <td>metaQuantome</td>
+      <td></td>
+      <td>metaQuantome</td>
+      <td>metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.</td>
+      <td>Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference</td>
+      <td>Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/galaxyproteomics/metaquantome/</td>
+      <td>Proteomics</td>
+      <td>metaquantome</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome</td>
+      <td>2.0.2</td>
+      <td>metaquantome</td>
+      <td>2.0.2</td>
+      <td>Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference</td>
+      <td>Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>2730</td>
+      <td>2831</td>
+      <td>260</td>
+      <td>262</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1540</td>
+      <td>1540</td>
+      <td>71</td>
+      <td>71</td>
+      <td>4270</td>
+      <td>4371</td>
+      <td>331</td>
+      <td>333</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metawrapmg</td>
+      <td>metawrapmg_binning</td>
+      <td>A flexible pipeline for genome-resolved metagenomic data analysis</td>
+      <td>metawrap</td>
+      <td>metawrap</td>
+      <td></td>
+      <td>MetaWRAP</td>
+      <td>MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.</td>
+      <td>Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing</td>
+      <td>Whole genome sequencing, Metagenomic sequencing, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bxlab/metaWRAP</td>
+      <td>Metagenomics</td>
+      <td>metawrapmg_binning</td>
+      <td>galaxy-australia</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg</td>
+      <td>1.3.0</td>
+      <td>metawrap-mg</td>
+      <td>1.3.0</td>
+      <td>Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing</td>
+      <td>Whole genome sequencing, Metagenomic sequencing, Metagenomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>142</td>
+      <td>142</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>379</td>
+      <td>379</td>
+      <td>47</td>
+      <td>47</td>
+      <td>521</td>
+      <td>521</td>
+      <td>79</td>
+      <td>79</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metfrag</td>
+      <td>metfrag</td>
+      <td>[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/computational-metabolomics/metfrag-galaxy</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>computational-metabolomics</td>
+      <td>https://github.com/computational-metabolomics/metfrag-galaxy</td>
+      <td>https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag</td>
+      <td>2.4.5+galaxy3</td>
+      <td>metfrag</td>
+      <td>2.4.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>192</td>
+      <td>192</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>192</td>
+      <td>192</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metfrag-vis</td>
+      <td>metfrag_vis</td>
+      <td>[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/computational-metabolomics/metfrag-galaxy</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>computational-metabolomics</td>
+      <td>https://github.com/computational-metabolomics/metfrag-galaxy</td>
+      <td>https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis</td>
+      <td>2.4.5+galaxy0</td>
+      <td>metfrag</td>
+      <td>2.4.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>50</td>
+      <td>50</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>50</td>
+      <td>50</td>
+      <td>14</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>methtools</td>
+      <td>methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling</td>
+      <td>tools for methylation analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methtools</td>
+      <td>Sequence Analysis</td>
+      <td>methtools</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methtools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methtools</td>
+      <td>0.1.1</td>
+      <td>methtools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>632</td>
+      <td>5461</td>
+      <td>155</td>
+      <td>453</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>632</td>
+      <td>5461</td>
+      <td>155</td>
+      <td>453</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>methyldackel</td>
+      <td>pileometh</td>
+      <td>A tool for processing bisulfite sequencing alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/dpryan79/MethylDackel</td>
+      <td>Sequence Analysis</td>
+      <td>pileometh</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel</td>
+      <td>0.5.2</td>
+      <td>methyldackel</td>
+      <td>0.6.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>14907</td>
+      <td>18971</td>
+      <td>638</td>
+      <td>894</td>
+      <td>2677</td>
+      <td>2677</td>
+      <td>230</td>
+      <td>230</td>
+      <td>2313</td>
+      <td>2313</td>
+      <td>83</td>
+      <td>83</td>
+      <td>19897</td>
+      <td>23961</td>
+      <td>951</td>
+      <td>1207</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>methylkit</td>
+      <td>methylkit</td>
+      <td>A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://bioconductor.org/packages/release/bioc/html/methylKit.html</td>
+      <td>Epigenetics</td>
+      <td>methylkit</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methylkit</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/methylkit</td>
+      <td>0.99.2</td>
+      <td>bioconductor-methylkit</td>
+      <td>1.28.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>metilene</td>
+      <td>metilene</td>
+      <td>Differential DNA methylation calling</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA, Statistics</td>
+      <td>metilene</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/metilene</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/metilene</td>
+      <td>0.2.6.1</td>
+      <td>metilene</td>
+      <td>0.2.8</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3209</td>
+      <td>4572</td>
+      <td>312</td>
+      <td>442</td>
+      <td>479</td>
+      <td>479</td>
+      <td>79</td>
+      <td>79</td>
+      <td>315</td>
+      <td>315</td>
+      <td>51</td>
+      <td>51</td>
+      <td>4003</td>
+      <td>5366</td>
+      <td>442</td>
+      <td>572</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mfassignr</td>
+      <td>mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot</td>
+      <td>The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements</td>
+      <td>mfassignr</td>
+      <td>mfassignr</td>
+      <td></td>
+      <td>MFAssignR</td>
+      <td>Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements.</td>
+      <td>Visualisation</td>
+      <td>Proteomics experiment, Molecular interactions, pathways and networks, Workflows</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/MFAssignR</td>
+      <td>Metabolomics</td>
+      <td>MFAssignR</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr</td>
+      <td>1.1.1</td>
+      <td>r-mfassignr</td>
+      <td>1.1.1</td>
+      <td>Visualisation</td>
+      <td>Proteomics experiment, Molecular interactions, pathways and networks, Workflows</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mg_toolkit</td>
+      <td>mg_toolkit_bulk_download, mg_toolkit_original_metadata</td>
+      <td>Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.</td>
+      <td>mg-toolkit</td>
+      <td>mg-toolkit</td>
+      <td></td>
+      <td>mg-toolkit</td>
+      <td>Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.</td>
+      <td>Data retrieval</td>
+      <td>Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/EBI-Metagenomics/emg-toolkit</td>
+      <td>Metagenomics</td>
+      <td>mg_toolkit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit</td>
+      <td>0.10.4</td>
+      <td>mg-toolkit</td>
+      <td>0.10.4</td>
+      <td>Data retrieval</td>
+      <td>Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mgf_formatter</td>
+      <td>mgf_formatter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td></td>
+      <td></td>
+      <td>mgf_formatter</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter</td>
+      <td>1.0.0</td>
+      <td>mgf-formatter</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mgnify_seqprep</td>
+      <td>mgnify_seqprep</td>
+      <td>A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.</td>
+      <td>seqprep</td>
+      <td>seqprep</td>
+      <td></td>
+      <td>SeqPrep</td>
+      <td>Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.</td>
+      <td>Nucleic acid design</td>
+      <td>Genomics, Sequence assembly, Sequencing, Probes and primers</td>
+      <td>To update</td>
+      <td>https://github.com/jstjohn/SeqPrep</td>
+      <td>Fastq Manipulation, Sequence Analysis</td>
+      <td>mgnify_seqprep</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep</td>
+      <td>1.2</td>
+      <td></td>
+      <td></td>
+      <td>Nucleic acid design</td>
+      <td>Genomics, Sequence assembly, Sequencing, Probes and primers</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>573</td>
+      <td>573</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>573</td>
+      <td>573</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>miclip</td>
+      <td>mi_clip</td>
+      <td>Identification of binding sites in CLIP-Seq data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/src/contrib/Archive/MiClip/</td>
+      <td>Sequence Analysis</td>
+      <td>miclip</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/miclip</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/miclip</td>
+      <td>1.2.0</td>
+      <td>Rscript</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>microsatbed</td>
+      <td>microsatbed</td>
+      <td>Select microsatellites for a bed file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/lmdu/pytrf</td>
+      <td>Sequence Analysis</td>
+      <td>microsatbed</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed</td>
+      <td>1.3.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>228</td>
+      <td>228</td>
+      <td>4</td>
+      <td>4</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>246</td>
+      <td>246</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>microsatellite_birthdeath</td>
+      <td>microsatellite_birthdeath</td>
+      <td>Identify microsatellite births and deaths</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>microsatellite_birthdeath</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>microsats_alignment_level</td>
+      <td>microsats_align1</td>
+      <td>Extract Orthologous Microsatellites from pair-wise alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>microsats_alignment_level</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level</td>
+      <td>1.0.0</td>
+      <td>sputnik</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>135</td>
+      <td>973</td>
+      <td>50</td>
+      <td>140</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>135</td>
+      <td>973</td>
+      <td>50</td>
+      <td>140</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>microsats_mutability</td>
+      <td>microsats_mutability1</td>
+      <td>Estimate microsatellite mutability by specified attributes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>microsats_mutability</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability</td>
+      <td>1.1.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>312</td>
+      <td>22</td>
+      <td>87</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>312</td>
+      <td>22</td>
+      <td>87</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>migmap</td>
+      <td>migmap</td>
+      <td>mapper for full-length T- and B-cell repertoire sequencing</td>
+      <td>MiGMAP</td>
+      <td>MiGMAP</td>
+      <td></td>
+      <td>MiGMAP</td>
+      <td>Mapper for full-length T- and B-cell repertoire sequencing.</td>
+      <td>Sequence analysis, Read mapping</td>
+      <td>Immunoproteins, genes and antigens, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/mikessh/migmap</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>migmap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap</td>
+      <td>1.0.3</td>
+      <td>migmap</td>
+      <td>1.0.3</td>
+      <td>Sequence analysis, Read mapping</td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1082</td>
+      <td>1229</td>
+      <td>25</td>
+      <td>33</td>
+      <td>1153</td>
+      <td>1376</td>
+      <td>70</td>
+      <td>89</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2235</td>
+      <td>2605</td>
+      <td>95</td>
+      <td>122</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>minced</td>
+      <td>minced</td>
+      <td>MinCED - Mining CRISPRs in Environmental Datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README</td>
+      <td>Sequence Analysis</td>
+      <td>minced</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/minced</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/minced</td>
+      <td>0.2.0</td>
+      <td>minced</td>
+      <td>0.4.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1213</td>
+      <td>1309</td>
+      <td>115</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1213</td>
+      <td>1309</td>
+      <td>115</td>
+      <td>124</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mine</td>
+      <td>maximal_information_based_nonparametric_exploration</td>
+      <td>Maximal Information-based Nonparametric Exploration</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>mine</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine</td>
+      <td>0.0.1</td>
+      <td>MINE</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9</td>
+      <td>11</td>
+      <td>8</td>
+      <td>8</td>
+      <td>17</td>
+      <td>63</td>
+      <td>6</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>74</td>
+      <td>14</td>
+      <td>27</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>minia</td>
+      <td>minia</td>
+      <td>Short-read assembler based on a de Bruijn graph</td>
+      <td>minia</td>
+      <td>minia</td>
+      <td></td>
+      <td>Minia</td>
+      <td>Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.</td>
+      <td>Genome assembly</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://gatb.inria.fr/software/minia/</td>
+      <td>Assembly</td>
+      <td>minia</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia</td>
+      <td>3.2.6</td>
+      <td>minia</td>
+      <td>3.2.6</td>
+      <td>Genome assembly</td>
+      <td>Sequence assembly</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7116</td>
+      <td>7116</td>
+      <td>256</td>
+      <td>256</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>278</td>
+      <td>278</td>
+      <td>60</td>
+      <td>60</td>
+      <td>7394</td>
+      <td>7394</td>
+      <td>316</td>
+      <td>316</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>miniasm</td>
+      <td>miniasm</td>
+      <td>Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)</td>
+      <td>miniasm</td>
+      <td>miniasm</td>
+      <td></td>
+      <td>miniasm</td>
+      <td>Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.</td>
+      <td>De-novo assembly</td>
+      <td>Genomics, Sequence assembly</td>
+      <td>To update</td>
+      <td>https://github.com/lh3/miniasm</td>
+      <td>Assembly</td>
+      <td>miniasm</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm</td>
+      <td>0.3_r179</td>
+      <td>miniasm</td>
+      <td>0.3</td>
+      <td>De-novo assembly</td>
+      <td>Genomics, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>13357</td>
+      <td>13479</td>
+      <td>554</td>
+      <td>562</td>
+      <td>8416</td>
+      <td>8416</td>
+      <td>448</td>
+      <td>448</td>
+      <td>898</td>
+      <td>898</td>
+      <td>85</td>
+      <td>85</td>
+      <td>22671</td>
+      <td>22793</td>
+      <td>1087</td>
+      <td>1095</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>minimap2</td>
+      <td>minimap2</td>
+      <td>A fast pairwise aligner for genomic and spliced nucleotide sequences</td>
+      <td>minimap2</td>
+      <td>minimap2</td>
+      <td></td>
+      <td>Minimap2</td>
+      <td>Pairwise aligner for genomic and spliced nucleotide sequences</td>
+      <td>Pairwise sequence alignment</td>
+      <td>Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lh3/minimap2</td>
+      <td>Next Gen Mappers</td>
+      <td>minimap2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2</td>
+      <td>2.28</td>
+      <td>minimap2</td>
+      <td>2.28</td>
+      <td>Pairwise sequence alignment</td>
+      <td>Mapping</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>346530</td>
+      <td>349075</td>
+      <td>4323</td>
+      <td>4419</td>
+      <td>108535</td>
+      <td>108535</td>
+      <td>4075</td>
+      <td>4075</td>
+      <td>22331</td>
+      <td>22331</td>
+      <td>1166</td>
+      <td>1166</td>
+      <td>477396</td>
+      <td>479941</td>
+      <td>9564</td>
+      <td>9660</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>minipolish</td>
+      <td>minipolish</td>
+      <td>Polishing miniasm assemblies</td>
+      <td>minipolish</td>
+      <td>minipolish</td>
+      <td></td>
+      <td>minipolish</td>
+      <td>A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.</td>
+      <td>Localised reassembly, Read depth analysis</td>
+      <td>Sequence assembly, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/rrwick/Minipolish</td>
+      <td>Sequence Analysis</td>
+      <td>minipolish</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/minipolish</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/minipolish</td>
+      <td>0.1.3</td>
+      <td>minipolish</td>
+      <td>0.1.3</td>
+      <td>Localised reassembly, Read depth analysis</td>
+      <td>Sequence assembly, Sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>229</td>
+      <td>229</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>229</td>
+      <td>229</td>
+      <td>32</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>miniprot</td>
+      <td>miniprot, miniprot_index</td>
+      <td>Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.</td>
+      <td>miniprot</td>
+      <td>miniprot</td>
+      <td></td>
+      <td>miniprot</td>
+      <td>Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.</td>
+      <td>Sequence alignment, Protein sequence analysis</td>
+      <td>Sequence sites, features and motifs, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lh3/miniprot</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot</td>
+      <td>0.13</td>
+      <td>miniprot</td>
+      <td>0.13</td>
+      <td>Sequence alignment, Protein sequence analysis</td>
+      <td>Sequence sites, features and motifs, Sequence analysis</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1244</td>
+      <td>1244</td>
+      <td>86</td>
+      <td>86</td>
+      <td>24</td>
+      <td>24</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1268</td>
+      <td>1268</td>
+      <td>101</td>
+      <td>101</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>miranda</td>
+      <td>miranda</td>
+      <td>Finds potential target sites for miRNAs in genomic sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.microrna.org/</td>
+      <td>RNA</td>
+      <td>miranda</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda</td>
+      <td>3.3a+galaxy1</td>
+      <td>miranda</td>
+      <td>3.3a</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6408</td>
+      <td>6514</td>
+      <td>94</td>
+      <td>99</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6408</td>
+      <td>6514</td>
+      <td>94</td>
+      <td>99</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>miranda2asko</td>
+      <td>miranda2asko</td>
+      <td>Converts miRanda output into AskOmics format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats</td>
+      <td>miranda2asko</td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko</td>
+      <td>0.2</td>
+      <td>perl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mircounts</td>
+      <td>mircounts</td>
+      <td>Generates miRNA count lists from read alignments to mirBase.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Transcriptomics</td>
+      <td>mircounts</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts</td>
+      <td>1.6</td>
+      <td>tar</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1458</td>
+      <td>1458</td>
+      <td>36</td>
+      <td>36</td>
+      <td>1458</td>
+      <td>1458</td>
+      <td>36</td>
+      <td>36</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mirmachine</td>
+      <td>mirmachine</td>
+      <td>Tool to detect miRNA in genome sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/sinanugur/MirMachine</td>
+      <td>Sequence Analysis</td>
+      <td>mirmachine</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine</td>
+      <td>0.2.13</td>
+      <td>mirmachine</td>
+      <td>0.2.13</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mirnature</td>
+      <td>mirnature</td>
+      <td>Computational detection of canonical microRNAs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Bierinformatik/miRNAture</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>mirnature</td>
+      <td>iuc</td>
+      <td>https://github.com/Bierinformatik/miRNAture</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature</td>
+      <td>1.1</td>
+      <td>mirnature</td>
+      <td>1.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>misc</td>
+      <td>target_screen, use_theoretical_mz_annotations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/misc</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/misc</td>
+      <td>1.0.0</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mitobim</td>
+      <td>mitobim</td>
+      <td>assemble mitochondrial genomes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/chrishah/MITObim</td>
+      <td>Assembly</td>
+      <td>mitobim</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim</td>
+      <td>1.9.1</td>
+      <td>mitobim</td>
+      <td>1.9.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1117</td>
+      <td>1117</td>
+      <td>116</td>
+      <td>116</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>295</td>
+      <td>295</td>
+      <td>25</td>
+      <td>25</td>
+      <td>1412</td>
+      <td>1412</td>
+      <td>141</td>
+      <td>141</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mitohifi</td>
+      <td>mitohifi</td>
+      <td>Assembly mitogenomes from Pacbio HiFi read.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2</td>
+      <td>Assembly</td>
+      <td>mitohifi</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi</td>
+      <td>3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1020</td>
+      <td>1020</td>
+      <td>176</td>
+      <td>176</td>
+      <td>414</td>
+      <td>414</td>
+      <td>73</td>
+      <td>73</td>
+      <td>277</td>
+      <td>277</td>
+      <td>20</td>
+      <td>20</td>
+      <td>1711</td>
+      <td>1711</td>
+      <td>269</td>
+      <td>269</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mitos</td>
+      <td>mitos, mitos2</td>
+      <td>de-novo annotation of metazoan mitochondrial genomes</td>
+      <td>mitos</td>
+      <td>mitos</td>
+      <td></td>
+      <td>MITOS</td>
+      <td>De novo metazoan mitochondrial genome annotation.</td>
+      <td>Genome annotation</td>
+      <td>Zoology, Whole genome sequencing</td>
+      <td>To update</td>
+      <td>http://mitos.bioinf.uni-leipzig.de/</td>
+      <td>Sequence Analysis</td>
+      <td>mitos</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos</td>
+      <td>1.1.7</td>
+      <td>mitos</td>
+      <td>2.1.9</td>
+      <td>Genome annotation</td>
+      <td>Zoology, Whole genome sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>0</td>
+      <td>191295</td>
+      <td>191295</td>
+      <td>1111</td>
+      <td>1111</td>
+      <td>42265</td>
+      <td>42265</td>
+      <td>320</td>
+      <td>320</td>
+      <td>10904</td>
+      <td>10904</td>
+      <td>83</td>
+      <td>83</td>
+      <td>244464</td>
+      <td>244464</td>
+      <td>1514</td>
+      <td>1514</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mixmodel4repeated_measures</td>
+      <td>mixmodel4repeated_measures</td>
+      <td>[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>mixmodel4repeated_measures</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures</td>
+      <td>3.1.0</td>
+      <td>r-lme4</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mlst</td>
+      <td>mlst, mlst_list</td>
+      <td>Scan contig files against PubMLST typing schemes</td>
+      <td>mlst</td>
+      <td>mlst</td>
+      <td></td>
+      <td>MLST</td>
+      <td>Multi Locus Sequence Typing from an assembled genome or from a set of reads.</td>
+      <td>Multilocus sequence typing</td>
+      <td>Immunoproteins and antigens</td>
+      <td>To update</td>
+      <td>https://github.com/tseemann/mlst</td>
+      <td>Sequence Analysis</td>
+      <td>mlst</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst</td>
+      <td>2.22.0</td>
+      <td>mlst</td>
+      <td>2.23.0</td>
+      <td>Multilocus sequence typing</td>
+      <td>Immunoproteins and antigens</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>13300</td>
+      <td>13471</td>
+      <td>1480</td>
+      <td>1501</td>
+      <td>6532</td>
+      <td>6532</td>
+      <td>1167</td>
+      <td>1167</td>
+      <td>10334</td>
+      <td>11841</td>
+      <td>1083</td>
+      <td>1300</td>
+      <td>30166</td>
+      <td>31844</td>
+      <td>3730</td>
+      <td>3968</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>moFF</td>
+      <td>proteomics_moff</td>
+      <td>moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/compomics/moFF</td>
+      <td>Proteomics</td>
+      <td>proteomics_moff</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF</td>
+      <td>2.0.3</td>
+      <td>moff</td>
+      <td>2.0.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>331</td>
+      <td>762</td>
+      <td>20</td>
+      <td>34</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>137</td>
+      <td>137</td>
+      <td>4</td>
+      <td>4</td>
+      <td>468</td>
+      <td>899</td>
+      <td>24</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>moabs</td>
+      <td>moabs</td>
+      <td>MOABS for differential methylation analysis on Bisulfite sequencing data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/sunnyisgalaxy/moabs</td>
+      <td>Epigenetics</td>
+      <td>moabs</td>
+      <td>iuc</td>
+      <td>https://github.com/sunnyisgalaxy/moabs</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs</td>
+      <td>1.3.4.6</td>
+      <td>moabs</td>
+      <td>1.3.9.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>339</td>
+      <td>339</td>
+      <td>56</td>
+      <td>56</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>339</td>
+      <td>339</td>
+      <td>56</td>
+      <td>56</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mob_suite</td>
+      <td>mob_recon, mob_typer</td>
+      <td>MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/mob-suite</td>
+      <td>Sequence Analysis</td>
+      <td>mob_suite</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/mob-suite</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite</td>
+      <td>3.0.3</td>
+      <td>mob_suite</td>
+      <td>3.1.9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>119024</td>
+      <td>119024</td>
+      <td>628</td>
+      <td>628</td>
+      <td>42</td>
+      <td>42</td>
+      <td>2</td>
+      <td>2</td>
+      <td>36310</td>
+      <td>36310</td>
+      <td>191</td>
+      <td>191</td>
+      <td>155376</td>
+      <td>155376</td>
+      <td>821</td>
+      <td>821</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>molecule2gspan</td>
+      <td>bg_mol2gspan</td>
+      <td>converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan</td>
+      <td>Convert Formats</td>
+      <td>molecule_to_gspan</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan</td>
+      <td>0.2</td>
+      <td>openbabel</td>
+      <td>2.3.90dev7d621d9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>monocle3</td>
+      <td>monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers</td>
+      <td>De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_monocle3</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3</td>
+      <td>0.1.4</td>
+      <td>monocle3-cli</td>
+      <td>0.0.9</td>
+      <td></td>
+      <td></td>
+      <td>9</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3610</td>
+      <td>3610</td>
+      <td>559</td>
+      <td>559</td>
+      <td>1728</td>
+      <td>1728</td>
+      <td>434</td>
+      <td>434</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5338</td>
+      <td>5338</td>
+      <td>993</td>
+      <td>993</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>morpheus</td>
+      <td>morpheus</td>
+      <td>Morpheus MS Search Application</td>
+      <td>morpheus</td>
+      <td>morpheus</td>
+      <td></td>
+      <td>Morpheus</td>
+      <td>A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.</td>
+      <td>Peptide database search</td>
+      <td>Proteomics</td>
+      <td>To update</td>
+      <td>https://cwenger.github.io/Morpheus</td>
+      <td>Proteomics</td>
+      <td>morpheus</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus</td>
+      <td>288</td>
+      <td>morpheus</td>
+      <td>290</td>
+      <td>Peptide database search</td>
+      <td>Proteomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>105</td>
+      <td>153</td>
+      <td>12</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>833</td>
+      <td>833</td>
+      <td>93</td>
+      <td>93</td>
+      <td>938</td>
+      <td>986</td>
+      <td>105</td>
+      <td>112</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>morphological_operations</td>
+      <td>morphological_operations</td>
+      <td>Apply morphological operations to images</td>
+      <td></td>
+      <td></td>
+      <td>scipy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>morphological_operations</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations</td>
+      <td>1.12.0</td>
+      <td>scipy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mosdepth</td>
+      <td>mosdepth</td>
+      <td>fast and flexible BAM/CRAM depth calculation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/brentp/mosdepth</td>
+      <td>SAM</td>
+      <td>mosdepth</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth</td>
+      <td>0.3.8</td>
+      <td>mosdepth</td>
+      <td>0.3.8</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1278</td>
+      <td>1278</td>
+      <td>87</td>
+      <td>87</td>
+      <td>168</td>
+      <td>168</td>
+      <td>24</td>
+      <td>24</td>
+      <td>102</td>
+      <td>102</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1548</td>
+      <td>1548</td>
+      <td>116</td>
+      <td>116</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mothur</td>
+      <td>mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn</td>
+      <td>Mothur wrappers</td>
+      <td>mothur</td>
+      <td>mothur</td>
+      <td></td>
+      <td>mothur</td>
+      <td>Open-source, platform-independent, community-supported software for describing and comparing microbial communities</td>
+      <td>DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis</td>
+      <td>Microbial ecology, Taxonomy, Sequence analysis, Phylogeny</td>
+      <td>To update</td>
+      <td>https://www.mothur.org</td>
+      <td>Metagenomics</td>
+      <td>mothur</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur</td>
+      <td>1.0</td>
+      <td>mothur</td>
+      <td>1.48.0</td>
+      <td>DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis</td>
+      <td>Microbial ecology, Taxonomy, Sequence analysis, Phylogeny</td>
+      <td>129</td>
+      <td>129</td>
+      <td>129</td>
+      <td>0</td>
+      <td>129</td>
+      <td>129</td>
+      <td>129</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>128</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>126</td>
+      <td>129</td>
+      <td>129</td>
+      <td>0</td>
+      <td>297546</td>
+      <td>326056</td>
+      <td>37506</td>
+      <td>41763</td>
+      <td>565218</td>
+      <td>682083</td>
+      <td>72163</td>
+      <td>89926</td>
+      <td>167400</td>
+      <td>182490</td>
+      <td>26963</td>
+      <td>28404</td>
+      <td>1030164</td>
+      <td>1190629</td>
+      <td>136632</td>
+      <td>160093</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>motus</td>
+      <td>mereg_mOTUs_tables, motus_profiler</td>
+      <td>Tool for profiling the abundance of microbial taxa.</td>
+      <td>mOTUs</td>
+      <td>mOTUs</td>
+      <td></td>
+      <td>Metagenomic operational taxonomic units (mOTUs)</td>
+      <td>Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/motu-tool/mOTUs</td>
+      <td>Metagenomics</td>
+      <td>motus</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/motus</td>
+      <td>3.1.0</td>
+      <td>motus</td>
+      <td>3.1.0</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mqc</td>
+      <td>mqc</td>
+      <td>Ribosome profiling mapping quality control tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/Biobix/mQC</td>
+      <td>Sequence Analysis</td>
+      <td>mqc</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc</td>
+      <td>1.9</td>
+      <td>mqc</td>
+      <td>1.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>71</td>
+      <td>76</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>71</td>
+      <td>76</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mqppep</td>
+      <td>mqppep_anova, mqppep_preproc</td>
+      <td>MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/</td>
+      <td>Proteomics</td>
+      <td>mqppep</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep</td>
+      <td>0.1.19</td>
+      <td>bioconductor-preprocesscore</td>
+      <td>1.64.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mrbayes</td>
+      <td>mrbayes</td>
+      <td>A program for the Bayesian estimation of phylogeny.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>mrbayes</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes</td>
+      <td>1.0.2</td>
+      <td>mrbayes</td>
+      <td>3.2.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ms2deepscore</td>
+      <td>ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training</td>
+      <td>Mass spectra similarity scoring using a trained ms2deepscore model.</td>
+      <td>ms2deepscore</td>
+      <td>ms2deepscore</td>
+      <td></td>
+      <td>MS2DeepScore</td>
+      <td>MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.</td>
+      <td>Spectrum calculation, Spectral library search, Network analysis</td>
+      <td>Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening</td>
+      <td>To update</td>
+      <td>https://github.com/matchms/ms2deepscore</td>
+      <td>Metabolomics</td>
+      <td>ms2deepscore</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore</td>
+      <td>2.0.0</td>
+      <td>ms2deepscore</td>
+      <td>2.1.0</td>
+      <td>Spectrum calculation, Spectral library search, Network analysis</td>
+      <td>Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ms2snoop</td>
+      <td>ms2snoop</td>
+      <td>[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>ms2snoop</td>
+      <td>workflow4metabolomics</td>
+      <td></td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop</td>
+      <td>2.2.1</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msPurity</td>
+      <td>mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching</td>
+      <td>[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/computational-metabolomics/mspurity-galaxy</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>computational-metabolomics</td>
+      <td>https://github.com/computational-metabolomics/mspurity-galaxy</td>
+      <td>https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity</td>
+      <td>1.28.0</td>
+      <td>bioconductor-mspurity</td>
+      <td>1.28.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>848</td>
+      <td>848</td>
+      <td>91</td>
+      <td>91</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>848</td>
+      <td>848</td>
+      <td>91</td>
+      <td>91</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msaboot</td>
+      <td>msaboot</td>
+      <td>A multiple sequences alignment bootstrapping tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/msaboot</td>
+      <td>Fasta Manipulation</td>
+      <td>msaboot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot</td>
+      <td>0.1.2</td>
+      <td>msaboot</td>
+      <td>0.1.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>864</td>
+      <td>929</td>
+      <td>91</td>
+      <td>101</td>
+      <td>1100</td>
+      <td>1100</td>
+      <td>175</td>
+      <td>175</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1964</td>
+      <td>2029</td>
+      <td>266</td>
+      <td>276</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msconvert</td>
+      <td>msconvert</td>
+      <td>msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container</td>
+      <td>msconvert</td>
+      <td>msconvert</td>
+      <td></td>
+      <td>msConvert</td>
+      <td>msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.</td>
+      <td>Filtering, Formatting</td>
+      <td>Proteomics, Proteomics experiment</td>
+      <td>To update</td>
+      <td>http://proteowizard.sourceforge.net/tools.shtml</td>
+      <td>Proteomics</td>
+      <td>msconvert</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert</td>
+      <td>3.0.20287</td>
+      <td></td>
+      <td></td>
+      <td>Filtering, Formatting</td>
+      <td>Proteomics, Proteomics experiment</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20749</td>
+      <td>22184</td>
+      <td>455</td>
+      <td>469</td>
+      <td>1239</td>
+      <td>1239</td>
+      <td>71</td>
+      <td>71</td>
+      <td>2666</td>
+      <td>2666</td>
+      <td>53</td>
+      <td>53</td>
+      <td>24654</td>
+      <td>26089</td>
+      <td>579</td>
+      <td>593</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msgfplus</td>
+      <td>msgfplus</td>
+      <td>MSGF+</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>msgfplus</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus</td>
+      <td>0.5</td>
+      <td>msgf_plus</td>
+      <td>2024.03.26</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>473</td>
+      <td>529</td>
+      <td>33</td>
+      <td>43</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>529</td>
+      <td>33</td>
+      <td>43</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msmetaenhancer</td>
+      <td>msmetaenhancer</td>
+      <td></td>
+      <td>msmetaenhancer</td>
+      <td>msmetaenhancer</td>
+      <td></td>
+      <td>MSMetaEnhancer</td>
+      <td>Tool for mass spectra metadata annotation.</td>
+      <td>Annotation, Standardisation and normalisation</td>
+      <td>Metabolomics, Compound libraries and screening, Data submission, annotation and curation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/MSMetaEnhancer</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer</td>
+      <td>0.4.0</td>
+      <td>msmetaenhancer</td>
+      <td>0.4.0</td>
+      <td>Annotation, Standardisation and normalisation</td>
+      <td>Metabolomics, Compound libraries and screening, Data submission, annotation and curation</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>203</td>
+      <td>203</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td>251</td>
+      <td>251</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msms_extractor</td>
+      <td>msms_extractor</td>
+      <td>Extract MS/MS scans from the mzML file(s) based on PSM report.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>msms_extractor</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor</td>
+      <td>1.0.0</td>
+      <td>proteowizard</td>
+      <td>3_0_9992</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>110</td>
+      <td>110</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>110</td>
+      <td>110</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msp_merge</td>
+      <td>msp_merge</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge</td>
+      <td>0.1.0</td>
+      <td>matchms</td>
+      <td>0.27.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msp_split</td>
+      <td>msp_split</td>
+      <td>[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/computational-metabolomics/mspurity-galaxy</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>tomnl</td>
+      <td>https://github.com/computational-metabolomics/mspurity-galaxy</td>
+      <td>https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split</td>
+      <td>0.0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msstats</td>
+      <td>msstats</td>
+      <td>MSstats tool for analyzing mass spectrometry proteomic datasets</td>
+      <td>msstatstmt</td>
+      <td>msstatstmt</td>
+      <td></td>
+      <td>MSstatsTMT</td>
+      <td>Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</td>
+      <td>Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling</td>
+      <td>Proteomics, Proteomics experiment, Protein expression</td>
+      <td>To update</td>
+      <td>https://github.com/MeenaChoi/MSstats</td>
+      <td>Proteomics</td>
+      <td></td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats</td>
+      <td>4.0.0</td>
+      <td>bioconductor-msstats</td>
+      <td>4.10.0</td>
+      <td>Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling</td>
+      <td>Proteomics, Proteomics experiment, Protein expression</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2353</td>
+      <td>2353</td>
+      <td>559</td>
+      <td>559</td>
+      <td>1122</td>
+      <td>1122</td>
+      <td>211</td>
+      <td>211</td>
+      <td>1091</td>
+      <td>1091</td>
+      <td>35</td>
+      <td>35</td>
+      <td>4566</td>
+      <td>4566</td>
+      <td>805</td>
+      <td>805</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>msstatstmt</td>
+      <td>msstatstmt</td>
+      <td>MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://msstats.org/msstatstmt/</td>
+      <td>Proteomics</td>
+      <td>msstatstmt</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt</td>
+      <td>2.0.0</td>
+      <td>bioconductor-msstatstmt</td>
+      <td>2.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>795</td>
+      <td>795</td>
+      <td>104</td>
+      <td>104</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>461</td>
+      <td>461</td>
+      <td>12</td>
+      <td>12</td>
+      <td>1256</td>
+      <td>1256</td>
+      <td>116</td>
+      <td>116</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mt2mq</td>
+      <td>mt2mq</td>
+      <td>Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>mt2mq</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq</td>
+      <td>1.1.0</td>
+      <td>r-tidyverse</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>275</td>
+      <td>275</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>275</td>
+      <td>275</td>
+      <td>38</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>multigps</td>
+      <td>multigps</td>
+      <td>Analyzes collections of multi-condition ChIP-seq data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://mahonylab.org/software/multigps/</td>
+      <td>ChIP-seq</td>
+      <td>multigps</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps</td>
+      <td>0.74.0</td>
+      <td>fonts-conda-ecosystem</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>485</td>
+      <td>871</td>
+      <td>159</td>
+      <td>298</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>485</td>
+      <td>871</td>
+      <td>159</td>
+      <td>298</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>multigsea</td>
+      <td>multigsea</td>
+      <td>GSEA-based pathway enrichment analysis for multi-omics data</td>
+      <td>multiGSEA</td>
+      <td>multiGSEA</td>
+      <td></td>
+      <td>multiGSEA</td>
+      <td>A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.</td>
+      <td>Gene-set enrichment analysis, Aggregation, Pathway analysis</td>
+      <td>Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules</td>
+      <td>Up-to-date</td>
+      <td>https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html</td>
+      <td>Transcriptomics, Proteomics, Statistics</td>
+      <td>multigsea</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea</td>
+      <td>1.12.0</td>
+      <td>bioconductor-multigsea</td>
+      <td>1.12.0</td>
+      <td>Gene-set enrichment analysis, Aggregation, Pathway analysis</td>
+      <td>Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>106</td>
+      <td>106</td>
+      <td>25</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>106</td>
+      <td>106</td>
+      <td>25</td>
+      <td>25</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>multiqc</td>
+      <td>multiqc</td>
+      <td>MultiQC aggregates results from bioinformatics analyses across many samples into a single report</td>
+      <td>multiqc</td>
+      <td>multiqc</td>
+      <td></td>
+      <td>MultiQC</td>
+      <td>MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.</td>
+      <td>Validation, Sequencing quality control</td>
+      <td>Sequencing, Bioinformatics, Sequence analysis, Genomics</td>
+      <td>To update</td>
+      <td>http://multiqc.info/</td>
+      <td>Fastq Manipulation, Statistics, Visualization</td>
+      <td>multiqc</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc</td>
+      <td>1.24.1</td>
+      <td>multiqc</td>
+      <td>1.25.1</td>
+      <td>Sequencing quality control</td>
+      <td>Sequencing, Bioinformatics, Sequence analysis, Genomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>182221</td>
+      <td>192389</td>
+      <td>19343</td>
+      <td>20494</td>
+      <td>163961</td>
+      <td>182413</td>
+      <td>26449</td>
+      <td>29758</td>
+      <td>40663</td>
+      <td>41855</td>
+      <td>5974</td>
+      <td>6157</td>
+      <td>386845</td>
+      <td>416657</td>
+      <td>51766</td>
+      <td>56409</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>multispecies_orthologous_microsats</td>
+      <td>multispecies_orthologous_microsats</td>
+      <td>Extract orthologous microsatellites</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>multispecies_orthologous_microsats</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats</td>
+      <td>1.0.0</td>
+      <td>bx-sputnik</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mummer</td>
+      <td>mummerplot_wrapper</td>
+      <td>Draw dotplots using mummer, mucmer, or promer with mummerplot</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://mummer.sourceforge.net/</td>
+      <td>Graphics, Sequence Analysis, Visualization</td>
+      <td>mummer</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer</td>
+      <td>0.0.8</td>
+      <td>ghostscript</td>
+      <td>9.18</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>883</td>
+      <td>921</td>
+      <td>199</td>
+      <td>211</td>
+      <td>730</td>
+      <td>730</td>
+      <td>199</td>
+      <td>199</td>
+      <td>136</td>
+      <td>202</td>
+      <td>34</td>
+      <td>49</td>
+      <td>1749</td>
+      <td>1853</td>
+      <td>432</td>
+      <td>459</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mummer4</td>
+      <td>mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords</td>
+      <td>Mummer4 Tools</td>
+      <td>mummer4</td>
+      <td>mummer4</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/mummer4/mummer</td>
+      <td>Sequence Analysis</td>
+      <td>mummer4</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4</td>
+      <td>4.0.0rc1</td>
+      <td>mummer4</td>
+      <td>4.0.0rc1</td>
+      <td></td>
+      <td></td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>21587</td>
+      <td>22119</td>
+      <td>1940</td>
+      <td>2033</td>
+      <td>29284</td>
+      <td>29284</td>
+      <td>3626</td>
+      <td>3626</td>
+      <td>8194</td>
+      <td>8194</td>
+      <td>545</td>
+      <td>545</td>
+      <td>59065</td>
+      <td>59597</td>
+      <td>6111</td>
+      <td>6204</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>music_deconvolution</td>
+      <td>music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution</td>
+      <td>Multi-subject Single Cell deconvolution (MuSiC)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/xuranw/MuSiC</td>
+      <td>Transcriptomics</td>
+      <td>music</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution</td>
+      <td>0.1.1</td>
+      <td>music-deconvolution</td>
+      <td>0.1.1</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>5</td>
+      <td>4</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2801</td>
+      <td>2801</td>
+      <td>289</td>
+      <td>289</td>
+      <td>364</td>
+      <td>364</td>
+      <td>80</td>
+      <td>80</td>
+      <td>1357</td>
+      <td>1357</td>
+      <td>21</td>
+      <td>21</td>
+      <td>4522</td>
+      <td>4522</td>
+      <td>390</td>
+      <td>390</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mutate_snp_codon</td>
+      <td>mutate_snp_codon_1</td>
+      <td>Mutate Codons with SNPs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>mutate_snp_codon</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>44</td>
+      <td>49</td>
+      <td>5</td>
+      <td>5</td>
+      <td>81</td>
+      <td>417</td>
+      <td>23</td>
+      <td>118</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>125</td>
+      <td>466</td>
+      <td>28</td>
+      <td>123</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mutational_patterns</td>
+      <td>mutational_patterns</td>
+      <td>Mutational patterns and signatures in base substitution catalogs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>mutational_patterns</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns</td>
+      <td>3.12.0</td>
+      <td>bioconductor-mutationalpatterns</td>
+      <td>3.12.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mykrobe</td>
+      <td>mykrobe_predict</td>
+      <td>Antibiotic resistance predictions</td>
+      <td>Mykrobe</td>
+      <td>Mykrobe</td>
+      <td></td>
+      <td>Mykrobe</td>
+      <td>Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed</td>
+      <td>Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming</td>
+      <td>Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics</td>
+      <td>To update</td>
+      <td>https://github.com/Mykrobe-tools/mykrobe</td>
+      <td>Sequence Analysis</td>
+      <td>mykrobe</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe</td>
+      <td>0.10.0</td>
+      <td>mykrobe</td>
+      <td>0.13.0</td>
+      <td>Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming</td>
+      <td>Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mykrobe_parser</td>
+      <td>mykrobe_parseR</td>
+      <td>RScript to parse the results of mykrobe predictor.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/mykrobe-parser</td>
+      <td>Sequence Analysis</td>
+      <td>mykrobe_parser</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/mykrobe-parser</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser</td>
+      <td>0.1.4.1</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mz_to_sqlite</td>
+      <td>mz_to_sqlite</td>
+      <td>Creates a SQLite database for proteomics data</td>
+      <td>mztosqlite</td>
+      <td>mztosqlite</td>
+      <td></td>
+      <td>mzToSQLite</td>
+      <td>Convert proteomics data files into a SQLite database</td>
+      <td>Conversion, Peptide database search</td>
+      <td>Proteomics, Biological databases</td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/mzToSQLite</td>
+      <td>Proteomics</td>
+      <td>mz_to_sqlite</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite</td>
+      <td>2.1.1+galaxy0</td>
+      <td>mztosqlite</td>
+      <td>2.1.1</td>
+      <td>Conversion, Peptide database search</td>
+      <td>Proteomics, Biological databases</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>854</td>
+      <td>860</td>
+      <td>110</td>
+      <td>111</td>
+      <td>79</td>
+      <td>79</td>
+      <td>15</td>
+      <td>15</td>
+      <td>274</td>
+      <td>274</td>
+      <td>13</td>
+      <td>13</td>
+      <td>1207</td>
+      <td>1213</td>
+      <td>138</td>
+      <td>139</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mzmine</td>
+      <td>mzmine_batch</td>
+      <td>mass-spectrometry data processing, with the main focus on LC-MS data</td>
+      <td>mzmine</td>
+      <td>mzmine</td>
+      <td></td>
+      <td>MZmine</td>
+      <td>Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.</td>
+      <td>Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation</td>
+      <td>Proteomics, Metabolomics, Proteomics experiment, Small molecules</td>
+      <td>Up-to-date</td>
+      <td>http://mzmine.github.io/</td>
+      <td>Metabolomics</td>
+      <td>mzmine_batch</td>
+      <td>iuc</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine</td>
+      <td>3.9.0</td>
+      <td>mzmine</td>
+      <td>3.9.0</td>
+      <td>Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation</td>
+      <td>Proteomics, Metabolomics, Proteomics experiment, Small molecules</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mzml_validator</td>
+      <td>mzml_validator</td>
+      <td>mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools</td>
+      <td>Metabolomics, Proteomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator</td>
+      <td>0.1.0+galaxy2</td>
+      <td>lxml</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>mzxmlshaper</td>
+      <td>mzxmlshaper</td>
+      <td>Convert mzML, mzXML or netCDF files to mzML or mzXML</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://rdrr.io/bioc/mzR/</td>
+      <td>Metabolomics</td>
+      <td>mzxmlshaper</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper</td>
+      <td>1.0.0+galaxy0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>naltorfs</td>
+      <td>bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs</td>
+      <td>nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BlankenbergLab/nAltORFs</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs</td>
+      <td>0.1.2</td>
+      <td>naltorfs</td>
+      <td>0.1.2</td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>204</td>
+      <td>204</td>
+      <td>75</td>
+      <td>75</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>204</td>
+      <td>204</td>
+      <td>75</td>
+      <td>75</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nanocompore</td>
+      <td>nanocompore_db, nanocompore_sampcomp</td>
+      <td>Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.</td>
+      <td>Nanocompore</td>
+      <td>Nanocompore</td>
+      <td></td>
+      <td>Nanocompore</td>
+      <td>RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro</td>
+      <td>Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting</td>
+      <td>Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites</td>
+      <td>To update</td>
+      <td>https://nanocompore.rna.rocks/</td>
+      <td>Sequence Analysis</td>
+      <td>nanocompore</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore</td>
+      <td>1.0.0rc3.post2</td>
+      <td>nanocompore</td>
+      <td>1.0.4</td>
+      <td>PolyA signal detection, Genotyping, k-mer counting</td>
+      <td>Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>839</td>
+      <td>839</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>269</td>
+      <td>269</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1108</td>
+      <td>1108</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nanoplot</td>
+      <td>nanoplot</td>
+      <td>Plotting tool for long read sequencing data and alignments</td>
+      <td>nanoplot</td>
+      <td>nanoplot</td>
+      <td></td>
+      <td>NanoPlot</td>
+      <td>NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences</td>
+      <td>Scatter plot plotting, Box-Whisker plot plotting</td>
+      <td>Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/wdecoster/NanoPlot</td>
+      <td>Visualization</td>
+      <td>nanoplot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot</td>
+      <td>1.43.0</td>
+      <td>nanoplot</td>
+      <td>1.43.0</td>
+      <td>Scatter plot plotting, Box-Whisker plot plotting</td>
+      <td>Genomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>99052</td>
+      <td>100009</td>
+      <td>5671</td>
+      <td>5755</td>
+      <td>40386</td>
+      <td>40386</td>
+      <td>3371</td>
+      <td>3371</td>
+      <td>17919</td>
+      <td>17919</td>
+      <td>2188</td>
+      <td>2188</td>
+      <td>157357</td>
+      <td>158314</td>
+      <td>11230</td>
+      <td>11314</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nanopolish</td>
+      <td>nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants</td>
+      <td>Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/jts/nanopolish</td>
+      <td></td>
+      <td>nanopolish</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish</td>
+      <td>0.14.0</td>
+      <td>nanopolish</td>
+      <td>0.14.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>9284</td>
+      <td>9694</td>
+      <td>215</td>
+      <td>229</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2358</td>
+      <td>2358</td>
+      <td>49</td>
+      <td>49</td>
+      <td>11642</td>
+      <td>12052</td>
+      <td>264</td>
+      <td>278</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nanopolishcomp</td>
+      <td>nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate</td>
+      <td>NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.</td>
+      <td>nanopolishcomp</td>
+      <td>nanopolishcomp</td>
+      <td></td>
+      <td>NanopolishComp</td>
+      <td>NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.</td>
+      <td>Methylation analysis, Collapsing methods</td>
+      <td>Sequence analysis, Sequencing, Genetic variation</td>
+      <td>To update</td>
+      <td>https://a-slide.github.io/NanopolishComp</td>
+      <td>Sequence Analysis</td>
+      <td>nanopolishcomp</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp</td>
+      <td>0.6.11</td>
+      <td>nanopolishcomp</td>
+      <td>0.6.12</td>
+      <td>Methylation analysis, Collapsing methods</td>
+      <td>Sequence analysis, Sequencing, Genetic variation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1091</td>
+      <td>1091</td>
+      <td>44</td>
+      <td>44</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1091</td>
+      <td>1091</td>
+      <td>44</td>
+      <td>44</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nastiseq</td>
+      <td>nastiseq</td>
+      <td>A method to identify cis-NATs using ssRNA-seq</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/</td>
+      <td>RNA</td>
+      <td>nastiseq</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq</td>
+      <td>1.0</td>
+      <td>r-nastiseq</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>36</td>
+      <td>40</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>36</td>
+      <td>40</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_acc_download</td>
+      <td>ncbi_acc_download</td>
+      <td>Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/kblin/ncbi-acc-download</td>
+      <td>Data Source</td>
+      <td>ncbi_acc_download</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download</td>
+      <td>0.2.8</td>
+      <td>ncbi-acc-download</td>
+      <td>0.2.8</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6873</td>
+      <td>6873</td>
+      <td>1664</td>
+      <td>1664</td>
+      <td>17651</td>
+      <td>17651</td>
+      <td>4513</td>
+      <td>4513</td>
+      <td>6228</td>
+      <td>6228</td>
+      <td>972</td>
+      <td>972</td>
+      <td>30752</td>
+      <td>30752</td>
+      <td>7149</td>
+      <td>7149</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_blast_plus</td>
+      <td>blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper</td>
+      <td>NCBI BLAST+</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://blast.ncbi.nlm.nih.gov/</td>
+      <td>Sequence Analysis</td>
+      <td>ncbi_blast_plus</td>
+      <td>devteam</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus</td>
+      <td>https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus</td>
+      <td>2.14.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>16</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>15</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>15</td>
+      <td>16</td>
+      <td>16</td>
+      <td>15</td>
+      <td>0</td>
+      <td>391141</td>
+      <td>443752</td>
+      <td>9760</td>
+      <td>10546</td>
+      <td>306361</td>
+      <td>350178</td>
+      <td>11767</td>
+      <td>13684</td>
+      <td>227235</td>
+      <td>244814</td>
+      <td>3192</td>
+      <td>3617</td>
+      <td>924737</td>
+      <td>1038744</td>
+      <td>24719</td>
+      <td>27847</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_datasets</td>
+      <td>datasets_download_gene, datasets_download_genome</td>
+      <td>NCBI datasets downloads biological sequence data across all domains of life from NCBI.</td>
+      <td>ncbi_datasets</td>
+      <td>ncbi_datasets</td>
+      <td></td>
+      <td>NCBI Datasets</td>
+      <td>NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.</td>
+      <td>Data handling, Sequence database search, Data retrieval</td>
+      <td>Biological databases</td>
+      <td>To update</td>
+      <td>https://github.com/ncbi/datasets</td>
+      <td>Data Source</td>
+      <td>ncbi_datasets</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets</td>
+      <td>16.20.0</td>
+      <td>ncbi-datasets-cli</td>
+      <td></td>
+      <td>Data handling, Sequence database search, Data retrieval</td>
+      <td>Biological databases</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>4417</td>
+      <td>4417</td>
+      <td>1024</td>
+      <td>1024</td>
+      <td>6940</td>
+      <td>6940</td>
+      <td>2275</td>
+      <td>2275</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>11358</td>
+      <td>11358</td>
+      <td>3300</td>
+      <td>3300</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_egapx</td>
+      <td>ncbi_egapx</td>
+      <td>Eukaryotic Genome Annotation Pipeline - External (EGAPx)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ncbi/egapx</td>
+      <td>Genome annotation</td>
+      <td>ncbi_egapx</td>
+      <td>richard-burhans</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx</td>
+      <td>0.2-alpha</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_entrez_direct</td>
+      <td>ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch</td>
+      <td>NCBI Entrez Direct allow fetching data from NCBI Databases</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://www.ncbi.nlm.nih.gov/books/NBK179288/</td>
+      <td>Data Source</td>
+      <td>ncbi_entrez_direct</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct</td>
+      <td>22.4</td>
+      <td>entrez-direct</td>
+      <td>22.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_entrez_eutils</td>
+      <td>ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary</td>
+      <td>NCBI Entrez E-Utilties allow fetching data from NCBI Databases</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.ncbi.nlm.nih.gov/books/NBK25501/</td>
+      <td>Data Source</td>
+      <td>ncbi_entrez_eutils</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils</td>
+      <td>1.70</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>2794</td>
+      <td>3191</td>
+      <td>533</td>
+      <td>664</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2794</td>
+      <td>3191</td>
+      <td>533</td>
+      <td>664</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_fcs_adaptor</td>
+      <td>ncbi_fcs_adaptor</td>
+      <td>FCS-adaptor detects adaptor and vector contamination in genome sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ncbi/fcs</td>
+      <td>Sequence Analysis</td>
+      <td>ncbi_fcs_adaptor</td>
+      <td>richard-burhans</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor</td>
+      <td>0.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>842</td>
+      <td>842</td>
+      <td>93</td>
+      <td>93</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>842</td>
+      <td>842</td>
+      <td>93</td>
+      <td>93</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ncbi_fcs_gx</td>
+      <td>ncbi_fcs_gx</td>
+      <td>FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).</td>
+      <td>ncbi_fcs</td>
+      <td>ncbi_fcs</td>
+      <td></td>
+      <td>NCBI fcs</td>
+      <td>The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.</td>
+      <td>Sequence assembly validation, Sequence trimming, Sequence contamination filtering</td>
+      <td>Sequence analysis, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/ncbi/fcs-gx</td>
+      <td>Sequence Analysis</td>
+      <td>ncbi_fcs_gx</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx</td>
+      <td>0.5.4</td>
+      <td>ncbi-fcs-gx</td>
+      <td>0.5.4</td>
+      <td>Sequence assembly validation, Sequence trimming, Sequence contamination filtering</td>
+      <td>Sequence analysis, Sequence assembly</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>125</td>
+      <td>125</td>
+      <td>26</td>
+      <td>26</td>
+      <td>2489</td>
+      <td>2489</td>
+      <td>139</td>
+      <td>139</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2614</td>
+      <td>2614</td>
+      <td>165</td>
+      <td>165</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>necat</td>
+      <td>necat</td>
+      <td>Error correction and de-novo assembly for ONT Nanopore reads</td>
+      <td>necat</td>
+      <td>necat</td>
+      <td></td>
+      <td>NECAT</td>
+      <td>NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.</td>
+      <td>De-novo assembly</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/xiaochuanle/NECAT</td>
+      <td>Assembly</td>
+      <td>necat</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat</td>
+      <td>0.0.1_update20200803</td>
+      <td>necat</td>
+      <td>0.0.1_update20200803</td>
+      <td>De-novo assembly</td>
+      <td>Sequence assembly</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>790</td>
+      <td>790</td>
+      <td>160</td>
+      <td>160</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>790</td>
+      <td>790</td>
+      <td>160</td>
+      <td>160</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>netboxr</td>
+      <td>netboxr</td>
+      <td>netboxr enables automated discovery of biological process modules by network analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Systems Biology</td>
+      <td>netboxr</td>
+      <td>bgruening</td>
+      <td></td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/netboxr</td>
+      <td>1.6.0</td>
+      <td>bioconductor-netboxr</td>
+      <td>1.9.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>newick_utils</td>
+      <td>newick_display</td>
+      <td>Perform operations on Newick trees</td>
+      <td>newick_utilities</td>
+      <td>newick_utilities</td>
+      <td></td>
+      <td>Newick Utilities</td>
+      <td>The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.</td>
+      <td>Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction</td>
+      <td>Phylogeny, Genomics, Computer science</td>
+      <td>To update</td>
+      <td>http://cegg.unige.ch/newick_utils</td>
+      <td>Visualization, Metagenomics</td>
+      <td>newick_utils</td>
+      <td>iuc</td>
+      <td>https://github.com/tjunier/newick_utils</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils</td>
+      <td>1.6+galaxy1</td>
+      <td>newick_utils</td>
+      <td>1.6</td>
+      <td></td>
+      <td>Phylogeny, Genomics, Computer science</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>33637</td>
+      <td>34195</td>
+      <td>1113</td>
+      <td>1172</td>
+      <td>16257</td>
+      <td>16257</td>
+      <td>1816</td>
+      <td>1816</td>
+      <td>7582</td>
+      <td>7582</td>
+      <td>899</td>
+      <td>899</td>
+      <td>57476</td>
+      <td>58034</td>
+      <td>3828</td>
+      <td>3887</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nextclade</td>
+      <td>nextalign, nextclade</td>
+      <td>Identify differences between your sequences and a reference sequence used by Nextstrain</td>
+      <td>nextclade</td>
+      <td>nextclade</td>
+      <td></td>
+      <td>Nextclade</td>
+      <td>Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.</td>
+      <td>Methylation analysis, Variant calling</td>
+      <td>Genomics, Sequence analysis, Cladistics</td>
+      <td>To update</td>
+      <td>https://github.com/nextstrain/nextclade</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade</td>
+      <td>2.7.0</td>
+      <td>nextalign</td>
+      <td>2.14.0</td>
+      <td>Methylation analysis, Variant calling</td>
+      <td>Genomics, Cladistics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4411</td>
+      <td>4411</td>
+      <td>396</td>
+      <td>396</td>
+      <td>9708</td>
+      <td>9708</td>
+      <td>279</td>
+      <td>279</td>
+      <td>2099</td>
+      <td>2099</td>
+      <td>212</td>
+      <td>212</td>
+      <td>16218</td>
+      <td>16218</td>
+      <td>887</td>
+      <td>887</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nextdenovo</td>
+      <td>nextdenovo</td>
+      <td>String graph-based de novo assembler for long reads</td>
+      <td>nextdenovo</td>
+      <td>nextdenovo</td>
+      <td></td>
+      <td>NextDenovo</td>
+      <td>NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages.</td>
+      <td>De-novo assembly, Genome assembly</td>
+      <td>Sequencing, Sequence assembly</td>
+      <td>To update</td>
+      <td>https://github.com/Nextomics/NextDenovo</td>
+      <td>Assembly</td>
+      <td>nextdenovo</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo</td>
+      <td>2.5.0</td>
+      <td>nextdenovo</td>
+      <td>2.5.2</td>
+      <td>De-novo assembly, Genome assembly</td>
+      <td>Sequencing, Sequence assembly</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>391</td>
+      <td>391</td>
+      <td>158</td>
+      <td>158</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>391</td>
+      <td>391</td>
+      <td>158</td>
+      <td>158</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ngmlr</td>
+      <td>ngmlr</td>
+      <td>CoNvex Gap-cost alignMents for Long Reads</td>
+      <td>ngmlr</td>
+      <td>ngmlr</td>
+      <td></td>
+      <td>NGMLR</td>
+      <td>An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.</td>
+      <td>DNA mapping, Sequence alignment, Genetic variation analysis</td>
+      <td>Sequencing, Mapping, DNA structural variation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/philres/ngmlr</td>
+      <td>Next Gen Mappers</td>
+      <td>ngmlr</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr</td>
+      <td>0.2.7</td>
+      <td>ngmlr</td>
+      <td>0.2.7</td>
+      <td>DNA mapping, Sequence alignment, Genetic variation analysis</td>
+      <td>Sequencing, Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1403</td>
+      <td>1403</td>
+      <td>49</td>
+      <td>49</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1403</td>
+      <td>1403</td>
+      <td>49</td>
+      <td>49</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ngsutils</td>
+      <td>ngsutils_bam_filter</td>
+      <td>NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.</td>
+      <td>ngsutils</td>
+      <td>ngsutils</td>
+      <td></td>
+      <td>NGSUtils</td>
+      <td>NGSUtils is a suite of software tools for working with next-generation sequencing datasets</td>
+      <td>Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering</td>
+      <td>Genomics, Transcriptomics</td>
+      <td>To update</td>
+      <td>https://github.com/ngsutils/ngsutils</td>
+      <td>SAM</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils</td>
+      <td></td>
+      <td>ngsutils</td>
+      <td>0.5.9</td>
+      <td>Read pre-processing, Variant calling, Formatting, Sequence contamination filtering</td>
+      <td>Transcriptomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>24611</td>
+      <td>29662</td>
+      <td>633</td>
+      <td>716</td>
+      <td>15523</td>
+      <td>21395</td>
+      <td>740</td>
+      <td>1128</td>
+      <td>7751</td>
+      <td>8972</td>
+      <td>125</td>
+      <td>145</td>
+      <td>47885</td>
+      <td>60029</td>
+      <td>1498</td>
+      <td>1989</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nlstradamus</td>
+      <td>nlstradamus</td>
+      <td>Find nuclear localization signals (NLSs) in protein sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.moseslab.csb.utoronto.ca/NLStradamus</td>
+      <td>Fasta Manipulation, Sequence Analysis</td>
+      <td>nlstradamus</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus</td>
+      <td>0.0.11</td>
+      <td>NLStradamus</td>
+      <td>1.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nmr_annotation</td>
+      <td>NmrAnnotation</td>
+      <td>[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>nmr_annotation</td>
+      <td>marie-tremblay-metatoul</td>
+      <td>https://github.com/workflow4metabolomics/nmr_annotation</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation</td>
+      <td>3.0.0</td>
+      <td>r-batch</td>
+      <td>1.1_4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>49</td>
+      <td>49</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>49</td>
+      <td>49</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nmr_annotation2d</td>
+      <td>2DNmrAnnotation</td>
+      <td>[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>2dnmrannotation</td>
+      <td>marie-tremblay-metatoul</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d</td>
+      <td>2.0.0</td>
+      <td>r-batch</td>
+      <td>1.1_4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nmr_preprocessing</td>
+      <td>NMR_Preprocessing, NMR_Read</td>
+      <td>[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>nmr_preprocessing</td>
+      <td>marie-tremblay-metatoul</td>
+      <td>https://github.com/workflow4metabolomics/nmr_preprocessing</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing</td>
+      <td></td>
+      <td>r-batch</td>
+      <td>1.1_4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>142</td>
+      <td>142</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>335</td>
+      <td>341</td>
+      <td>9</td>
+      <td>9</td>
+      <td>477</td>
+      <td>483</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nonpareil</td>
+      <td>nonpareil</td>
+      <td>Estimate average coverage in metagenomic datasets</td>
+      <td>nonpareil</td>
+      <td>nonpareil</td>
+      <td></td>
+      <td>nonpareil</td>
+      <td>Estimate metagenomic coverage and sequence diversity</td>
+      <td>Operation</td>
+      <td></td>
+      <td>To update</td>
+      <td>http://nonpareil.readthedocs.io</td>
+      <td>Metagenomics</td>
+      <td>nonpareil</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil</td>
+      <td>3.1.1</td>
+      <td>nonpareil</td>
+      <td>3.5.5</td>
+      <td>Operation</td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>107</td>
+      <td>143</td>
+      <td>13</td>
+      <td>15</td>
+      <td>148</td>
+      <td>148</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>255</td>
+      <td>291</td>
+      <td>33</td>
+      <td>35</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>normalization</td>
+      <td>normalization</td>
+      <td>[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>normalization</td>
+      <td>marie-tremblay-metatoul</td>
+      <td>https://github.com/workflow4metabolomics/normalization</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization</td>
+      <td>1.0.7</td>
+      <td>r-batch</td>
+      <td>1.1_4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>152</td>
+      <td>162</td>
+      <td>39</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>233</td>
+      <td>236</td>
+      <td>12</td>
+      <td>12</td>
+      <td>385</td>
+      <td>398</td>
+      <td>51</td>
+      <td>52</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>novoplasty</td>
+      <td>novoplasty</td>
+      <td>NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ndierckx/NOVOPlasty</td>
+      <td>Assembly</td>
+      <td>novoplasty</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty</td>
+      <td>4.3.1</td>
+      <td>novoplasty</td>
+      <td>4.3.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7780</td>
+      <td>7780</td>
+      <td>337</td>
+      <td>337</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2323</td>
+      <td>2323</td>
+      <td>99</td>
+      <td>99</td>
+      <td>10104</td>
+      <td>10104</td>
+      <td>437</td>
+      <td>437</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nucleosome_prediction</td>
+      <td>Nucleosome</td>
+      <td>Prediction of Nucleosomes Positions on the Genome</td>
+      <td>nucleosome_prediction</td>
+      <td>nucleosome_prediction</td>
+      <td></td>
+      <td>nucleosome_prediction</td>
+      <td>Prediction of Nucleosomes Positions on the Genome</td>
+      <td>Prediction and recognition, Nucleosome position prediction, Sequence analysis</td>
+      <td>Structural genomics, Nucleic acid sites, features and motifs</td>
+      <td>Up-to-date</td>
+      <td>https://genie.weizmann.ac.il/software/nucleo_exe.html</td>
+      <td>Sequence Analysis</td>
+      <td>nucleosome_prediction</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction</td>
+      <td>3.0</td>
+      <td>nucleosome_prediction</td>
+      <td>3.0</td>
+      <td>Prediction and recognition, Nucleosome position prediction, Sequence analysis</td>
+      <td>Structural genomics, Nucleic acid sites, features and motifs</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>118</td>
+      <td>863</td>
+      <td>19</td>
+      <td>26</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>118</td>
+      <td>863</td>
+      <td>19</td>
+      <td>26</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>nugen_nudup</td>
+      <td>nugen_nudup</td>
+      <td>Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.</td>
+      <td>nudup</td>
+      <td>nudup</td>
+      <td></td>
+      <td>NuDup</td>
+      <td>Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.</td>
+      <td>Duplication detection</td>
+      <td>Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tecangenomics/nudup</td>
+      <td>SAM, Metagenomics, Sequence Analysis, Transcriptomics</td>
+      <td>nugen_nudup</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup</td>
+      <td>2.3.3</td>
+      <td>nudup</td>
+      <td>2.3.3</td>
+      <td>Duplication detection</td>
+      <td>Sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>numeric_clustering</td>
+      <td>numeric_clustering</td>
+      <td>Clustering tool for numberic values</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://scikit-learn.org/stable/index.html</td>
+      <td>Statistics</td>
+      <td>numeric_clustering</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering</td>
+      <td>0.9</td>
+      <td>anaconda</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>391</td>
+      <td>486</td>
+      <td>5</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>391</td>
+      <td>486</td>
+      <td>5</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>oases</td>
+      <td>oasesoptimiserv</td>
+      <td>Short read assembler</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Assembly, RNA</td>
+      <td>oases</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/oases</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/oases</td>
+      <td>1.4.0</td>
+      <td>oases</td>
+      <td>0.2.09</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>obisindicators</td>
+      <td>obisindicators, obis_data</td>
+      <td>Compute biodiveristy indicators for marine data from obis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/Marie59/obisindicators</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators</td>
+      <td>0.0.2</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>352</td>
+      <td>352</td>
+      <td>42</td>
+      <td>42</td>
+      <td>8</td>
+      <td>8</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>360</td>
+      <td>360</td>
+      <td>48</td>
+      <td>48</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>obitools</td>
+      <td>obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq</td>
+      <td>OBITools is a set of programs developed to simplify the manipulation of sequence files</td>
+      <td>obitools</td>
+      <td>obitools</td>
+      <td></td>
+      <td>OBITools</td>
+      <td>Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.</td>
+      <td>Sequence analysis, Sequence analysis</td>
+      <td>Sequence analysis, DNA, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>http://metabarcoding.org/obitools</td>
+      <td>Sequence Analysis</td>
+      <td>obitools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools</td>
+      <td>1.2.13</td>
+      <td>obitools</td>
+      <td>1.2.13</td>
+      <td>Sequence analysis, Sequence analysis</td>
+      <td>Sequence analysis, DNA, Sequencing</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>37598</td>
+      <td>37598</td>
+      <td>1277</td>
+      <td>1277</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3862</td>
+      <td>3862</td>
+      <td>280</td>
+      <td>280</td>
+      <td>41460</td>
+      <td>41460</td>
+      <td>1557</td>
+      <td>1557</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ocean</td>
+      <td>argo_getdata, divand_full_analysis</td>
+      <td>Access, process, visualise oceanographic data for the Earth System</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/Marie59/FE-ft-ESG/tree/main/argo</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean</td>
+      <td>0.1.15</td>
+      <td>julia</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>54</td>
+      <td>54</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ococo</td>
+      <td>ococo</td>
+      <td>Variant detection of SNVs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/karel-brinda/ococo</td>
+      <td>Variant Analysis</td>
+      <td>ococo</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo</td>
+      <td>0.1.2.6</td>
+      <td>ococo</td>
+      <td>0.1.2.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1850</td>
+      <td>1963</td>
+      <td>79</td>
+      <td>93</td>
+      <td>1370</td>
+      <td>1370</td>
+      <td>194</td>
+      <td>194</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3220</td>
+      <td>3333</td>
+      <td>273</td>
+      <td>287</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>odgi</td>
+      <td>odgi_build, odgi_viz</td>
+      <td>Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/vgteam/odgi</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi</td>
+      <td>0.3</td>
+      <td>odgi</td>
+      <td>0.8.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ogcProcess_otb_bandmath</td>
+      <td>otb_band_math</td>
+      <td>Outputs a monoband image which is the result of a mathematical operation on several multi-band images.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AquaINFRA/galaxy</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath</td>
+      <td>1.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>98</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>98</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ogcProcess_otb_meanShiftSmoothing</td>
+      <td>otb_mean_shift_smoothing</td>
+      <td>This application smooths an image using the MeanShift algorithm.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AquaINFRA/galaxy</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing</td>
+      <td>1.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omark</td>
+      <td>omark</td>
+      <td>Proteome quality assessment software</td>
+      <td>omark</td>
+      <td>omark</td>
+      <td></td>
+      <td>OMArk</td>
+      <td>Proteome quality assessment software</td>
+      <td>Sequence assembly validation, Differential protein expression profiling</td>
+      <td>Proteomics, Sequence analysis, Statistics and probability</td>
+      <td>To update</td>
+      <td>https://github.com/DessimozLab/OMArk</td>
+      <td>Sequence Analysis</td>
+      <td>omark</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark</td>
+      <td>0.3.0</td>
+      <td></td>
+      <td></td>
+      <td>Sequence assembly validation, Differential protein expression profiling</td>
+      <td>Proteomics, Sequence analysis, Statistics and probability</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>12</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omero</td>
+      <td>omero_import, omero_metadata_import, omero_roi_import</td>
+      <td>Import images, region of interest, metadata into an OMERO.server using omero-py</td>
+      <td>omero</td>
+      <td>omero</td>
+      <td></td>
+      <td>OMERO</td>
+      <td>Client-server Java software for visualisation, management and analysis of biological microscope images.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Data visualisation</td>
+      <td>To update</td>
+      <td>https://github.com/ome/omero-py/</td>
+      <td>Imaging</td>
+      <td>omero_upload</td>
+      <td>ufz</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero</td>
+      <td>5.18.0</td>
+      <td>omero-py</td>
+      <td>5.11.1</td>
+      <td>Image analysis</td>
+      <td>Imaging, Data visualisation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omero_clean_rois_tables</td>
+      <td>omero_clean_rois_tables</td>
+      <td>Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>omero_clean_rois_tables</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables</td>
+      <td>20230623</td>
+      <td>fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omero_get_children_ids</td>
+      <td>omero_get_children_ids</td>
+      <td>Get omero id of children of an omero object id</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>omero_get_children_ids</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids</td>
+      <td>0.2.0</td>
+      <td>omero-py</td>
+      <td>5.11.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omero_get_full_images</td>
+      <td>omero_get_full_images</td>
+      <td>Get full images from omero</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>omero_get_full_images</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images</td>
+      <td>20240521</td>
+      <td>fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omero_hyperstack_to_fluo_measurements_on_gastruloid</td>
+      <td>omero_hyperstack_to_fluo_measurements_on_gastruloid</td>
+      <td>Analyse Hyperstack on OMERO server to measure fluorescence levels</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>omero_hyperstack_to_fluo_measurements_on_gastruloid</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid</td>
+      <td>20230809</td>
+      <td>fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>omero_hyperstack_to_gastruloid_measurements</td>
+      <td>omero_hyperstack_to_gastruloid_measurements</td>
+      <td>Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>omero_hyperstack_to_gastruloid_measurements</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements</td>
+      <td>20240214</td>
+      <td>fiji</td>
+      <td>20240614</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ont_fast5_api</td>
+      <td>ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5</td>
+      <td>ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/nanoporetech/ont_fast5_api/</td>
+      <td>Nanopore</td>
+      <td>ont_fast5_api</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api</td>
+      <td>3.1.3</td>
+      <td>ont-fast5-api</td>
+      <td>4.1.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>87</td>
+      <td>87</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3051</td>
+      <td>3051</td>
+      <td>87</td>
+      <td>87</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>onto_toolkit</td>
+      <td>onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def</td>
+      <td>ONTO-Toolkit is a collection of tools for managing ontologies.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://search.cpan.org/~easr/ONTO-PERL-1.45/</td>
+      <td>Ontology Manipulation</td>
+      <td>onto_toolkit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit</td>
+      <td>1.45</td>
+      <td>perl-onto-perl</td>
+      <td>1.45</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>582</td>
+      <td>663</td>
+      <td>68</td>
+      <td>69</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>582</td>
+      <td>663</td>
+      <td>68</td>
+      <td>69</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>openlabcds2csv</td>
+      <td>openlabcds2csv</td>
+      <td>Creates a summary of several "Internal Standard Report" OpenLabCDS results.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Metabolomics</td>
+      <td>openlabcds2csv</td>
+      <td>genouest</td>
+      <td></td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv</td>
+      <td>0.1.0</td>
+      <td>openjdk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>openmm</td>
+      <td>pdbfixer</td>
+      <td>OpenMM is a toolkit for molecular simulation using high performance GPU code.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/openmm</td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>openmm</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm</td>
+      <td>1.8.1</td>
+      <td>pdbfixer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>491</td>
+      <td>491</td>
+      <td>52</td>
+      <td>52</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>491</td>
+      <td>491</td>
+      <td>52</td>
+      <td>52</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>openms</td>
+      <td>AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter</td>
+      <td>OpenMS Suite for LC/MS data management and analyses</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.openms.de/</td>
+      <td>Proteomics</td>
+      <td>openms</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms</td>
+      <td>3.1</td>
+      <td>openms</td>
+      <td>3.2.0</td>
+      <td></td>
+      <td></td>
+      <td>8</td>
+      <td>34</td>
+      <td>144</td>
+      <td>0</td>
+      <td>8</td>
+      <td>34</td>
+      <td>144</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>141</td>
+      <td>124</td>
+      <td>0</td>
+      <td>32169</td>
+      <td>108654</td>
+      <td>3316</td>
+      <td>4889</td>
+      <td>50</td>
+      <td>50</td>
+      <td>15</td>
+      <td>15</td>
+      <td>940</td>
+      <td>940</td>
+      <td>245</td>
+      <td>245</td>
+      <td>33159</td>
+      <td>109644</td>
+      <td>3576</td>
+      <td>5149</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>openms</td>
+      <td>AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter</td>
+      <td>OpenMS in version 2.1.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>openms</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/openms</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/openms</td>
+      <td>2.1.0</td>
+      <td>openms</td>
+      <td>3.2.0</td>
+      <td></td>
+      <td></td>
+      <td>7</td>
+      <td>34</td>
+      <td>135</td>
+      <td>0</td>
+      <td>7</td>
+      <td>34</td>
+      <td>135</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>135</td>
+      <td>134</td>
+      <td>0</td>
+      <td>31121</td>
+      <td>108907</td>
+      <td>3369</td>
+      <td>5029</td>
+      <td>50</td>
+      <td>50</td>
+      <td>15</td>
+      <td>15</td>
+      <td>933</td>
+      <td>933</td>
+      <td>242</td>
+      <td>242</td>
+      <td>32104</td>
+      <td>109890</td>
+      <td>3626</td>
+      <td>5286</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>optdoe</td>
+      <td>optdoe</td>
+      <td>Optimal Design Of Experiment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/pablocarb/doebase</td>
+      <td>Synthetic Biology</td>
+      <td>optdoe</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe</td>
+      <td>v2.0.2</td>
+      <td>doebase</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>optitype</td>
+      <td>optitype</td>
+      <td>Precision HLA typing from NGS data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/FRED-2/OptiType</td>
+      <td>Sequence Analysis</td>
+      <td>optitype</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype</td>
+      <td>1.3.5</td>
+      <td>optitype</td>
+      <td>1.3.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>500</td>
+      <td>500</td>
+      <td>45</td>
+      <td>45</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>500</td>
+      <td>500</td>
+      <td>45</td>
+      <td>45</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>orfipy</td>
+      <td>orfipy</td>
+      <td>Galaxy wrapper for ORFIPY</td>
+      <td>orfipy</td>
+      <td>orfipy</td>
+      <td></td>
+      <td>orfipy</td>
+      <td>A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.</td>
+      <td>Coding region prediction, Database search, Transcriptome assembly, De-novo assembly</td>
+      <td>Computer science, RNA-Seq, Transcriptomics, Small molecules</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/urmi-21/orfipy</td>
+      <td>Sequence Analysis</td>
+      <td>orfipy</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy</td>
+      <td>0.0.4</td>
+      <td>orfipy</td>
+      <td>0.0.4</td>
+      <td>Coding region prediction, Database search, Transcriptome assembly, De-novo assembly</td>
+      <td>Computer science, RNA-Seq, Transcriptomics, Small molecules</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>897</td>
+      <td>897</td>
+      <td>99</td>
+      <td>99</td>
+      <td>1792</td>
+      <td>1792</td>
+      <td>239</td>
+      <td>239</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2689</td>
+      <td>2689</td>
+      <td>338</td>
+      <td>338</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>orientationpy</td>
+      <td>orientationpy</td>
+      <td>Compute image orientation</td>
+      <td></td>
+      <td></td>
+      <td>orientationj</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>orientationpy</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy</td>
+      <td>0.2.0.4</td>
+      <td>orientationpy</td>
+      <td>0.2.0.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>orthofinder</td>
+      <td>orthofinder_onlygroups</td>
+      <td>Accurate inference of orthologous gene groups made easy</td>
+      <td>OrthoFinder</td>
+      <td>OrthoFinder</td>
+      <td></td>
+      <td>OrthoFinder</td>
+      <td>OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.</td>
+      <td>Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment</td>
+      <td>Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/davidemms/OrthoFinder</td>
+      <td>Phylogenetics, Sequence Analysis</td>
+      <td>orthofinder</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder</td>
+      <td>2.5.5</td>
+      <td>orthofinder</td>
+      <td>3.0.1b1</td>
+      <td>Genome comparison, Genome alignment</td>
+      <td>Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2018</td>
+      <td>2018</td>
+      <td>419</td>
+      <td>419</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>438</td>
+      <td>438</td>
+      <td>58</td>
+      <td>58</td>
+      <td>2456</td>
+      <td>2456</td>
+      <td>477</td>
+      <td>477</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>overlay_images</td>
+      <td>ip_overlay_images</td>
+      <td>Overlay two images</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis</td>
+      <td>Imaging</td>
+      <td>overlay_images</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images</td>
+      <td>0.0.4</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>149</td>
+      <td>149</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td>167</td>
+      <td>167</td>
+      <td>32</td>
+      <td>32</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>packaged_annotation_loader</td>
+      <td>packaged_annotation_loader</td>
+      <td>Tool to make cached genome annotation data available as a list of datasets collection</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader</td>
+      <td>Data Source</td>
+      <td>packaged_annotation_loader</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader</td>
+      <td>0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>packmol</td>
+      <td>packmol</td>
+      <td>PACKMOL is a package for creating starting structures for Molecular Dynamics simulations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://m3g.iqm.unicamp.br/packmol/home.shtml</td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>packmol</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol</td>
+      <td>18.169.1</td>
+      <td>packmol</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>282</td>
+      <td>295</td>
+      <td>32</td>
+      <td>33</td>
+      <td>420</td>
+      <td>420</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>702</td>
+      <td>715</td>
+      <td>40</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pacu</td>
+      <td>pacu_map, pacu_snp</td>
+      <td>PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.</td>
+      <td>pacu</td>
+      <td>pacu</td>
+      <td></td>
+      <td>PACU</td>
+      <td>PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).</td>
+      <td>Clustering</td>
+      <td>Phylogenetics, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BioinformaticsPlatformWIV-ISP/PACU</td>
+      <td>Sequence Analysis, Phylogenetics</td>
+      <td>pacu</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu</td>
+      <td>0.0.5</td>
+      <td>pacu_snp</td>
+      <td>0.0.5</td>
+      <td>Clustering</td>
+      <td>Phylogenetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pairtools</td>
+      <td>pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats</td>
+      <td>Flexible tools for Hi-C data processing</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://pairtools.readthedocs.io</td>
+      <td>Sequence Analysis</td>
+      <td>pairtools</td>
+      <td>iuc</td>
+      <td>https://github.com/open2c/pairtools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools</td>
+      <td>1.1.0</td>
+      <td>pairtools</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>196</td>
+      <td>196</td>
+      <td>16</td>
+      <td>16</td>
+      <td>19</td>
+      <td>19</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>215</td>
+      <td>215</td>
+      <td>30</td>
+      <td>30</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pandas_rolling_window</td>
+      <td>pandas_rolling_window</td>
+      <td>Rolling window calculations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html</td>
+      <td>Statistics</td>
+      <td>pandas_rolling_window</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window</td>
+      <td>0.1</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>261</td>
+      <td>275</td>
+      <td>12</td>
+      <td>12</td>
+      <td>63</td>
+      <td>63</td>
+      <td>22</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>324</td>
+      <td>338</td>
+      <td>34</td>
+      <td>34</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pangolin</td>
+      <td>pangolin</td>
+      <td>Phylogenetic Assignment of Named Global Outbreak LINeages</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/hCoV-2019/pangolin</td>
+      <td>Sequence Analysis</td>
+      <td>pangolin</td>
+      <td>nml</td>
+      <td>https://github.com/hCoV-2019/pangolin</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin</td>
+      <td>1.1.14</td>
+      <td>pangolin</td>
+      <td>4.3</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7457</td>
+      <td>7457</td>
+      <td>508</td>
+      <td>508</td>
+      <td>8518</td>
+      <td>8518</td>
+      <td>377</td>
+      <td>377</td>
+      <td>2760</td>
+      <td>2760</td>
+      <td>259</td>
+      <td>259</td>
+      <td>18735</td>
+      <td>18735</td>
+      <td>1144</td>
+      <td>1144</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pangolin</td>
+      <td>pangolin</td>
+      <td>Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.</td>
+      <td>pangolin_cov-lineages</td>
+      <td>pangolin_cov-lineages</td>
+      <td></td>
+      <td>pangolin</td>
+      <td>Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages</td>
+      <td>Tree-based sequence alignment, Variant classification</td>
+      <td>Virology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cov-lineages/pangolin</td>
+      <td>Sequence Analysis</td>
+      <td>pangolin</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin</td>
+      <td>4.3</td>
+      <td>pangolin</td>
+      <td>4.3</td>
+      <td>Tree-based sequence alignment, Variant classification</td>
+      <td>Virology</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7457</td>
+      <td>7457</td>
+      <td>508</td>
+      <td>508</td>
+      <td>8518</td>
+      <td>8518</td>
+      <td>377</td>
+      <td>377</td>
+      <td>2760</td>
+      <td>2760</td>
+      <td>259</td>
+      <td>259</td>
+      <td>18735</td>
+      <td>18735</td>
+      <td>1144</td>
+      <td>1144</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>paralyzer</td>
+      <td>paralyzer</td>
+      <td>A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/</td>
+      <td>RNA</td>
+      <td>paralyzer</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer</td>
+      <td>1.5</td>
+      <td>paralyzer</td>
+      <td>1.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>322</td>
+      <td>349</td>
+      <td>24</td>
+      <td>29</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>322</td>
+      <td>349</td>
+      <td>24</td>
+      <td>29</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>parse_mito_blast</td>
+      <td>parse_mito_blast</td>
+      <td>Filtering blast out from querying assembly against mitochondrial database.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py</td>
+      <td>Sequence Analysis</td>
+      <td>parse_mito_blast</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast</td>
+      <td>1.0.2</td>
+      <td>parse_mito_blast</td>
+      <td>1.0.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>203</td>
+      <td>203</td>
+      <td>65</td>
+      <td>65</td>
+      <td>288</td>
+      <td>288</td>
+      <td>62</td>
+      <td>62</td>
+      <td>110</td>
+      <td>110</td>
+      <td>20</td>
+      <td>20</td>
+      <td>601</td>
+      <td>601</td>
+      <td>147</td>
+      <td>147</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>partialr_square</td>
+      <td>partialRsq</td>
+      <td>Compute partial R square</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>partialr_square</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square</td>
+      <td>1.0.0</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>142</td>
+      <td>8</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>142</td>
+      <td>8</td>
+      <td>42</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pathifier</td>
+      <td>pathifier</td>
+      <td>pathifier</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://</td>
+      <td>Transcriptomics, Statistics</td>
+      <td>pathifier</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier</td>
+      <td>1.40.0</td>
+      <td>bioconductor-pathifier</td>
+      <td>1.40.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>245</td>
+      <td>245</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>245</td>
+      <td>245</td>
+      <td>10</td>
+      <td>10</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pathview</td>
+      <td>pathview</td>
+      <td>Pathview is a tool set for pathway based data integration and visualization.</td>
+      <td>pathview</td>
+      <td>pathview</td>
+      <td></td>
+      <td>pathview</td>
+      <td>Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.</td>
+      <td>Pathway or network analysis, Pathway or network visualisation</td>
+      <td>Molecular interactions, pathways and networks, Systems biology, Data visualisation</td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/pathview.html</td>
+      <td>Statistics, RNA, Micro-array Analysis</td>
+      <td>pathview</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview</td>
+      <td>1.34.0</td>
+      <td>bioconductor-pathview</td>
+      <td>1.42.0</td>
+      <td>Pathway or network analysis, Pathway or network visualisation</td>
+      <td>Molecular interactions, pathways and networks, Systems biology, Data visualisation</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6204</td>
+      <td>6211</td>
+      <td>1261</td>
+      <td>1261</td>
+      <td>6667</td>
+      <td>6667</td>
+      <td>1143</td>
+      <td>1143</td>
+      <td>1160</td>
+      <td>1160</td>
+      <td>189</td>
+      <td>189</td>
+      <td>14031</td>
+      <td>14038</td>
+      <td>2593</td>
+      <td>2593</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pathwaymatcher</td>
+      <td>reactome_pathwaymatcher</td>
+      <td>Reactome Pathway Matcher</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/LuisFranciscoHS/PathwayMatcher</td>
+      <td>Proteomics</td>
+      <td>reactome_pathwaymatcher</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher</td>
+      <td></td>
+      <td>pathwaymatcher</td>
+      <td>1.9.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>174</td>
+      <td>244</td>
+      <td>65</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>174</td>
+      <td>244</td>
+      <td>65</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>patrist</td>
+      <td>patrist</td>
+      <td>Extract Patristic Distance From a Tree</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02</td>
+      <td>Phylogenetics</td>
+      <td>patrist</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/patrist</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist</td>
+      <td>0.1.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pbgcpp</td>
+      <td>pbgcpp</td>
+      <td>Compute genomic consensus and call variants using PacBio reads mapped to a reference</td>
+      <td>genomicconsensus</td>
+      <td>genomicconsensus</td>
+      <td></td>
+      <td>GenomicConsensus</td>
+      <td>The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.</td>
+      <td>Variant calling</td>
+      <td>Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/PacificBiosciences/gcpp</td>
+      <td>Variant Analysis</td>
+      <td>pbgcpp</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp</td>
+      <td>2.0.2</td>
+      <td>pbgcpp</td>
+      <td>2.0.2</td>
+      <td>Variant calling</td>
+      <td>Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pbmm2</td>
+      <td>pbmm2</td>
+      <td>A minimap2 SMRT wrapper for PacBio data.</td>
+      <td>pbmm2</td>
+      <td>pbmm2</td>
+      <td></td>
+      <td>pbmm2</td>
+      <td>pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.</td>
+      <td>Pairwise sequence alignment, Sorting</td>
+      <td>Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/PacificBiosciences/pbmm2</td>
+      <td>Next Gen Mappers</td>
+      <td>pbmm2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2</td>
+      <td>1.14.99</td>
+      <td>pbmm2</td>
+      <td>1.14.99</td>
+      <td>Pairwise sequence alignment, Sorting</td>
+      <td>Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pbtk</td>
+      <td>bam2fastx</td>
+      <td>Convert PacBio Bam File to fasta or fastq file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/PacificBiosciences/pbtk</td>
+      <td>Convert Formats, Fasta Manipulation, Fastq Manipulation</td>
+      <td>bam2fastx</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk</td>
+      <td>3.1.1</td>
+      <td>pbtk</td>
+      <td>3.1.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>22</td>
+      <td>22</td>
+      <td>109</td>
+      <td>109</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>167</td>
+      <td>167</td>
+      <td>41</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pe_histogram</td>
+      <td>pe_histogram</td>
+      <td>Contains a tool that produces an insert size histogram for a paired-end BAM file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram</td>
+      <td>Graphics</td>
+      <td>pe_histogram</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram</td>
+      <td>1.0.2</td>
+      <td>openjdk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5505</td>
+      <td>5505</td>
+      <td>510</td>
+      <td>510</td>
+      <td>7932</td>
+      <td>8582</td>
+      <td>811</td>
+      <td>909</td>
+      <td>736</td>
+      <td>736</td>
+      <td>119</td>
+      <td>119</td>
+      <td>14173</td>
+      <td>14823</td>
+      <td>1440</td>
+      <td>1538</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>peakachu</td>
+      <td>peakachu</td>
+      <td>PEAKachu is a peak-caller for CLIP- and RIP-Seq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, RNA</td>
+      <td>peakachu</td>
+      <td>rnateam</td>
+      <td>https://github.com/tbischler/PEAKachu</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/peakachu</td>
+      <td>0.2.0+galaxy1</td>
+      <td>peakachu</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2807</td>
+      <td>3337</td>
+      <td>178</td>
+      <td>196</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2807</td>
+      <td>3337</td>
+      <td>178</td>
+      <td>196</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>peakzilla</td>
+      <td>peakzilla</td>
+      <td>Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/steinmann/peakzilla</td>
+      <td>ChIP-seq</td>
+      <td>peakzilla</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla</td>
+      <td>1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pear</td>
+      <td>iuc_pear</td>
+      <td>PEAR evaluates all possible paired-end read overlaps</td>
+      <td>pear</td>
+      <td>pear</td>
+      <td></td>
+      <td>PEAR</td>
+      <td>Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.</td>
+      <td>Sequence merging</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://cme.h-its.org/exelixis/web/software/pear/</td>
+      <td>Fastq Manipulation</td>
+      <td>pear</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear</td>
+      <td>0.9.6</td>
+      <td>pear</td>
+      <td>0.9.6</td>
+      <td>Sequence merging</td>
+      <td>Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6269</td>
+      <td>6866</td>
+      <td>260</td>
+      <td>292</td>
+      <td>5530</td>
+      <td>20068</td>
+      <td>467</td>
+      <td>1664</td>
+      <td>5647</td>
+      <td>8471</td>
+      <td>198</td>
+      <td>300</td>
+      <td>17446</td>
+      <td>35405</td>
+      <td>925</td>
+      <td>2256</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pearson_correlation</td>
+      <td>Pearson_and_apos_Correlation1</td>
+      <td>Pearson and apos Correlation between any two numeric columns</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>pearson_correlation</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pep_pointer</td>
+      <td>pep_pointer</td>
+      <td>PepPointer categorizes peptides by their genomic coordinates.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Genomic Interval Operations, Proteomics</td>
+      <td>pep_pointer</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer</td>
+      <td>0.1.3+galaxy1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>506</td>
+      <td>511</td>
+      <td>54</td>
+      <td>55</td>
+      <td>21</td>
+      <td>21</td>
+      <td>12</td>
+      <td>12</td>
+      <td>163</td>
+      <td>163</td>
+      <td>8</td>
+      <td>8</td>
+      <td>690</td>
+      <td>695</td>
+      <td>74</td>
+      <td>75</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pepquery</td>
+      <td>pepquery</td>
+      <td>A peptide-centric MS search engine for novel peptide identification and validation.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pepquery.org</td>
+      <td>Proteomics</td>
+      <td>pepquery</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery</td>
+      <td>1.6.2</td>
+      <td>pepquery</td>
+      <td>2.0.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7047</td>
+      <td>7047</td>
+      <td>76</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7047</td>
+      <td>7047</td>
+      <td>76</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pepquery2</td>
+      <td>pepquery2, pepquery2_index, pepquery2_show_sets</td>
+      <td>PepQuery2 peptide-centric MS search for peptide identification and validation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://pepquery.org</td>
+      <td>Proteomics</td>
+      <td>pepquery2</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2</td>
+      <td>2.0.2</td>
+      <td>pepquery</td>
+      <td>2.0.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1222</td>
+      <td>1222</td>
+      <td>28</td>
+      <td>28</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1222</td>
+      <td>1222</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>peptide_genomic_coordinate</td>
+      <td>peptide_genomic_coordinate</td>
+      <td>Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>peptide_genomic_coordinate</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate</td>
+      <td>1.0.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>472</td>
+      <td>472</td>
+      <td>56</td>
+      <td>56</td>
+      <td>16</td>
+      <td>16</td>
+      <td>10</td>
+      <td>10</td>
+      <td>149</td>
+      <td>149</td>
+      <td>5</td>
+      <td>5</td>
+      <td>637</td>
+      <td>637</td>
+      <td>71</td>
+      <td>71</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>peptideshaker</td>
+      <td>fasta_cli, ident_params, peptide_shaker, search_gui</td>
+      <td>PeptideShaker and SearchGUI</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://compomics.github.io</td>
+      <td>Proteomics</td>
+      <td>peptideshaker</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker</td>
+      <td></td>
+      <td>searchgui</td>
+      <td>4.3.11</td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>4</td>
+      <td>2</td>
+      <td>0</td>
+      <td>11986</td>
+      <td>17898</td>
+      <td>1046</td>
+      <td>1153</td>
+      <td>1314</td>
+      <td>1314</td>
+      <td>389</td>
+      <td>389</td>
+      <td>3034</td>
+      <td>3034</td>
+      <td>118</td>
+      <td>118</td>
+      <td>16334</td>
+      <td>22246</td>
+      <td>1553</td>
+      <td>1660</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>peptimapper</td>
+      <td>peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag</td>
+      <td>Proteogenomics workflow for the expert annotation of eukaryotic genomes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9</td>
+      <td>Proteomics</td>
+      <td></td>
+      <td>genouest</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper</td>
+      <td>https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper</td>
+      <td>2.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pepxml_to_xls</td>
+      <td></td>
+      <td>Convert PepXML to Tabular</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>pepxml_to_xls</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>percolator</td>
+      <td>batched_set_list_creator, percolator, percolator_input_converters, pout2mzid</td>
+      <td>Percolator</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>percolator</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator</td>
+      <td>3.5</td>
+      <td>percolator</td>
+      <td>3.7.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>338</td>
+      <td>378</td>
+      <td>15</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1059</td>
+      <td>1059</td>
+      <td>13</td>
+      <td>13</td>
+      <td>1397</td>
+      <td>1437</td>
+      <td>28</td>
+      <td>29</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>perf</td>
+      <td>stats_perf_tool</td>
+      <td>suitable for boolean classification problems</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://osmot.cs.cornell.edu/kddcup/software.html</td>
+      <td></td>
+      <td>stats_perf_tool</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/perf</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/perf</td>
+      <td>5.11.0</td>
+      <td>perf</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>permutate_axis</td>
+      <td>ip_permutate_axis</td>
+      <td>Permutates axes</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>permutate_axis</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis</td>
+      <td>0.2-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>36</td>
+      <td>42</td>
+      <td>1</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>36</td>
+      <td>42</td>
+      <td>1</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pfamscan</td>
+      <td>pfamscan</td>
+      <td>Search a FASTA sequence against a library of Pfam HMM.</td>
+      <td>pfamscan</td>
+      <td>pfamscan</td>
+      <td></td>
+      <td>PfamScan</td>
+      <td>This tool is used to search a FASTA sequence against a library of Pfam HMM.</td>
+      <td>Protein sequence analysis</td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/</td>
+      <td>Sequence Analysis</td>
+      <td>pfamscan</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan</td>
+      <td>1.6</td>
+      <td>pfam_scan</td>
+      <td>1.6</td>
+      <td>Protein sequence analysis</td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>773</td>
+      <td>773</td>
+      <td>60</td>
+      <td>60</td>
+      <td>495</td>
+      <td>495</td>
+      <td>72</td>
+      <td>72</td>
+      <td>246</td>
+      <td>246</td>
+      <td>17</td>
+      <td>17</td>
+      <td>1514</td>
+      <td>1514</td>
+      <td>149</td>
+      <td>149</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pg_tools</td>
+      <td>pg_dump, pg_import, pg_query</td>
+      <td>tool suite for dealing with Postgresql databases from Galaxy's history</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.postgresql.org</td>
+      <td>Data Export, Data Source</td>
+      <td>pgtools</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tools/pgtools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools</td>
+      <td></td>
+      <td>postgresql</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pgsnp2gd_snp</td>
+      <td>pgSnp2gd_snp</td>
+      <td>Convert from pgSnp to gd_snp</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>pgsnp2gd_snp</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pharmcat</td>
+      <td>pharmcat</td>
+      <td>Pharmacogenomics Clinical Annotation Tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pharmcat.org/</td>
+      <td>Variant Analysis</td>
+      <td>pharmcat</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>109</td>
+      <td>109</td>
+      <td>29</td>
+      <td>29</td>
+      <td>250</td>
+      <td>250</td>
+      <td>84</td>
+      <td>84</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>359</td>
+      <td>359</td>
+      <td>113</td>
+      <td>113</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pharokka</td>
+      <td>pharokka</td>
+      <td>rapid standardised annotation tool for bacteriophage genomes and metagenomes</td>
+      <td>pharokka</td>
+      <td>pharokka</td>
+      <td></td>
+      <td>Pharokka</td>
+      <td>Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.</td>
+      <td>Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly</td>
+      <td>Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA</td>
+      <td>To update</td>
+      <td>https://github.com/gbouras13/pharokka</td>
+      <td>Genome annotation</td>
+      <td>pharokka</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka</td>
+      <td>1.3.2</td>
+      <td>\n                pharokka\n</td>
+      <td></td>
+      <td>Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly</td>
+      <td>Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5462</td>
+      <td>5462</td>
+      <td>334</td>
+      <td>334</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>309</td>
+      <td>309</td>
+      <td>52</td>
+      <td>52</td>
+      <td>5771</td>
+      <td>5771</td>
+      <td>386</td>
+      <td>386</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>phyloseq</td>
+      <td>phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness</td>
+      <td>Handling and analysis of high-throughput microbiome census data</td>
+      <td>phyloseq</td>
+      <td>phyloseq</td>
+      <td></td>
+      <td>phyloseq</td>
+      <td>Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.</td>
+      <td>Deposition, Analysis, Visualisation</td>
+      <td>Microbiology, Sequence analysis, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html</td>
+      <td>Metagenomics</td>
+      <td>phyloseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq</td>
+      <td>1.46.0</td>
+      <td>bioconductor-phyloseq</td>
+      <td>1.46.0</td>
+      <td>Deposition, Analysis, Visualisation</td>
+      <td>Microbiology, Sequence analysis, Metagenomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>1199</td>
+      <td>1199</td>
+      <td>193</td>
+      <td>193</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1205</td>
+      <td>1205</td>
+      <td>194</td>
+      <td>194</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>phyml</td>
+      <td>phyml</td>
+      <td>PhyML is a phylogeny software based on the maximum-likelihood principle.</td>
+      <td>phyml</td>
+      <td>phyml</td>
+      <td></td>
+      <td>PhyML</td>
+      <td>Phylogenetic estimation software using Maximum Likelihood</td>
+      <td>Phylogenetic tree generation (maximum likelihood and Bayesian methods)</td>
+      <td>Phylogenetics, Bioinformatics, Phylogenetics</td>
+      <td>Up-to-date</td>
+      <td>http://www.atgc-montpellier.fr/phyml/</td>
+      <td>Phylogenetics</td>
+      <td>phyml</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml</td>
+      <td>3.3.20220408</td>
+      <td>phyml</td>
+      <td>3.3.20220408</td>
+      <td></td>
+      <td>Phylogenetics, Bioinformatics, Phylogenetics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1975</td>
+      <td>2034</td>
+      <td>246</td>
+      <td>258</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>553</td>
+      <td>564</td>
+      <td>140</td>
+      <td>144</td>
+      <td>2528</td>
+      <td>2598</td>
+      <td>386</td>
+      <td>402</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>physiofit</td>
+      <td>physiofit</td>
+      <td>PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake &amp; production fluxes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>physiofit.readthedocs.io</td>
+      <td>Metabolomics</td>
+      <td>physiofit</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/MetaSys-LISBP/PhysioFit</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit</td>
+      <td>3.4.0</td>
+      <td>physiofit</td>
+      <td>3.4.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>physiofit_manager</td>
+      <td>physiofit_data_manager</td>
+      <td>Handling of physiofit input files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>physiofit.readthedocs.io</td>
+      <td>Metabolomics</td>
+      <td>physiofit_manager</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager</td>
+      <td>1.0.1</td>
+      <td>physiofit_data_manager</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pi_db_tools</td>
+      <td>calc_delta_pi, pi_db_split, pi_dbspec_align</td>
+      <td>HiRIEF tools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>hirieftools</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools</td>
+      <td>1.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>picard</td>
+      <td>picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile</td>
+      <td>Picard SAM/BAM manipulation tools.</td>
+      <td>picard_samtofastq</td>
+      <td>picard_samtofastq, picard_replacesamheader, picard_fastqtosam, picard_reordersam</td>
+      <td></td>
+      <td>picard_samtofastq</td>
+      <td>Create a FASTQ file.</td>
+      <td>Formatting</td>
+      <td>Sequencing</td>
+      <td>To update</td>
+      <td>http://broadinstitute.github.io/picard/</td>
+      <td>SAM</td>
+      <td>picard</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard</td>
+      <td>3.1.1</td>
+      <td>picard</td>
+      <td>3.2.0</td>
+      <td>Formatting</td>
+      <td>Sequencing</td>
+      <td>31</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>4</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>386934</td>
+      <td>399039</td>
+      <td>11024</td>
+      <td>11956</td>
+      <td>366646</td>
+      <td>589980</td>
+      <td>32000</td>
+      <td>57111</td>
+      <td>56622</td>
+      <td>62258</td>
+      <td>2845</td>
+      <td>3398</td>
+      <td>810202</td>
+      <td>1051277</td>
+      <td>45869</td>
+      <td>72465</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pick_value</td>
+      <td>pick_value</td>
+      <td>Compose a text parameter value using text, integer and float values</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>pick_value</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1607</td>
+      <td>1607</td>
+      <td>41</td>
+      <td>41</td>
+      <td>490</td>
+      <td>490</td>
+      <td>53</td>
+      <td>53</td>
+      <td>127</td>
+      <td>127</td>
+      <td>4</td>
+      <td>4</td>
+      <td>2224</td>
+      <td>2224</td>
+      <td>98</td>
+      <td>98</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>picrust</td>
+      <td>picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes</td>
+      <td>PICRUSt wrappers</td>
+      <td>picrust</td>
+      <td>picrust</td>
+      <td></td>
+      <td>PICRUSt</td>
+      <td>PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.</td>
+      <td>Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding</td>
+      <td>Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing</td>
+      <td>To update</td>
+      <td>https://picrust.github.io/picrust/</td>
+      <td>Metagenomics</td>
+      <td>picrust</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust</td>
+      <td>1.1.1</td>
+      <td>picrust</td>
+      <td>1.1.4</td>
+      <td>Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding</td>
+      <td>Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing</td>
+      <td>0</td>
+      <td>6</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>867</td>
+      <td>1128</td>
+      <td>144</td>
+      <td>165</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2106</td>
+      <td>2106</td>
+      <td>121</td>
+      <td>121</td>
+      <td>2973</td>
+      <td>3234</td>
+      <td>265</td>
+      <td>286</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>picrust2</td>
+      <td>picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions</td>
+      <td>PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States</td>
+      <td>picrust2</td>
+      <td>picrust2</td>
+      <td></td>
+      <td>PICRUSt2</td>
+      <td>PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.</td>
+      <td>Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis</td>
+      <td>Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/picrust/picrust2/wiki</td>
+      <td>Metagenomics</td>
+      <td>picrust2</td>
+      <td>iuc</td>
+      <td>https://github.com/picrust/picrust2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2</td>
+      <td>2.5.3</td>
+      <td>picrust2</td>
+      <td>2.5.3</td>
+      <td>Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis</td>
+      <td>Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2532</td>
+      <td>2532</td>
+      <td>382</td>
+      <td>382</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1311</td>
+      <td>1311</td>
+      <td>83</td>
+      <td>83</td>
+      <td>3844</td>
+      <td>3844</td>
+      <td>466</td>
+      <td>466</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pileup_interval</td>
+      <td>pileup_interval</td>
+      <td>Pileup-to-Interval condenses pileup format into ranges of bases</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>SAM</td>
+      <td>pileup_interval</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval</td>
+      <td>1.0.3</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>613</td>
+      <td>640</td>
+      <td>48</td>
+      <td>54</td>
+      <td>1381</td>
+      <td>7804</td>
+      <td>201</td>
+      <td>1552</td>
+      <td>756</td>
+      <td>815</td>
+      <td>22</td>
+      <td>30</td>
+      <td>2750</td>
+      <td>9259</td>
+      <td>271</td>
+      <td>1636</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pileup_parser</td>
+      <td>pileup_parser</td>
+      <td>Filter pileup on coverage and SNPs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-devteam/</td>
+      <td>SAM</td>
+      <td>pileup_parser</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser</td>
+      <td>1.0.2</td>
+      <td>perl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3639</td>
+      <td>3774</td>
+      <td>414</td>
+      <td>461</td>
+      <td>9754</td>
+      <td>52522</td>
+      <td>1247</td>
+      <td>4531</td>
+      <td>1893</td>
+      <td>2433</td>
+      <td>191</td>
+      <td>318</td>
+      <td>15286</td>
+      <td>58729</td>
+      <td>1852</td>
+      <td>5310</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pilon</td>
+      <td>pilon</td>
+      <td>pilon is a tool for assembly improvement and variant analysis in bacteria</td>
+      <td>pilon</td>
+      <td>pilon</td>
+      <td></td>
+      <td>pilon</td>
+      <td>Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.</td>
+      <td>Sequence assembly, Analysis, Read alignment</td>
+      <td>Assembly</td>
+      <td>To update</td>
+      <td>https://github.com/broadinstitute/pilon/wiki</td>
+      <td>Variant Analysis</td>
+      <td>pilon</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon</td>
+      <td>1.20.1</td>
+      <td>pilon</td>
+      <td>1.24</td>
+      <td>Sequence assembly, Analysis</td>
+      <td>Assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9045</td>
+      <td>9458</td>
+      <td>1115</td>
+      <td>1144</td>
+      <td>7989</td>
+      <td>7989</td>
+      <td>1070</td>
+      <td>1070</td>
+      <td>3945</td>
+      <td>4137</td>
+      <td>726</td>
+      <td>741</td>
+      <td>20979</td>
+      <td>21584</td>
+      <td>2911</td>
+      <td>2955</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pindel</td>
+      <td>pindel</td>
+      <td>Pindel detects genome-wide structural variation.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>pindel</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel</td>
+      <td>0.2.5b9</td>
+      <td>pindel</td>
+      <td>0.2.5b9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pipelign</td>
+      <td>pipelign</td>
+      <td>Multipe sequence alignment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/asmmhossain/pipelign/</td>
+      <td>Next Gen Mappers</td>
+      <td>pipelign</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign</td>
+      <td>0.2</td>
+      <td>pipelign</td>
+      <td>0.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1245</td>
+      <td>1245</td>
+      <td>231</td>
+      <td>231</td>
+      <td>9046</td>
+      <td>9046</td>
+      <td>630</td>
+      <td>630</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10291</td>
+      <td>10291</td>
+      <td>861</td>
+      <td>861</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pipmir</td>
+      <td>pipmir</td>
+      <td>A method to identify novel plant miRNA.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/</td>
+      <td>RNA</td>
+      <td>pipmir</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir</td>
+      <td>0.1.0</td>
+      <td>pipmir</td>
+      <td>1.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>238</td>
+      <td>283</td>
+      <td>42</td>
+      <td>45</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>238</td>
+      <td>283</td>
+      <td>42</td>
+      <td>45</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>piranha</td>
+      <td>piranha</td>
+      <td>Piranha is a peak-caller for CLIP- and RIP-Seq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, RNA</td>
+      <td>piranha</td>
+      <td>rnateam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/piranha</td>
+      <td>1.2.1.0</td>
+      <td>piranha</td>
+      <td>1.2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1408</td>
+      <td>2068</td>
+      <td>94</td>
+      <td>119</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1408</td>
+      <td>2068</td>
+      <td>94</td>
+      <td>119</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pizzly</td>
+      <td>pizzly</td>
+      <td>Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/pmelsted/pizzly/</td>
+      <td>Transcriptomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly</td>
+      <td>0.37.3.1</td>
+      <td>pizzly</td>
+      <td>0.37.3</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>201</td>
+      <td>210</td>
+      <td>23</td>
+      <td>24</td>
+      <td>998</td>
+      <td>998</td>
+      <td>76</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1199</td>
+      <td>1208</td>
+      <td>99</td>
+      <td>100</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plantseg</td>
+      <td>plantseg</td>
+      <td>Tool for cell instance aware segmentation in densely packed 3D volumetric images</td>
+      <td>plantseg</td>
+      <td>plantseg</td>
+      <td></td>
+      <td>PlantSeg</td>
+      <td>Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.</td>
+      <td>Network analysis, Quantification, Microscope image visualisation</td>
+      <td>Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>plantseg</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg</td>
+      <td>1.8.1</td>
+      <td>plant-seg</td>
+      <td></td>
+      <td>Network analysis, Quantification, Microscope image visualisation</td>
+      <td>Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plasflow</td>
+      <td>PlasFlow</td>
+      <td>PlasFlow - Prediction of plasmid sequences in metagenomic contigs.</td>
+      <td>plasflow</td>
+      <td>plasflow</td>
+      <td></td>
+      <td>PlasFlow</td>
+      <td>PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.</td>
+      <td>Sequence analysis</td>
+      <td>Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/smaegol/PlasFlow</td>
+      <td>Sequence Analysis</td>
+      <td>plasflow</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow</td>
+      <td>1.1.0</td>
+      <td>plasflow</td>
+      <td>1.1.0</td>
+      <td>Sequence analysis</td>
+      <td>Metagenomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>37086</td>
+      <td>37272</td>
+      <td>711</td>
+      <td>734</td>
+      <td>6346</td>
+      <td>6346</td>
+      <td>583</td>
+      <td>583</td>
+      <td>3065</td>
+      <td>3065</td>
+      <td>61</td>
+      <td>61</td>
+      <td>46497</td>
+      <td>46683</td>
+      <td>1355</td>
+      <td>1378</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plasmid_profiler</td>
+      <td>plasmid_profiler</td>
+      <td>Explores plasmid content in WGS data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>plasmid_profiler</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler</td>
+      <td>0.1.6</td>
+      <td>r</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plasmid_profiler_suite</td>
+      <td></td>
+      <td>Plasmid Profiler suite defining all dependencies for Plasmid Profiler</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>suite_plasmid_profiler</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plasmidfinder</td>
+      <td>plasmidfinder</td>
+      <td>"PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"</td>
+      <td>PlasmidFinder</td>
+      <td>PlasmidFinder</td>
+      <td></td>
+      <td>PlasmidFinder</td>
+      <td>PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).</td>
+      <td>Genome assembly, Scaffolding, Multilocus sequence typing</td>
+      <td>Whole genome sequencing, Sequence assembly, Mapping, Probes and primers</td>
+      <td>Up-to-date</td>
+      <td>https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/</td>
+      <td>Sequence Analysis</td>
+      <td>plasmidfinder</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder</td>
+      <td>2.1.6</td>
+      <td>plasmidfinder</td>
+      <td>2.1.6</td>
+      <td>Genome assembly, Scaffolding, Multilocus sequence typing</td>
+      <td>Whole genome sequencing, Sequence assembly, Mapping, Probes and primers</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14652</td>
+      <td>14652</td>
+      <td>251</td>
+      <td>251</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>101</td>
+      <td>101</td>
+      <td>18</td>
+      <td>18</td>
+      <td>14753</td>
+      <td>14753</td>
+      <td>269</td>
+      <td>269</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plasmidspades</td>
+      <td>plasmidspades</td>
+      <td>Genome assembler for assemblying plasmid</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Assembly</td>
+      <td>plasmidspades</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades</td>
+      <td>1.1</td>
+      <td>spades</td>
+      <td>4.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>platypus</td>
+      <td>bg_platypus</td>
+      <td>efficient and accurate variant-detection in high-throughput sequencing data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.well.ox.ac.uk/platypus</td>
+      <td>Sequence Analysis</td>
+      <td>platypus</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/platypus</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/platypus</td>
+      <td>0.0.11</td>
+      <td>platypus</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plink</td>
+      <td>plink</td>
+      <td>Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.</td>
+      <td>plink</td>
+      <td>plink</td>
+      <td></td>
+      <td>PLINK</td>
+      <td>Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.</td>
+      <td>Genetic variation analysis</td>
+      <td>GWAS study</td>
+      <td>Up-to-date</td>
+      <td>https://www.cog-genomics.org/plink</td>
+      <td>Genome-Wide Association Study</td>
+      <td>plink</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink</td>
+      <td>1.90b6.21</td>
+      <td>plink</td>
+      <td>1.90b6.21</td>
+      <td>Genetic variation analysis</td>
+      <td>GWAS study</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>851</td>
+      <td>851</td>
+      <td>127</td>
+      <td>127</td>
+      <td>249</td>
+      <td>249</td>
+      <td>43</td>
+      <td>43</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1100</td>
+      <td>1100</td>
+      <td>170</td>
+      <td>170</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plot_from_lda</td>
+      <td>plot_for_lda_output1</td>
+      <td>Draw ROC plot on "Perform LDA" output</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Statistics</td>
+      <td>plot_from_lda</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda</td>
+      <td>1.0.1</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>65</td>
+      <td>77</td>
+      <td>19</td>
+      <td>25</td>
+      <td>153</td>
+      <td>886</td>
+      <td>38</td>
+      <td>343</td>
+      <td>142</td>
+      <td>155</td>
+      <td>8</td>
+      <td>10</td>
+      <td>360</td>
+      <td>1118</td>
+      <td>65</td>
+      <td>378</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plotheatmap</td>
+      <td>plotheatmap</td>
+      <td>This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Computational chemistry</td>
+      <td>plotheatmap</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap</td>
+      <td>1.0</td>
+      <td>bioconductor-preprocesscore</td>
+      <td>1.64.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plotly_ml_performance_plots</td>
+      <td>plotly_ml_performance_plots</td>
+      <td>performance plots for machine learning problems</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics</td>
+      <td>Visualization</td>
+      <td>plotly_ml_performance_plots</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots</td>
+      <td>0.4</td>
+      <td>galaxy-ml</td>
+      <td>0.10.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1342</td>
+      <td>1472</td>
+      <td>184</td>
+      <td>197</td>
+      <td>902</td>
+      <td>902</td>
+      <td>156</td>
+      <td>156</td>
+      <td>630</td>
+      <td>630</td>
+      <td>24</td>
+      <td>24</td>
+      <td>2874</td>
+      <td>3004</td>
+      <td>364</td>
+      <td>377</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plotly_parallel_coordinates_plot</td>
+      <td>plotly_parallel_coordinates_plot</td>
+      <td>parallel coordinates plot produced with plotly</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://plot.ly/python/parallel-coordinates-plot/</td>
+      <td>Visualization</td>
+      <td>plotly_parallel_coordinates_plot</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot</td>
+      <td>0.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>408</td>
+      <td>664</td>
+      <td>91</td>
+      <td>122</td>
+      <td>627</td>
+      <td>627</td>
+      <td>118</td>
+      <td>118</td>
+      <td>605</td>
+      <td>605</td>
+      <td>26</td>
+      <td>26</td>
+      <td>1640</td>
+      <td>1896</td>
+      <td>235</td>
+      <td>266</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>plotly_regression_performance_plots</td>
+      <td>plotly_regression_performance_plots</td>
+      <td>performance plots for regression problems</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://scikit-learn.org/stable/supervised_learning.html#supervised-learning</td>
+      <td>Visualization</td>
+      <td>plotly_regression_performance_plots</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots</td>
+      <td>0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>764</td>
+      <td>879</td>
+      <td>213</td>
+      <td>237</td>
+      <td>304</td>
+      <td>304</td>
+      <td>95</td>
+      <td>95</td>
+      <td>193</td>
+      <td>193</td>
+      <td>26</td>
+      <td>26</td>
+      <td>1261</td>
+      <td>1376</td>
+      <td>334</td>
+      <td>358</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pmd_fdr</td>
+      <td>pmd_fdr</td>
+      <td>Calculate Precursor Mass Discrepancy (PMD) for MS/MS</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/slhubler/PMD-FDR-for-Galaxy-P</td>
+      <td>Proteomics</td>
+      <td>pmd_fdr</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr</td>
+      <td>1.4.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pneumocat</td>
+      <td>pneumocat</td>
+      <td>Pneumococcal Capsular Typing of illumina fastq reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phe-bioinformatics/PneumoCaT</td>
+      <td>Variant Analysis</td>
+      <td>pneumocat</td>
+      <td>nml</td>
+      <td>https://github.com/phe-bioinformatics/PneumoCaT</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat</td>
+      <td>1.2.1</td>
+      <td>pneumocat</td>
+      <td>1.2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>points2labelimage</td>
+      <td>ip_points_to_label</td>
+      <td>Points to label image</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>points2labelimage</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage</td>
+      <td>0.4</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>33</td>
+      <td>33</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>points_association_nn</td>
+      <td>ip_points_association_nn</td>
+      <td>Association of points in consecutive frames</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis</td>
+      <td>Imaging</td>
+      <td>points_association_nn</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn</td>
+      <td>0.0.3-2</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>poisson2test</td>
+      <td>poisson2test</td>
+      <td>Poisson two-sample test</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Statistics, Metagenomics</td>
+      <td>poisson2test</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test</td>
+      <td>1.0.0</td>
+      <td>taxonomy</td>
+      <td>0.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
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+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>112</td>
+      <td>120</td>
+      <td>16</td>
+      <td>16</td>
+      <td>4</td>
+      <td>562</td>
+      <td>1</td>
+      <td>140</td>
+      <td>320</td>
+      <td>347</td>
+      <td>7</td>
+      <td>8</td>
+      <td>436</td>
+      <td>1029</td>
+      <td>24</td>
+      <td>164</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>polypolish</td>
+      <td>polypolish</td>
+      <td>"Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."</td>
+      <td>Polypolish</td>
+      <td>Polypolish</td>
+      <td></td>
+      <td>Polypolish</td>
+      <td>Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.</td>
+      <td>Genome assembly, Read mapping, Mapping assembly, Sequencing error detection</td>
+      <td>Sequence assembly, Sequence composition, complexity and repeats, Mapping</td>
+      <td>To update</td>
+      <td>https://github.com/rrwick/Polypolish</td>
+      <td>Sequence Analysis</td>
+      <td>polypolish</td>
+      <td>iuc</td>
+      <td>https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish</td>
+      <td>0.5.0</td>
+      <td>polypolish</td>
+      <td>0.6.0</td>
+      <td>Genome assembly, Read mapping, Mapping assembly, Sequencing error detection</td>
+      <td>Sequence assembly, Sequence composition, complexity and repeats, Mapping</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>731</td>
+      <td>731</td>
+      <td>86</td>
+      <td>86</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>4</td>
+      <td>4</td>
+      <td>773</td>
+      <td>773</td>
+      <td>90</td>
+      <td>90</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>porechop</td>
+      <td>porechop</td>
+      <td>Porechop - Finding and removing adapters from Oxford Nanopore reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/rrwick/Porechop</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td>porechop</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop</td>
+      <td></td>
+      <td>porechop</td>
+      <td>0.2.4</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>262015</td>
+      <td>262852</td>
+      <td>2627</td>
+      <td>2711</td>
+      <td>83623</td>
+      <td>83623</td>
+      <td>1918</td>
+      <td>1918</td>
+      <td>52558</td>
+      <td>52558</td>
+      <td>1037</td>
+      <td>1037</td>
+      <td>398196</td>
+      <td>399033</td>
+      <td>5582</td>
+      <td>5666</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>poretools</td>
+      <td>poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot</td>
+      <td>A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.</td>
+      <td>poretools</td>
+      <td>poretools</td>
+      <td></td>
+      <td>Poretools</td>
+      <td>Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>DNA, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://poretools.readthedocs.io/en/latest/</td>
+      <td>Fasta Manipulation, Fastq Manipulation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools</td>
+      <td>0.6.1a1</td>
+      <td>poretools</td>
+      <td>0.6.1a1</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>DNA, Sequencing</td>
+      <td>13</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>13</td>
+      <td>0</td>
+      <td>19942</td>
+      <td>20587</td>
+      <td>1055</td>
+      <td>1245</td>
+      <td>33619</td>
+      <td>40808</td>
+      <td>2183</td>
+      <td>2594</td>
+      <td>9261</td>
+      <td>9261</td>
+      <td>365</td>
+      <td>365</td>
+      <td>62822</td>
+      <td>70656</td>
+      <td>3603</td>
+      <td>4204</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>positions2snv_alignment</td>
+      <td>positions2snv_alignment</td>
+      <td>Generate alignment of SNVs from SNVPhyl variant table.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Variant Analysis</td>
+      <td>positions2snv_alignment</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>positions2snv_invariant_alignment</td>
+      <td>positions2snv_invariant_alignment</td>
+      <td>Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Variant Analysis</td>
+      <td>positions2snv_invariant_alignment</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>predictnls</td>
+      <td>predictnls</td>
+      <td>Python reimplementation of predictNLS for Galaxy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls</td>
+      <td>Sequence Analysis</td>
+      <td>predictnls</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls</td>
+      <td>0.0.10</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>presto</td>
+      <td>presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3</td>
+      <td>pRESTO toolkit for immune repertoire analysis.</td>
+      <td>presto</td>
+      <td>presto</td>
+      <td></td>
+      <td>pRESTO</td>
+      <td>Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Sequencing, DNA, Immunology</td>
+      <td>To update</td>
+      <td>https://presto.readthedocs.io/</td>
+      <td>Sequence Analysis</td>
+      <td>presto</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto</td>
+      <td>0.6.2</td>
+      <td>presto</td>
+      <td>0.7.2</td>
+      <td>Nucleic acid sequence analysis</td>
+      <td>Sequencing, DNA, Immunology</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>63244</td>
+      <td>65177</td>
+      <td>1392</td>
+      <td>1599</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>63244</td>
+      <td>65177</td>
+      <td>1392</td>
+      <td>1599</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pretext</td>
+      <td>pretext_graph, pretext_map, pretext_snapshot</td>
+      <td>Process genome contacts maps processing images.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/wtsi-hpag/PretextSnapshot</td>
+      <td>Sequence Analysis</td>
+      <td>suite_pretext</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext</td>
+      <td>0.0.6</td>
+      <td>pretextgraph</td>
+      <td>0.0.6</td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3463</td>
+      <td>3463</td>
+      <td>538</td>
+      <td>538</td>
+      <td>1853</td>
+      <td>1853</td>
+      <td>256</td>
+      <td>256</td>
+      <td>1097</td>
+      <td>1097</td>
+      <td>70</td>
+      <td>70</td>
+      <td>6413</td>
+      <td>6413</td>
+      <td>864</td>
+      <td>864</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>principal_component_analysis</td>
+      <td>pca1</td>
+      <td>Principal Component Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>principal_component_analysis</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis</td>
+      <td>1.0.2</td>
+      <td>rpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>9788</td>
+      <td>10032</td>
+      <td>207</td>
+      <td>244</td>
+      <td>3072</td>
+      <td>8054</td>
+      <td>607</td>
+      <td>1488</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12860</td>
+      <td>18086</td>
+      <td>814</td>
+      <td>1732</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>prinseq</td>
+      <td>prinseq</td>
+      <td>PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets</td>
+      <td>prinseq</td>
+      <td>prinseq</td>
+      <td></td>
+      <td>PRINSEQ</td>
+      <td>PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.</td>
+      <td>Read pre-processing, Sequence trimming, Sequence contamination filtering</td>
+      <td>Transcriptomics, Metagenomics, Genomics</td>
+      <td>To update</td>
+      <td>http://prinseq.sourceforge.net/manual.html</td>
+      <td>Fastq Manipulation, Metagenomics</td>
+      <td>prinseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq</td>
+      <td>@TOOL_VERSION+galaxy2</td>
+      <td>prinseq</td>
+      <td>0.20.4</td>
+      <td>Read pre-processing, Sequence trimming, Sequence contamination filtering</td>
+      <td>Transcriptomics, Metagenomics</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>10152</td>
+      <td>10626</td>
+      <td>253</td>
+      <td>281</td>
+      <td>10581</td>
+      <td>10581</td>
+      <td>1240</td>
+      <td>1240</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20733</td>
+      <td>21207</td>
+      <td>1493</td>
+      <td>1521</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>probecoverage</td>
+      <td>probecoverage</td>
+      <td>computes and plots read coverage of genomic regions by sequencing datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Sequence Analysis, Genomic Interval Operations, Graphics, Statistics</td>
+      <td>probecoverage</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage</td>
+      <td>0.22.0</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>prodigal</td>
+      <td>prodigal</td>
+      <td>A protein-coding gene prediction software tool for bacterial and archaeal genomes</td>
+      <td>prodigal</td>
+      <td>prodigal</td>
+      <td></td>
+      <td>Prodigal</td>
+      <td>Fast, reliable protein-coding gene prediction for prokaryotic genomes.</td>
+      <td>Genome annotation</td>
+      <td>Genomics, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/hyattpd/Prodigal</td>
+      <td>Genome annotation</td>
+      <td>prodigal</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal</td>
+      <td>2.6.3</td>
+      <td>prodigal</td>
+      <td>2.6.3</td>
+      <td>Genome annotation</td>
+      <td>Genomics, Sequence analysis</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1902</td>
+      <td>1902</td>
+      <td>167</td>
+      <td>167</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1902</td>
+      <td>1902</td>
+      <td>167</td>
+      <td>167</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>progressivemauve</td>
+      <td>progressivemauve, xmfa2gff3</td>
+      <td>Mauve/ProgressiveMauve Multiple Sequence Aligner</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://darlinglab.org/mauve/user-guide/progressivemauve.html</td>
+      <td>Sequence Analysis</td>
+      <td>progressivemauve</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve</td>
+      <td></td>
+      <td>progressivemauve</td>
+      <td>snapshot_2015_02_13</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2064</td>
+      <td>2173</td>
+      <td>678</td>
+      <td>695</td>
+      <td>2900</td>
+      <td>2900</td>
+      <td>1034</td>
+      <td>1034</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4964</td>
+      <td>5073</td>
+      <td>1712</td>
+      <td>1729</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>projective_transformation</td>
+      <td>ip_projective_transformation</td>
+      <td>Projective transformation</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>projective_transformation</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation</td>
+      <td>0.1.2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>40</td>
+      <td>86</td>
+      <td>4</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>86</td>
+      <td>4</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>projective_transformation_points</td>
+      <td>ip_projective_transformation_points</td>
+      <td>Projective transformation of ROIs defined by pixel (point) coordinates</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>projective_transformation_points</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points</td>
+      <td>0.1.1</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20858</td>
+      <td>21444</td>
+      <td>14</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20858</td>
+      <td>21444</td>
+      <td>14</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>prokka</td>
+      <td>prokka</td>
+      <td>Rapid annotation of prokaryotic genomes</td>
+      <td>prokka</td>
+      <td>prokka</td>
+      <td></td>
+      <td>Prokka</td>
+      <td>Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.</td>
+      <td>Gene prediction, Coding region prediction, Genome annotation</td>
+      <td>Genomics, Model organisms, Virology</td>
+      <td>Up-to-date</td>
+      <td>http://github.com/tseemann/prokka</td>
+      <td>Sequence Analysis</td>
+      <td>prokka</td>
+      <td>crs4</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka</td>
+      <td>1.14.6</td>
+      <td>prokka</td>
+      <td>1.14.6</td>
+      <td>Coding region prediction, Genome annotation</td>
+      <td>Genomics, Model organisms, Virology</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>464359</td>
+      <td>476554</td>
+      <td>7475</td>
+      <td>7721</td>
+      <td>313285</td>
+      <td>331256</td>
+      <td>11243</td>
+      <td>12384</td>
+      <td>131211</td>
+      <td>141875</td>
+      <td>4358</td>
+      <td>4947</td>
+      <td>908855</td>
+      <td>949685</td>
+      <td>23076</td>
+      <td>25052</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>promer</td>
+      <td>promer4_substitutions</td>
+      <td>Aligns two sets of contigs and reports amino acid substitutions between them</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/promer</td>
+      <td>Assembly</td>
+      <td>promer</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/promer</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer</td>
+      <td>1.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>prot-scriber</td>
+      <td>prot_scriber</td>
+      <td>Protein annotation of short human readable descriptions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/usadellab/prot-scriber</td>
+      <td>Proteomics</td>
+      <td>prot_scriber</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber</td>
+      <td>0.1.6</td>
+      <td>prot-scriber</td>
+      <td>0.1.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>protease_prediction</td>
+      <td>eden_protease_prediction</td>
+      <td>This tool can learn the cleavage specificity of a given class of proteases.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/fabriziocosta/eden</td>
+      <td>Sequence Analysis, Proteomics</td>
+      <td>protease_prediction</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction</td>
+      <td>0.9</td>
+      <td>eden</td>
+      <td>2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>129</td>
+      <td>155</td>
+      <td>15</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>129</td>
+      <td>155</td>
+      <td>15</td>
+      <td>21</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>protein_analysis</td>
+      <td>promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort</td>
+      <td>TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis</td>
+      <td>Sequence Analysis</td>
+      <td>tmhmm_and_signalp</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis</td>
+      <td>0.0.13</td>
+      <td>promoter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>11743</td>
+      <td>12752</td>
+      <td>1137</td>
+      <td>1278</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11745</td>
+      <td>12754</td>
+      <td>1138</td>
+      <td>1279</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>protein_properties</td>
+      <td>bg_protein_properties</td>
+      <td>Calculation of various properties from given protein sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>protein_properties</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties</td>
+      <td>0.2.0</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>465</td>
+      <td>638</td>
+      <td>81</td>
+      <td>100</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>465</td>
+      <td>638</td>
+      <td>81</td>
+      <td>100</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteinortho</td>
+      <td>proteinortho, proteinortho_grab_proteins, proteinortho_summary</td>
+      <td>Proteinortho is a tool to detect orthologous proteins/genes within different species.</td>
+      <td>proteinortho</td>
+      <td>proteinortho</td>
+      <td></td>
+      <td>Proteinortho</td>
+      <td>Proteinortho is a tool to detect orthologous genes within different species</td>
+      <td>Sequence clustering, Sequence analysis</td>
+      <td>Comparative genomics</td>
+      <td>To update</td>
+      <td>https://gitlab.com/paulklemm_PHD/proteinortho</td>
+      <td>Proteomics</td>
+      <td>proteinortho</td>
+      <td>iuc</td>
+      <td>https://gitlab.com/paulklemm_PHD/proteinortho</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho</td>
+      <td>6.3.1</td>
+      <td>proteinortho</td>
+      <td>6.3.2</td>
+      <td>Sequence clustering, Sequence analysis</td>
+      <td>Comparative genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3962</td>
+      <td>3962</td>
+      <td>501</td>
+      <td>501</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3962</td>
+      <td>3962</td>
+      <td>501</td>
+      <td>501</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteinpilot</td>
+      <td>convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>proteinpilot</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_joinquantpepionswithproteins</td>
+      <td>proteomiqon_joinquantpepionswithproteins</td>
+      <td>The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_joinquantpepionswithproteins</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins</td>
+      <td>0.0.1</td>
+      <td>proteomiqon-joinquantpepionswithproteins</td>
+      <td>0.0.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>366</td>
+      <td>366</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>366</td>
+      <td>366</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_labeledproteinquantification</td>
+      <td>proteomiqon_labeledproteinquantification</td>
+      <td>The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_labeledproteinquantification</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification</td>
+      <td>0.0.1</td>
+      <td>proteomiqon-labeledproteinquantification</td>
+      <td>0.0.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_labelfreeproteinquantification</td>
+      <td>proteomiqon_labelfreeproteinquantification</td>
+      <td>The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_labelfreeproteinquantification</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification</td>
+      <td>0.0.1</td>
+      <td>proteomiqon-labelfreeproteinquantification</td>
+      <td>0.0.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_mzmltomzlite</td>
+      <td>proteomiqon_mzmltomzlite</td>
+      <td>The tool MzMLToMzLite allows to convert mzML files to mzLite files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_mzmltomzlite</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite</td>
+      <td>0.0.8</td>
+      <td>proteomiqon-mzmltomzlite</td>
+      <td>0.0.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>721</td>
+      <td>721</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>721</td>
+      <td>721</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_peptidedb</td>
+      <td>proteomiqon_peptidedb</td>
+      <td>The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_peptidedb</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb</td>
+      <td>0.0.7</td>
+      <td>proteomiqon-peptidedb</td>
+      <td>0.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>96</td>
+      <td>96</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>96</td>
+      <td>96</td>
+      <td>12</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_peptidespectrummatching</td>
+      <td>proteomiqon_peptidespectrummatching</td>
+      <td>Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_peptidespectrummatching</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching</td>
+      <td>0.0.7</td>
+      <td>proteomiqon-peptidespectrummatching</td>
+      <td>0.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>686</td>
+      <td>686</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>686</td>
+      <td>686</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_proteininference</td>
+      <td>proteomiqon_proteininference</td>
+      <td>MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_proteininference</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference</td>
+      <td>0.0.7</td>
+      <td>proteomiqon-proteininference</td>
+      <td>0.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>89</td>
+      <td>89</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>89</td>
+      <td>89</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_psmbasedquantification</td>
+      <td>proteomiqon_psmbasedquantification</td>
+      <td>The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_psmbasedquantification</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification</td>
+      <td>0.0.8</td>
+      <td>proteomiqon-psmbasedquantification</td>
+      <td>0.0.9</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>604</td>
+      <td>604</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>604</td>
+      <td>604</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteomiqon_psmstatistics</td>
+      <td>proteomiqon_psmstatistics</td>
+      <td>The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html</td>
+      <td>Proteomics</td>
+      <td>proteomiqon_psmstatistics</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics</td>
+      <td>0.0.8</td>
+      <td>proteomiqon-psmstatistics</td>
+      <td>0.0.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>694</td>
+      <td>694</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>694</td>
+      <td>694</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>proteore_venn_diagram</td>
+      <td>proteore_venn_diagram</td>
+      <td>ProteoRE JVenn Diagram</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>proteore_venn_diagram</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram</td>
+      <td>2021.06.08</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>protxml_to_xls</td>
+      <td>protxml_to_xls</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>protxml_to_xls</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls</td>
+      <td>0.1.0</td>
+      <td>trans_proteomic_pipeline</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pseudogenome</td>
+      <td>pseudogenome</td>
+      <td>Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Sequence Analysis</td>
+      <td>pseudogenome</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome</td>
+      <td>1.0.0</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>psiclass</td>
+      <td>psiclass</td>
+      <td>PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.</td>
+      <td>psiclass</td>
+      <td>psiclass</td>
+      <td></td>
+      <td>PsiCLASS</td>
+      <td>Reference-based transcriptome assembler for single or multiple RNA-seq samples</td>
+      <td>Transcriptome assembly</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/splicebox/PsiCLASS</td>
+      <td>Transcriptomics</td>
+      <td>psiclass</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass</td>
+      <td>1.0.3</td>
+      <td>psiclass</td>
+      <td>1.0.3</td>
+      <td>Transcriptome assembly</td>
+      <td>Sequence assembly</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>24</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>24</td>
+      <td>24</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>psm2sam</td>
+      <td>PSMtoSAM</td>
+      <td>PSM to SAM</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bioconductor.org/packages/release/bioc/html/proBAMr.html</td>
+      <td>Proteomics</td>
+      <td>psm_to_sam</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam</td>
+      <td>1.3.2.1</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>psm_eval</td>
+      <td>psm_eval</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>psm_eval</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval</td>
+      <td>0.1.0</td>
+      <td>binaries_for_psm_eval</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>psm_validation</td>
+      <td>psmvalidator</td>
+      <td>Validate PSM from Ion Fragmentation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/psm_fragments.git</td>
+      <td>Proteomics</td>
+      <td>psm_validation</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation</td>
+      <td>1.0.3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>20</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>20</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>psy-maps</td>
+      <td>psy_maps</td>
+      <td>Visualization of regular geographical data on a map with psyplot</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/Chilipp/psy-maps</td>
+      <td>Visualization, Climate Analysis</td>
+      <td>psy_maps</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps</td>
+      <td>1.3.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>333</td>
+      <td>502</td>
+      <td>62</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>333</td>
+      <td>502</td>
+      <td>62</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pureclip</td>
+      <td>pureclip</td>
+      <td>PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/skrakau/PureCLIP</td>
+      <td>Sequence Analysis, RNA, CLIP-seq</td>
+      <td>pureclip</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip</td>
+      <td>1.0.4</td>
+      <td>pureclip</td>
+      <td>1.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1319</td>
+      <td>1507</td>
+      <td>81</td>
+      <td>92</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1319</td>
+      <td>1507</td>
+      <td>81</td>
+      <td>92</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>purge_dups</td>
+      <td>purge_dups</td>
+      <td>Purge haplotigs and overlaps in an assembly based on read depth</td>
+      <td>purge_dups</td>
+      <td>purge_dups</td>
+      <td></td>
+      <td>purge_dups</td>
+      <td>Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences</td>
+      <td>Genome assembly, Read binning, Scaffolding</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/dfguan/purge_dups</td>
+      <td>Assembly</td>
+      <td>purge_dups</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups</td>
+      <td>1.2.6</td>
+      <td>purge_dups</td>
+      <td>1.2.6</td>
+      <td>Genome assembly, Read binning, Scaffolding</td>
+      <td>Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17782</td>
+      <td>17782</td>
+      <td>287</td>
+      <td>287</td>
+      <td>853</td>
+      <td>853</td>
+      <td>65</td>
+      <td>65</td>
+      <td>2224</td>
+      <td>2224</td>
+      <td>65</td>
+      <td>65</td>
+      <td>20859</td>
+      <td>20859</td>
+      <td>417</td>
+      <td>417</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pycoqc</td>
+      <td>pycoqc</td>
+      <td>QC metrics for ONT Basecalling</td>
+      <td>pycoqc</td>
+      <td>pycoqc</td>
+      <td></td>
+      <td>pycoQC</td>
+      <td>PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.</td>
+      <td>Sequencing quality control, Statistical calculation</td>
+      <td>Sequence analysis, Data quality management, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tleonardi/pycoQC</td>
+      <td>Nanopore</td>
+      <td>pycoqc</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc</td>
+      <td>2.5.2</td>
+      <td>pycoqc</td>
+      <td>2.5.2</td>
+      <td>Sequencing quality control, Statistical calculation</td>
+      <td>Sequence analysis, Data quality management, Sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22742</td>
+      <td>22742</td>
+      <td>557</td>
+      <td>557</td>
+      <td>2159</td>
+      <td>2159</td>
+      <td>716</td>
+      <td>716</td>
+      <td>776</td>
+      <td>776</td>
+      <td>448</td>
+      <td>448</td>
+      <td>25677</td>
+      <td>25677</td>
+      <td>1721</td>
+      <td>1721</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pyega3</td>
+      <td>pyega3</td>
+      <td>EGA python client uses the EGA REST API to download authorized datasets and files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/EGA-archive/ega-download-client</td>
+      <td>Data Source</td>
+      <td>ega_download_client</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3</td>
+      <td>5.0.2</td>
+      <td>pyega3</td>
+      <td>5.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2716</td>
+      <td>2716</td>
+      <td>104</td>
+      <td>104</td>
+      <td>134</td>
+      <td>134</td>
+      <td>43</td>
+      <td>43</td>
+      <td>40</td>
+      <td>40</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2890</td>
+      <td>2890</td>
+      <td>148</td>
+      <td>148</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pygenometracks</td>
+      <td>pygenomeTracks</td>
+      <td>pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.</td>
+      <td>pygenometracks</td>
+      <td>pygenometracks</td>
+      <td></td>
+      <td>pyGenomeTracks</td>
+      <td>reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.</td>
+      <td>Visualisation, Formatting</td>
+      <td>Model organisms, Imaging, Workflows</td>
+      <td>To update</td>
+      <td>https://github.com/deeptools/pyGenomeTracks</td>
+      <td>Visualization</td>
+      <td>pygenometracks</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks</td>
+      <td>3.8</td>
+      <td>pygenometracks</td>
+      <td>3.9</td>
+      <td>Visualisation, Formatting</td>
+      <td>Model organisms, Imaging, Workflows</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>12858</td>
+      <td>13232</td>
+      <td>986</td>
+      <td>996</td>
+      <td>8092</td>
+      <td>8092</td>
+      <td>943</td>
+      <td>943</td>
+      <td>3238</td>
+      <td>3238</td>
+      <td>124</td>
+      <td>124</td>
+      <td>24188</td>
+      <td>24562</td>
+      <td>2053</td>
+      <td>2063</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pyprophet</td>
+      <td>pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample</td>
+      <td>Semi-supervised learning and scoring of OpenSWATH results.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/PyProphet/pyprophet</td>
+      <td>Proteomics</td>
+      <td></td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet</td>
+      <td>2.1.4</td>
+      <td>pyprophet</td>
+      <td>2.2.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>5</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>2626</td>
+      <td>2626</td>
+      <td>150</td>
+      <td>150</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>609</td>
+      <td>609</td>
+      <td>9</td>
+      <td>9</td>
+      <td>3235</td>
+      <td>3235</td>
+      <td>159</td>
+      <td>159</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pyscenic</td>
+      <td>pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn</td>
+      <td>PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Sequence Analysis</td>
+      <td>suite_pyscenic</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic</td>
+      <td>0.12.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pysradb</td>
+      <td>pysradb_search</td>
+      <td>pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.</td>
+      <td>pysradb</td>
+      <td>pysradb</td>
+      <td></td>
+      <td>pysradb</td>
+      <td>Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.</td>
+      <td>Deposition, Data retrieval</td>
+      <td>Sequencing, Gene transcripts, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/saketkc/pysradb</td>
+      <td>Sequence Analysis</td>
+      <td>pysradb_search</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb</td>
+      <td>1.4.2</td>
+      <td>pysradb</td>
+      <td>2.2.2</td>
+      <td>Deposition, Data retrieval</td>
+      <td>Sequencing, Gene transcripts, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>163</td>
+      <td>163</td>
+      <td>35</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>163</td>
+      <td>163</td>
+      <td>35</td>
+      <td>35</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pyteomics</td>
+      <td>mztab2tsv</td>
+      <td>Tools using the pyteomics library</td>
+      <td>pyteomics</td>
+      <td>pyteomics</td>
+      <td></td>
+      <td>Pyteomics</td>
+      <td>Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.</td>
+      <td>Protein identification</td>
+      <td>Proteomics, Proteomics experiment</td>
+      <td>To update</td>
+      <td>https://pyteomics.readthedocs.io/en/latest/</td>
+      <td>Proteomics, Metabolomics</td>
+      <td>pyteomics</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics</td>
+      <td>4.4.1</td>
+      <td>pyteomics</td>
+      <td>4.7.4</td>
+      <td>Protein identification</td>
+      <td>Proteomics, Proteomics experiment</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>92</td>
+      <td>92</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>92</td>
+      <td>92</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>pyvo_integration</td>
+      <td>astronomical_archives</td>
+      <td>Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Data Source</td>
+      <td>astronomicalarchivestool</td>
+      <td>astroteam</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration</td>
+      <td>0.10.0</td>
+      <td>astropy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>53</td>
+      <td>53</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>53</td>
+      <td>53</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qcxms</td>
+      <td>qcxms_getres, qcxms_neutral_run, qcxms_production_run</td>
+      <td>QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/grimme-lab/QCxMS</td>
+      <td>Computational chemistry, Molecular Dynamics</td>
+      <td>QCxMS</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms</td>
+      <td>5.2.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11246</td>
+      <td>11246</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11246</td>
+      <td>11246</td>
+      <td>13</td>
+      <td>13</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qfilt</td>
+      <td>qfilt</td>
+      <td>Filter sequencing data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/veg/qfilt</td>
+      <td>Fastq Manipulation</td>
+      <td>qfilt</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt</td>
+      <td>1.0.0+galaxy1</td>
+      <td>qfilt</td>
+      <td>0.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qiime_add_on</td>
+      <td>qiime_collapse_samples, qiime_make_otu_table</td>
+      <td>QIIME to perform microbial community analysis</td>
+      <td>qiime_add_on</td>
+      <td>qiime_add_on, qiime_core</td>
+      <td></td>
+      <td>qiime_add_on</td>
+      <td>QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.</td>
+      <td>Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control</td>
+      <td>Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics</td>
+      <td>To update</td>
+      <td>http://www.qiime.org</td>
+      <td>Metagenomics</td>
+      <td>qiime</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on</td>
+      <td></td>
+      <td>qiime</td>
+      <td>1.9.1</td>
+      <td>Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control</td>
+      <td>Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2092</td>
+      <td>2342</td>
+      <td>209</td>
+      <td>238</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2094</td>
+      <td>2344</td>
+      <td>210</td>
+      <td>239</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qiime_core</td>
+      <td>qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file</td>
+      <td>QIIME to perform microbial community analysis</td>
+      <td>qiime_core</td>
+      <td>qiime_core</td>
+      <td></td>
+      <td>qiime_core</td>
+      <td>QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.</td>
+      <td>Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control</td>
+      <td>Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics</td>
+      <td>To update</td>
+      <td>http://www.qiime.org</td>
+      <td>Metagenomics</td>
+      <td>qiime</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core</td>
+      <td></td>
+      <td>qiime</td>
+      <td>1.9.1</td>
+      <td>Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control</td>
+      <td>Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>31825</td>
+      <td>34677</td>
+      <td>3375</td>
+      <td>3785</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>14</td>
+      <td>14</td>
+      <td>4</td>
+      <td>4</td>
+      <td>31840</td>
+      <td>34692</td>
+      <td>3380</td>
+      <td>3790</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qiime_extract_viz</td>
+      <td>qiime_extract_viz</td>
+      <td>Extract vizualization from QIIME artifacts</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.qiime.org</td>
+      <td>Metagenomics</td>
+      <td>qiime_extract_viz</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz</td>
+      <td>0.1.0</td>
+      <td>unzip</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qq_tools</td>
+      <td>qq_manhattan</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://CRAN.R-project.org/package=qqman</td>
+      <td>Visualization, Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td></td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools</td>
+      <td>0.1.0</td>
+      <td>r-qqman</td>
+      <td>0.1.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qualimap</td>
+      <td>qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq</td>
+      <td>Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.</td>
+      <td>qualimap</td>
+      <td>qualimap</td>
+      <td></td>
+      <td>QualiMap</td>
+      <td>Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.</td>
+      <td>Sequencing quality control</td>
+      <td>Data quality management</td>
+      <td>Up-to-date</td>
+      <td>http://qualimap.bioinfo.cipf.es/</td>
+      <td>Sequence Analysis, Transcriptomics, SAM</td>
+      <td>qualimap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap</td>
+      <td>2.3</td>
+      <td>qualimap</td>
+      <td>2.3</td>
+      <td>Sequencing quality control</td>
+      <td>Data quality management</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>684820</td>
+      <td>684820</td>
+      <td>3239</td>
+      <td>3239</td>
+      <td>90503</td>
+      <td>90503</td>
+      <td>3881</td>
+      <td>3881</td>
+      <td>29018</td>
+      <td>29018</td>
+      <td>826</td>
+      <td>826</td>
+      <td>804341</td>
+      <td>804341</td>
+      <td>7946</td>
+      <td>7946</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>quality_filter</td>
+      <td>qualityFilter</td>
+      <td>Filter nucleotides based on quality scores</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>quality_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter</td>
+      <td>1.0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>724</td>
+      <td>35</td>
+      <td>62</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>98</td>
+      <td>724</td>
+      <td>35</td>
+      <td>62</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>quantp</td>
+      <td>quantp</td>
+      <td>Correlation between protein and transcript abundance</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>quantp</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp</td>
+      <td>1.1.2</td>
+      <td>r-data.table</td>
+      <td>1.11.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>197</td>
+      <td>241</td>
+      <td>17</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>197</td>
+      <td>241</td>
+      <td>17</td>
+      <td>22</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>quantwiz_iq</td>
+      <td>quantwiz_iq</td>
+      <td>Isobaric Quantitation using QuantWiz-IQ</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://sourceforge.net/projects/quantwiz/</td>
+      <td>Proteomics</td>
+      <td>quantwiz_iq</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq</td>
+      <td>2.0</td>
+      <td>quantwiz-iq</td>
+      <td>2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>32</td>
+      <td>32</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>32</td>
+      <td>32</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>quasitools</td>
+      <td>aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality</td>
+      <td>A collection of tools for analysing Viral Quasispecies</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/quasitools</td>
+      <td>Sequence Analysis</td>
+      <td>quasitools</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/quasitools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools</td>
+      <td>0.7.0</td>
+      <td>quasitools</td>
+      <td>0.7.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13483</td>
+      <td>13483</td>
+      <td>434</td>
+      <td>434</td>
+      <td>13483</td>
+      <td>13483</td>
+      <td>434</td>
+      <td>434</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>quast</td>
+      <td>quast</td>
+      <td>Quast (Quality ASsessment Tool) evaluates genome assemblies.</td>
+      <td>quast</td>
+      <td>quast</td>
+      <td></td>
+      <td>QUAST</td>
+      <td>QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.</td>
+      <td>Visualisation, Sequence assembly validation</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>http://quast.bioinf.spbau.ru/</td>
+      <td>Assembly</td>
+      <td>quast</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast</td>
+      <td>5.2.0</td>
+      <td>quast</td>
+      <td>5.2.0</td>
+      <td>Visualisation, Sequence assembly validation</td>
+      <td>Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>67737</td>
+      <td>69738</td>
+      <td>7787</td>
+      <td>7971</td>
+      <td>51925</td>
+      <td>56602</td>
+      <td>9692</td>
+      <td>10646</td>
+      <td>32003</td>
+      <td>34145</td>
+      <td>3890</td>
+      <td>4127</td>
+      <td>151665</td>
+      <td>160485</td>
+      <td>21369</td>
+      <td>22744</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>query</td>
+      <td>query</td>
+      <td>Execute an SQL statement on a set of tables</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>query</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/query</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/query</td>
+      <td>0.2</td>
+      <td>click</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>query_impc</td>
+      <td>query_impc</td>
+      <td>Contains a tool to query the IMPC database.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc</td>
+      <td>Convert Formats, Web Services</td>
+      <td>query_impc</td>
+      <td>iuc</td>
+      <td>https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc</td>
+      <td>0.9.0</td>
+      <td>requests</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>query_tabular</td>
+      <td>filter_tabular, query_tabular, sqlite_to_tabular</td>
+      <td>Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular</td>
+      <td>Text Manipulation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular</td>
+      <td>3.3.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>130124</td>
+      <td>135361</td>
+      <td>1265</td>
+      <td>1305</td>
+      <td>11135</td>
+      <td>11135</td>
+      <td>922</td>
+      <td>922</td>
+      <td>5939</td>
+      <td>5939</td>
+      <td>153</td>
+      <td>153</td>
+      <td>147198</td>
+      <td>152435</td>
+      <td>2340</td>
+      <td>2380</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>quickmerge</td>
+      <td>quickmerge</td>
+      <td>Merge long-read and hybrid assemblies to increase contiguity</td>
+      <td>quickmerge</td>
+      <td>quickmerge</td>
+      <td></td>
+      <td>quickmerge</td>
+      <td>Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.</td>
+      <td>Genome assembly, Scaffolding, De-novo assembly, Genotyping</td>
+      <td>Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/mahulchak/quickmerge</td>
+      <td>Assembly</td>
+      <td>quickmerge</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge</td>
+      <td>0.3</td>
+      <td>quickmerge</td>
+      <td>0.3</td>
+      <td>Genome assembly, Scaffolding, De-novo assembly, Genotyping</td>
+      <td>Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>qupath_roi_splitter</td>
+      <td>qupath_roi_splitter</td>
+      <td>Split ROI coordinates of QuPath TMA annotation by cell type</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/npinter/ROIsplitter</td>
+      <td>Imaging</td>
+      <td>qupath_roi_splitter</td>
+      <td>galaxyp</td>
+      <td>hhttps://github.com/npinter/ROIsplitter</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter</td>
+      <td>0.3.2</td>
+      <td>geojson</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>172</td>
+      <td>172</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>172</td>
+      <td>172</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rRNA</td>
+      <td>meta_rna</td>
+      <td>Identification of ribosomal RNA genes in metagenomic fragments.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://weizhong-lab.ucsd.edu/meta_rna/</td>
+      <td>RNA</td>
+      <td>rrna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rRNA</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA</td>
+      <td>0.1</td>
+      <td>hmmsearch3.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>raceid</td>
+      <td>raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory</td>
+      <td>RaceID3, StemID2, FateID - scRNA analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/dgrun/RaceID3_StemID2_package/</td>
+      <td>Single Cell, Transcriptomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid</td>
+      <td>0.2.3</td>
+      <td>r-raceid</td>
+      <td>0.1.3</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>3077</td>
+      <td>4581</td>
+      <td>395</td>
+      <td>518</td>
+      <td>2856</td>
+      <td>2856</td>
+      <td>1093</td>
+      <td>1093</td>
+      <td>1977</td>
+      <td>1977</td>
+      <td>19</td>
+      <td>19</td>
+      <td>7910</td>
+      <td>9414</td>
+      <td>1507</td>
+      <td>1630</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>racon</td>
+      <td>racon</td>
+      <td>Consensus module for raw de novo DNA assembly of long uncorrected reads.</td>
+      <td>Racon</td>
+      <td>Racon</td>
+      <td></td>
+      <td>Racon</td>
+      <td>Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.</td>
+      <td>Genome assembly, Mapping assembly</td>
+      <td>Whole genome sequencing, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/isovic/racon</td>
+      <td>Sequence Analysis</td>
+      <td>racon</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/racon</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/racon</td>
+      <td>1.5.0</td>
+      <td>racon</td>
+      <td>1.5.0</td>
+      <td>Genome assembly, Mapping assembly</td>
+      <td>Whole genome sequencing, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>27113</td>
+      <td>27315</td>
+      <td>839</td>
+      <td>850</td>
+      <td>9089</td>
+      <td>9089</td>
+      <td>475</td>
+      <td>475</td>
+      <td>5452</td>
+      <td>5452</td>
+      <td>171</td>
+      <td>171</td>
+      <td>41654</td>
+      <td>41856</td>
+      <td>1485</td>
+      <td>1496</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ragtag</td>
+      <td>ragtag</td>
+      <td>Reference-guided scaffolding of draft genomes tool.</td>
+      <td>ragtag</td>
+      <td>ragtag</td>
+      <td></td>
+      <td>ragtag</td>
+      <td>RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.</td>
+      <td>Genome assembly</td>
+      <td>Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/malonge/RagTag</td>
+      <td>Assembly</td>
+      <td>ragtag</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag</td>
+      <td>2.1.0</td>
+      <td>ragtag</td>
+      <td>2.1.0</td>
+      <td>Genome assembly</td>
+      <td>Sequence assembly</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4844</td>
+      <td>4844</td>
+      <td>480</td>
+      <td>480</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>3</td>
+      <td>3</td>
+      <td>4851</td>
+      <td>4851</td>
+      <td>483</td>
+      <td>483</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ramclustr</td>
+      <td>ramclustr, ramclustr_define_experiment</td>
+      <td></td>
+      <td>ramclustr</td>
+      <td>ramclustr</td>
+      <td></td>
+      <td>RAMClustR</td>
+      <td>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</td>
+      <td>Imputation, Standardisation and normalisation, Clustering, Correlation</td>
+      <td>Metabolomics</td>
+      <td>To update</td>
+      <td>https://rdrr.io/cran/RAMClustR/</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr</td>
+      <td>1.3.0</td>
+      <td>r-ramclustr</td>
+      <td>1.3.1</td>
+      <td>Imputation, Standardisation and normalisation, Clustering, Correlation</td>
+      <td>Metabolomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>22</td>
+      <td>22</td>
+      <td>29</td>
+      <td>29</td>
+      <td>14</td>
+      <td>14</td>
+      <td>344</td>
+      <td>344</td>
+      <td>4</td>
+      <td>4</td>
+      <td>431</td>
+      <td>431</td>
+      <td>40</td>
+      <td>40</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rapidnj</td>
+      <td>rapidnj</td>
+      <td>Galaxy wrapper for the RapidNJ tool</td>
+      <td>rapidnj</td>
+      <td>rapidnj</td>
+      <td></td>
+      <td>RapidNJ</td>
+      <td>A tool for fast canonical neighbor-joining tree construction.</td>
+      <td>Phylogenetic tree generation</td>
+      <td>Phylogeny</td>
+      <td>Up-to-date</td>
+      <td>https://birc.au.dk/software/rapidnj/</td>
+      <td>Phylogenetics</td>
+      <td>rapidnj</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj</td>
+      <td>2.3.2</td>
+      <td>rapidnj</td>
+      <td>2.3.2</td>
+      <td></td>
+      <td>Phylogeny</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>339</td>
+      <td>339</td>
+      <td>30</td>
+      <td>30</td>
+      <td>1737</td>
+      <td>1737</td>
+      <td>256</td>
+      <td>256</td>
+      <td>6</td>
+      <td>6</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2082</td>
+      <td>2082</td>
+      <td>287</td>
+      <td>287</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rasusa</td>
+      <td>rasusa</td>
+      <td>Randomly subsample sequencing reads to a specified coverage</td>
+      <td>rasusa</td>
+      <td>rasusa</td>
+      <td></td>
+      <td>rasusa</td>
+      <td>Produces an unbiased subsample of your reads</td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/mbhall88/rasusa</td>
+      <td>Sequence Analysis</td>
+      <td>rasusa</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa</td>
+      <td>2.0.0</td>
+      <td>rasusa</td>
+      <td>2.1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>42</td>
+      <td>42</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>raven</td>
+      <td>raven</td>
+      <td>Raven is a de novo genome assembler for long uncorrected reads.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lbcb-sci/raven</td>
+      <td>Assembly</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven</td>
+      <td>1.8.3</td>
+      <td>raven-assembler</td>
+      <td>1.8.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>9477</td>
+      <td>9477</td>
+      <td>438</td>
+      <td>438</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10585</td>
+      <td>10585</td>
+      <td>182</td>
+      <td>182</td>
+      <td>20062</td>
+      <td>20062</td>
+      <td>620</td>
+      <td>620</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rawtools</td>
+      <td>rawtools</td>
+      <td>Raw Tools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/kevinkovalchik/RawTools</td>
+      <td>Proteomics</td>
+      <td>rawtools</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools</td>
+      <td></td>
+      <td>rawtools</td>
+      <td>2.0.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>166</td>
+      <td>179</td>
+      <td>32</td>
+      <td>33</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>414</td>
+      <td>414</td>
+      <td>13</td>
+      <td>13</td>
+      <td>580</td>
+      <td>593</td>
+      <td>45</td>
+      <td>46</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>raxml</td>
+      <td>raxml</td>
+      <td>RAxML - A Maximum Likelihood based phylogenetic inference</td>
+      <td>raxml</td>
+      <td>raxml</td>
+      <td></td>
+      <td>RAxML</td>
+      <td>A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.</td>
+      <td>Sequence analysis, Phylogenetic tree analysis</td>
+      <td>Phylogenetics, Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.exelixis-lab.org/web/software/raxml/</td>
+      <td>Phylogenetics</td>
+      <td>raxml</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml</td>
+      <td>8.2.12</td>
+      <td>raxml</td>
+      <td>8.2.13</td>
+      <td>Sequence analysis</td>
+      <td>Phylogenetics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>10905</td>
+      <td>10905</td>
+      <td>966</td>
+      <td>966</td>
+      <td>5100</td>
+      <td>5114</td>
+      <td>587</td>
+      <td>587</td>
+      <td>4955</td>
+      <td>6094</td>
+      <td>765</td>
+      <td>892</td>
+      <td>20960</td>
+      <td>22113</td>
+      <td>2318</td>
+      <td>2445</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rbpbench</td>
+      <td>rbpbench</td>
+      <td>Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs</td>
+      <td>rbpbench</td>
+      <td>rbpbench</td>
+      <td></td>
+      <td>RBPBench</td>
+      <td>Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs</td>
+      <td></td>
+      <td>RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/michauhl/RBPBench</td>
+      <td>Sequence Analysis, RNA, CLIP-seq</td>
+      <td>rbpbench</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench</td>
+      <td>0.8.1</td>
+      <td>rbpbench</td>
+      <td>1.0</td>
+      <td></td>
+      <td>RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>90</td>
+      <td>90</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>90</td>
+      <td>90</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rcas</td>
+      <td>rcas</td>
+      <td>RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/BIMSBbioinfo/RCAS</td>
+      <td>RNA</td>
+      <td>rcas</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas</td>
+      <td>1.5.4</td>
+      <td>bioconductor-rcas</td>
+      <td>1.28.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>860</td>
+      <td>1257</td>
+      <td>88</td>
+      <td>98</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>860</td>
+      <td>1257</td>
+      <td>88</td>
+      <td>98</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rcorrector</td>
+      <td>rcorrector</td>
+      <td>Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.</td>
+      <td>rcorrector</td>
+      <td>rcorrector</td>
+      <td></td>
+      <td>Rcorrector</td>
+      <td>This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.</td>
+      <td>Sequencing error detection</td>
+      <td>RNA, RNA-Seq, Sequencing</td>
+      <td>To update</td>
+      <td>https://github.com/mourisl/Rcorrector</td>
+      <td>Fastq Manipulation</td>
+      <td>rcorrector</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector</td>
+      <td>1.0.3+galaxy1</td>
+      <td>rcorrector</td>
+      <td>1.0.7</td>
+      <td>Sequencing error detection</td>
+      <td>RNA, RNA-Seq</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>655</td>
+      <td>655</td>
+      <td>57</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>655</td>
+      <td>655</td>
+      <td>57</td>
+      <td>57</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rcve</td>
+      <td>rcve1</td>
+      <td>Compute RCVE</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>rcve</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve</td>
+      <td>1.0.0</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>49</td>
+      <td>191</td>
+      <td>5</td>
+      <td>46</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>49</td>
+      <td>191</td>
+      <td>5</td>
+      <td>46</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rcx-tk</td>
+      <td>rcx-tk</td>
+      <td>Tools to process metadata or alkane files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/rcx-tk</td>
+      <td>Metabolomics</td>
+      <td>rcx_tk</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk</td>
+      <td>0.1.0+galaxy0</td>
+      <td>rcx-tk</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rdock</td>
+      <td>rdock</td>
+      <td>Docking ligands to proteins and nucleic acids</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rdock.sourceforge.net/</td>
+      <td>Computational chemistry</td>
+      <td>rdock</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock</td>
+      <td>1.0</td>
+      <td>rDock</td>
+      <td>2013.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>read_it_and_keep</td>
+      <td>read_it_and_keep</td>
+      <td>Rapid decontamination of SARS-CoV-2 sequencing reads</td>
+      <td>read_it_and_keep</td>
+      <td>read_it_and_keep</td>
+      <td></td>
+      <td>read_it_and_keep</td>
+      <td>Read contamination removal</td>
+      <td>Filtering, Genome alignment</td>
+      <td>Pathology, Genomics</td>
+      <td>To update</td>
+      <td>https://github.com/GenomePathogenAnalysisService/read-it-and-keep</td>
+      <td>Sequence Analysis</td>
+      <td>read_it_and_keep</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep</td>
+      <td>0.2.2</td>
+      <td>read-it-and-keep</td>
+      <td>0.3.0</td>
+      <td>Filtering, Genome alignment</td>
+      <td>Pathology, Genomics</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3710</td>
+      <td>3710</td>
+      <td>80</td>
+      <td>80</td>
+      <td>7</td>
+      <td>7</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3717</td>
+      <td>3717</td>
+      <td>86</td>
+      <td>86</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>reago</td>
+      <td>reago</td>
+      <td>Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.</td>
+      <td>reago</td>
+      <td>reago</td>
+      <td></td>
+      <td>REAGO</td>
+      <td>This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly, RNA, Metagenomics, Microbiology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/chengyuan/reago-1.1</td>
+      <td>Metagenomics, RNA</td>
+      <td>reago</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago</td>
+      <td>1.1</td>
+      <td>reago</td>
+      <td>1.1</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly, RNA, Metagenomics, Microbiology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>recentrifuge</td>
+      <td>recentrifuge</td>
+      <td>"With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."</td>
+      <td>Recentrifuge</td>
+      <td>Recentrifuge</td>
+      <td></td>
+      <td>Recentrifuge</td>
+      <td>Robust comparative analysis and contamination removal for metagenomics.</td>
+      <td>Taxonomic classification, Expression analysis, Cross-assembly</td>
+      <td>Metagenomics, Microbial ecology, Metagenomic sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/khyox/recentrifuge</td>
+      <td>Metagenomics</td>
+      <td>recentrifuge</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge</td>
+      <td>1.15.0</td>
+      <td>recentrifuge</td>
+      <td>1.15.0</td>
+      <td>Taxonomic classification, Expression analysis, Cross-assembly</td>
+      <td>Metagenomics, Microbial ecology, Metagenomic sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>472</td>
+      <td>472</td>
+      <td>92</td>
+      <td>92</td>
+      <td>32</td>
+      <td>32</td>
+      <td>13</td>
+      <td>13</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td>510</td>
+      <td>510</td>
+      <td>109</td>
+      <td>109</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>recetox_aplcms</td>
+      <td>recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise</td>
+      <td>Peak detection tool for HRMS profile data.</td>
+      <td>recetox-aplcms</td>
+      <td>recetox-aplcms</td>
+      <td></td>
+      <td>recetox-aplcms</td>
+      <td>recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.</td>
+      <td>Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment</td>
+      <td>Metabolomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/recetox-aplcms</td>
+      <td>Metabolomics</td>
+      <td>recetox-aplcms</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms</td>
+      <td>0.13.3</td>
+      <td>r-recetox-aplcms</td>
+      <td>0.13.3</td>
+      <td>Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment</td>
+      <td>Metabolomics</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>862</td>
+      <td>862</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td>910</td>
+      <td>910</td>
+      <td>13</td>
+      <td>13</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>recetox_msfinder</td>
+      <td>recetox_msfinder</td>
+      <td></td>
+      <td>recetox-msfinder</td>
+      <td>recetox-msfinder</td>
+      <td></td>
+      <td>recetox-msfinder</td>
+      <td>This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.</td>
+      <td>Annotation</td>
+      <td>Metabolomics</td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/recetox-msfinder</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder</td>
+      <td>v3.5.2</td>
+      <td></td>
+      <td></td>
+      <td>Annotation</td>
+      <td>Metabolomics</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>47</td>
+      <td>47</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>47</td>
+      <td>47</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>recetox_xmsannotator</td>
+      <td>recetox_xmsannotator_advanced</td>
+      <td></td>
+      <td>recetox-xmsannotator</td>
+      <td>recetox-xmsannotator</td>
+      <td></td>
+      <td>recetox-xMSannotator</td>
+      <td>Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.</td>
+      <td>Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/recetox-xMSannotator</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator</td>
+      <td>0.10.0</td>
+      <td>r-recetox-xmsannotator</td>
+      <td>0.10.0</td>
+      <td>Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation</td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>93</td>
+      <td>93</td>
+      <td>2</td>
+      <td>2</td>
+      <td>93</td>
+      <td>93</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>red</td>
+      <td>red</td>
+      <td>Red (REpeat Detector)</td>
+      <td>red</td>
+      <td>red</td>
+      <td></td>
+      <td>RED</td>
+      <td>This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.</td>
+      <td>RNA-Seq analysis, Editing</td>
+      <td>RNA, Sequencing, Data visualisation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/BioinformaticsToolsmith/Red</td>
+      <td>Sequence Analysis</td>
+      <td>red</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/red</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/red</td>
+      <td>2018.09.10</td>
+      <td>red</td>
+      <td>2018.09.10</td>
+      <td>RNA-Seq analysis, Editing</td>
+      <td>RNA, Sequencing, Data visualisation</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>859</td>
+      <td>859</td>
+      <td>203</td>
+      <td>203</td>
+      <td>305</td>
+      <td>305</td>
+      <td>142</td>
+      <td>142</td>
+      <td>227</td>
+      <td>227</td>
+      <td>58</td>
+      <td>58</td>
+      <td>1391</td>
+      <td>1391</td>
+      <td>403</td>
+      <td>403</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>refseq_masher</td>
+      <td>refseq_masher_contains, refseq_masher_matches</td>
+      <td>Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/refseq_masher</td>
+      <td>Sequence Analysis</td>
+      <td>refseq_masher</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/refseq_masher</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher</td>
+      <td>0.1.2</td>
+      <td>refseq_masher</td>
+      <td>0.1.2</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>428</td>
+      <td>428</td>
+      <td>35</td>
+      <td>35</td>
+      <td>141</td>
+      <td>141</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>569</td>
+      <td>569</td>
+      <td>77</td>
+      <td>77</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>regex_find_replace</td>
+      <td>regex1, regexColumn1</td>
+      <td>Use python regular expressions to find and replace text</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>regex_find_replace</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace</td>
+      <td>1.0.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>78648</td>
+      <td>78834</td>
+      <td>1144</td>
+      <td>1156</td>
+      <td>18063</td>
+      <td>18063</td>
+      <td>870</td>
+      <td>870</td>
+      <td>4455</td>
+      <td>6051</td>
+      <td>194</td>
+      <td>289</td>
+      <td>101166</td>
+      <td>102948</td>
+      <td>2208</td>
+      <td>2315</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>regionalgam</td>
+      <td>regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RetoSchmucki/regionalGAM</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam</td>
+      <td>1.5</td>
+      <td>r-mgcv</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>438</td>
+      <td>542</td>
+      <td>128</td>
+      <td>157</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>438</td>
+      <td>542</td>
+      <td>128</td>
+      <td>157</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rem_complex</td>
+      <td>rem_complex</td>
+      <td>Removes molecular coordination complexes.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools</td>
+      <td>Metabolomics</td>
+      <td>rem_complex</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex</td>
+      <td>1.0.0</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18</td>
+      <td>18</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>remove_beginning</td>
+      <td>Remove beginning1</td>
+      <td>Remove lines from the beginning of a file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>remove_beginning</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>148572</td>
+      <td>169964</td>
+      <td>3525</td>
+      <td>3682</td>
+      <td>36694</td>
+      <td>113826</td>
+      <td>3910</td>
+      <td>8163</td>
+      <td>9713</td>
+      <td>10577</td>
+      <td>1475</td>
+      <td>1598</td>
+      <td>194979</td>
+      <td>294367</td>
+      <td>8910</td>
+      <td>13443</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>remurna</td>
+      <td>remurna</td>
+      <td>remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna</td>
+      <td>RNA</td>
+      <td>remurna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna</td>
+      <td>1.0.0</td>
+      <td>remurna</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>39</td>
+      <td>44</td>
+      <td>6</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>44</td>
+      <td>6</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rename_annotated_feature</td>
+      <td>rename_annotated_feature</td>
+      <td>Update column names in an abundance table using a annotation table with spectral matching results</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/RECETOX/galaxytools/</td>
+      <td>Metabolomics</td>
+      <td>rename_annotated_feature</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature</td>
+      <td>1.0.0</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repeat_channels</td>
+      <td>repeat_channels</td>
+      <td>Convert single-channel to multi-channel image</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>repeat_channels</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels</td>
+      <td>1.26.4</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repeat_masker</td>
+      <td>repeatmasker_wrapper</td>
+      <td>RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.repeatmasker.org/</td>
+      <td>Sequence Analysis</td>
+      <td>repeat_masker</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker</td>
+      <td>0.1.2</td>
+      <td>RepeatMasker</td>
+      <td>4.0.9_p2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5998</td>
+      <td>5998</td>
+      <td>810</td>
+      <td>810</td>
+      <td>7618</td>
+      <td>7618</td>
+      <td>803</td>
+      <td>803</td>
+      <td>3135</td>
+      <td>3135</td>
+      <td>292</td>
+      <td>292</td>
+      <td>16751</td>
+      <td>16751</td>
+      <td>1905</td>
+      <td>1905</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repeatexplorer2</td>
+      <td>repeatexplorer_clustering</td>
+      <td>Tool for annotation of repeats from unassembled shotgun reads.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/repeatexplorer/repex_tarean</td>
+      <td>Genome annotation</td>
+      <td>repeatexplorer2</td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2</td>
+      <td>2.3.8</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>95</td>
+      <td>95</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>95</td>
+      <td>95</td>
+      <td>38</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repeatmasker</td>
+      <td>repeatmasker_wrapper</td>
+      <td>RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.</td>
+      <td>repeatmasker</td>
+      <td>repeatmasker</td>
+      <td></td>
+      <td>RepeatMasker</td>
+      <td>A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).</td>
+      <td>Genome annotation</td>
+      <td>Sequence analysis, Sequence composition, complexity and repeats</td>
+      <td>To update</td>
+      <td>http://www.repeatmasker.org/</td>
+      <td>Sequence Analysis</td>
+      <td>repeat_masker</td>
+      <td>bgruening</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker</td>
+      <td>4.1.5</td>
+      <td>repeatmasker</td>
+      <td>4.0.9_p2</td>
+      <td>Genome annotation</td>
+      <td>Sequence composition, complexity and repeats</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5998</td>
+      <td>5998</td>
+      <td>810</td>
+      <td>810</td>
+      <td>7618</td>
+      <td>7618</td>
+      <td>803</td>
+      <td>803</td>
+      <td>3135</td>
+      <td>3135</td>
+      <td>292</td>
+      <td>292</td>
+      <td>16751</td>
+      <td>16751</td>
+      <td>1905</td>
+      <td>1905</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repeatmodeler</td>
+      <td>repeatmodeler</td>
+      <td>RepeatModeler - Model repetitive DNA</td>
+      <td>repeatmodeler</td>
+      <td>repeatmodeler</td>
+      <td></td>
+      <td>RepeatModeler</td>
+      <td>De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.</td>
+      <td>Repeat sequence detection</td>
+      <td>Sequence composition, complexity and repeats, Sequence composition, complexity and repeats</td>
+      <td>To update</td>
+      <td>https://www.repeatmasker.org/RepeatModeler/</td>
+      <td>Genome annotation</td>
+      <td>repeatmodeler</td>
+      <td>csbl</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler</td>
+      <td>2.0.5</td>
+      <td></td>
+      <td></td>
+      <td>Repeat sequence detection</td>
+      <td>Sequence composition, complexity and repeats, Sequence composition, complexity and repeats</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7963</td>
+      <td>7963</td>
+      <td>413</td>
+      <td>413</td>
+      <td>1485</td>
+      <td>1485</td>
+      <td>220</td>
+      <td>220</td>
+      <td>8402</td>
+      <td>8402</td>
+      <td>168</td>
+      <td>168</td>
+      <td>17850</td>
+      <td>17850</td>
+      <td>801</td>
+      <td>801</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repenrich</td>
+      <td>edger-repenrich, repenrich</td>
+      <td>Repeat element profiling</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich</td>
+      <td>Transcriptomics</td>
+      <td>repenrich</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich</td>
+      <td>2.31.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1725</td>
+      <td>1790</td>
+      <td>56</td>
+      <td>57</td>
+      <td>1725</td>
+      <td>1790</td>
+      <td>56</td>
+      <td>57</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repenrich2</td>
+      <td>edger-repenrich2, repenrich2</td>
+      <td>Repeat element profiling using bowtie2 aligner</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2</td>
+      <td>Transcriptomics</td>
+      <td>repenrich2</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2</td>
+      <td>2.31.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>replaceColumn</td>
+      <td>replace_column_with_key_value_file</td>
+      <td>A tool to replace all column entries of a file given by values of a key-value file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>replace_column_by_key_value_file</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn</td>
+      <td>0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>577184</td>
+      <td>577312</td>
+      <td>463</td>
+      <td>492</td>
+      <td>43900</td>
+      <td>44233</td>
+      <td>283</td>
+      <td>373</td>
+      <td>2190</td>
+      <td>2190</td>
+      <td>112</td>
+      <td>112</td>
+      <td>623274</td>
+      <td>623735</td>
+      <td>858</td>
+      <td>977</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>replace_chromosome_names</td>
+      <td>replace_chromosome_names</td>
+      <td>Replace chromosome names</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>replace_chromosome_names</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names</td>
+      <td>0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>514</td>
+      <td>573</td>
+      <td>69</td>
+      <td>83</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>514</td>
+      <td>573</td>
+      <td>69</td>
+      <td>83</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>repmatch_gff3</td>
+      <td>repmatch_gff3</td>
+      <td>Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>ChIP-seq</td>
+      <td>repmatch_gff3</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3</td>
+      <td></td>
+      <td>matplotlib</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>415</td>
+      <td>721</td>
+      <td>128</td>
+      <td>219</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>415</td>
+      <td>721</td>
+      <td>128</td>
+      <td>219</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>reshape2</td>
+      <td>cast, melt</td>
+      <td>Flexibly restructure and aggregate data using just the two functions melt and dcast</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/web/packages/reshape2/index.html</td>
+      <td>Text Manipulation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2</td>
+      <td>1.4.2</td>
+      <td>r-reshape2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>3543</td>
+      <td>3619</td>
+      <td>108</td>
+      <td>111</td>
+      <td>536</td>
+      <td>536</td>
+      <td>157</td>
+      <td>157</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4079</td>
+      <td>4155</td>
+      <td>265</td>
+      <td>268</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>resize_coordinate_window</td>
+      <td>resize_coordinate_window</td>
+      <td>Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Genomic Interval Operations</td>
+      <td>resize_coordinate_window</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window</td>
+      <td>1.0.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>75</td>
+      <td>86</td>
+      <td>8</td>
+      <td>9</td>
+      <td>138</td>
+      <td>216</td>
+      <td>30</td>
+      <td>57</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>213</td>
+      <td>302</td>
+      <td>38</td>
+      <td>66</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rest_tool</td>
+      <td>pubchem_rest_tool</td>
+      <td>This tool fetches data from pubchem via the PubChem REST API.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html</td>
+      <td>Data Source</td>
+      <td>pubchem_rest_tool</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>retip</td>
+      <td>retip_apply, retip_descriptors, retip_filter_rt, retip_train</td>
+      <td></td>
+      <td>retip</td>
+      <td>retip</td>
+      <td></td>
+      <td>Retip</td>
+      <td>Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.</td>
+      <td>Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition</td>
+      <td>Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry</td>
+      <td>To update</td>
+      <td>https://github.com/PaoloBnn/Retip</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/retip</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/retip</td>
+      <td>0.5.4</td>
+      <td></td>
+      <td></td>
+      <td>Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition</td>
+      <td>Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>retrieve_bold</td>
+      <td>retrieve_bold</td>
+      <td>Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://anaconda.org/conda-forge/r-bold</td>
+      <td>Ecology</td>
+      <td>retrieve_bold</td>
+      <td>ecology</td>
+      <td>https://github.com/wpearman1996/MARES_database_pipeline/tree/master</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold</td>
+      <td>1.3.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>retrieve_ensembl_bed</td>
+      <td>retrieve_ensembl_bed</td>
+      <td>Retrieve cDNA features from Ensembl REST API in BED format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rest.ensembl.org/</td>
+      <td>Data Source</td>
+      <td>retrieve_ensembl_bed</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>revertR2orientationInBam</td>
+      <td>revertR2orientationInBam</td>
+      <td>Revert the mapped orientation of R2 mates in a bam.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>SAM</td>
+      <td>revertr2orientationinbam</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam</td>
+      <td>0.0.2</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>40</td>
+      <td>40</td>
+      <td>11</td>
+      <td>11</td>
+      <td>520</td>
+      <td>520</td>
+      <td>31</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>560</td>
+      <td>560</td>
+      <td>42</td>
+      <td>42</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>revoluzer</td>
+      <td>revoluzer_crex, revoluzer_distmat</td>
+      <td>revoluzer wrappers</td>
+      <td>revoluzer</td>
+      <td>revoluzer</td>
+      <td></td>
+      <td>revoluzer</td>
+      <td>Various tools for genome rearrangement analysis. CREx, TreeREx, etc</td>
+      <td>Structural variation detection</td>
+      <td>Molecular evolution, Phylogeny</td>
+      <td>Up-to-date</td>
+      <td>https://gitlab.com/Bernt/revoluzer/</td>
+      <td>Phylogenetics</td>
+      <td>revoluzer</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer</td>
+      <td>0.1.6</td>
+      <td>revoluzer</td>
+      <td>0.1.6</td>
+      <td>Structural variation detection</td>
+      <td>Molecular evolution, Phylogeny</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2444</td>
+      <td>2444</td>
+      <td>52</td>
+      <td>52</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2444</td>
+      <td>2444</td>
+      <td>52</td>
+      <td>52</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rfove</td>
+      <td>rfove</td>
+      <td>Perform segmentation region-based fitting of overlapping ellipses</td>
+      <td>rfove</td>
+      <td>rfove</td>
+      <td></td>
+      <td>RFOVE</td>
+      <td>RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.</td>
+      <td>Image analysis</td>
+      <td>Cell biology, Biomedical science, Imaging</td>
+      <td>To update</td>
+      <td>https://sites.google.com/site/costaspanagiotakis/research/cs</td>
+      <td>Imaging</td>
+      <td>rfove</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove</td>
+      <td>2023.11.12</td>
+      <td></td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Cell biology, Biomedical science, Imaging</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rgcca</td>
+      <td>rgcca</td>
+      <td>multi-block analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/rgcca-factory/RGCCA</td>
+      <td>Statistics</td>
+      <td>rgcca</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca</td>
+      <td>3.0.2</td>
+      <td>rgccacmd</td>
+      <td>3.0.3</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>44</td>
+      <td>44</td>
+      <td>6</td>
+      <td>6</td>
+      <td>77</td>
+      <td>77</td>
+      <td>35</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>41</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rgrnastar</td>
+      <td>rna_star, rna_starsolo</td>
+      <td>RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper</td>
+      <td>star</td>
+      <td>star</td>
+      <td></td>
+      <td>STAR</td>
+      <td>Ultrafast universal RNA-seq data aligner</td>
+      <td>Sequence alignment</td>
+      <td>RNA-Seq, Transcriptomics</td>
+      <td>To update</td>
+      <td>https://github.com/alexdobin/STAR</td>
+      <td>Next Gen Mappers, Transcriptomics</td>
+      <td>rgrnastar</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar</td>
+      <td>2.7.11a</td>
+      <td>star</td>
+      <td>2.7.11b</td>
+      <td>Sequence alignment</td>
+      <td>RNA-Seq, Transcriptomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>438078</td>
+      <td>473957</td>
+      <td>10142</td>
+      <td>10900</td>
+      <td>325474</td>
+      <td>403925</td>
+      <td>15284</td>
+      <td>18791</td>
+      <td>49662</td>
+      <td>53138</td>
+      <td>1359</td>
+      <td>1449</td>
+      <td>813214</td>
+      <td>931020</td>
+      <td>26785</td>
+      <td>31140</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>riassigner</td>
+      <td>riassigner, riassigner_from_comment</td>
+      <td></td>
+      <td>riassigner</td>
+      <td>riassigner</td>
+      <td></td>
+      <td>RIAssigner</td>
+      <td>RIAssigner is a python tool for retention index (RI) computation for GC-MS data.</td>
+      <td>Standardisation and normalisation</td>
+      <td>Metabolomics, Compound libraries and screening, Data submission, annotation and curation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/RIAssigner</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner</td>
+      <td>0.4.1</td>
+      <td>riassigner</td>
+      <td>0.4.1</td>
+      <td>Standardisation and normalisation</td>
+      <td>Metabolomics, Compound libraries and screening, Data submission, annotation and curation</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>46</td>
+      <td>46</td>
+      <td>19</td>
+      <td>19</td>
+      <td>15</td>
+      <td>15</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>62</td>
+      <td>62</td>
+      <td>24</td>
+      <td>24</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ribotaper</td>
+      <td>ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling</td>
+      <td>A method for defining traslated ORFs using Ribosome Profiling data.</td>
+      <td>ribotaper</td>
+      <td>ribotaper</td>
+      <td></td>
+      <td>RiboTaper</td>
+      <td>New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.</td>
+      <td>Gene expression profiling</td>
+      <td>Functional genomics</td>
+      <td>To update</td>
+      <td>https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/</td>
+      <td>RNA</td>
+      <td>ribotaper</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper</td>
+      <td>1.3.1a</td>
+      <td>ribotaper</td>
+      <td>1.3.1</td>
+      <td>Gene expression profiling</td>
+      <td>Functional genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>661</td>
+      <td>681</td>
+      <td>78</td>
+      <td>78</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>661</td>
+      <td>681</td>
+      <td>78</td>
+      <td>78</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ribowaltz</td>
+      <td>ribowaltz_process, ribowaltz_plot</td>
+      <td>Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data</td>
+      <td>riboWaltz</td>
+      <td>riboWaltz</td>
+      <td></td>
+      <td>riboWaltz</td>
+      <td>riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.</td>
+      <td></td>
+      <td>Computational biology</td>
+      <td>To update</td>
+      <td>https://github.com/LabTranslationalArchitectomics/riboWaltz</td>
+      <td>Transcriptomics, RNA</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz</td>
+      <td>1.2.0</td>
+      <td>ribowaltz</td>
+      <td>2.0</td>
+      <td></td>
+      <td>Computational biology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>171</td>
+      <td>171</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>171</td>
+      <td>171</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rmap</td>
+      <td>rmap_wrapper</td>
+      <td>RMAP for Solexa Short Reads Alignment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Next Gen Mappers</td>
+      <td>rmap</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap</td>
+      <td>1.0.0</td>
+      <td>rmap</td>
+      <td>2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rmapq</td>
+      <td>rmapq_wrapper</td>
+      <td>RMAPQ for Solexa Short Reads Alignment with Quality Scores</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Next Gen Mappers</td>
+      <td>rmapq</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq</td>
+      <td>1.0.0</td>
+      <td>rmap</td>
+      <td>2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rmassbank</td>
+      <td>rmassbank</td>
+      <td>RMassBank is an R package for processing tandem MS files and building of MassBank records.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/MassBank/RMassBank</td>
+      <td>Metabolomics</td>
+      <td>rmassbank</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank</td>
+      <td>3.0.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td>48</td>
+      <td>48</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rna_shapes</td>
+      <td>RNAshapes</td>
+      <td>Compute secondary structures of RNA</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>rnashapes</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes</td>
+      <td>3.3.0</td>
+      <td>@EXECUTABLE@</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>137</td>
+      <td>173</td>
+      <td>40</td>
+      <td>49</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>137</td>
+      <td>173</td>
+      <td>40</td>
+      <td>49</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnabob</td>
+      <td>rbc_rnabob</td>
+      <td>Fast pattern searching for RNA structural motifs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://eddylab.org/software.html</td>
+      <td>RNA</td>
+      <td>rnabob</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob</td>
+      <td>2.2.1.0</td>
+      <td>rnabob</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>90</td>
+      <td>196</td>
+      <td>9</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>90</td>
+      <td>196</td>
+      <td>9</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnacode</td>
+      <td>rbc_rnacode</td>
+      <td>Analyze the protein coding potential in MSA</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA</td>
+      <td>rnacode</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode</td>
+      <td>0.3.2</td>
+      <td>rnacode</td>
+      <td>0.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>878</td>
+      <td>1363</td>
+      <td>29</td>
+      <td>35</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>878</td>
+      <td>1363</td>
+      <td>29</td>
+      <td>35</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnacommender</td>
+      <td>rbc_rnacommender</td>
+      <td>RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/gianlucacorrado/RNAcommender</td>
+      <td>RNA</td>
+      <td>rnacommender</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender</td>
+      <td>0.1.1</td>
+      <td>sam</td>
+      <td>3.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1024</td>
+      <td>1077</td>
+      <td>18</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1024</td>
+      <td>1077</td>
+      <td>18</td>
+      <td>21</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnaformer</td>
+      <td>infer_rnaformer</td>
+      <td>RNAformer: RNA secondary structure prediction</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/automl/RNAformer</td>
+      <td>RNA</td>
+      <td>rnaformer</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer</td>
+      <td>1.0.0</td>
+      <td>rnaformer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnalien</td>
+      <td>RNAlien</td>
+      <td>RNAlien unsupervized RNA family model construction</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rna.tbi.univie.ac.at/rnalien/</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>rnalien</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien</td>
+      <td>1.3.6</td>
+      <td>rnalien</td>
+      <td>1.8.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>23</td>
+      <td>33</td>
+      <td>10</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>23</td>
+      <td>33</td>
+      <td>10</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnaquast</td>
+      <td>rna_quast</td>
+      <td>rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.</td>
+      <td>rnaQUAST</td>
+      <td>rnaQUAST</td>
+      <td></td>
+      <td>rnaQUAST</td>
+      <td>Quality assessment tool for de novo transcriptome assemblies.</td>
+      <td>De-novo assembly, Transcriptome assembly, Sequence assembly validation</td>
+      <td>Sequence assembly, Transcriptomics, RNA-seq</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/ablab/rnaquast</td>
+      <td>Assembly, RNA</td>
+      <td>rnaquast</td>
+      <td>iuc</td>
+      <td>https://git.ufz.de/lehmanju/rnaquast</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast</td>
+      <td>2.3.0</td>
+      <td>rnaquast</td>
+      <td>2.3.0</td>
+      <td>De-novo assembly, Transcriptome assembly, Sequence assembly validation</td>
+      <td>Sequence assembly, Transcriptomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1522</td>
+      <td>1522</td>
+      <td>254</td>
+      <td>254</td>
+      <td>372</td>
+      <td>372</td>
+      <td>75</td>
+      <td>75</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1899</td>
+      <td>1899</td>
+      <td>330</td>
+      <td>330</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnasnp</td>
+      <td>rnasnp</td>
+      <td>RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rth.dk/resources/rnasnp/</td>
+      <td>RNA</td>
+      <td>rnasnp</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp</td>
+      <td>1.2.0</td>
+      <td>rnasnp</td>
+      <td>1.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>65</td>
+      <td>89</td>
+      <td>14</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>89</td>
+      <td>14</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rnaz</td>
+      <td>rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window</td>
+      <td>RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://www.tbi.univie.ac.at/~wash/RNAz/</td>
+      <td>RNA</td>
+      <td>rnaz</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz</td>
+      <td>2.1.1</td>
+      <td>rnaz</td>
+      <td>2.1.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>1156</td>
+      <td>43309</td>
+      <td>93</td>
+      <td>121</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1156</td>
+      <td>43309</td>
+      <td>93</td>
+      <td>121</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>roary</td>
+      <td>roary</td>
+      <td>Roary the pangenome pipeline</td>
+      <td>roary</td>
+      <td>roary</td>
+      <td></td>
+      <td>Roary</td>
+      <td>A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.</td>
+      <td>Genome assembly</td>
+      <td>DNA, Genomics, Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://sanger-pathogens.github.io/Roary/</td>
+      <td>Sequence Analysis</td>
+      <td>roary</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary</td>
+      <td>3.13.0</td>
+      <td>roary</td>
+      <td>3.13.0</td>
+      <td>Genome assembly</td>
+      <td>DNA, Genomics, Mapping</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15196</td>
+      <td>15685</td>
+      <td>1459</td>
+      <td>1501</td>
+      <td>12188</td>
+      <td>12188</td>
+      <td>1768</td>
+      <td>1768</td>
+      <td>4881</td>
+      <td>5539</td>
+      <td>518</td>
+      <td>555</td>
+      <td>32265</td>
+      <td>33412</td>
+      <td>3745</td>
+      <td>3824</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rp2biosensor</td>
+      <td>rp2biosensor</td>
+      <td>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/rp2biosensor</td>
+      <td>Synthetic Biology</td>
+      <td>rp2biosensor</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor</td>
+      <td>3.2.1</td>
+      <td>rp2biosensor</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rp2paths</td>
+      <td>rp2paths</td>
+      <td>Enumerate and seperate the different pathways generated by RetroPath2.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/rp2paths</td>
+      <td>Synthetic Biology</td>
+      <td>rp2paths</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths</td>
+      <td>1.5.1</td>
+      <td>rp2paths</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rpbasicdesign</td>
+      <td>rpbasicdesign</td>
+      <td>Extracting enzyme IDs from rpSBML files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/rpbasicdesign</td>
+      <td>Synthetic Biology</td>
+      <td>rpbasicdesign</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign</td>
+      <td>1.2.2</td>
+      <td>rpbasicdesign</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rpfba</td>
+      <td>rpfba</td>
+      <td>Perform FBA for the RetroPath2.0 heterologous pathways</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/rptools/releases</td>
+      <td>Synthetic Biology</td>
+      <td>rpfba</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba</td>
+      <td>5.12.3</td>
+      <td>rptools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rptools</td>
+      <td>rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz</td>
+      <td>Suite of tools that work on rpSBML format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/rptools</td>
+      <td>Synthetic Biology</td>
+      <td>rptools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools</td>
+      <td>5.13.1</td>
+      <td>rptools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rrparser</td>
+      <td>rrparser</td>
+      <td>Reaction Rules Parser</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/RRParser</td>
+      <td>Synthetic Biology</td>
+      <td>rrparser</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser</td>
+      <td>2.5.2</td>
+      <td>rrparser</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rsat_filter_snps</td>
+      <td>rsat_filter_snps</td>
+      <td>Filter SNPs in RSAT Matrix Scan output</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/</td>
+      <td>ChIP-seq, Systems Biology</td>
+      <td>rsat_filter_snps</td>
+      <td>earlham</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rsem</td>
+      <td>extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie</td>
+      <td>transcript quantification from RNA-Seq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/deweylab/RSEM</td>
+      <td>Transcriptomics, RNA</td>
+      <td>rsem</td>
+      <td>artbio</td>
+      <td>https://github.com/artbio/tools-artbio/tree/master/tools/rsem</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem</td>
+      <td></td>
+      <td>rsem</td>
+      <td>1.3.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>363</td>
+      <td>430</td>
+      <td>158</td>
+      <td>183</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>67</td>
+      <td>146</td>
+      <td>13</td>
+      <td>39</td>
+      <td>430</td>
+      <td>576</td>
+      <td>171</td>
+      <td>222</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>rseqc</td>
+      <td>rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin</td>
+      <td>an RNA-seq quality control package</td>
+      <td>rseqc</td>
+      <td>rseqc</td>
+      <td></td>
+      <td>RSeQC</td>
+      <td>Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.</td>
+      <td>Data handling</td>
+      <td>Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://code.google.com/p/rseqc/</td>
+      <td>Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization</td>
+      <td>rseqc</td>
+      <td>nilesh</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc</td>
+      <td>5.0.3</td>
+      <td>rseqc</td>
+      <td>5.0.3</td>
+      <td>Data handling</td>
+      <td>Sequencing</td>
+      <td>22</td>
+      <td>22</td>
+      <td>22</td>
+      <td>0</td>
+      <td>22</td>
+      <td>22</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>22</td>
+      <td>22</td>
+      <td>22</td>
+      <td>0</td>
+      <td>136315</td>
+      <td>147595</td>
+      <td>8341</td>
+      <td>9385</td>
+      <td>138707</td>
+      <td>161046</td>
+      <td>10696</td>
+      <td>12789</td>
+      <td>22718</td>
+      <td>23767</td>
+      <td>1593</td>
+      <td>1695</td>
+      <td>297740</td>
+      <td>332408</td>
+      <td>20630</td>
+      <td>23869</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ruvseq</td>
+      <td>ruvseq</td>
+      <td>Remove Unwanted Variation from RNA-Seq Data</td>
+      <td>ruvseq</td>
+      <td>ruvseq</td>
+      <td></td>
+      <td>RUVSeq</td>
+      <td>This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.</td>
+      <td>Differential gene expression analysis</td>
+      <td>Gene expression, RNA-seq</td>
+      <td>To update</td>
+      <td>https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>ruvseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq</td>
+      <td>1.26.0</td>
+      <td>bioconductor-ruvseq</td>
+      <td>1.36.0</td>
+      <td>Differential gene expression analysis</td>
+      <td>Gene expression</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1286</td>
+      <td>1364</td>
+      <td>178</td>
+      <td>193</td>
+      <td>2220</td>
+      <td>2220</td>
+      <td>299</td>
+      <td>299</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3506</td>
+      <td>3584</td>
+      <td>477</td>
+      <td>492</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sailfish</td>
+      <td>sailfish</td>
+      <td>Sailfish is a tool for transcript quantification from RNA-seq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.cs.cmu.edu/~ckingsf/software/sailfish/</td>
+      <td>Sequence Analysis, RNA</td>
+      <td>sailfish</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sailfish</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sailfish</td>
+      <td>0.10.1.1</td>
+      <td>bzip2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3628</td>
+      <td>4168</td>
+      <td>165</td>
+      <td>199</td>
+      <td>8399</td>
+      <td>14473</td>
+      <td>573</td>
+      <td>1147</td>
+      <td>2710</td>
+      <td>3000</td>
+      <td>151</td>
+      <td>175</td>
+      <td>14737</td>
+      <td>21641</td>
+      <td>889</td>
+      <td>1521</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>salmon</td>
+      <td>alevin, salmon, salmonquantmerge</td>
+      <td>Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.</td>
+      <td>salmon</td>
+      <td>salmon</td>
+      <td></td>
+      <td>Salmon</td>
+      <td>A tool for transcript expression quantification from RNA-seq data</td>
+      <td>Sequence composition calculation, RNA-Seq quantification, Gene expression analysis</td>
+      <td>RNA-Seq, Gene expression, Transcriptomics</td>
+      <td>To update</td>
+      <td>https://github.com/COMBINE-lab/salmon</td>
+      <td>Sequence Analysis, RNA, Transcriptomics</td>
+      <td></td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/salmon</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/salmon</td>
+      <td>1.10.1</td>
+      <td>salmon</td>
+      <td>1.10.3</td>
+      <td>Sequence composition calculation, RNA-Seq quantification, Gene expression analysis</td>
+      <td>RNA-Seq, Transcriptomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>73085</td>
+      <td>77081</td>
+      <td>2243</td>
+      <td>2319</td>
+      <td>90634</td>
+      <td>122835</td>
+      <td>3402</td>
+      <td>4726</td>
+      <td>13371</td>
+      <td>15818</td>
+      <td>513</td>
+      <td>586</td>
+      <td>177090</td>
+      <td>215734</td>
+      <td>6158</td>
+      <td>7631</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>salmon-kallisto-mtx-to-10x</td>
+      <td>_salmon_kallisto_mtx_to_10x</td>
+      <td>Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary</td>
+      <td>Sequence Analysis</td>
+      <td>salmon_kallisto_mtx_to_10x</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x</td>
+      <td>0.0.1+galaxy6</td>
+      <td>scipy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>682</td>
+      <td>682</td>
+      <td>172</td>
+      <td>172</td>
+      <td>322</td>
+      <td>322</td>
+      <td>74</td>
+      <td>74</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1007</td>
+      <td>1007</td>
+      <td>249</td>
+      <td>249</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>salsa2</td>
+      <td>salsa</td>
+      <td>A tool to scaffold long read assemblies with Hi-C</td>
+      <td>SALSA</td>
+      <td>SALSA</td>
+      <td></td>
+      <td>SALSA</td>
+      <td>&gt; VERY_LOW CONFIDENCE! | &gt; CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch</td>
+      <td>Genome assembly, De-novo assembly, Scaffolding</td>
+      <td>Sequence assembly, DNA binding sites, Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/marbl/SALSA</td>
+      <td>Assembly</td>
+      <td>salsa</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2</td>
+      <td>2.3</td>
+      <td>salsa2</td>
+      <td>2.3</td>
+      <td>Genome assembly, De-novo assembly, Scaffolding</td>
+      <td>Sequence assembly, DNA binding sites, Mapping</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>463</td>
+      <td>463</td>
+      <td>119</td>
+      <td>119</td>
+      <td>1038</td>
+      <td>1038</td>
+      <td>87</td>
+      <td>87</td>
+      <td>410</td>
+      <td>410</td>
+      <td>24</td>
+      <td>24</td>
+      <td>1911</td>
+      <td>1911</td>
+      <td>230</td>
+      <td>230</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sam2interval</td>
+      <td>sam2interval</td>
+      <td>Convert SAM to interval.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>SAM</td>
+      <td>sam2interval</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval</td>
+      <td>1.0.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1155</td>
+      <td>1251</td>
+      <td>57</td>
+      <td>63</td>
+      <td>2264</td>
+      <td>18187</td>
+      <td>189</td>
+      <td>1748</td>
+      <td>525</td>
+      <td>590</td>
+      <td>10</td>
+      <td>17</td>
+      <td>3944</td>
+      <td>20028</td>
+      <td>256</td>
+      <td>1828</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sam_bitwise_flag_filter</td>
+      <td>sam_bw_filter</td>
+      <td>Filter SAM on bitwise flag values</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>SAM</td>
+      <td>sam_bitwise_flag_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter</td>
+      <td>1.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>96</td>
+      <td>278</td>
+      <td>12</td>
+      <td>26</td>
+      <td>3554</td>
+      <td>76029</td>
+      <td>450</td>
+      <td>6346</td>
+      <td>229</td>
+      <td>345</td>
+      <td>16</td>
+      <td>29</td>
+      <td>3879</td>
+      <td>76652</td>
+      <td>478</td>
+      <td>6401</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sambamba</td>
+      <td>sambamba_sample_or_filter</td>
+      <td>filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>SAM</td>
+      <td>sambamba</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba</td>
+      <td>0.7.1+galaxy1</td>
+      <td>sambamba</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>684</td>
+      <td>684</td>
+      <td>17</td>
+      <td>17</td>
+      <td>684</td>
+      <td>684</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sambamba</td>
+      <td>sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort</td>
+      <td>Sambamba: process your BAM data faster!</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/biod/sambamba</td>
+      <td>SAM</td>
+      <td>sambamba</td>
+      <td>bgruening</td>
+      <td>https://github.com/biod/sambamba</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sambamba</td>
+      <td>1.0.1</td>
+      <td>sambamba</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>297</td>
+      <td>297</td>
+      <td>51</td>
+      <td>51</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>297</td>
+      <td>297</td>
+      <td>51</td>
+      <td>51</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>samblaster</td>
+      <td>samblaster</td>
+      <td>samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files</td>
+      <td>samblaster</td>
+      <td>samblaster</td>
+      <td></td>
+      <td>SAMBLASTER</td>
+      <td>A tool to mark duplicates and extract discordant and split reads from SAM files.</td>
+      <td>Split read mapping</td>
+      <td>DNA, Sequencing, Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/GregoryFaust/samblaster</td>
+      <td>SAM, Fastq Manipulation, Variant Analysis</td>
+      <td>samblaster</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster</td>
+      <td>0.1.26</td>
+      <td>samblaster</td>
+      <td>0.1.26</td>
+      <td>Split read mapping</td>
+      <td>DNA, Sequencing, Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sample_seqs</td>
+      <td>sample_seqs</td>
+      <td>Sub-sample sequences files (e.g. to reduce coverage)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs</td>
+      <td>Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis</td>
+      <td>sample_seqs</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs</td>
+      <td>0.2.6</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3421</td>
+      <td>3859</td>
+      <td>340</td>
+      <td>382</td>
+      <td>883</td>
+      <td>883</td>
+      <td>109</td>
+      <td>109</td>
+      <td>1138</td>
+      <td>1138</td>
+      <td>15</td>
+      <td>15</td>
+      <td>5442</td>
+      <td>5880</td>
+      <td>464</td>
+      <td>506</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>samtools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/samtools/samtools</td>
+      <td>SAM</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools</td>
+      <td>1.20</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>samtools_depad</td>
+      <td>samtools_depad</td>
+      <td>Re-align a SAM/BAM file with a padded reference (using samtools depad)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.htslib.org/</td>
+      <td>Assembly, SAM, Sequence Analysis</td>
+      <td>samtools_depad</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad</td>
+      <td>0.0.5</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>samtools_depth</td>
+      <td>samtools_depth</td>
+      <td>Coverage depth via samtools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.htslib.org/</td>
+      <td>Assembly, Sequence Analysis, SAM</td>
+      <td>samtools_depth</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth</td>
+      <td>0.0.3</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>6485</td>
+      <td>6549</td>
+      <td>720</td>
+      <td>726</td>
+      <td>10127</td>
+      <td>10127</td>
+      <td>1518</td>
+      <td>1518</td>
+      <td>238</td>
+      <td>238</td>
+      <td>37</td>
+      <td>37</td>
+      <td>16850</td>
+      <td>16914</td>
+      <td>2275</td>
+      <td>2281</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>samtools_idxstats</td>
+      <td>samtools_idxstats</td>
+      <td>BAM mapping statistics (using samtools idxstats)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.htslib.org/</td>
+      <td>Assembly, Next Gen Mappers, SAM</td>
+      <td>samtools_idxstats</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats</td>
+      <td>0.0.6</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>52099</td>
+      <td>55110</td>
+      <td>4053</td>
+      <td>4497</td>
+      <td>73194</td>
+      <td>108684</td>
+      <td>6930</td>
+      <td>9936</td>
+      <td>14771</td>
+      <td>15714</td>
+      <td>1222</td>
+      <td>1419</td>
+      <td>140064</td>
+      <td>179508</td>
+      <td>12205</td>
+      <td>15852</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sansa</td>
+      <td>sansa_annotate</td>
+      <td>Sansa is a tool for structural variant annotation.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/dellytools/sansa</td>
+      <td>Variant Analysis</td>
+      <td>sansa</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa</td>
+      <td>0.2.1</td>
+      <td>sansa</td>
+      <td>0.2.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>138</td>
+      <td>138</td>
+      <td>36</td>
+      <td>36</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>138</td>
+      <td>138</td>
+      <td>36</td>
+      <td>36</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sarscov2formatter</td>
+      <td>sarscov2formatter</td>
+      <td>sarscov2formatter custom script</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/nickeener/sarscov2formatter</td>
+      <td>Sequence Analysis</td>
+      <td>sarscov2formatter</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter</td>
+      <td>1.0</td>
+      <td>sarscov2formatter</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>174</td>
+      <td>174</td>
+      <td>16</td>
+      <td>16</td>
+      <td>399</td>
+      <td>399</td>
+      <td>29</td>
+      <td>29</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>573</td>
+      <td>573</td>
+      <td>45</td>
+      <td>45</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sarscov2summary</td>
+      <td>sarscov2summary</td>
+      <td>sarscov2summary custom script</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/nickeener/sarscov2summary</td>
+      <td>Sequence Analysis</td>
+      <td>sarscov2summary</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary</td>
+      <td>0.1</td>
+      <td>sarscov2summary</td>
+      <td>0.5</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>140</td>
+      <td>140</td>
+      <td>5</td>
+      <td>5</td>
+      <td>253</td>
+      <td>253</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>393</td>
+      <td>393</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sashimi_plot</td>
+      <td>sashimi_plot</td>
+      <td>Generates a sashimi plot from bam files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Transcriptomics, Graphics, Visualization</td>
+      <td>sashimi_plot</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot</td>
+      <td>0.1.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sbml2sbol</td>
+      <td>sbml2sbol</td>
+      <td>Convert SBML to SBOL format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/neilswainston/SbmlToSbol</td>
+      <td>Synthetic Biology</td>
+      <td>sbml2sbol</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol</td>
+      <td>0.1.13</td>
+      <td>sbml2sbol</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sc3</td>
+      <td>sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare</td>
+      <td>De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_sc3</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3</td>
+      <td>1.8.0</td>
+      <td>sc3-scripts</td>
+      <td>0.0.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>10</td>
+      <td>10</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scaffold</td>
+      <td>scaffold, scaffold_export</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td>scaffold</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold</td>
+      <td>0.1.0</td>
+      <td>scaffold</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scale_image</td>
+      <td>ip_scale_image</td>
+      <td>Scale image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.</td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>scale_image</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image</td>
+      <td>0.18.3</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>477</td>
+      <td>520</td>
+      <td>13</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>477</td>
+      <td>520</td>
+      <td>13</td>
+      <td>16</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scanpy</td>
+      <td>anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data</td>
+      <td>scanpy-scripts, command-line wrapper scripts around Scanpy.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://scanpy.readthedocs.io</td>
+      <td>Transcriptomics, Sequence Analysis, RNA</td>
+      <td>scanpy_scripts</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy</td>
+      <td>1.9.3</td>
+      <td>scanpy-scripts</td>
+      <td>1.9.301</td>
+      <td></td>
+      <td></td>
+      <td>27</td>
+      <td>27</td>
+      <td>27</td>
+      <td>0</td>
+      <td>27</td>
+      <td>27</td>
+      <td>27</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>13</td>
+      <td>0</td>
+      <td>45501</td>
+      <td>45666</td>
+      <td>4832</td>
+      <td>4868</td>
+      <td>7304</td>
+      <td>7304</td>
+      <td>1846</td>
+      <td>1846</td>
+      <td>3106</td>
+      <td>3106</td>
+      <td>457</td>
+      <td>457</td>
+      <td>55911</td>
+      <td>56076</td>
+      <td>7135</td>
+      <td>7171</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scanpy</td>
+      <td>scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders</td>
+      <td>Scanpy – Single-Cell Analysis in Python</td>
+      <td>scanpy</td>
+      <td>scanpy</td>
+      <td></td>
+      <td>SCANPY</td>
+      <td>Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.</td>
+      <td>Differential gene expression analysis</td>
+      <td>Gene expression, Cell biology, Genetics</td>
+      <td>To update</td>
+      <td>https://scanpy.readthedocs.io</td>
+      <td>Single Cell, Spatial Omics, Transcriptomics</td>
+      <td>scanpy</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy</td>
+      <td>1.10.2</td>
+      <td>scanpy</td>
+      <td>1.7.2</td>
+      <td>Differential gene expression analysis</td>
+      <td>Gene expression, Cell biology, Genetics</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>63789</td>
+      <td>64034</td>
+      <td>2543</td>
+      <td>2547</td>
+      <td>29962</td>
+      <td>29962</td>
+      <td>1185</td>
+      <td>1185</td>
+      <td>18028</td>
+      <td>18028</td>
+      <td>379</td>
+      <td>379</td>
+      <td>111779</td>
+      <td>112024</td>
+      <td>4107</td>
+      <td>4111</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scater</td>
+      <td>scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results</td>
+      <td>De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_scater</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater</td>
+      <td>1.10.0</td>
+      <td>scater-scripts</td>
+      <td>0.0.5</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>2</td>
+      <td>6</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>381</td>
+      <td>388</td>
+      <td>99</td>
+      <td>100</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>297</td>
+      <td>297</td>
+      <td>9</td>
+      <td>9</td>
+      <td>678</td>
+      <td>685</td>
+      <td>108</td>
+      <td>109</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scater</td>
+      <td>scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne</td>
+      <td>Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.</td>
+      <td>scater</td>
+      <td>scater</td>
+      <td></td>
+      <td>scater</td>
+      <td>Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.</td>
+      <td>Read pre-processing, Sequencing quality control, Sequence visualisation</td>
+      <td>RNA-seq, Quality affairs, Molecular genetics</td>
+      <td>To update</td>
+      <td>http://bioconductor.org/packages/scater/</td>
+      <td>Single Cell, Transcriptomics, Visualization</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater</td>
+      <td>1.22.0</td>
+      <td>bioconductor-scater</td>
+      <td>1.30.1</td>
+      <td>Read pre-processing, Sequence visualisation</td>
+      <td>Quality affairs, Molecular genetics</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>1345</td>
+      <td>1371</td>
+      <td>350</td>
+      <td>351</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>903</td>
+      <td>903</td>
+      <td>29</td>
+      <td>29</td>
+      <td>2248</td>
+      <td>2274</td>
+      <td>379</td>
+      <td>380</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scatterplot</td>
+      <td>scatterplot_rpy</td>
+      <td>Scatterplot of two numeric columns</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Statistics</td>
+      <td>scatterplot</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot</td>
+      <td>1.0.3</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1234</td>
+      <td>1752</td>
+      <td>179</td>
+      <td>261</td>
+      <td>680</td>
+      <td>9223</td>
+      <td>231</td>
+      <td>1927</td>
+      <td>0</td>
+      <td>49</td>
+      <td>0</td>
+      <td>18</td>
+      <td>1914</td>
+      <td>11024</td>
+      <td>410</td>
+      <td>2206</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sccaf</td>
+      <td>run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out</td>
+      <td>SCCAF: Single Cell Clustering Assessment Framework.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/sccaf/sccaf</td>
+      <td>Transcriptomics</td>
+      <td>SCCAF</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf</td>
+      <td>0.0.9</td>
+      <td>sccaf</td>
+      <td>0.0.10</td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>3</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>3</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>110</td>
+      <td>110</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>110</td>
+      <td>110</td>
+      <td>19</td>
+      <td>19</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sceasy</td>
+      <td>sceasy_convert</td>
+      <td>Convert scRNA data object between popular formats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics</td>
+      <td>sceasy</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy</td>
+      <td>0.0.5</td>
+      <td>r-sceasy</td>
+      <td>0.0.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1059</td>
+      <td>1059</td>
+      <td>222</td>
+      <td>222</td>
+      <td>426</td>
+      <td>426</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1486</td>
+      <td>1486</td>
+      <td>294</td>
+      <td>294</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sceasy</td>
+      <td>sceasy_convert</td>
+      <td>Converter between difference single-cell formats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cellgeni/sceasy/</td>
+      <td>Single Cell, Spatial Omics, Convert Formats</td>
+      <td>sceasy_convert</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy</td>
+      <td>0.0.7</td>
+      <td>r-sceasy</td>
+      <td>0.0.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1059</td>
+      <td>1059</td>
+      <td>222</td>
+      <td>222</td>
+      <td>426</td>
+      <td>426</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1486</td>
+      <td>1486</td>
+      <td>294</td>
+      <td>294</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>schicexplorer</td>
+      <td>schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol</td>
+      <td>scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/joachimwolff/schicexplorer</td>
+      <td>Sequence Analysis, Transcriptomics, Visualization, Single Cell</td>
+      <td>schicexplorer</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer</td>
+      <td>4</td>
+      <td>schicexplorer</td>
+      <td>7</td>
+      <td></td>
+      <td></td>
+      <td>16</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>809</td>
+      <td>809</td>
+      <td>78</td>
+      <td>78</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>105</td>
+      <td>105</td>
+      <td>16</td>
+      <td>16</td>
+      <td>917</td>
+      <td>917</td>
+      <td>96</td>
+      <td>96</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scikit-bio</td>
+      <td>scikit_bio_diversity_beta_diversity</td>
+      <td>scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://scikit-bio.org/</td>
+      <td>Sequence Analysis</td>
+      <td>scikit_bio</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio</td>
+      <td>0.4.2</td>
+      <td>scikit-bio</td>
+      <td>0.4.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1503</td>
+      <td>1955</td>
+      <td>283</td>
+      <td>402</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1504</td>
+      <td>1956</td>
+      <td>284</td>
+      <td>403</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scmap</td>
+      <td>scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features</td>
+      <td>De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_scmap</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap</td>
+      <td>1.6.4</td>
+      <td>scmap-cli</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>97</td>
+      <td>97</td>
+      <td>41</td>
+      <td>41</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>97</td>
+      <td>97</td>
+      <td>41</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scoary</td>
+      <td>scoary</td>
+      <td>Scoary calculates the assocations between all genes in the accessory genome and the traits.</td>
+      <td>scoary</td>
+      <td>scoary</td>
+      <td></td>
+      <td>Scoary</td>
+      <td>Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 &lt; i &lt; N) and the traits. It reports a list of genes sorted by strength of association per trait.</td>
+      <td>Analysis</td>
+      <td>Genotype and phenotype, Model organisms, GWAS study, Functional genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/AdmiralenOla/Scoary</td>
+      <td>Metagenomics</td>
+      <td>scoary</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary</td>
+      <td>1.6.16</td>
+      <td>scoary</td>
+      <td>1.6.16</td>
+      <td>Analysis</td>
+      <td>Genotype and phenotype, Model organisms, GWAS study, Functional genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>901</td>
+      <td>901</td>
+      <td>90</td>
+      <td>90</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>901</td>
+      <td>901</td>
+      <td>90</td>
+      <td>90</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scpipe</td>
+      <td>scpipe</td>
+      <td>A flexible preprocessing pipeline for single-cell RNA-sequencing data</td>
+      <td>scpipe</td>
+      <td>scpipe</td>
+      <td></td>
+      <td>scPipe</td>
+      <td>A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.</td>
+      <td>Genome annotation, Validation, Alignment, Visualisation</td>
+      <td>Gene expression, RNA-Seq, Sequencing</td>
+      <td>To update</td>
+      <td>http://bioconductor.org/packages/release/bioc/html/scPipe.html</td>
+      <td>Transcriptomics, Single Cell</td>
+      <td>scpipe</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe</td>
+      <td>1.0.0+galaxy2</td>
+      <td>bioconductor-scpipe</td>
+      <td>2.2.0</td>
+      <td>Genome annotation, Validation, Alignment, Visualisation</td>
+      <td>Gene expression, RNA-Seq</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>284</td>
+      <td>632</td>
+      <td>34</td>
+      <td>38</td>
+      <td>786</td>
+      <td>786</td>
+      <td>61</td>
+      <td>61</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1071</td>
+      <td>1419</td>
+      <td>96</td>
+      <td>100</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scpred</td>
+      <td>scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model</td>
+      <td>De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_scpred</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred</td>
+      <td>1.0.2</td>
+      <td>scpred-cli</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25</td>
+      <td>25</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25</td>
+      <td>25</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>scripting</td>
+      <td>singularity_scriptrunner</td>
+      <td>suite_scripting</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/</td>
+      <td>Text Manipulation</td>
+      <td>scripting tools</td>
+      <td>mbernt</td>
+      <td>https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting</td>
+      <td>0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sdmpredictors</td>
+      <td>sdmpredictors_list_layers</td>
+      <td>Terrestrial and marine predictors for species distribution modelling.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/web/packages/sdmpredictors/index.html</td>
+      <td>Ecology</td>
+      <td>sdmpredictors</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors</td>
+      <td>0.2.15</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seacr</td>
+      <td>seacr</td>
+      <td>SEACR is intended to call peaks and enriched regions from sparse CUT&amp;RUN or chromatin profiling data in which background is dominated by zeroes.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/FredHutch/SEACR</td>
+      <td>Epigenetics, ChIP-seq</td>
+      <td>seacr</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr</td>
+      <td>1.3</td>
+      <td>seacr</td>
+      <td>1.3</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5106</td>
+      <td>5106</td>
+      <td>116</td>
+      <td>116</td>
+      <td>6419</td>
+      <td>6419</td>
+      <td>241</td>
+      <td>241</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11525</td>
+      <td>11525</td>
+      <td>357</td>
+      <td>357</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sed</td>
+      <td>sed_stream_editor</td>
+      <td>Manipulate your data with the sed command line tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sed</td>
+      <td>Text Manipulation</td>
+      <td>sed_wrapper</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sed</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sed</td>
+      <td>0.0.1</td>
+      <td>sed</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>281</td>
+      <td>2284</td>
+      <td>10</td>
+      <td>53</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>281</td>
+      <td>2284</td>
+      <td>10</td>
+      <td>53</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>segalign</td>
+      <td>segalign</td>
+      <td>A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/gsneha26/SegAlign</td>
+      <td>Next Gen Mappers</td>
+      <td>segalign</td>
+      <td>richard-burhans</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign</td>
+      <td>https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign</td>
+      <td>0.1.2.7</td>
+      <td>segalign-galaxy</td>
+      <td>0.1.2.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>252</td>
+      <td>252</td>
+      <td>47</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>252</td>
+      <td>252</td>
+      <td>47</td>
+      <td>47</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>segemehl</td>
+      <td>segemehl</td>
+      <td>segemehl - short read mapping with gaps</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.bioinf.uni-leipzig.de/Software/segemehl/</td>
+      <td>Next Gen Mappers</td>
+      <td>segemehl</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/segemehl</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/segemehl</td>
+      <td>0.2.0.4</td>
+      <td>segemehl</td>
+      <td>0.3.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1095</td>
+      <td>1306</td>
+      <td>98</td>
+      <td>113</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1095</td>
+      <td>1306</td>
+      <td>98</td>
+      <td>113</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>segmetrics</td>
+      <td>ip_segmetrics</td>
+      <td>Image segmentation and object detection performance measures</td>
+      <td>segmetrics</td>
+      <td>segmetrics</td>
+      <td>segmetrics</td>
+      <td>SegMetrics</td>
+      <td>Image segmentation and object detection performance measures</td>
+      <td>Image analysis</td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>segmetrics</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics</td>
+      <td>1.4</td>
+      <td>segmetrics</td>
+      <td>1.5</td>
+      <td>Image analysis</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>selectsequencesfrommsa</td>
+      <td>selectsequencesfrommsa</td>
+      <td>SelectSequences - selects representative entries from a multiple sequence alignment in clustal format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/eggzilla/SelectSequences</td>
+      <td>RNA, Sequence Analysis</td>
+      <td>selectsequencesfrommsa</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa</td>
+      <td>1.0.5</td>
+      <td>selectsequencesfrommsa</td>
+      <td>1.0.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>305</td>
+      <td>463</td>
+      <td>43</td>
+      <td>50</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>305</td>
+      <td>463</td>
+      <td>43</td>
+      <td>50</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>selenzy_wrapper</td>
+      <td>selenzy_wrapper</td>
+      <td>Performs enzyme selection from a reaction query.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/brsynth/selenzy-wrapper</td>
+      <td>Synthetic Biology</td>
+      <td>selenzy_wrapper</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper</td>
+      <td>0.3.0</td>
+      <td>selenzy_wrapper</td>
+      <td>0.3.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>semibin</td>
+      <td>semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train</td>
+      <td>SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks</td>
+      <td>semibin</td>
+      <td>semibin</td>
+      <td></td>
+      <td>SemiBin</td>
+      <td>Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.</td>
+      <td>Sequence assembly, Read binning</td>
+      <td>Metagenomics, Machine learning, Microbial ecology, Sequence assembly</td>
+      <td>To update</td>
+      <td>https://semibin.readthedocs.io/en/latest/</td>
+      <td>Metagenomics</td>
+      <td>semibin</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin</td>
+      <td>2.0.2</td>
+      <td>semibin</td>
+      <td>2.1.0</td>
+      <td>Sequence assembly, Read binning</td>
+      <td>Metagenomics, Machine learning, Microbial ecology, Sequence assembly</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>931</td>
+      <td>931</td>
+      <td>93</td>
+      <td>93</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>931</td>
+      <td>931</td>
+      <td>93</td>
+      <td>93</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq2hla</td>
+      <td>seq2hla</td>
+      <td>Precision HLA typing and expression from RNAseq data</td>
+      <td>seq2hla</td>
+      <td>seq2hla</td>
+      <td></td>
+      <td>Seq2HLA</td>
+      <td>seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.</td>
+      <td>Read mapping, Genetic variation analysis</td>
+      <td>Transcriptomics, Mapping</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/TRON-Bioinformatics/seq2HLA</td>
+      <td>Sequence Analysis</td>
+      <td>seq2hla</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla</td>
+      <td>2.3</td>
+      <td>seq2hla</td>
+      <td>2.3</td>
+      <td>Read mapping, Genetic variation analysis</td>
+      <td>Transcriptomics, Mapping</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>342</td>
+      <td>342</td>
+      <td>40</td>
+      <td>40</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>342</td>
+      <td>342</td>
+      <td>40</td>
+      <td>40</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_composition</td>
+      <td>seq_composition</td>
+      <td>Sequence composition</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition</td>
+      <td>Sequence Analysis</td>
+      <td>seq_composition</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition</td>
+      <td>0.0.5</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1053</td>
+      <td>1186</td>
+      <td>137</td>
+      <td>195</td>
+      <td>680</td>
+      <td>680</td>
+      <td>206</td>
+      <td>206</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1733</td>
+      <td>1866</td>
+      <td>343</td>
+      <td>401</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_filter_by_id</td>
+      <td>seq_filter_by_id</td>
+      <td>Filter sequences by ID</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id</td>
+      <td>Fasta Manipulation, Sequence Analysis, Text Manipulation</td>
+      <td>seq_filter_by_id</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id</td>
+      <td>0.2.9</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>30300</td>
+      <td>32553</td>
+      <td>732</td>
+      <td>799</td>
+      <td>21726</td>
+      <td>31891</td>
+      <td>619</td>
+      <td>621</td>
+      <td>2886</td>
+      <td>2886</td>
+      <td>144</td>
+      <td>144</td>
+      <td>54912</td>
+      <td>67330</td>
+      <td>1495</td>
+      <td>1564</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_filter_by_mapping</td>
+      <td>seq_filter_by_mapping</td>
+      <td>Filter sequencing reads using SAM/BAM mapping files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping</td>
+      <td>Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis</td>
+      <td>seq_filter_by_mapping</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping</td>
+      <td>0.0.8</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4322</td>
+      <td>4714</td>
+      <td>180</td>
+      <td>205</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4322</td>
+      <td>4714</td>
+      <td>180</td>
+      <td>205</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_length</td>
+      <td>seq_length</td>
+      <td>Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length</td>
+      <td>Fasta Manipulation, Fastq Manipulation, Sequence Analysis</td>
+      <td>seq_length</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length</td>
+      <td>0.0.5</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_primer_clip</td>
+      <td>seq_primer_clip</td>
+      <td>Trim off 5' or 3' primers</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip</td>
+      <td>Assembly, Fasta Manipulation, Text Manipulation</td>
+      <td>seq_primer_clip</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip</td>
+      <td>0.0.18</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_rename</td>
+      <td>seq_rename</td>
+      <td>Rename sequences with ID mapping from a tabular file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename</td>
+      <td>Fasta Manipulation, Sequence Analysis, Text Manipulation</td>
+      <td>seq_rename</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename</td>
+      <td>0.0.10</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seq_select_by_id</td>
+      <td>seq_select_by_id</td>
+      <td>Select sequences by ID</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id</td>
+      <td>Fasta Manipulation, Sequence Analysis, Text Manipulation</td>
+      <td>seq_select_by_id</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id</td>
+      <td>0.0.15</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2196</td>
+      <td>3529</td>
+      <td>260</td>
+      <td>289</td>
+      <td>2196</td>
+      <td>3529</td>
+      <td>260</td>
+      <td>289</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqcomplexity</td>
+      <td>seqcomplexity</td>
+      <td>Sequence complexity for raw reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/stevenweaver/seqcomplexity</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity</td>
+      <td>0.1.2</td>
+      <td>seqcomplexity</td>
+      <td>0.1.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>19</td>
+      <td>19</td>
+      <td>109</td>
+      <td>109</td>
+      <td>47</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>179</td>
+      <td>179</td>
+      <td>66</td>
+      <td>66</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqkit</td>
+      <td>seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate</td>
+      <td>A cross-platform and ultrafast toolkit for FASTA/Q file manipulation</td>
+      <td>seqkit</td>
+      <td>seqkit</td>
+      <td></td>
+      <td>seqkit</td>
+      <td>FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.</td>
+      <td>DNA transcription, Sequence trimming, DNA translation, Sequence conversion</td>
+      <td>Database management, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://bioinf.shenwei.me/seqkit/</td>
+      <td>Sequence Analysis</td>
+      <td>seqkit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit</td>
+      <td>2.8.2</td>
+      <td>seqkit</td>
+      <td>2.8.2</td>
+      <td>DNA transcription, Sequence trimming, DNA translation</td>
+      <td>Database management, Sequence analysis</td>
+      <td>0</td>
+      <td>2</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3364</td>
+      <td>3364</td>
+      <td>247</td>
+      <td>247</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>244</td>
+      <td>244</td>
+      <td>33</td>
+      <td>33</td>
+      <td>3608</td>
+      <td>3608</td>
+      <td>280</td>
+      <td>280</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqprep</td>
+      <td>seqprep</td>
+      <td>Tool for merging paired-end Illumina reads and trimming adapters.</td>
+      <td>seqprep</td>
+      <td>seqprep</td>
+      <td></td>
+      <td>SeqPrep</td>
+      <td>Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.</td>
+      <td>Nucleic acid design</td>
+      <td>Genomics, Sequence assembly, Sequencing, Probes and primers</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/jstjohn/SeqPrep</td>
+      <td>Fastq Manipulation, Sequence Analysis</td>
+      <td>seqprep</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep</td>
+      <td>1.3.2</td>
+      <td>seqprep</td>
+      <td>1.3.2</td>
+      <td>Nucleic acid design</td>
+      <td>Genomics, Sequence assembly, Sequencing, Probes and primers</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2424</td>
+      <td>2424</td>
+      <td>102</td>
+      <td>102</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2424</td>
+      <td>2424</td>
+      <td>102</td>
+      <td>102</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqsero2</td>
+      <td>seqsero2</td>
+      <td>Salmonella serotype prediction from genome sequencing data</td>
+      <td>seqsero2</td>
+      <td>seqsero2</td>
+      <td></td>
+      <td>SeqSero2</td>
+      <td>rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode)</td>
+      <td>Genome indexing, Antimicrobial resistance prediction, Genome alignment</td>
+      <td>Whole genome sequencing, Sequence assembly, Genomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/denglab/SeqSero2</td>
+      <td>Sequence Analysis</td>
+      <td>seqsero2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2</td>
+      <td>1.3.1</td>
+      <td>seqsero2</td>
+      <td>1.3.1</td>
+      <td>Genome indexing, Antimicrobial resistance prediction, Genome alignment</td>
+      <td>Whole genome sequencing, Sequence assembly, Genomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4182</td>
+      <td>4182</td>
+      <td>42</td>
+      <td>42</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4182</td>
+      <td>4182</td>
+      <td>42</td>
+      <td>42</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqtk</td>
+      <td>seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq</td>
+      <td>Toolkit for processing sequences in FASTA/Q formats</td>
+      <td>seqtk</td>
+      <td>seqtk</td>
+      <td></td>
+      <td>seqtk</td>
+      <td>A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.</td>
+      <td>Data handling, Sequence file editing</td>
+      <td>Data management</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/lh3/seqtk</td>
+      <td>Sequence Analysis</td>
+      <td>seqtk</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk</td>
+      <td>1.4</td>
+      <td>seqtk</td>
+      <td>1.4</td>
+      <td>Data handling, Sequence file editing</td>
+      <td></td>
+      <td>15</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>0</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>14</td>
+      <td>14</td>
+      <td>72816</td>
+      <td>73514</td>
+      <td>2210</td>
+      <td>2300</td>
+      <td>102777</td>
+      <td>107831</td>
+      <td>2313</td>
+      <td>2669</td>
+      <td>154613</td>
+      <td>154613</td>
+      <td>682</td>
+      <td>682</td>
+      <td>330206</td>
+      <td>335958</td>
+      <td>5205</td>
+      <td>5651</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqtk_nml</td>
+      <td>seqtk_nml_sample</td>
+      <td>Tool to downsample fastq reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/lh3/seqtk</td>
+      <td>Sequence Analysis</td>
+      <td>seqtk_nml</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml</td>
+      <td>1.0.1</td>
+      <td>seqtk</td>
+      <td>1.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sequence_format_converter</td>
+      <td>sequence_format_converter</td>
+      <td>various fasta to tabular conversions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Convert Formats, Fasta Manipulation</td>
+      <td>sequence_format_converter</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter</td>
+      <td>2.2.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seqwish</td>
+      <td>seqwish</td>
+      <td>Alignment to variation graph inducer</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/seqwish</td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish</td>
+      <td>0.7.5</td>
+      <td>seqwish</td>
+      <td>0.7.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>271</td>
+      <td>271</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>271</td>
+      <td>271</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seurat</td>
+      <td>seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension</td>
+      <td>Seurat - R toolkit for single cell genomics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://satijalab.org/seurat/</td>
+      <td>Single Cell, Transcriptomics, Sequence Analysis</td>
+      <td>seurat</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat</td>
+      <td>5.0</td>
+      <td>r-seurat</td>
+      <td>3.0.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>7</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>11</td>
+      <td>11</td>
+      <td>32</td>
+      <td>32</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>153</td>
+      <td>153</td>
+      <td>16</td>
+      <td>16</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>seurat</td>
+      <td>seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features</td>
+      <td>De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/</td>
+      <td>Transcriptomics, RNA, Statistics, Sequence Analysis</td>
+      <td>suite_seurat</td>
+      <td>ebi-gxa</td>
+      <td></td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat</td>
+      <td>4.0.0</td>
+      <td>seurat-scripts</td>
+      <td>4.4.0</td>
+      <td></td>
+      <td></td>
+      <td>14</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>14</td>
+      <td>14</td>
+      <td>14</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2296</td>
+      <td>2328</td>
+      <td>673</td>
+      <td>676</td>
+      <td>141</td>
+      <td>141</td>
+      <td>39</td>
+      <td>39</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2437</td>
+      <td>2469</td>
+      <td>712</td>
+      <td>715</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sgwb</td>
+      <td>sgwb_astro_tool</td>
+      <td>SGWB</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Astronomy</td>
+      <td>sgwb_astro_tool</td>
+      <td>astroteam</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools</td>
+      <td>https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb</td>
+      <td>0.0.1+galaxy0</td>
+      <td>ipython</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>shasta</td>
+      <td>shasta</td>
+      <td>Fast de novo assembly of long read sequencing data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/chanzuckerberg/shasta</td>
+      <td>Assembly, Nanopore</td>
+      <td>shasta</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta</td>
+      <td>0.6.0</td>
+      <td>shasta</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>913</td>
+      <td>913</td>
+      <td>308</td>
+      <td>308</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>568</td>
+      <td>568</td>
+      <td>73</td>
+      <td>73</td>
+      <td>1481</td>
+      <td>1481</td>
+      <td>381</td>
+      <td>381</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>shift-longitudes</td>
+      <td>shyft_longitudes</td>
+      <td>Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/</td>
+      <td>Climate Analysis</td>
+      <td>shift_longitudes</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes</td>
+      <td>0.1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>54</td>
+      <td>64</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>54</td>
+      <td>64</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>shorah</td>
+      <td>shorah_amplicon</td>
+      <td>Reconstruct haplotypes using ShoRAH in amplicon mode</td>
+      <td>shorah</td>
+      <td>shorah</td>
+      <td></td>
+      <td>ShoRAH</td>
+      <td>Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.</td>
+      <td>Haplotype mapping, Variant calling</td>
+      <td>Metagenomics, Sequencing, Genetics</td>
+      <td>To update</td>
+      <td>https://github.com/cbg-ethz/shorah/blob/master/README.md</td>
+      <td>Sequence Analysis</td>
+      <td>shorah_amplicon</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah</td>
+      <td>1.1.3</td>
+      <td>shorah</td>
+      <td>1.99.2</td>
+      <td>Haplotype mapping, Variant calling</td>
+      <td>Metagenomics, Sequencing, Genetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>short_reads_figure_high_quality_length</td>
+      <td>hist_high_quality_score</td>
+      <td>Histogram of high quality score reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Graphics</td>
+      <td>short_reads_figure_high_quality_length</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length</td>
+      <td>1.0.0</td>
+      <td>rpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>short_reads_figure_score</td>
+      <td>quality_score_distribution</td>
+      <td>Build base quality distribution</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Graphics</td>
+      <td>short_reads_figure_score</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score</td>
+      <td>1.0.2</td>
+      <td>fontconfig</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>145</td>
+      <td>163</td>
+      <td>25</td>
+      <td>30</td>
+      <td>196</td>
+      <td>3360</td>
+      <td>23</td>
+      <td>711</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>341</td>
+      <td>3523</td>
+      <td>48</td>
+      <td>741</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>short_reads_trim_seq</td>
+      <td>trim_reads</td>
+      <td>Select high quality segments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fastq Manipulation</td>
+      <td>short_reads_trim_seq</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>175</td>
+      <td>220</td>
+      <td>51</td>
+      <td>60</td>
+      <td>350</td>
+      <td>6657</td>
+      <td>85</td>
+      <td>1602</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>525</td>
+      <td>6877</td>
+      <td>136</td>
+      <td>1662</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>shovill</td>
+      <td>shovill</td>
+      <td>Faster de novo assembly pipeline based around Spades</td>
+      <td>shovill</td>
+      <td>shovill</td>
+      <td></td>
+      <td>shovill</td>
+      <td>Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.</td>
+      <td>Genome assembly</td>
+      <td>Genomics, Microbiology, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tseemann/shovill</td>
+      <td>Assembly</td>
+      <td>shovill</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill</td>
+      <td>1.1.0</td>
+      <td>shovill</td>
+      <td>1.1.0</td>
+      <td>Genome assembly</td>
+      <td>Genomics, Microbiology, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>46125</td>
+      <td>47376</td>
+      <td>2273</td>
+      <td>2356</td>
+      <td>40577</td>
+      <td>40577</td>
+      <td>3971</td>
+      <td>3971</td>
+      <td>19960</td>
+      <td>21130</td>
+      <td>1085</td>
+      <td>1199</td>
+      <td>106662</td>
+      <td>109083</td>
+      <td>7329</td>
+      <td>7526</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>show_beginning</td>
+      <td>Show beginning1</td>
+      <td>Select lines from the beginning of a file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>show_beginning</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>27232</td>
+      <td>36366</td>
+      <td>2184</td>
+      <td>2789</td>
+      <td>16648</td>
+      <td>84460</td>
+      <td>4191</td>
+      <td>18767</td>
+      <td>2785</td>
+      <td>3276</td>
+      <td>373</td>
+      <td>452</td>
+      <td>46665</td>
+      <td>124102</td>
+      <td>6748</td>
+      <td>22008</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>show_tail</td>
+      <td>Show tail1</td>
+      <td>Select lines from the end of a file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>show_tail</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1620</td>
+      <td>2660</td>
+      <td>378</td>
+      <td>589</td>
+      <td>10551</td>
+      <td>24579</td>
+      <td>682</td>
+      <td>1851</td>
+      <td>284</td>
+      <td>398</td>
+      <td>67</td>
+      <td>83</td>
+      <td>12455</td>
+      <td>27637</td>
+      <td>1127</td>
+      <td>2523</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sicer</td>
+      <td>peakcalling_sicer</td>
+      <td>Statistical approach for the Identification of ChIP-Enriched Regions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://home.gwu.edu/~wpeng/Software.htm</td>
+      <td>ChIP-seq</td>
+      <td>sicer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer</td>
+      <td>1.1</td>
+      <td>SICER</td>
+      <td>1.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>276</td>
+      <td>379</td>
+      <td>30</td>
+      <td>42</td>
+      <td>972</td>
+      <td>9053</td>
+      <td>146</td>
+      <td>1008</td>
+      <td>644</td>
+      <td>689</td>
+      <td>5</td>
+      <td>7</td>
+      <td>1892</td>
+      <td>10121</td>
+      <td>181</td>
+      <td>1057</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sickle</td>
+      <td>sickle</td>
+      <td>A windowed adaptive trimming tool for FASTQ files using quality</td>
+      <td>sickle</td>
+      <td>sickle</td>
+      <td></td>
+      <td>sickle</td>
+      <td>A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.</td>
+      <td>Sequence trimming</td>
+      <td>Data quality management</td>
+      <td>To update</td>
+      <td>https://github.com/najoshi/sickle</td>
+      <td>Fastq Manipulation, Sequence Analysis</td>
+      <td>sickle</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle</td>
+      <td>1.33.2</td>
+      <td>sickle-trim</td>
+      <td>1.33</td>
+      <td>Sequence trimming</td>
+      <td>Data quality management</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>18184</td>
+      <td>18937</td>
+      <td>555</td>
+      <td>608</td>
+      <td>10514</td>
+      <td>10514</td>
+      <td>1063</td>
+      <td>1063</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>28698</td>
+      <td>29451</td>
+      <td>1618</td>
+      <td>1671</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>simtext</td>
+      <td>abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix</td>
+      <td>A text mining framework for interactive analysis and visualization of similarities among biomedical entities.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/dlal-group/simtext</td>
+      <td>Text Manipulation</td>
+      <td>simtext</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tools/simtext</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext</td>
+      <td>0.0.2</td>
+      <td>r-argparse</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>2</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>220</td>
+      <td>220</td>
+      <td>68</td>
+      <td>68</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>416</td>
+      <td>416</td>
+      <td>10</td>
+      <td>10</td>
+      <td>636</td>
+      <td>636</td>
+      <td>78</td>
+      <td>78</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sina</td>
+      <td>sina</td>
+      <td>SINA reference based multiple sequence alignment</td>
+      <td>sina</td>
+      <td>sina</td>
+      <td></td>
+      <td>SINA</td>
+      <td>Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment</td>
+      <td>Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment</td>
+      <td>Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy</td>
+      <td>Up-to-date</td>
+      <td>https://sina.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>sina</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina</td>
+      <td>1.7.2</td>
+      <td>sina</td>
+      <td>1.7.2</td>
+      <td>Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment</td>
+      <td>Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1369</td>
+      <td>1369</td>
+      <td>125</td>
+      <td>125</td>
+      <td>2398</td>
+      <td>2398</td>
+      <td>420</td>
+      <td>420</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3767</td>
+      <td>3767</td>
+      <td>545</td>
+      <td>545</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sinto</td>
+      <td>sinto_barcode, sinto_fragments</td>
+      <td>Sinto single-cell analysis tools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/timoast/sinto</td>
+      <td>Single Cell, Epigenetics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto</td>
+      <td>0.10.1</td>
+      <td>sinto</td>
+      <td>0.10.1</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>284</td>
+      <td>284</td>
+      <td>70</td>
+      <td>70</td>
+      <td>165</td>
+      <td>165</td>
+      <td>38</td>
+      <td>38</td>
+      <td>14</td>
+      <td>14</td>
+      <td>2</td>
+      <td>2</td>
+      <td>463</td>
+      <td>463</td>
+      <td>110</td>
+      <td>110</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sistr_cmd</td>
+      <td>sistr_cmd</td>
+      <td>SISTR in silico serotyping tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/sistr_cmd</td>
+      <td>Sequence Analysis</td>
+      <td>sistr_cmd</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd</td>
+      <td>1.1.1</td>
+      <td>sistr_cmd</td>
+      <td>1.1.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3457</td>
+      <td>3457</td>
+      <td>301</td>
+      <td>301</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>556</td>
+      <td>556</td>
+      <td>65</td>
+      <td>65</td>
+      <td>4013</td>
+      <td>4013</td>
+      <td>366</td>
+      <td>366</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sixgill</td>
+      <td>sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge</td>
+      <td>Six-frame Genome-Inferred Libraries for LC-MS/MS</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td></td>
+      <td>Proteomics, MetaProteomics</td>
+      <td>sixgill</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill</td>
+      <td>0.2.4</td>
+      <td>sixgill</td>
+      <td>0.2.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>312</td>
+      <td>312</td>
+      <td>71</td>
+      <td>71</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>312</td>
+      <td>312</td>
+      <td>71</td>
+      <td>71</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sklearn</td>
+      <td>sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split</td>
+      <td>Machine Learning tool suite from Scikit-learn</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://scikit-learn.org</td>
+      <td>Machine Learning, Statistics</td>
+      <td>sklearn</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sklearn</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/sklearn</td>
+      <td>1.0.11.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>30</td>
+      <td>14</td>
+      <td>31</td>
+      <td>0</td>
+      <td>30</td>
+      <td>14</td>
+      <td>31</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>31</td>
+      <td>27</td>
+      <td>0</td>
+      <td>82169</td>
+      <td>116810</td>
+      <td>2402</td>
+      <td>2666</td>
+      <td>18101</td>
+      <td>18101</td>
+      <td>2375</td>
+      <td>2375</td>
+      <td>17549</td>
+      <td>17549</td>
+      <td>321</td>
+      <td>321</td>
+      <td>117819</td>
+      <td>152460</td>
+      <td>5098</td>
+      <td>5362</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>skyline2isocor</td>
+      <td>skyline2isocor</td>
+      <td>Converting skyline output to IsoCor input</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor</td>
+      <td>Metabolomics</td>
+      <td>skyline2isocor</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor</td>
+      <td>1.0.0</td>
+      <td>skyline2isocor</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>slamdunk</td>
+      <td>alleyoop, slamdunk</td>
+      <td>Slamdunk maps and quantifies SLAMseq reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://t-neumann.github.io/slamdunk</td>
+      <td>RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers</td>
+      <td>slamdunk</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk</td>
+      <td>0.4.3</td>
+      <td>slamdunk</td>
+      <td>0.4.3</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>346</td>
+      <td>362</td>
+      <td>16</td>
+      <td>16</td>
+      <td>872</td>
+      <td>872</td>
+      <td>67</td>
+      <td>67</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1218</td>
+      <td>1234</td>
+      <td>83</td>
+      <td>83</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sleuth</td>
+      <td>sleuth</td>
+      <td>Sleuth is a program for differential analysis of RNA-Seq data.</td>
+      <td>sleuth</td>
+      <td>sleuth</td>
+      <td></td>
+      <td>sleuth</td>
+      <td>A statistical model and software application for RNA-seq differential expression analysis.</td>
+      <td>Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation</td>
+      <td>RNA-seq, Gene expression, Statistics and probability</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/pachterlab/sleuth</td>
+      <td>Transcriptomics, RNA, Statistics</td>
+      <td>sleuth</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth</td>
+      <td>0.30.1</td>
+      <td>r-sleuth</td>
+      <td>0.30.1</td>
+      <td>Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation</td>
+      <td>Gene expression, Statistics and probability</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>141</td>
+      <td>141</td>
+      <td>26</td>
+      <td>26</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>141</td>
+      <td>141</td>
+      <td>26</td>
+      <td>26</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>slice_image</td>
+      <td>ip_slice_image</td>
+      <td>Slice image</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>slice_image</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image</td>
+      <td>0.3-4</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>96</td>
+      <td>103</td>
+      <td>4</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>100</td>
+      <td>107</td>
+      <td>5</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>small_rna_clusters</td>
+      <td>small_rna_clusters</td>
+      <td>clusters small rna reads in alignment BAM files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, SAM, Graphics, Next Gen Mappers</td>
+      <td>small_rna_clusters</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters</td>
+      <td>1.3.0</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>small_rna_maps</td>
+      <td>small_rna_maps</td>
+      <td>Generates small read maps from alignment BAM files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, SAM, Graphics, Next Gen Mappers</td>
+      <td>small_rna_maps</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps</td>
+      <td>3.1.1</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>small_rna_signatures</td>
+      <td>overlapping_reads, signature</td>
+      <td>Computes the tendency of small RNAs to overlap with each other.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA</td>
+      <td>small_rna_signatures</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures</td>
+      <td>3.4.2</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>smallgenomeutilities</td>
+      <td>smgu_frameshift_deletions_checks</td>
+      <td>Set of utilities for manipulating small viral genome data.</td>
+      <td>v-pipe</td>
+      <td>v-pipe</td>
+      <td></td>
+      <td>V-pipe</td>
+      <td>Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.</td>
+      <td>Read pre-processing, Sequence alignment, Genetic variation analysis</td>
+      <td>Genomics, Population genetics, Workflows, Virology, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cbg-ethz/smallgenomeutilities</td>
+      <td>Sequence Analysis</td>
+      <td>smallgenomeutilities</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities</td>
+      <td>0.4.1</td>
+      <td>smallgenomeutilities</td>
+      <td>0.4.1</td>
+      <td>Read pre-processing, Sequence alignment, Genetic variation analysis</td>
+      <td>Genomics, Population genetics, Workflows, Virology, Sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>158</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>smalt</td>
+      <td>smalt</td>
+      <td>SMALT aligns DNA sequencing reads with a reference genome.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://www.sanger.ac.uk/science/tools/smalt-0</td>
+      <td>Sequence Analysis</td>
+      <td>smalt</td>
+      <td>nml</td>
+      <td>https://sourceforge.net/projects/smalt/</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt</td>
+      <td>0.7.6</td>
+      <td>smalt</td>
+      <td>0.7.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>smart_domains</td>
+      <td>smart_domains</td>
+      <td>SMART domains</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://smart.embl.de/</td>
+      <td>Sequence Analysis</td>
+      <td>smart_domains</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains</td>
+      <td>0.1.0</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>smina</td>
+      <td>smina</td>
+      <td>smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://sourceforge.net/projects/smina/</td>
+      <td>Computational chemistry</td>
+      <td>smina</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina</td>
+      <td>1.0</td>
+      <td>smina</td>
+      <td>2017.11.9</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>499</td>
+      <td>499</td>
+      <td>16</td>
+      <td>16</td>
+      <td>44</td>
+      <td>44</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>543</td>
+      <td>543</td>
+      <td>26</td>
+      <td>26</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>smithsonian-volcanoes</td>
+      <td>smithsonian_volcanoes</td>
+      <td>Retrieve data from Volcanoes of the World (VOTW) Database</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://volcano.si.edu/gvp_votw.cfm</td>
+      <td>Retrieve Data</td>
+      <td>smithsonian_volcanoes</td>
+      <td>climate</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes</td>
+      <td>https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes</td>
+      <td>0.1.0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>smudgeplot</td>
+      <td>smudgeplot</td>
+      <td>Inference of ploidy and heterozygosity structure using whole genome sequencing</td>
+      <td>smudgeplots</td>
+      <td>smudgeplots</td>
+      <td></td>
+      <td>Smudgeplots</td>
+      <td>Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568</td>
+      <td>Sequence trimming, Genotyping, k-mer counting</td>
+      <td>Sequence assembly, Genetic variation, Mathematics</td>
+      <td>To update</td>
+      <td>https://github.com/KamilSJaron/smudgeplot</td>
+      <td>Assembly</td>
+      <td>smudgeplot</td>
+      <td>galaxy-australia</td>
+      <td>https://github.com/galaxyproject/tools-iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot</td>
+      <td>0.2.5</td>
+      <td>smudgeplot</td>
+      <td>0.3.0</td>
+      <td>Sequence trimming, Genotyping, k-mer counting</td>
+      <td>Sequence assembly, Genetic variation, Mathematics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>325</td>
+      <td>325</td>
+      <td>61</td>
+      <td>61</td>
+      <td>137</td>
+      <td>137</td>
+      <td>54</td>
+      <td>54</td>
+      <td>843</td>
+      <td>843</td>
+      <td>63</td>
+      <td>63</td>
+      <td>1305</td>
+      <td>1305</td>
+      <td>178</td>
+      <td>178</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snap</td>
+      <td>snap, snap_training</td>
+      <td>SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.</td>
+      <td>snap</td>
+      <td>snap</td>
+      <td></td>
+      <td>SNAP</td>
+      <td>The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.</td>
+      <td>Gene prediction</td>
+      <td>DNA, DNA polymorphism, Genetics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/KorfLab/SNAP</td>
+      <td>Sequence Analysis</td>
+      <td>snap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap</td>
+      <td>2013_11_29</td>
+      <td>snap</td>
+      <td>2013_11_29</td>
+      <td>Gene prediction</td>
+      <td>DNA polymorphism, Genetics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1499</td>
+      <td>1638</td>
+      <td>331</td>
+      <td>358</td>
+      <td>779</td>
+      <td>779</td>
+      <td>244</td>
+      <td>244</td>
+      <td>467</td>
+      <td>467</td>
+      <td>83</td>
+      <td>83</td>
+      <td>2745</td>
+      <td>2884</td>
+      <td>658</td>
+      <td>685</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snapatac2</td>
+      <td>snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing</td>
+      <td>SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://kzhang.org/SnapATAC2/</td>
+      <td>Single Cell, Epigenetics</td>
+      <td>snapatac2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2</td>
+      <td>2.6.4</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1817</td>
+      <td>1817</td>
+      <td>14</td>
+      <td>14</td>
+      <td>4</td>
+      <td>4</td>
+      <td>2</td>
+      <td>2</td>
+      <td>136</td>
+      <td>136</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1957</td>
+      <td>1957</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sniffles</td>
+      <td>sniffles</td>
+      <td>Galaxy wrapper for sniffles</td>
+      <td>sniffles</td>
+      <td>sniffles</td>
+      <td></td>
+      <td>Sniffles</td>
+      <td>An algorithm for structural variation detection from third generation sequencing alignment.</td>
+      <td>Sequence analysis, Structural variation detection</td>
+      <td>DNA structural variation, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/fritzsedlazeck/Sniffles</td>
+      <td>Sequence Analysis</td>
+      <td>sniffles</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles</td>
+      <td>2.4</td>
+      <td>sniffles</td>
+      <td>2.4</td>
+      <td>Sequence analysis, Structural variation detection</td>
+      <td>Sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1141</td>
+      <td>1141</td>
+      <td>134</td>
+      <td>134</td>
+      <td>606</td>
+      <td>606</td>
+      <td>156</td>
+      <td>156</td>
+      <td>2267</td>
+      <td>2267</td>
+      <td>80</td>
+      <td>80</td>
+      <td>4014</td>
+      <td>4014</td>
+      <td>370</td>
+      <td>370</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snipit</td>
+      <td>snipit</td>
+      <td>Summarise snps relative to a reference sequence</td>
+      <td>snipit</td>
+      <td>snipit</td>
+      <td></td>
+      <td>snipit</td>
+      <td>Summarise snps relative to a reference sequence</td>
+      <td>Base position variability plotting</td>
+      <td>Virology</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/aineniamh/snipit</td>
+      <td>Variant Analysis, Sequence Analysis</td>
+      <td>snipit</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit</td>
+      <td>1.2</td>
+      <td>snipit</td>
+      <td>1.2</td>
+      <td>Base position variability plotting</td>
+      <td>Virology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>905</td>
+      <td>905</td>
+      <td>44</td>
+      <td>44</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>905</td>
+      <td>905</td>
+      <td>44</td>
+      <td>44</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snippy</td>
+      <td>snippy_core, snippy, snippy_clean_full_aln</td>
+      <td>Contains the snippy tool for characterising microbial snps</td>
+      <td>snippy</td>
+      <td>snippy</td>
+      <td></td>
+      <td>snippy</td>
+      <td>Rapid haploid variant calling and core SNP phylogeny generation.</td>
+      <td>Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling</td>
+      <td>Genomics, Model organisms, DNA polymorphism, Phylogenetics</td>
+      <td>To update</td>
+      <td>https://github.com/tseemann/snippy</td>
+      <td>Sequence Analysis</td>
+      <td>snippy</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy</td>
+      <td></td>
+      <td>snippy</td>
+      <td>4.6.0</td>
+      <td>Phylogenetic tree visualisation, Variant calling</td>
+      <td>Genomics, Model organisms, DNA polymorphism, Phylogenetics</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>0</td>
+      <td>121363</td>
+      <td>124773</td>
+      <td>3448</td>
+      <td>3602</td>
+      <td>92504</td>
+      <td>92504</td>
+      <td>3945</td>
+      <td>3945</td>
+      <td>48068</td>
+      <td>52034</td>
+      <td>2705</td>
+      <td>3073</td>
+      <td>261935</td>
+      <td>269311</td>
+      <td>10098</td>
+      <td>10620</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snp-dists</td>
+      <td>snp_dists</td>
+      <td>Compute pairwise SNP distance matrix from a FASTA sequence alignment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/tseemann/snp-dists</td>
+      <td>Variant Analysis</td>
+      <td>snp_dists</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists</td>
+      <td>0.8.2</td>
+      <td>snp-dists</td>
+      <td>0.8.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6555</td>
+      <td>6555</td>
+      <td>807</td>
+      <td>807</td>
+      <td>5336</td>
+      <td>5336</td>
+      <td>171</td>
+      <td>171</td>
+      <td>1143</td>
+      <td>1143</td>
+      <td>182</td>
+      <td>182</td>
+      <td>13034</td>
+      <td>13034</td>
+      <td>1160</td>
+      <td>1160</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snp-sites</td>
+      <td>snp_sites</td>
+      <td>Finds SNP sites from a multi-FASTA alignment file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/sanger-pathogens/snp-sites</td>
+      <td>Variant Analysis</td>
+      <td>snp_sites</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites</td>
+      <td>2.5.1</td>
+      <td>snp-sites</td>
+      <td>2.5.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6597</td>
+      <td>6597</td>
+      <td>663</td>
+      <td>663</td>
+      <td>1467</td>
+      <td>1467</td>
+      <td>256</td>
+      <td>256</td>
+      <td>1279</td>
+      <td>1279</td>
+      <td>114</td>
+      <td>114</td>
+      <td>9343</td>
+      <td>9343</td>
+      <td>1033</td>
+      <td>1033</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpeff</td>
+      <td>snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names</td>
+      <td>SnpEff is a genetic variant annotation and effect prediction toolbox</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://snpeff.sourceforge.net/</td>
+      <td>Genome-Wide Association Study, Variant Analysis</td>
+      <td>snpeff</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff</td>
+      <td></td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>103826</td>
+      <td>108296</td>
+      <td>7181</td>
+      <td>7908</td>
+      <td>115727</td>
+      <td>178110</td>
+      <td>15871</td>
+      <td>22769</td>
+      <td>11817</td>
+      <td>13155</td>
+      <td>2148</td>
+      <td>2321</td>
+      <td>231370</td>
+      <td>299561</td>
+      <td>25200</td>
+      <td>32998</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpeff-covid19</td>
+      <td>snpeff_sars_cov_2</td>
+      <td>SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox</td>
+      <td>snpeff</td>
+      <td>snpeff</td>
+      <td></td>
+      <td>snpEff</td>
+      <td>Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).</td>
+      <td>SNP detection</td>
+      <td>DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs</td>
+      <td>To update</td>
+      <td>http://snpeff.sourceforge.net/</td>
+      <td>Genome-Wide Association Study, Variant Analysis</td>
+      <td>snpeff_sars_cov_2</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>SNP detection</td>
+      <td>DNA polymorphism, Nucleic acid sites, features and motifs</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>764895</td>
+      <td>764895</td>
+      <td>1276</td>
+      <td>1276</td>
+      <td>94572</td>
+      <td>94572</td>
+      <td>1636</td>
+      <td>1636</td>
+      <td>26990</td>
+      <td>26990</td>
+      <td>561</td>
+      <td>561</td>
+      <td>886457</td>
+      <td>886457</td>
+      <td>3473</td>
+      <td>3473</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpfreq</td>
+      <td>hgv_snpFreq</td>
+      <td>snpFreq significant SNPs in case-control data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis, Statistics</td>
+      <td>snpfreq</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq</td>
+      <td>1.0.1</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>35</td>
+      <td>44</td>
+      <td>10</td>
+      <td>12</td>
+      <td>307</td>
+      <td>649</td>
+      <td>68</td>
+      <td>181</td>
+      <td>227</td>
+      <td>260</td>
+      <td>16</td>
+      <td>23</td>
+      <td>569</td>
+      <td>953</td>
+      <td>94</td>
+      <td>216</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpfreqplot</td>
+      <td>snpfreqplot</td>
+      <td>A plotting app to visualise the SNPs across a region</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/BrownfieldPlantLab/SNPFreqPlot</td>
+      <td>Variant Analysis</td>
+      <td>snpfreqplot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot</td>
+      <td>1.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3683</td>
+      <td>3683</td>
+      <td>338</td>
+      <td>338</td>
+      <td>1401</td>
+      <td>1401</td>
+      <td>433</td>
+      <td>433</td>
+      <td>1029</td>
+      <td>1029</td>
+      <td>95</td>
+      <td>95</td>
+      <td>6113</td>
+      <td>6113</td>
+      <td>866</td>
+      <td>866</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpsift</td>
+      <td>snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck</td>
+      <td>snpEff SnpSift tools from Pablo Cingolani</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://snpeff.sourceforge.net/SnpSift.html</td>
+      <td>Variant Analysis</td>
+      <td>snpsift</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift</td>
+      <td></td>
+      <td>snpsift</td>
+      <td>5.2</td>
+      <td></td>
+      <td></td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>5142904</td>
+      <td>5146618</td>
+      <td>3602</td>
+      <td>4283</td>
+      <td>382391</td>
+      <td>421190</td>
+      <td>7013</td>
+      <td>9678</td>
+      <td>104030</td>
+      <td>105024</td>
+      <td>960</td>
+      <td>1184</td>
+      <td>5629325</td>
+      <td>5672832</td>
+      <td>11575</td>
+      <td>15145</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpsift_dbnsfp</td>
+      <td>snpSift_dbnsfp</td>
+      <td>snpEff SnpSift dbnsfp tool from Pablo Cingolani</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://snpeff.sourceforge.net/SnpSift.html#dbNSFP</td>
+      <td>Variant Analysis</td>
+      <td>snpsift_dbnsfp</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp</td>
+      <td></td>
+      <td>snpsift</td>
+      <td>5.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>52</td>
+      <td>55</td>
+      <td>23</td>
+      <td>24</td>
+      <td>421</td>
+      <td>421</td>
+      <td>75</td>
+      <td>75</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>473</td>
+      <td>476</td>
+      <td>98</td>
+      <td>99</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snpsift_genesets</td>
+      <td>snpSift_geneSets</td>
+      <td>Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://snpeff.sourceforge.net/SnpSift.html#geneSets</td>
+      <td>Variant Analysis</td>
+      <td>snpsift_genesets</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets</td>
+      <td></td>
+      <td>snpsift</td>
+      <td>5.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>509</td>
+      <td>554</td>
+      <td>107</td>
+      <td>128</td>
+      <td>474</td>
+      <td>474</td>
+      <td>190</td>
+      <td>190</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>983</td>
+      <td>1028</td>
+      <td>297</td>
+      <td>318</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snv_matrix</td>
+      <td>snvmatrix</td>
+      <td>Generate matrix of SNV distances</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>snv_matrix</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>snvtocnv</td>
+      <td>sequenzaindex, snvtocnv</td>
+      <td>infer copy number variations from a vcf file with SNVs using R sequenza</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>snvtocnv</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv</td>
+      <td>3.0.0+galaxy1</td>
+      <td>sequenza-utils</td>
+      <td>3.0.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>socru</td>
+      <td>socru</td>
+      <td>Order and orientation of complete bacterial genomes</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/quadram-institute-bioscience/socru</td>
+      <td>Sequence Analysis</td>
+      <td>socru</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru</td>
+      <td>2.1.7</td>
+      <td>socru</td>
+      <td>2.2.4</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>659</td>
+      <td>659</td>
+      <td>42</td>
+      <td>42</td>
+      <td>296</td>
+      <td>296</td>
+      <td>92</td>
+      <td>92</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>955</td>
+      <td>955</td>
+      <td>134</td>
+      <td>134</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sonneityping</td>
+      <td>sonneityping</td>
+      <td>Scripts for parsing Mykrobe predict results for Shigella sonnei.</td>
+      <td>sonneityping</td>
+      <td>sonneityping</td>
+      <td></td>
+      <td>sonneityping</td>
+      <td>Scripts for parsing Mykrobe predict results for Shigella sonnei.</td>
+      <td>Antimicrobial resistance prediction, Variant calling, Genotyping</td>
+      <td>Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/katholt/sonneityping</td>
+      <td>Sequence Analysis</td>
+      <td>sonneityping</td>
+      <td>iuc</td>
+      <td>https://github.com/katholt/sonneityping</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping</td>
+      <td>20210201</td>
+      <td>sonneityping</td>
+      <td>20210201</td>
+      <td>Antimicrobial resistance prediction, Variant calling, Genotyping</td>
+      <td>Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sortmerna</td>
+      <td>bg_sortmerna</td>
+      <td>SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.</td>
+      <td>sortmerna</td>
+      <td>sortmerna</td>
+      <td></td>
+      <td>SortMeRNA</td>
+      <td>Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.</td>
+      <td>Sequence similarity search, Sequence comparison, Sequence alignment analysis</td>
+      <td>Metatranscriptomics, Metagenomics</td>
+      <td>To update</td>
+      <td>http://bioinfo.lifl.fr/RNA/sortmerna/</td>
+      <td>RNA</td>
+      <td>sortmerna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna</td>
+      <td>4.3.6</td>
+      <td>sortmerna</td>
+      <td>4.3.7</td>
+      <td>Sequence similarity search, Sequence alignment analysis</td>
+      <td>Metatranscriptomics, Metagenomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>19865</td>
+      <td>21034</td>
+      <td>1047</td>
+      <td>1126</td>
+      <td>3141</td>
+      <td>3141</td>
+      <td>328</td>
+      <td>328</td>
+      <td>3304</td>
+      <td>3304</td>
+      <td>189</td>
+      <td>189</td>
+      <td>26310</td>
+      <td>27479</td>
+      <td>1564</td>
+      <td>1643</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spades</td>
+      <td>spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades</td>
+      <td>SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.</td>
+      <td>spades</td>
+      <td>spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades</td>
+      <td></td>
+      <td>SPAdes</td>
+      <td>St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.</td>
+      <td>Genome assembly</td>
+      <td>Sequence assembly</td>
+      <td>To update</td>
+      <td>https://github.com/ablab/spades</td>
+      <td>Assembly, RNA, Metagenomics</td>
+      <td>spades</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades</td>
+      <td>3.15.5</td>
+      <td>spades</td>
+      <td>4.0.0</td>
+      <td>Genome assembly</td>
+      <td>Sequence assembly</td>
+      <td>9</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>9</td>
+      <td>9</td>
+      <td>9</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>3</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>9</td>
+      <td>3</td>
+      <td>0</td>
+      <td>82716</td>
+      <td>87113</td>
+      <td>8209</td>
+      <td>8526</td>
+      <td>120471</td>
+      <td>120475</td>
+      <td>14787</td>
+      <td>14790</td>
+      <td>54067</td>
+      <td>61541</td>
+      <td>5817</td>
+      <td>6653</td>
+      <td>257254</td>
+      <td>269129</td>
+      <td>28813</td>
+      <td>29969</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spades_header_fixer</td>
+      <td>spades_header_fixer</td>
+      <td>Fixes Spades Fasta ids</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>Fasta Manipulation</td>
+      <td>spades_fasta_header_fixer</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer</td>
+      <td>1.1.2+galaxy1</td>
+      <td>sed</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spaln</td>
+      <td>list_spaln_tables, spaln</td>
+      <td>Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/</td>
+      <td>Sequence Analysis, Genome annotation</td>
+      <td>spaln</td>
+      <td>iuc</td>
+      <td>https://github.com/ogotoh/spaln</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln</td>
+      <td>2.4.9</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>450</td>
+      <td>491</td>
+      <td>91</td>
+      <td>100</td>
+      <td>4270</td>
+      <td>4270</td>
+      <td>288</td>
+      <td>288</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4720</td>
+      <td>4761</td>
+      <td>379</td>
+      <td>388</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spapros</td>
+      <td>spapros_evaluation, spapros_selection</td>
+      <td>Select and evaluate probe sets for targeted spatial transcriptomics.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/theislab/spapros</td>
+      <td>Single Cell, Transcriptomics, Sequence Analysis</td>
+      <td>spapros</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros</td>
+      <td>0.1.5</td>
+      <td>spapros</td>
+      <td>0.1.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spatyper</td>
+      <td>spatyper</td>
+      <td>Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/HCGB-IGTP/spaTyper</td>
+      <td>Sequence Analysis</td>
+      <td>spatyper</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper</td>
+      <td>0.3.3</td>
+      <td>spatyper</td>
+      <td>0.3.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spec2vec</td>
+      <td>spec2vec_similarity, spec2vec_training</td>
+      <td>Mass spectra similarity scoring using a trained Spec2Vec model.</td>
+      <td>spec2vec</td>
+      <td>spec2vec</td>
+      <td></td>
+      <td>Spec2Vec</td>
+      <td>Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.</td>
+      <td>Spectrum calculation, Spectral library search, Database search, Natural product identification</td>
+      <td>Proteomics experiment, Metabolomics, Natural language processing, Proteomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/iomega/spec2vec</td>
+      <td>Metabolomics</td>
+      <td>spec2vec</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec</td>
+      <td>0.8.0</td>
+      <td>spec2vec</td>
+      <td>0.8.0</td>
+      <td>Spectrum calculation, Spectral library search, Database search, Natural product identification</td>
+      <td>Proteomics experiment, Metabolomics, Natural language processing, Proteomics</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spectrast2spectrast_irt</td>
+      <td>gp_spectrast2spectrast_irt</td>
+      <td>Filter from spectraST files to swath input files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>spectrast2spectrast_irt</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt</td>
+      <td>0.1.0</td>
+      <td>msproteomicstools</td>
+      <td>0.11.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spectrast2tsv</td>
+      <td>gp_spectrast2tsv</td>
+      <td>Filter from spectraST files to swath input files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>spectrast2tsv</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv</td>
+      <td>0.1.0</td>
+      <td>msproteomicstools</td>
+      <td>0.11.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>split_file_on_column</td>
+      <td>tp_split_on_column</td>
+      <td>Split a file on a specific column.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>split_file_on_column</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column</td>
+      <td>0.6</td>
+      <td>gawk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5995</td>
+      <td>6261</td>
+      <td>408</td>
+      <td>453</td>
+      <td>2150</td>
+      <td>2150</td>
+      <td>311</td>
+      <td>311</td>
+      <td>26</td>
+      <td>26</td>
+      <td>2</td>
+      <td>2</td>
+      <td>8171</td>
+      <td>8437</td>
+      <td>721</td>
+      <td>766</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>split_file_to_collection</td>
+      <td>split_file_to_collection</td>
+      <td>Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection</td>
+      <td>Text Manipulation</td>
+      <td>split_file_to_collection</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection</td>
+      <td>0.5.2</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>16415</td>
+      <td>16623</td>
+      <td>968</td>
+      <td>984</td>
+      <td>9133</td>
+      <td>9133</td>
+      <td>672</td>
+      <td>672</td>
+      <td>4140</td>
+      <td>4140</td>
+      <td>148</td>
+      <td>148</td>
+      <td>29688</td>
+      <td>29896</td>
+      <td>1788</td>
+      <td>1804</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>split_labelmap</td>
+      <td>ip_split_labelmap</td>
+      <td>Split Labelmaps</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>split_labelmap</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap</td>
+      <td>0.2-3</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>44</td>
+      <td>51</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>44</td>
+      <td>51</td>
+      <td>2</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>split_paired_reads</td>
+      <td>split_paired_reads</td>
+      <td>Split paired end reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fastq Manipulation</td>
+      <td>split_paired_reads</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>0</td>
+      <td>3</td>
+      <td>200</td>
+      <td>384</td>
+      <td>31</td>
+      <td>66</td>
+      <td>200</td>
+      <td>397</td>
+      <td>31</td>
+      <td>69</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>splitfasta</td>
+      <td>rbc_splitfasta</td>
+      <td>Split a multi-sequence fasta file into files containing single sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>splitfasta</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta</td>
+      <td>0.4.0</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1772</td>
+      <td>1811</td>
+      <td>278</td>
+      <td>294</td>
+      <td>3012</td>
+      <td>3012</td>
+      <td>564</td>
+      <td>564</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4784</td>
+      <td>4823</td>
+      <td>842</td>
+      <td>858</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spocc</td>
+      <td>spocc_occ</td>
+      <td>Get species occurences data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/web/packages/spocc/index.html</td>
+      <td>Ecology</td>
+      <td>spocc_occ</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc</td>
+      <td>1.2.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>789</td>
+      <td>840</td>
+      <td>130</td>
+      <td>134</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>789</td>
+      <td>840</td>
+      <td>130</td>
+      <td>134</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spolpred</td>
+      <td>spolpred</td>
+      <td>A program for predicting the spoligotype from raw sequence reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>spolpred</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred</td>
+      <td>1.0.1</td>
+      <td>spolpred</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spot_detection_2d</td>
+      <td>ip_spot_detection_2d</td>
+      <td>Spot detection in 2D image sequence</td>
+      <td>galaxy_image_analysis</td>
+      <td>galaxy_image_analysis</td>
+      <td></td>
+      <td>Galaxy Image Analysis</td>
+      <td>Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>To update</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis</td>
+      <td>Imaging</td>
+      <td>spot_detection_2d</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d</td>
+      <td>0.1</td>
+      <td>giatools</td>
+      <td>0.3.1</td>
+      <td>Image analysis</td>
+      <td>Imaging, Bioinformatics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>16</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spotyping</td>
+      <td>spotyping</td>
+      <td>SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads</td>
+      <td>spotyping</td>
+      <td>spotyping</td>
+      <td></td>
+      <td>SpoTyping</td>
+      <td>Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.</td>
+      <td>Variant pattern analysis</td>
+      <td>Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/xiaeryu/SpoTyping-v2.0</td>
+      <td>Sequence Analysis</td>
+      <td>spotyping</td>
+      <td>iuc</td>
+      <td>https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping</td>
+      <td>2.1</td>
+      <td>spotyping</td>
+      <td>2.1</td>
+      <td>Variant pattern analysis</td>
+      <td>Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1436</td>
+      <td>1436</td>
+      <td>23</td>
+      <td>23</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1436</td>
+      <td>1436</td>
+      <td>23</td>
+      <td>23</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>spyboat</td>
+      <td>spyboat</td>
+      <td>Wavelet analysis for 3d-image stacks</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://github.com/tensionhead/spyboat</td>
+      <td>Imaging, Graphics</td>
+      <td>spyboat</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat</td>
+      <td>0.1.2</td>
+      <td>spyboat</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>142</td>
+      <td>142</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>142</td>
+      <td>142</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sr_bowtie</td>
+      <td>bowtieForSmallRNA</td>
+      <td>bowtie wrapper tool to align small RNA sequencing reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Next Gen Mappers</td>
+      <td>sr_bowtie</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie</td>
+      <td>2.3.0</td>
+      <td>bowtie</td>
+      <td>1.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>80</td>
+      <td>80</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>80</td>
+      <td>80</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sr_bowtie_dataset_annotation</td>
+      <td>sr_bowtie_dataset_annotation</td>
+      <td>Maps iteratively small RNA sequencing datasets to reference sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA</td>
+      <td>sr_bowtie_dataset_annotation</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation</td>
+      <td>2.8</td>
+      <td>bowtie</td>
+      <td>1.3.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sra-tools</td>
+      <td>fasterq_dump, fastq_dump, sam_dump</td>
+      <td>NCBI Sequence Read Archive toolkit utilities</td>
+      <td>sra-tools</td>
+      <td>sra-tools</td>
+      <td></td>
+      <td>SRA Software Toolkit</td>
+      <td>The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.</td>
+      <td>Data handling</td>
+      <td>DNA, Genomics, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/ncbi/sra-tools</td>
+      <td>Data Source, Fastq Manipulation</td>
+      <td>sra_tools</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools</td>
+      <td>3.1.1</td>
+      <td>sra-tools</td>
+      <td>3.1.1</td>
+      <td>Data handling</td>
+      <td>DNA, Genomics, Sequencing</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>364871</td>
+      <td>376580</td>
+      <td>16710</td>
+      <td>17342</td>
+      <td>583675</td>
+      <td>678448</td>
+      <td>53271</td>
+      <td>59638</td>
+      <td>48131</td>
+      <td>50455</td>
+      <td>5910</td>
+      <td>6181</td>
+      <td>996677</td>
+      <td>1105483</td>
+      <td>75891</td>
+      <td>83161</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>srs_tools</td>
+      <td>srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata</td>
+      <td>Compute biodiversity indicators for remote sensing data from Sentinel 2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/Marie59/Sentinel_2A/srs_tools</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools</td>
+      <td>0.0.1</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>239</td>
+      <td>239</td>
+      <td>34</td>
+      <td>34</td>
+      <td>44</td>
+      <td>44</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>283</td>
+      <td>283</td>
+      <td>47</td>
+      <td>47</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>srst2</td>
+      <td>srst2</td>
+      <td>Short Read Sequence Typing for Bacterial Pathogens</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>srst2</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2</td>
+      <td>0.3.7</td>
+      <td>srst2</td>
+      <td>0.2.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>297</td>
+      <td>297</td>
+      <td>40</td>
+      <td>40</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>368</td>
+      <td>368</td>
+      <td>41</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>srst2</td>
+      <td>srst2</td>
+      <td>SRST2 Short Read Sequence Typing for Bacterial Pathogens</td>
+      <td>srst2</td>
+      <td>srst2</td>
+      <td></td>
+      <td>srst2</td>
+      <td>Short Read Sequence Typing for Bacterial Pathogens</td>
+      <td>Multilocus sequence typing</td>
+      <td>Whole genome sequencing, Public health and epidemiology</td>
+      <td>To update</td>
+      <td>http://katholt.github.io/srst2/</td>
+      <td>Metagenomics</td>
+      <td>srst2</td>
+      <td>iuc</td>
+      <td>https://github.com/katholt/srst2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2</td>
+      <td>0.2.0</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td>Multilocus sequence typing</td>
+      <td>Whole genome sequencing, Public health and epidemiology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>297</td>
+      <td>297</td>
+      <td>40</td>
+      <td>40</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>368</td>
+      <td>368</td>
+      <td>41</td>
+      <td>41</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>sshmm</td>
+      <td>sshmm</td>
+      <td>ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.molgen.mpg.de/heller/ssHMM</td>
+      <td>Sequence Analysis, RNA</td>
+      <td>sshmm</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm</td>
+      <td>1.0.7</td>
+      <td>sshmm</td>
+      <td>1.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>214</td>
+      <td>225</td>
+      <td>17</td>
+      <td>18</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>214</td>
+      <td>225</td>
+      <td>17</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>stacks</td>
+      <td>stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks</td>
+      <td>Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq</td>
+      <td>stacks</td>
+      <td>stacks</td>
+      <td></td>
+      <td>Stacks</td>
+      <td>Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.</td>
+      <td>Data handling</td>
+      <td>Mapping, Population genetics</td>
+      <td>To update</td>
+      <td>http://catchenlab.life.illinois.edu/stacks/</td>
+      <td>Sequence Analysis</td>
+      <td>stacks</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks</td>
+      <td></td>
+      <td>stacks</td>
+      <td>2.65</td>
+      <td>Data handling</td>
+      <td>Mapping, Population genetics</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>6440</td>
+      <td>11998</td>
+      <td>465</td>
+      <td>593</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4070</td>
+      <td>4070</td>
+      <td>76</td>
+      <td>76</td>
+      <td>10510</td>
+      <td>16068</td>
+      <td>541</td>
+      <td>669</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>stacks2</td>
+      <td>stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks</td>
+      <td>Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://catchenlab.life.illinois.edu/stacks/</td>
+      <td>Sequence Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2</td>
+      <td>2.55</td>
+      <td>stacks</td>
+      <td>2.65</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>8437</td>
+      <td>8592</td>
+      <td>626</td>
+      <td>646</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>18016</td>
+      <td>18016</td>
+      <td>270</td>
+      <td>270</td>
+      <td>26453</td>
+      <td>26608</td>
+      <td>896</td>
+      <td>916</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>star_fusion</td>
+      <td>star_fusion</td>
+      <td>STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/STAR-Fusion/STAR-Fusion</td>
+      <td>Sequence Analysis, Transcriptomics</td>
+      <td>star_fusion</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion</td>
+      <td>0.5.4-3+galaxy1</td>
+      <td>star-fusion</td>
+      <td>1.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1312</td>
+      <td>1383</td>
+      <td>82</td>
+      <td>95</td>
+      <td>2198</td>
+      <td>3076</td>
+      <td>234</td>
+      <td>303</td>
+      <td>173</td>
+      <td>173</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3683</td>
+      <td>4632</td>
+      <td>319</td>
+      <td>401</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>staramr</td>
+      <td>staramr_search</td>
+      <td>Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/phac-nml/staramr</td>
+      <td>Sequence Analysis</td>
+      <td>staramr</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr</td>
+      <td>0.10.0</td>
+      <td>staramr</td>
+      <td>0.10.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20778</td>
+      <td>20891</td>
+      <td>2030</td>
+      <td>2045</td>
+      <td>9520</td>
+      <td>9520</td>
+      <td>1424</td>
+      <td>1424</td>
+      <td>6753</td>
+      <td>6753</td>
+      <td>864</td>
+      <td>864</td>
+      <td>37051</td>
+      <td>37164</td>
+      <td>4318</td>
+      <td>4333</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>statistics</td>
+      <td>bg_statistical_hypothesis_testing</td>
+      <td>Tool for computing statistical tests.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/statistics</td>
+      <td>Statistics</td>
+      <td>bg_statistical_hypothesis_testing</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/statistics</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/statistics</td>
+      <td>0.3</td>
+      <td>numpy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>169</td>
+      <td>346</td>
+      <td>46</td>
+      <td>61</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>169</td>
+      <td>346</td>
+      <td>46</td>
+      <td>61</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>stoc</td>
+      <td>stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic</td>
+      <td>Tools to analyse STOC data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Ecology</td>
+      <td>stoceps</td>
+      <td>ecology</td>
+      <td>https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc</td>
+      <td>0.0.2</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>328</td>
+      <td>328</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>328</td>
+      <td>328</td>
+      <td>38</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>straindesign</td>
+      <td>straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion</td>
+      <td>Toolbox to optimize biological model</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/brsynth/straindesign</td>
+      <td>Systems Biology, Synthetic Biology</td>
+      <td>straindesign</td>
+      <td>iuc</td>
+      <td>https://github.com/brsynth/straindesign</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign</td>
+      <td>3.2.2</td>
+      <td>straindesign</td>
+      <td>3.2.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>strelka</td>
+      <td>strelka_germline, strelka_somatic</td>
+      <td>Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Illumina/strelka/</td>
+      <td>Variant Analysis</td>
+      <td>strelka</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka</td>
+      <td>2.9.10</td>
+      <td>strelka</td>
+      <td>2.9.10</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>669</td>
+      <td>669</td>
+      <td>112</td>
+      <td>112</td>
+      <td>1261</td>
+      <td>1261</td>
+      <td>417</td>
+      <td>417</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1930</td>
+      <td>1930</td>
+      <td>529</td>
+      <td>529</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>stress_ng</td>
+      <td>stress_ng</td>
+      <td>stress test a computer system in various selectable ways</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Web Services</td>
+      <td>stress_ng</td>
+      <td>bgruening-util</td>
+      <td>https://github.com/ColinIanKing/stress-ng</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng</td>
+      <td>0.12.04</td>
+      <td>stress-ng</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>62</td>
+      <td>62</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>62</td>
+      <td>62</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>stringmlst</td>
+      <td>stringmlst</td>
+      <td>Rapid and accurate identification of the sequence type (ST)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>stringmlst</td>
+      <td>nml</td>
+      <td></td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst</td>
+      <td>1.1.0</td>
+      <td>stringMLST</td>
+      <td>0.6.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>stringtie</td>
+      <td>stringtie, stringtie_merge</td>
+      <td>StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.</td>
+      <td>stringtie</td>
+      <td>stringtie</td>
+      <td></td>
+      <td>StringTie</td>
+      <td>Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.</td>
+      <td>Transcriptome assembly, RNA-Seq analysis</td>
+      <td>Transcriptomics, RNA-seq</td>
+      <td>Up-to-date</td>
+      <td>http://ccb.jhu.edu/software/stringtie/</td>
+      <td>Transcriptomics</td>
+      <td>stringtie</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie</td>
+      <td>2.2.3</td>
+      <td>stringtie</td>
+      <td>2.2.3</td>
+      <td>Transcriptome assembly, RNA-Seq analysis</td>
+      <td>Transcriptomics</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>178677</td>
+      <td>187728</td>
+      <td>4972</td>
+      <td>5347</td>
+      <td>320780</td>
+      <td>407379</td>
+      <td>10825</td>
+      <td>15171</td>
+      <td>26375</td>
+      <td>28921</td>
+      <td>1032</td>
+      <td>1167</td>
+      <td>525832</td>
+      <td>624028</td>
+      <td>16829</td>
+      <td>21685</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>structure</td>
+      <td>structure</td>
+      <td>for using multi-locus genotype data to investigate population structure.</td>
+      <td>structure</td>
+      <td>structure</td>
+      <td></td>
+      <td>Structure</td>
+      <td>The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.</td>
+      <td>Genetic variation analysis</td>
+      <td>Population genetics</td>
+      <td>Up-to-date</td>
+      <td>https://web.stanford.edu/group/pritchardlab/structure.html</td>
+      <td>Phylogenetics, Variant Analysis</td>
+      <td>structure</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure</td>
+      <td>2.3.4</td>
+      <td>structure</td>
+      <td>2.3.4</td>
+      <td>Genetic variation analysis</td>
+      <td>Population genetics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2858</td>
+      <td>3001</td>
+      <td>118</td>
+      <td>123</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2858</td>
+      <td>3001</td>
+      <td>118</td>
+      <td>123</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>structureharvester</td>
+      <td>structureharvester</td>
+      <td>for parsing STRUCTURE outputs and for performing the Evanno method</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/</td>
+      <td>Phylogenetics, Variant Analysis</td>
+      <td>structureharvester</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester</td>
+      <td>0.6.94</td>
+      <td>structureharvester</td>
+      <td>0.6.94</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>substitution_rates</td>
+      <td>subRate1</td>
+      <td>Estimate substitution rates for non-coding regions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>substitution_rates</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>121</td>
+      <td>3901</td>
+      <td>34</td>
+      <td>747</td>
+      <td>105</td>
+      <td>114</td>
+      <td>4</td>
+      <td>4</td>
+      <td>226</td>
+      <td>4015</td>
+      <td>38</td>
+      <td>751</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>substitutions</td>
+      <td>substitutions1</td>
+      <td>Fetch substitutions from pairwise alignments</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>substitutions</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions</td>
+      <td>1.0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>93</td>
+      <td>901</td>
+      <td>13</td>
+      <td>84</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>93</td>
+      <td>901</td>
+      <td>13</td>
+      <td>84</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>subtract</td>
+      <td>gops_subtract_1</td>
+      <td>Subtract the intervals of two datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>subtract</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract</td>
+      <td>1.0.0</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>566512</td>
+      <td>567199</td>
+      <td>410</td>
+      <td>470</td>
+      <td>49985</td>
+      <td>184650</td>
+      <td>1473</td>
+      <td>7631</td>
+      <td>20648</td>
+      <td>20897</td>
+      <td>155</td>
+      <td>188</td>
+      <td>637145</td>
+      <td>772746</td>
+      <td>2038</td>
+      <td>8289</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>subtract_query</td>
+      <td>subtract_query1</td>
+      <td>Subtract Whole Dataset from another dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>subtract_query</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query</td>
+      <td>0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1178</td>
+      <td>1450</td>
+      <td>124</td>
+      <td>141</td>
+      <td>3169</td>
+      <td>40539</td>
+      <td>636</td>
+      <td>3435</td>
+      <td>799</td>
+      <td>950</td>
+      <td>26</td>
+      <td>38</td>
+      <td>5146</td>
+      <td>42939</td>
+      <td>786</td>
+      <td>3614</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__alignment</td>
+      <td>qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-alignment</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>249</td>
+      <td>249</td>
+      <td>32</td>
+      <td>32</td>
+      <td>16</td>
+      <td>16</td>
+      <td>10</td>
+      <td>10</td>
+      <td>102</td>
+      <td>102</td>
+      <td>16</td>
+      <td>16</td>
+      <td>367</td>
+      <td>367</td>
+      <td>58</td>
+      <td>58</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__composition</td>
+      <td>qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-composition</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>117</td>
+      <td>117</td>
+      <td>41</td>
+      <td>41</td>
+      <td>84</td>
+      <td>84</td>
+      <td>24</td>
+      <td>24</td>
+      <td>161</td>
+      <td>161</td>
+      <td>13</td>
+      <td>13</td>
+      <td>362</td>
+      <td>362</td>
+      <td>78</td>
+      <td>78</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__cutadapt</td>
+      <td>qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-cutadapt</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>217</td>
+      <td>217</td>
+      <td>47</td>
+      <td>47</td>
+      <td>42</td>
+      <td>42</td>
+      <td>20</td>
+      <td>20</td>
+      <td>96</td>
+      <td>96</td>
+      <td>12</td>
+      <td>12</td>
+      <td>355</td>
+      <td>355</td>
+      <td>79</td>
+      <td>79</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__dada2</td>
+      <td>qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://benjjneb.github.io/dada2/</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>721</td>
+      <td>721</td>
+      <td>160</td>
+      <td>160</td>
+      <td>350</td>
+      <td>350</td>
+      <td>91</td>
+      <td>91</td>
+      <td>214</td>
+      <td>214</td>
+      <td>35</td>
+      <td>35</td>
+      <td>1285</td>
+      <td>1285</td>
+      <td>286</td>
+      <td>286</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__deblur</td>
+      <td>qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/biocore/deblur</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>125</td>
+      <td>125</td>
+      <td>30</td>
+      <td>30</td>
+      <td>13</td>
+      <td>13</td>
+      <td>9</td>
+      <td>9</td>
+      <td>83</td>
+      <td>83</td>
+      <td>8</td>
+      <td>8</td>
+      <td>221</td>
+      <td>221</td>
+      <td>47</td>
+      <td>47</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__demux</td>
+      <td>qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-demux</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>396</td>
+      <td>396</td>
+      <td>134</td>
+      <td>134</td>
+      <td>121</td>
+      <td>121</td>
+      <td>57</td>
+      <td>57</td>
+      <td>144</td>
+      <td>144</td>
+      <td>39</td>
+      <td>39</td>
+      <td>661</td>
+      <td>661</td>
+      <td>230</td>
+      <td>230</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__diversity</td>
+      <td>qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-diversity</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>21</td>
+      <td>21</td>
+      <td>22</td>
+      <td>0</td>
+      <td>21</td>
+      <td>21</td>
+      <td>22</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>964</td>
+      <td>964</td>
+      <td>318</td>
+      <td>318</td>
+      <td>249</td>
+      <td>249</td>
+      <td>118</td>
+      <td>118</td>
+      <td>475</td>
+      <td>475</td>
+      <td>108</td>
+      <td>108</td>
+      <td>1688</td>
+      <td>1688</td>
+      <td>544</td>
+      <td>544</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__diversity_lib</td>
+      <td>qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-diversity-lib</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>12</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>13</td>
+      <td>13</td>
+      <td>11</td>
+      <td>11</td>
+      <td>1302</td>
+      <td>1302</td>
+      <td>19</td>
+      <td>19</td>
+      <td>1323</td>
+      <td>1323</td>
+      <td>38</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__emperor</td>
+      <td>qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://emperor.microbio.me</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>58</td>
+      <td>58</td>
+      <td>23</td>
+      <td>23</td>
+      <td>24</td>
+      <td>24</td>
+      <td>11</td>
+      <td>11</td>
+      <td>92</td>
+      <td>92</td>
+      <td>11</td>
+      <td>11</td>
+      <td>174</td>
+      <td>174</td>
+      <td>45</td>
+      <td>45</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__feature_classifier</td>
+      <td>qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-feature-classifier</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>863</td>
+      <td>863</td>
+      <td>220</td>
+      <td>220</td>
+      <td>237</td>
+      <td>237</td>
+      <td>98</td>
+      <td>98</td>
+      <td>181</td>
+      <td>181</td>
+      <td>41</td>
+      <td>41</td>
+      <td>1281</td>
+      <td>1281</td>
+      <td>359</td>
+      <td>359</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__feature_table</td>
+      <td>qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-feature-table</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>17</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>983</td>
+      <td>983</td>
+      <td>287</td>
+      <td>287</td>
+      <td>375</td>
+      <td>375</td>
+      <td>144</td>
+      <td>144</td>
+      <td>907</td>
+      <td>907</td>
+      <td>106</td>
+      <td>106</td>
+      <td>2265</td>
+      <td>2265</td>
+      <td>537</td>
+      <td>537</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__fragment_insertion</td>
+      <td>qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-fragment-insertion</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>46</td>
+      <td>46</td>
+      <td>13</td>
+      <td>13</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>55</td>
+      <td>55</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__longitudinal</td>
+      <td>qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-longitudinal</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>11</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>11</td>
+      <td>11</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>37</td>
+      <td>37</td>
+      <td>16</td>
+      <td>16</td>
+      <td>22</td>
+      <td>22</td>
+      <td>7</td>
+      <td>7</td>
+      <td>89</td>
+      <td>89</td>
+      <td>14</td>
+      <td>14</td>
+      <td>148</td>
+      <td>148</td>
+      <td>37</td>
+      <td>37</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__metadata</td>
+      <td>qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-metadata</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>615</td>
+      <td>615</td>
+      <td>143</td>
+      <td>143</td>
+      <td>246</td>
+      <td>246</td>
+      <td>75</td>
+      <td>75</td>
+      <td>115</td>
+      <td>115</td>
+      <td>27</td>
+      <td>27</td>
+      <td>976</td>
+      <td>976</td>
+      <td>245</td>
+      <td>245</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__phylogeny</td>
+      <td>qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-phylogeny</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>12</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>330</td>
+      <td>330</td>
+      <td>83</td>
+      <td>83</td>
+      <td>64</td>
+      <td>64</td>
+      <td>40</td>
+      <td>40</td>
+      <td>195</td>
+      <td>195</td>
+      <td>49</td>
+      <td>49</td>
+      <td>589</td>
+      <td>589</td>
+      <td>172</td>
+      <td>172</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__quality_control</td>
+      <td>qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-quality-control</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>6</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td>10</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__quality_filter</td>
+      <td>qiime2__quality_filter__q_score</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-quality-filter</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>29</td>
+      <td>29</td>
+      <td>14</td>
+      <td>14</td>
+      <td>16</td>
+      <td>16</td>
+      <td>6</td>
+      <td>6</td>
+      <td>37</td>
+      <td>37</td>
+      <td>2</td>
+      <td>2</td>
+      <td>82</td>
+      <td>82</td>
+      <td>22</td>
+      <td>22</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__rescript</td>
+      <td>qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/nbokulich/RESCRIPt</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__sample_classifier</td>
+      <td>qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-sample-classifier</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>15</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>3</td>
+      <td>3</td>
+      <td>14</td>
+      <td>14</td>
+      <td>10</td>
+      <td>10</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>29</td>
+      <td>29</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__taxa</td>
+      <td>qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-taxa</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>664</td>
+      <td>664</td>
+      <td>145</td>
+      <td>145</td>
+      <td>113</td>
+      <td>113</td>
+      <td>43</td>
+      <td>43</td>
+      <td>255</td>
+      <td>255</td>
+      <td>50</td>
+      <td>50</td>
+      <td>1032</td>
+      <td>1032</td>
+      <td>238</td>
+      <td>238</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2__vsearch</td>
+      <td>qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/qiime2/q2-vsearch</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch</td>
+      <td>2024.5.0+q2galaxy.2024.5.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>84</td>
+      <td>84</td>
+      <td>52</td>
+      <td>52</td>
+      <td>25</td>
+      <td>25</td>
+      <td>16</td>
+      <td>16</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>118</td>
+      <td>118</td>
+      <td>73</td>
+      <td>73</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2_core</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics, Metagenomics, Sequence Analysis</td>
+      <td></td>
+      <td>q2d2</td>
+      <td></td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_qiime2_core__tools</td>
+      <td>qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://qiime2.org</td>
+      <td>Metagenomics, Sequence Analysis, Statistics</td>
+      <td></td>
+      <td>q2d2</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools</td>
+      <td>https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools</td>
+      <td>2024.5.0+dist.he540b0b0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14941</td>
+      <td>14941</td>
+      <td>383</td>
+      <td>383</td>
+      <td>25941</td>
+      <td>25941</td>
+      <td>255</td>
+      <td>255</td>
+      <td>2856</td>
+      <td>2856</td>
+      <td>112</td>
+      <td>112</td>
+      <td>43738</td>
+      <td>43738</td>
+      <td>750</td>
+      <td>750</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>suite_snvphyl</td>
+      <td></td>
+      <td>SNVPhyl suite defining all dependencies for SNVPhyl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>suite_snvphyl_1_2_3</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>superdsm</td>
+      <td>ip_superdsm</td>
+      <td>Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</td>
+      <td>superdsm</td>
+      <td>superdsm</td>
+      <td>superdsm</td>
+      <td>SuperDSM</td>
+      <td>SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.</td>
+      <td>Image analysis</td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>superdsm</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm</td>
+      <td>0.2.0</td>
+      <td>superdsm</td>
+      <td>0.4.0</td>
+      <td>Image analysis</td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>swift</td>
+      <td>swiftlink</td>
+      <td>Parallel MCMC Linkage Analysis</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/ajm/swiftlink</td>
+      <td>Variant Analysis</td>
+      <td>swiftlink</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift</td>
+      <td>1.0</td>
+      <td>swiftlink</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>syndiva</td>
+      <td>syndiva</td>
+      <td>SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>syndiva</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva</td>
+      <td>1.0</td>
+      <td>clustalo</td>
+      <td>1.2.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>30</td>
+      <td>30</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>30</td>
+      <td>30</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>t2ps</td>
+      <td>Draw_phylogram</td>
+      <td>Draw phylogeny</td>
+      <td>t2ps</td>
+      <td>t2ps</td>
+      <td></td>
+      <td>Draw phylogeny</td>
+      <td>"Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format." - Galaxy tool wrapper</td>
+      <td>Phylogenetic tree visualisation</td>
+      <td>Phylogenomics</td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Metagenomics</td>
+      <td>t2ps</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps</td>
+      <td>1.0.0</td>
+      <td>taxonomy</td>
+      <td>0.10.0</td>
+      <td>Phylogenetic tree visualisation</td>
+      <td>Phylogenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>411</td>
+      <td>472</td>
+      <td>68</td>
+      <td>90</td>
+      <td>102</td>
+      <td>7952</td>
+      <td>13</td>
+      <td>1240</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>513</td>
+      <td>8424</td>
+      <td>81</td>
+      <td>1330</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>t2t_report</td>
+      <td>t2t_report</td>
+      <td>Summarize taxonomy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://bitbucket.org/natefoo/taxonomy</td>
+      <td>Metagenomics</td>
+      <td>t2t_report</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report</td>
+      <td>1.0.0</td>
+      <td>taxonomy</td>
+      <td>0.10.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>927</td>
+      <td>959</td>
+      <td>65</td>
+      <td>78</td>
+      <td>130</td>
+      <td>7194</td>
+      <td>18</td>
+      <td>1143</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1057</td>
+      <td>8153</td>
+      <td>83</td>
+      <td>1221</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>t_coffee</td>
+      <td>t_coffee</td>
+      <td>T-Coffee</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.tcoffee.org/</td>
+      <td>Sequence Analysis</td>
+      <td>t_coffee</td>
+      <td>earlhaminst</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee</td>
+      <td>https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee</td>
+      <td>13.45.0.4846264</td>
+      <td>t-coffee</td>
+      <td>13.46.0.919e8c6b</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3783</td>
+      <td>9125</td>
+      <td>211</td>
+      <td>229</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3784</td>
+      <td>9126</td>
+      <td>212</td>
+      <td>230</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>t_test_two_samples</td>
+      <td>t_test_two_samples</td>
+      <td>T Test for Two Samples</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Statistics</td>
+      <td>t_test_two_samples</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples</td>
+      <td>1.0.1</td>
+      <td>R</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>141</td>
+      <td>215</td>
+      <td>20</td>
+      <td>31</td>
+      <td>520</td>
+      <td>1166</td>
+      <td>79</td>
+      <td>274</td>
+      <td>1025</td>
+      <td>1118</td>
+      <td>11</td>
+      <td>12</td>
+      <td>1686</td>
+      <td>2499</td>
+      <td>110</td>
+      <td>317</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>table_annovar</td>
+      <td>table_annovar</td>
+      <td>Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>table_annovar</td>
+      <td>devteam</td>
+      <td>Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar</td>
+      <td>0.2</td>
+      <td>annovar</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16526</td>
+      <td>64515</td>
+      <td>2803</td>
+      <td>7456</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16526</td>
+      <td>64515</td>
+      <td>2803</td>
+      <td>7456</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>table_compute</td>
+      <td>table_compute</td>
+      <td>Perform general-purpose table operations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute</td>
+      <td>Text Manipulation</td>
+      <td>table_compute</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute</td>
+      <td>1.2.4</td>
+      <td>pandas</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>216072</td>
+      <td>216115</td>
+      <td>1811</td>
+      <td>1814</td>
+      <td>12326</td>
+      <td>12326</td>
+      <td>1558</td>
+      <td>1558</td>
+      <td>16136</td>
+      <td>16136</td>
+      <td>256</td>
+      <td>256</td>
+      <td>244534</td>
+      <td>244577</td>
+      <td>3625</td>
+      <td>3628</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tables_arithmetic_operations</td>
+      <td>tables_arithmetic_operations</td>
+      <td>Arithmetic Operations on tables</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/gops</td>
+      <td>Genomic Interval Operations</td>
+      <td>tables_arithmetic_operations</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations</td>
+      <td>1.0.0</td>
+      <td>perl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2188</td>
+      <td>2220</td>
+      <td>33</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2188</td>
+      <td>2220</td>
+      <td>33</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tabular_to_fasta</td>
+      <td>tab2fasta</td>
+      <td>Tabular-to-FASTA</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats</td>
+      <td>tabular_to_fasta</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta</td>
+      <td>1.1.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>329032</td>
+      <td>333057</td>
+      <td>1489</td>
+      <td>1702</td>
+      <td>79033</td>
+      <td>215770</td>
+      <td>2441</td>
+      <td>8587</td>
+      <td>27876</td>
+      <td>33727</td>
+      <td>296</td>
+      <td>360</td>
+      <td>435941</td>
+      <td>582554</td>
+      <td>4226</td>
+      <td>10649</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tabular_to_fastq</td>
+      <td>tabular_to_fastq</td>
+      <td>Tabular to FASTQ converter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/sequence_utils</td>
+      <td>Fastq Manipulation</td>
+      <td>tabular_to_fastq</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq</td>
+      <td>1.1.5</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>7011</td>
+      <td>8135</td>
+      <td>449</td>
+      <td>482</td>
+      <td>9473</td>
+      <td>28494</td>
+      <td>626</td>
+      <td>2183</td>
+      <td>850</td>
+      <td>1090</td>
+      <td>80</td>
+      <td>104</td>
+      <td>17334</td>
+      <td>37719</td>
+      <td>1155</td>
+      <td>2769</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tag_pileup_frequency</td>
+      <td>tag_pileup_frequency</td>
+      <td>Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup</td>
+      <td>Statistics, SAM, Genomic Interval Operations</td>
+      <td>tag_pileup_frequency</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency</td>
+      <td>1.0.2</td>
+      <td>openjdk</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>158</td>
+      <td>164</td>
+      <td>15</td>
+      <td>16</td>
+      <td>722</td>
+      <td>865</td>
+      <td>40</td>
+      <td>73</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>880</td>
+      <td>1029</td>
+      <td>55</td>
+      <td>89</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tapscan</td>
+      <td>tapscan_classify</td>
+      <td>Search for transcription associated proteins (TAPs)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://plantcode.cup.uni-freiburg.de/tapscan/</td>
+      <td>Proteomics</td>
+      <td>tapscan</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tapscan</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tapscan</td>
+      <td>4.76+galaxy0</td>
+      <td>hmmer</td>
+      <td>3.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>19</td>
+      <td>6</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>19</td>
+      <td>6</td>
+      <td>6</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tarfast5</td>
+      <td>tarfast5</td>
+      <td>produces a tar.gz archive of fast5 sequence files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Nanopore</td>
+      <td>tarfast5</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5</td>
+      <td>0.6.1</td>
+      <td>pigz</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>targetfinder</td>
+      <td>targetfinder</td>
+      <td>Plant small RNA target prediction tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/carringtonlab/TargetFinder.git</td>
+      <td>RNA</td>
+      <td>targetfinder</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder</td>
+      <td>1.7</td>
+      <td>targetfinder</td>
+      <td>1.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>827</td>
+      <td>838</td>
+      <td>89</td>
+      <td>92</td>
+      <td>114</td>
+      <td>114</td>
+      <td>41</td>
+      <td>41</td>
+      <td>900</td>
+      <td>900</td>
+      <td>29</td>
+      <td>29</td>
+      <td>1841</td>
+      <td>1852</td>
+      <td>159</td>
+      <td>162</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tasmanian_mismatch</td>
+      <td>tasmanian_mismatch</td>
+      <td>Analysis of positional mismatches</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/nebiolabs/tasmanian-mismatch</td>
+      <td>Sequence Analysis</td>
+      <td>tasmanian_mismatch</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch</td>
+      <td>1.0.7</td>
+      <td>tasmanian-mismatch</td>
+      <td>1.0.7</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>4</td>
+      <td>61</td>
+      <td>61</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>taxonkit</td>
+      <td>name2taxid, profile2cami</td>
+      <td>TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit</td>
+      <td>taxonkit</td>
+      <td>taxonkit</td>
+      <td></td>
+      <td>TaxonKit</td>
+      <td>TaxonKit is a practical and efficient NCBI taxonomy toolkit.</td>
+      <td>Formatting, Data retrieval</td>
+      <td>Taxonomy, Biotechnology, Ecology</td>
+      <td>Up-to-date</td>
+      <td>https://bioinf.shenwei.me/taxonkit/</td>
+      <td>Metagenomics</td>
+      <td>taxonkit</td>
+      <td>iuc</td>
+      <td>https://github.com/shenwei356/taxonkit</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit</td>
+      <td>0.17.0</td>
+      <td>taxonkit</td>
+      <td>0.17.0</td>
+      <td>Formatting, Data retrieval</td>
+      <td>Taxonomy, Biotechnology, Ecology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>taxonomy_filter_refseq</td>
+      <td>taxonomy_filter_refseq</td>
+      <td>Filter RefSeq by taxonomy</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/pvanheus/ncbitaxonomy</td>
+      <td>Sequence Analysis, Genome annotation</td>
+      <td>taxonomy_filter_refseq</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq</td>
+      <td>0.3.0</td>
+      <td>rust-ncbitaxonomy</td>
+      <td>1.0.7</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>taxonomy_krona_chart</td>
+      <td>taxonomy_krona_chart</td>
+      <td>Krona pie chart from taxonomic profile</td>
+      <td>krona</td>
+      <td>krona</td>
+      <td></td>
+      <td>Krona</td>
+      <td>Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).</td>
+      <td>Visualisation</td>
+      <td>Metagenomics</td>
+      <td>To update</td>
+      <td>http://sourceforge.net/projects/krona/</td>
+      <td>Assembly</td>
+      <td>taxonomy_krona_chart</td>
+      <td>crs4</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart</td>
+      <td>2.7.1+galaxy0</td>
+      <td>krona</td>
+      <td>2.8.1</td>
+      <td>Visualisation</td>
+      <td>Metagenomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>36069</td>
+      <td>36922</td>
+      <td>5257</td>
+      <td>5431</td>
+      <td>25255</td>
+      <td>30822</td>
+      <td>5066</td>
+      <td>5826</td>
+      <td>7949</td>
+      <td>7949</td>
+      <td>1584</td>
+      <td>1584</td>
+      <td>69273</td>
+      <td>75693</td>
+      <td>11907</td>
+      <td>12841</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>taxpasta</td>
+      <td>taxpasta</td>
+      <td>standardise taxonomic profiles</td>
+      <td>taxpasta</td>
+      <td>taxpasta</td>
+      <td></td>
+      <td>taxpasta</td>
+      <td>TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.</td>
+      <td>Standardisation and normalisation, Aggregation, Formatting, Conversion</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://taxpasta.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>taxpasta</td>
+      <td>iuc</td>
+      <td>https://github.com/taxprofiler/taxpasta</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta</td>
+      <td>0.7.0</td>
+      <td>taxpasta</td>
+      <td>0.7.0</td>
+      <td>Standardisation and normalisation, Aggregation, Formatting, Conversion</td>
+      <td>Taxonomy, Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>34</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>34</td>
+      <td>34</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tb-profiler</td>
+      <td>tb_profiler_profile</td>
+      <td>Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.</td>
+      <td>tb-profiler</td>
+      <td>tb-profiler</td>
+      <td></td>
+      <td>tb-profiler</td>
+      <td>A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/jodyphelan/TBProfiler</td>
+      <td>Sequence Analysis</td>
+      <td>tbprofiler</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler</td>
+      <td>6.2.1</td>
+      <td>tb-profiler</td>
+      <td>6.3.0</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6372</td>
+      <td>6395</td>
+      <td>372</td>
+      <td>379</td>
+      <td>7339</td>
+      <td>7339</td>
+      <td>378</td>
+      <td>378</td>
+      <td>6966</td>
+      <td>6966</td>
+      <td>154</td>
+      <td>154</td>
+      <td>20677</td>
+      <td>20700</td>
+      <td>904</td>
+      <td>911</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tb_variant_filter</td>
+      <td>tb_variant_filter</td>
+      <td>M. tuberculosis H37Rv VCF filter</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/COMBAT-TB/tb_variant_filter</td>
+      <td>Variant Analysis</td>
+      <td>tb_variant_filter</td>
+      <td>iuc</td>
+      <td>https://github.com/COMBAT-TB/tb_variant_filter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter</td>
+      <td>0.4.0</td>
+      <td>tb_variant_filter</td>
+      <td>0.4.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>22977</td>
+      <td>22977</td>
+      <td>461</td>
+      <td>461</td>
+      <td>3888</td>
+      <td>3888</td>
+      <td>274</td>
+      <td>274</td>
+      <td>3611</td>
+      <td>3611</td>
+      <td>80</td>
+      <td>80</td>
+      <td>30476</td>
+      <td>30476</td>
+      <td>815</td>
+      <td>815</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tbl2gff3</td>
+      <td>tbl2gff3</td>
+      <td>Table to GFF3</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3</td>
+      <td>Convert Formats, Sequence Analysis</td>
+      <td>tbl2gff3</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3</td>
+      <td>1.2</td>
+      <td>bcbiogff</td>
+      <td>0.6.6</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1941</td>
+      <td>1941</td>
+      <td>466</td>
+      <td>466</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>463</td>
+      <td>463</td>
+      <td>112</td>
+      <td>112</td>
+      <td>2404</td>
+      <td>2404</td>
+      <td>578</td>
+      <td>578</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tbvcfreport</td>
+      <td>tbvcfreport</td>
+      <td>Generate HTML report from SnpEff M.tuberculosis VCF(s)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/COMBAT-TB/tbvcfreport</td>
+      <td>Variant Analysis</td>
+      <td>tbvcfreport</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport</td>
+      <td>1.0.1</td>
+      <td>tbvcfreport</td>
+      <td>1.0.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2955</td>
+      <td>2955</td>
+      <td>335</td>
+      <td>335</td>
+      <td>6090</td>
+      <td>6090</td>
+      <td>348</td>
+      <td>348</td>
+      <td>2347</td>
+      <td>2347</td>
+      <td>72</td>
+      <td>72</td>
+      <td>11392</td>
+      <td>11392</td>
+      <td>755</td>
+      <td>755</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>te_finder</td>
+      <td>te_finder</td>
+      <td>Transposable element insertions finder</td>
+      <td>tefinder</td>
+      <td>tefinder</td>
+      <td></td>
+      <td>TEfinder</td>
+      <td>A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.</td>
+      <td>Genome indexing, Variant calling, PCR primer design</td>
+      <td>Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation</td>
+      <td>To update</td>
+      <td>https://github.com/VistaSohrab/TEfinder</td>
+      <td>Sequence Analysis</td>
+      <td>te_finder</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder</td>
+      <td>1.0.1</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td>Genome indexing, Variant calling, PCR primer design</td>
+      <td>Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>203</td>
+      <td>203</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>203</td>
+      <td>203</td>
+      <td>20</td>
+      <td>20</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>telescope</td>
+      <td>telescope_assign</td>
+      <td>Single locus resolution of Transposable ELEment expression.</td>
+      <td>Telescope-expression</td>
+      <td>Telescope-expression</td>
+      <td></td>
+      <td>Telescope</td>
+      <td>Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.</td>
+      <td>Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping</td>
+      <td>RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/mlbendall/telescope/</td>
+      <td>Genome annotation</td>
+      <td>telescope_assign</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope</td>
+      <td>1.0.3</td>
+      <td>telescope</td>
+      <td>1.0.3</td>
+      <td>Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping</td>
+      <td>RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tetoolkit</td>
+      <td>tetoolkit_tetranscripts</td>
+      <td>The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://hammelllab.labsites.cshl.edu/software/</td>
+      <td>Sequence Analysis</td>
+      <td>tetoolkit</td>
+      <td>iuc</td>
+      <td>https://github.com/mhammell-laboratory/TEtranscripts</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit</td>
+      <td>2.2.3</td>
+      <td>tetranscripts</td>
+      <td>2.2.3</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1013</td>
+      <td>1013</td>
+      <td>74</td>
+      <td>74</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>70</td>
+      <td>70</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1083</td>
+      <td>1083</td>
+      <td>78</td>
+      <td>78</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tetyper</td>
+      <td>tetyper</td>
+      <td>Type a specific transposable element (TE) of interest from paired-end sequencing data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/aesheppard/TETyper</td>
+      <td>Sequence Analysis</td>
+      <td>tetyper</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper</td>
+      <td>1.1</td>
+      <td>tetyper</td>
+      <td>1.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>106</td>
+      <td>106</td>
+      <td>16</td>
+      <td>16</td>
+      <td>155</td>
+      <td>155</td>
+      <td>47</td>
+      <td>47</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>261</td>
+      <td>261</td>
+      <td>63</td>
+      <td>63</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>text_processing</td>
+      <td>tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq</td>
+      <td>High performance text processing tools using the GNU coreutils, sed, awk and friends.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.gnu.org/software/</td>
+      <td>Text Manipulation</td>
+      <td>text_processing</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing</td>
+      <td>9.3</td>
+      <td>coreutils</td>
+      <td>8.25</td>
+      <td></td>
+      <td></td>
+      <td>20</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>20</td>
+      <td>20</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>1</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>19</td>
+      <td>19</td>
+      <td>0</td>
+      <td>3898014</td>
+      <td>4015573</td>
+      <td>37698</td>
+      <td>42095</td>
+      <td>648268</td>
+      <td>915282</td>
+      <td>47636</td>
+      <td>69828</td>
+      <td>103365</td>
+      <td>105214</td>
+      <td>7778</td>
+      <td>7953</td>
+      <td>4649647</td>
+      <td>5036069</td>
+      <td>93112</td>
+      <td>119876</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tgsgapcloser</td>
+      <td>tgsgapcloser</td>
+      <td>TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.</td>
+      <td>TGS-GapCloser</td>
+      <td>TGS-GapCloser</td>
+      <td></td>
+      <td>TGS-GapCloser</td>
+      <td>TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.</td>
+      <td>Genome assembly, Read mapping, Scaffolding, Localised reassembly</td>
+      <td>Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping</td>
+      <td>To update</td>
+      <td>https://github.com/BGI-Qingdao/TGS-GapCloser</td>
+      <td>Assembly</td>
+      <td>tgsgapcloser</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser</td>
+      <td>1.0.3</td>
+      <td>tgsgapcloser</td>
+      <td>1.2.1</td>
+      <td>Genome assembly, Read mapping, Scaffolding, Localised reassembly</td>
+      <td>Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>547</td>
+      <td>547</td>
+      <td>51</td>
+      <td>51</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>547</td>
+      <td>547</td>
+      <td>51</td>
+      <td>51</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tiara</td>
+      <td>tiara</td>
+      <td>Tool for identification of eukaryotic sequences in the metagenomic datasets.</td>
+      <td>Tiara</td>
+      <td>Tiara</td>
+      <td></td>
+      <td>TIARA</td>
+      <td>Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).</td>
+      <td>Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection</td>
+      <td>Sequencing, Genomics, DNA polymorphism, DNA structural variation</td>
+      <td>To update</td>
+      <td>https://github.com/ibe-uw/tiara</td>
+      <td>Metagenomics, Sequence Analysis</td>
+      <td>tiara</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tiara</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tiara</td>
+      <td>1.0.3</td>
+      <td>tiara</td>
+      <td></td>
+      <td>Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection</td>
+      <td>Sequencing, Genomics, DNA polymorphism</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>15</td>
+      <td>15</td>
+      <td>8</td>
+      <td>8</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tn93</td>
+      <td>tn93_readreduce, tn93, tn93_cluster, tn93_filter</td>
+      <td>Compute distances between sequences</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/veg/tn93/</td>
+      <td>Sequence Analysis</td>
+      <td>tn93</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93</td>
+      <td>1.0.14</td>
+      <td>tn93</td>
+      <td>1.0.14</td>
+      <td></td>
+      <td></td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1915</td>
+      <td>1915</td>
+      <td>42</td>
+      <td>42</td>
+      <td>1972</td>
+      <td>1972</td>
+      <td>225</td>
+      <td>225</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3887</td>
+      <td>3887</td>
+      <td>267</td>
+      <td>267</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tool_recommendation_model</td>
+      <td>create_tool_recommendation_model</td>
+      <td>Create model to recommend tools</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools</td>
+      <td>Machine Learning</td>
+      <td>create_tool_recommendation_model</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model</td>
+      <td>0.0.5</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>445</td>
+      <td>445</td>
+      <td>25</td>
+      <td>25</td>
+      <td>71</td>
+      <td>71</td>
+      <td>32</td>
+      <td>32</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>516</td>
+      <td>516</td>
+      <td>57</td>
+      <td>57</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tooldistillator</td>
+      <td>tooldistillator, tooldistillator_summarize</td>
+      <td>ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files</td>
+      <td>tooldistillator</td>
+      <td>tooldistillator</td>
+      <td></td>
+      <td>ToolDistillator</td>
+      <td>ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.</td>
+      <td>Data handling, Parsing</td>
+      <td>Microbiology, Bioinformatics, Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://gitlab.com/ifb-elixirfr/abromics/tooldistillator</td>
+      <td>Sequence Analysis</td>
+      <td>tooldistillator</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator</td>
+      <td>0.9.1</td>
+      <td>tooldistillator</td>
+      <td>0.9.1</td>
+      <td>Parsing</td>
+      <td>Microbiology, Bioinformatics, Sequence analysis</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>9</td>
+      <td>9</td>
+      <td>6</td>
+      <td>6</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>71</td>
+      <td>71</td>
+      <td>14</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tophat</td>
+      <td>tophat</td>
+      <td>Tophat for Illumina</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>RNA, Next Gen Mappers</td>
+      <td>tophat</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat</td>
+      <td>1.5.0</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>158</td>
+      <td>66524</td>
+      <td>28</td>
+      <td>7228</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>158</td>
+      <td>66525</td>
+      <td>28</td>
+      <td>7229</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tophat2</td>
+      <td>tophat2</td>
+      <td>Tophat - fast splice junction mapper for RNA-Seq reads</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://ccb.jhu.edu/software/tophat/index.shtml</td>
+      <td>RNA, Next Gen Mappers</td>
+      <td>tophat2</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2</td>
+      <td>2.1.1</td>
+      <td>bowtie2</td>
+      <td>2.5.4</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>15496</td>
+      <td>26623</td>
+      <td>1076</td>
+      <td>1664</td>
+      <td>83063</td>
+      <td>343017</td>
+      <td>8372</td>
+      <td>27829</td>
+      <td>5388</td>
+      <td>14057</td>
+      <td>508</td>
+      <td>1012</td>
+      <td>103947</td>
+      <td>383697</td>
+      <td>9956</td>
+      <td>30505</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tophat_fusion_post</td>
+      <td>tophat_fusion_post</td>
+      <td>Wrapper for Tophat-Fusion post step</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Transcriptomics</td>
+      <td>tophat_fusion_post</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post</td>
+      <td>0.1</td>
+      <td>blast+</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>220</td>
+      <td>242</td>
+      <td>41</td>
+      <td>46</td>
+      <td>6</td>
+      <td>814</td>
+      <td>2</td>
+      <td>191</td>
+      <td>100</td>
+      <td>120</td>
+      <td>8</td>
+      <td>12</td>
+      <td>326</td>
+      <td>1176</td>
+      <td>51</td>
+      <td>249</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>topologyeditors</td>
+      <td>gromacs_modify_topology, gromacs_extract_topology</td>
+      <td>Set of python scripts and associated tool files that can be used to modify topology files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors</td>
+      <td>Molecular Dynamics, Computational chemistry</td>
+      <td>topologyeditors</td>
+      <td>chemteam</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors</td>
+      <td>0</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>57</td>
+      <td>57</td>
+      <td>10</td>
+      <td>10</td>
+      <td>20</td>
+      <td>20</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>77</td>
+      <td>77</td>
+      <td>18</td>
+      <td>18</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tracegroomer</td>
+      <td>tracegroomer</td>
+      <td>TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/cbib/TraceGroomer</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer</td>
+      <td>0.1.4</td>
+      <td>tracegroomer</td>
+      <td>0.1.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tracy</td>
+      <td>tracy_align, tracy_assemble, tracy_basecall, tracy_decompose</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy</td>
+      <td>0.6.1</td>
+      <td>tracy</td>
+      <td>0.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3314</td>
+      <td>3314</td>
+      <td>124</td>
+      <td>124</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3314</td>
+      <td>3314</td>
+      <td>124</td>
+      <td>124</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>transdecoder</td>
+      <td>transdecoder</td>
+      <td>TransDecoder finds coding regions within transcripts</td>
+      <td>TransDecoder</td>
+      <td>TransDecoder</td>
+      <td></td>
+      <td>TransDecoder</td>
+      <td>TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.</td>
+      <td>Coding region prediction, de Novo sequencing, De-novo assembly</td>
+      <td>Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing</td>
+      <td>To update</td>
+      <td>https://transdecoder.github.io/</td>
+      <td>Transcriptomics, RNA</td>
+      <td>transdecoder</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder</td>
+      <td>5.5.0</td>
+      <td>transdecoder</td>
+      <td>5.7.1</td>
+      <td>Coding region prediction, de Novo sequencing, De-novo assembly</td>
+      <td>Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5964</td>
+      <td>6418</td>
+      <td>944</td>
+      <td>970</td>
+      <td>5450</td>
+      <td>5450</td>
+      <td>1066</td>
+      <td>1066</td>
+      <td>2610</td>
+      <td>2796</td>
+      <td>317</td>
+      <td>344</td>
+      <td>14024</td>
+      <td>14664</td>
+      <td>2327</td>
+      <td>2380</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>transit</td>
+      <td>gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps</td>
+      <td>TRANSIT</td>
+      <td>transit</td>
+      <td>transit</td>
+      <td></td>
+      <td>TRANSIT</td>
+      <td>A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.</td>
+      <td>Transposon prediction</td>
+      <td>DNA, Sequencing, Mobile genetic elements</td>
+      <td>To update</td>
+      <td>https://github.com/mad-lab/transit/</td>
+      <td>Genome annotation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit</td>
+      <td>3.0.2</td>
+      <td>transit</td>
+      <td>3.2.3</td>
+      <td>Transposon prediction</td>
+      <td>DNA, Sequencing, Mobile genetic elements</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>1039</td>
+      <td>1039</td>
+      <td>189</td>
+      <td>189</td>
+      <td>2672</td>
+      <td>3349</td>
+      <td>467</td>
+      <td>485</td>
+      <td>358</td>
+      <td>358</td>
+      <td>47</td>
+      <td>47</td>
+      <td>4069</td>
+      <td>4746</td>
+      <td>703</td>
+      <td>721</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>translate_bed</td>
+      <td>translate_bed</td>
+      <td>Translate BED transcript CDS or cDNA in 3 frames</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://rest.ensembl.org/</td>
+      <td>Proteomics</td>
+      <td>translate_bed</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed</td>
+      <td>0.1.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>649</td>
+      <td>685</td>
+      <td>138</td>
+      <td>142</td>
+      <td>473</td>
+      <td>473</td>
+      <td>105</td>
+      <td>105</td>
+      <td>761</td>
+      <td>761</td>
+      <td>18</td>
+      <td>18</td>
+      <td>1883</td>
+      <td>1919</td>
+      <td>261</td>
+      <td>265</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>translate_bed_sequences</td>
+      <td>translate_bed_sequences</td>
+      <td>Perform 3 frame translation of BED file augmented with a sequence column</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>translate_bed_sequences</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences</td>
+      <td>0.2.0</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>57</td>
+      <td>69</td>
+      <td>16</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>57</td>
+      <td>69</td>
+      <td>16</td>
+      <td>21</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>transtermhp</td>
+      <td>transtermhp</td>
+      <td>Finds rho-independent transcription terminators in bacterial genomes</td>
+      <td>transtermhp</td>
+      <td>transtermhp</td>
+      <td></td>
+      <td>TransTermHP</td>
+      <td>TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator</td>
+      <td>Transcriptional regulatory element prediction</td>
+      <td>Transcription factors and regulatory sites</td>
+      <td>To update</td>
+      <td>https://transterm.cbcb.umd.edu</td>
+      <td>Sequence Analysis</td>
+      <td>transtermhp</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp</td>
+      <td></td>
+      <td>transtermhp</td>
+      <td>2.09</td>
+      <td>Transcriptional regulatory element prediction</td>
+      <td>Transcription factors and regulatory sites</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>250</td>
+      <td>254</td>
+      <td>31</td>
+      <td>31</td>
+      <td>174</td>
+      <td>174</td>
+      <td>45</td>
+      <td>45</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>424</td>
+      <td>428</td>
+      <td>76</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tree_relabeler</td>
+      <td>tree_relabel</td>
+      <td>Relabels the tips of a newick formatted tree.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>tree_relabeler</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler</td>
+      <td>1.1.0</td>
+      <td>perl-bioperl</td>
+      <td>1.7.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trim_galore</td>
+      <td>trim_galore</td>
+      <td>Trim Galore adaptive quality and adapter trimmer</td>
+      <td>trim_galore</td>
+      <td>trim_galore</td>
+      <td></td>
+      <td>Trim Galore</td>
+      <td>A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.</td>
+      <td>Sequence trimming, Primer removal, Read pre-processing</td>
+      <td>Sequence analysis</td>
+      <td>To update</td>
+      <td>http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/</td>
+      <td>Sequence Analysis, Fastq Manipulation</td>
+      <td>trim_galore</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore</td>
+      <td>0.6.7</td>
+      <td>trim-galore</td>
+      <td>0.6.10</td>
+      <td>Sequence trimming, Primer removal, Read pre-processing</td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>229489</td>
+      <td>275008</td>
+      <td>5733</td>
+      <td>6500</td>
+      <td>228708</td>
+      <td>324716</td>
+      <td>11708</td>
+      <td>16638</td>
+      <td>22644</td>
+      <td>23869</td>
+      <td>1439</td>
+      <td>1527</td>
+      <td>480841</td>
+      <td>623593</td>
+      <td>18880</td>
+      <td>24665</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trimmer</td>
+      <td>trimmer</td>
+      <td>Trim leading or trailing characters.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Text Manipulation</td>
+      <td>trimmer</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer</td>
+      <td>0.0.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
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+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
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+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>5304</td>
+      <td>7438</td>
+      <td>447</td>
+      <td>512</td>
+      <td>15698</td>
+      <td>108672</td>
+      <td>658</td>
+      <td>2946</td>
+      <td>266</td>
+      <td>822</td>
+      <td>53</td>
+      <td>81</td>
+      <td>21268</td>
+      <td>116932</td>
+      <td>1158</td>
+      <td>3539</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trimmomatic</td>
+      <td>trimmomatic</td>
+      <td>A flexible read trimming tool for Illumina NGS data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://www.usadellab.org/cms/?page=trimmomatic</td>
+      <td>Fastq Manipulation</td>
+      <td>trimmomatic</td>
+      <td>pjbriggs</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic</td>
+      <td>0.39</td>
+      <td>trimmomatic</td>
+      <td>0.39</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
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+      <td>1</td>
+      <td>0</td>
+      <td>352353</td>
+      <td>383014</td>
+      <td>14547</td>
+      <td>15408</td>
+      <td>632385</td>
+      <td>839058</td>
+      <td>39323</td>
+      <td>49850</td>
+      <td>125340</td>
+      <td>139097</td>
+      <td>5268</td>
+      <td>5975</td>
+      <td>1110078</td>
+      <td>1361169</td>
+      <td>59138</td>
+      <td>71233</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trinity</td>
+      <td>trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats</td>
+      <td>Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq</td>
+      <td>trinity</td>
+      <td>trinity</td>
+      <td></td>
+      <td>Trinity</td>
+      <td>Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.</td>
+      <td>Transcriptome assembly</td>
+      <td>Transcriptomics, Gene expression, Gene transcripts</td>
+      <td>To update</td>
+      <td>https://github.com/trinityrnaseq/trinityrnaseq</td>
+      <td>Transcriptomics, RNA</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity</td>
+      <td>2.15.1</td>
+      <td>trinity</td>
+      <td>2.15.2</td>
+      <td>Transcriptome assembly</td>
+      <td>Transcriptomics, Gene transcripts</td>
+      <td>9</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>9</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>2</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>13</td>
+      <td>12</td>
+      <td>0</td>
+      <td>35698</td>
+      <td>39132</td>
+      <td>4376</td>
+      <td>4632</td>
+      <td>44509</td>
+      <td>44509</td>
+      <td>6714</td>
+      <td>6714</td>
+      <td>21883</td>
+      <td>23889</td>
+      <td>1924</td>
+      <td>2070</td>
+      <td>102090</td>
+      <td>107530</td>
+      <td>13014</td>
+      <td>13416</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trinotate</td>
+      <td>trinotate</td>
+      <td>Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.</td>
+      <td>trinotate</td>
+      <td>trinotate</td>
+      <td></td>
+      <td>Trinotate</td>
+      <td>Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.</td>
+      <td>Gene functional annotation</td>
+      <td>Gene expression, Transcriptomics</td>
+      <td>To update</td>
+      <td>https://trinotate.github.io/</td>
+      <td>Transcriptomics, RNA</td>
+      <td>trinotate</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate</td>
+      <td>3.2.2</td>
+      <td>trinotate</td>
+      <td>4.0.2</td>
+      <td>Gene functional annotation</td>
+      <td>Transcriptomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1968</td>
+      <td>2080</td>
+      <td>374</td>
+      <td>390</td>
+      <td>1825</td>
+      <td>1825</td>
+      <td>527</td>
+      <td>527</td>
+      <td>862</td>
+      <td>1060</td>
+      <td>161</td>
+      <td>195</td>
+      <td>4655</td>
+      <td>4965</td>
+      <td>1062</td>
+      <td>1112</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tripal</td>
+      <td>analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync</td>
+      <td>Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxy-genome-annotation/python-tripal</td>
+      <td>Web Services</td>
+      <td></td>
+      <td>gga</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal</td>
+      <td>https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal</td>
+      <td></td>
+      <td>python-tripal</td>
+      <td>3.2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trna_prediction</td>
+      <td>aragorn_trna, trnascan</td>
+      <td>Aragorn predicts tRNA and tmRNA in nucleotide sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://mbioserv2.mbioekol.lu.se/ARAGORN/</td>
+      <td>RNA</td>
+      <td>trna_prediction</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction</td>
+      <td>0.6</td>
+      <td>aragorn</td>
+      <td>1.2.41</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>4361</td>
+      <td>4601</td>
+      <td>741</td>
+      <td>807</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2469</td>
+      <td>2469</td>
+      <td>190</td>
+      <td>190</td>
+      <td>6830</td>
+      <td>7070</td>
+      <td>931</td>
+      <td>997</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>trycycler</td>
+      <td>trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample</td>
+      <td>Trycycler toolkit wrappers</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/rrwick/Trycycler</td>
+      <td>Assembly</td>
+      <td>trycycler</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler</td>
+      <td>0.5.5</td>
+      <td>trycycler</td>
+      <td>0.5.5</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14681</td>
+      <td>14681</td>
+      <td>265</td>
+      <td>265</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4488</td>
+      <td>4488</td>
+      <td>147</td>
+      <td>147</td>
+      <td>19169</td>
+      <td>19169</td>
+      <td>412</td>
+      <td>412</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tsebra</td>
+      <td>tsebra</td>
+      <td>This tool has been developed to combine BRAKER predictions.</td>
+      <td>tsebra</td>
+      <td>tsebra</td>
+      <td></td>
+      <td>TSEBRA</td>
+      <td>TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.</td>
+      <td>Homology-based gene prediction, Alternative splicing prediction</td>
+      <td>Gene expression, RNA-Seq, Gene transcripts, Model organisms</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/Gaius-Augustus/TSEBRA</td>
+      <td>Genome annotation</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra</td>
+      <td>1.1.2.5</td>
+      <td>tsebra</td>
+      <td>1.1.2.5</td>
+      <td>Homology-based gene prediction, Alternative splicing prediction</td>
+      <td>Gene expression, RNA-Seq, Gene transcripts, Model organisms</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>17</td>
+      <td>17</td>
+      <td>7</td>
+      <td>7</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tsne</td>
+      <td>tsne</td>
+      <td>T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/web/packages/Rtsne/</td>
+      <td>Text Manipulation</td>
+      <td>tsne</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne</td>
+      <td>0.0.2</td>
+      <td>r-rtsne</td>
+      <td>0.13</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>255</td>
+      <td>379</td>
+      <td>31</td>
+      <td>37</td>
+      <td>281</td>
+      <td>281</td>
+      <td>64</td>
+      <td>64</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>536</td>
+      <td>660</td>
+      <td>95</td>
+      <td>101</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>twobittofa</td>
+      <td>ucsc-twobittofa</td>
+      <td>twoBitToFa is a tool to convert all or part of .2bit file to FASTA</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://genome.ucsc.edu/goldenpath/help/twoBit.html</td>
+      <td>Convert Formats</td>
+      <td>ucsc_twobittofa</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa</td>
+      <td>469</td>
+      <td>ucsc-twobittofa</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>413</td>
+      <td>511</td>
+      <td>84</td>
+      <td>118</td>
+      <td>441</td>
+      <td>441</td>
+      <td>123</td>
+      <td>123</td>
+      <td>21</td>
+      <td>21</td>
+      <td>2</td>
+      <td>2</td>
+      <td>875</td>
+      <td>973</td>
+      <td>209</td>
+      <td>243</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>tximport</td>
+      <td>tximport</td>
+      <td>Wrapper for the Bioconductor package tximport</td>
+      <td>tximport</td>
+      <td>tximport</td>
+      <td></td>
+      <td>tximport</td>
+      <td>An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.</td>
+      <td>Pathway or network analysis, Formatting, RNA-Seq analysis</td>
+      <td>Transcriptomics, Gene transcripts, Workflows</td>
+      <td>Up-to-date</td>
+      <td>http://bioconductor.org/packages/tximport/</td>
+      <td>Transcriptomics</td>
+      <td>tximport</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport</td>
+      <td>1.30.0</td>
+      <td>bioconductor-tximport</td>
+      <td>1.30.0</td>
+      <td>Pathway or network analysis, Formatting, RNA-Seq analysis</td>
+      <td>Transcriptomics, Gene transcripts, Workflows</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1802</td>
+      <td>1802</td>
+      <td>225</td>
+      <td>225</td>
+      <td>6963</td>
+      <td>6963</td>
+      <td>904</td>
+      <td>904</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8765</td>
+      <td>8765</td>
+      <td>1129</td>
+      <td>1129</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc-cell-browser</td>
+      <td>ucsc_cell_browser</td>
+      <td>Python pipeline and Javascript scatter plot library for single-cell datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://cells.ucsc.edu/</td>
+      <td>Transcriptomics</td>
+      <td>ucsc_cell_browser</td>
+      <td>ebi-gxa</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml</td>
+      <td>https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser</td>
+      <td>1.0.0+galaxy1</td>
+      <td>ucsc-cell-browser</td>
+      <td>1.2.8</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>965</td>
+      <td>975</td>
+      <td>178</td>
+      <td>181</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>965</td>
+      <td>975</td>
+      <td>178</td>
+      <td>181</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_axtchain</td>
+      <td>ucsc_axtchain</td>
+      <td>Chain together genome alignments</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_axtchain</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain</td>
+      <td>469</td>
+      <td>ucsc-axtchain</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_axttomaf</td>
+      <td>ucsc_axtomaf</td>
+      <td>Convert dataset from axt to MAF format.</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Convert Formats</td>
+      <td>ucsc_axttomaf</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf</td>
+      <td>469</td>
+      <td>ucsc-axttomaf</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_blat</td>
+      <td>ucsc_blat</td>
+      <td>Standalone blat sequence search command line tool</td>
+      <td>blat</td>
+      <td>blat</td>
+      <td></td>
+      <td>BLAT</td>
+      <td>Fast, accurate spliced alignment of DNA sequences.</td>
+      <td>Sequence alignment</td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://genome.ucsc.edu/goldenPath/help/blatSpec.html</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_blat</td>
+      <td>yating-l</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat</td>
+      <td>469</td>
+      <td>ucsc-blat</td>
+      <td>469</td>
+      <td>Sequence alignment</td>
+      <td>Sequence analysis</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_chainnet</td>
+      <td>ucsc_chainnet</td>
+      <td>Make alignment nets out of chains</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_chainnet</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet</td>
+      <td>469</td>
+      <td>ucsc-chainnet</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_chainprenet</td>
+      <td>ucsc_chainprenet</td>
+      <td>Remove chains that don't have a chance of being netted</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_chainprenet</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet</td>
+      <td>469</td>
+      <td>ucsc-chainprenet</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_chainsort</td>
+      <td>ucsc_chainsort</td>
+      <td>Sort chains. By default sorts by score.</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_chainsort</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort</td>
+      <td>469</td>
+      <td>ucsc-chainsort</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_custom_track</td>
+      <td>build_ucsc_custom_track_1</td>
+      <td>Build custom track for UCSC genome browser</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_custom_track</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track</td>
+      <td>1.0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>373</td>
+      <td>463</td>
+      <td>134</td>
+      <td>151</td>
+      <td>2249</td>
+      <td>18611</td>
+      <td>638</td>
+      <td>4080</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2622</td>
+      <td>19074</td>
+      <td>772</td>
+      <td>4231</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_netfilter</td>
+      <td>ucsc_netfilter</td>
+      <td>Filter out parts of net</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_netfilter</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter</td>
+      <td>469</td>
+      <td>ucsc-netfilter</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_netsyntenic</td>
+      <td>ucsc_netsyntenic</td>
+      <td>Add synteny info to a net dataset</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Sequence Analysis</td>
+      <td>ucsc_netsyntenic</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic</td>
+      <td>469</td>
+      <td>ucsc-netsyntenic</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>ucsc_nettoaxt</td>
+      <td>ucsc_nettoaxt</td>
+      <td>Convert net (and chain) to axt format.</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>http://hgdownload.cse.ucsc.edu/admin/exe/</td>
+      <td>Convert Formats</td>
+      <td>ucsc_nettoaxt</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt</td>
+      <td>469</td>
+      <td>ucsc-nettoaxt</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>umi_tools</td>
+      <td>umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist</td>
+      <td>UMI-tools extract - Extract UMIs from fastq</td>
+      <td>umi-tools</td>
+      <td>umi-tools</td>
+      <td></td>
+      <td>UMI-tools</td>
+      <td>Tools for handling Unique Molecular Identifiers in NGS data sets.</td>
+      <td>Sequencing quality control</td>
+      <td>NGS, Sequence sites, features and motifs, Quality affairs</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/CGATOxford/UMI-tools</td>
+      <td>Sequence Analysis, Transcriptomics, Single Cell</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools</td>
+      <td>1.1.5</td>
+      <td>umi_tools</td>
+      <td>1.1.5</td>
+      <td>Sequencing quality control</td>
+      <td>Sequence sites, features and motifs, Quality affairs</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>5</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>55050</td>
+      <td>68123</td>
+      <td>1090</td>
+      <td>1223</td>
+      <td>9001</td>
+      <td>9001</td>
+      <td>906</td>
+      <td>906</td>
+      <td>12444</td>
+      <td>12444</td>
+      <td>187</td>
+      <td>187</td>
+      <td>76495</td>
+      <td>89568</td>
+      <td>2183</td>
+      <td>2316</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>unicycler</td>
+      <td>unicycler</td>
+      <td>Unicycler is a hybrid assembly pipeline for bacterial genomes.</td>
+      <td>unicycler</td>
+      <td>unicycler</td>
+      <td></td>
+      <td>Unicycler</td>
+      <td>A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.</td>
+      <td>Genome assembly, Aggregation</td>
+      <td>Microbiology, Genomics, Sequencing, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/rrwick/Unicycler</td>
+      <td>Assembly</td>
+      <td>unicycler</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler</td>
+      <td>0.5.1</td>
+      <td>unicycler</td>
+      <td>0.5.1</td>
+      <td>Genome assembly, Aggregation</td>
+      <td>Microbiology, Genomics, Sequencing, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>74120</td>
+      <td>77648</td>
+      <td>3798</td>
+      <td>3963</td>
+      <td>64946</td>
+      <td>90075</td>
+      <td>5451</td>
+      <td>7380</td>
+      <td>19516</td>
+      <td>20422</td>
+      <td>2010</td>
+      <td>2080</td>
+      <td>158582</td>
+      <td>188145</td>
+      <td>11259</td>
+      <td>13423</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>unipept</td>
+      <td>unipept</td>
+      <td>Unipept retrieves metaproteomics information</td>
+      <td>unipept</td>
+      <td>unipept</td>
+      <td></td>
+      <td>Unipept</td>
+      <td>Metaproteomics data analysis with a focus on interactive data visualizations.</td>
+      <td>Prediction and recognition, Visualisation</td>
+      <td>Proteomics, Proteogenomics, Biodiversity, Workflows</td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp</td>
+      <td>Proteomics</td>
+      <td>unipept</td>
+      <td>galaxyp</td>
+      <td>https://unipept.ugent.be/apidocs</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept</td>
+      <td>4.5.1</td>
+      <td>python</td>
+      <td></td>
+      <td>Prediction and recognition, Visualisation</td>
+      <td>Proteomics, Proteogenomics, Biodiversity, Workflows</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4900</td>
+      <td>5146</td>
+      <td>257</td>
+      <td>270</td>
+      <td>251</td>
+      <td>251</td>
+      <td>81</td>
+      <td>81</td>
+      <td>1069</td>
+      <td>1069</td>
+      <td>29</td>
+      <td>29</td>
+      <td>6220</td>
+      <td>6466</td>
+      <td>367</td>
+      <td>380</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>uniprot_rest_interface</td>
+      <td>uniprot</td>
+      <td>UniProt ID mapping and sequence retrieval</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/jdrudolph/uniprot</td>
+      <td>Proteomics, Sequence Analysis</td>
+      <td>uniprot_rest_interface</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface</td>
+      <td>0.6</td>
+      <td>requests</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2117</td>
+      <td>2725</td>
+      <td>341</td>
+      <td>412</td>
+      <td>3111</td>
+      <td>5779</td>
+      <td>594</td>
+      <td>1011</td>
+      <td>806</td>
+      <td>806</td>
+      <td>50</td>
+      <td>50</td>
+      <td>6034</td>
+      <td>9310</td>
+      <td>985</td>
+      <td>1473</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>uniprotxml_downloader</td>
+      <td>uniprotxml_downloader</td>
+      <td>Download UniProt proteome in XML or fasta format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Proteomics</td>
+      <td>uniprotxml_downloader</td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader</td>
+      <td>2.4.0</td>
+      <td>requests</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1488</td>
+      <td>1596</td>
+      <td>230</td>
+      <td>266</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>743</td>
+      <td>743</td>
+      <td>35</td>
+      <td>35</td>
+      <td>2231</td>
+      <td>2339</td>
+      <td>265</td>
+      <td>301</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>unzip</td>
+      <td>unzip</td>
+      <td>Unzip file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Convert Formats</td>
+      <td>unzip</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip</td>
+      <td>6.0</td>
+      <td>unzip</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6942</td>
+      <td>7024</td>
+      <td>1345</td>
+      <td>1356</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>2461</td>
+      <td>2461</td>
+      <td>266</td>
+      <td>266</td>
+      <td>9404</td>
+      <td>9486</td>
+      <td>1612</td>
+      <td>1623</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>upload_roi_and_measures_to_omero</td>
+      <td>uploadROIandMeasuresToOMERO</td>
+      <td>Upload the ROI coordinates and the measurements to the omero server</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Imaging</td>
+      <td>upload_roi_and_measures_to_omero</td>
+      <td>lldelisle</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero</td>
+      <td>https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero</td>
+      <td>0.0.5</td>
+      <td>omero-py</td>
+      <td>5.11.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>usher</td>
+      <td>usher_matutils, usher</td>
+      <td>UShER toolkit wrappers</td>
+      <td>usher</td>
+      <td>usher</td>
+      <td></td>
+      <td>usher</td>
+      <td>The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.</td>
+      <td>Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)</td>
+      <td>Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics</td>
+      <td>To update</td>
+      <td>https://github.com/yatisht/usher</td>
+      <td>Phylogenetics</td>
+      <td>usher</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher</td>
+      <td>0.2.1</td>
+      <td>usher</td>
+      <td>0.6.3</td>
+      <td>Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)</td>
+      <td>Cladistics, Genotype and phenotype, Phylogenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1060</td>
+      <td>1060</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1060</td>
+      <td>1060</td>
+      <td>5</td>
+      <td>5</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>valet</td>
+      <td>valet</td>
+      <td>A pipeline for detecting mis-assemblies in metagenomic assemblies.</td>
+      <td>valet</td>
+      <td>valet</td>
+      <td></td>
+      <td>VALET</td>
+      <td>VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.</td>
+      <td>Sequence assembly, Sequence assembly visualisation</td>
+      <td>Metagenomics, Sequence assembly</td>
+      <td>To update</td>
+      <td>https://github.com/marbl/VALET</td>
+      <td>Metagenomics</td>
+      <td>valet</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet</td>
+      <td></td>
+      <td>valet</td>
+      <td>1.0</td>
+      <td>Sequence assembly, Sequence assembly visualisation</td>
+      <td>Metagenomics, Sequence assembly</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>518</td>
+      <td>677</td>
+      <td>75</td>
+      <td>87</td>
+      <td>234</td>
+      <td>234</td>
+      <td>65</td>
+      <td>65</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>752</td>
+      <td>911</td>
+      <td>140</td>
+      <td>152</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>validate_fasta_database</td>
+      <td>validate_fasta_database</td>
+      <td>runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Fasta Manipulation, Proteomics</td>
+      <td>validate_fasta_database</td>
+      <td>galaxyp</td>
+      <td></td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database</td>
+      <td>0.1.5</td>
+      <td>validate-fasta-database</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>112</td>
+      <td>112</td>
+      <td>38</td>
+      <td>38</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>112</td>
+      <td>112</td>
+      <td>38</td>
+      <td>38</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vapor</td>
+      <td>vapor</td>
+      <td>Classify Influenza samples from raw short read sequence data</td>
+      <td>vapor</td>
+      <td>vapor</td>
+      <td></td>
+      <td>VAPOR</td>
+      <td>VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (&gt; 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.</td>
+      <td>Data retrieval, De-novo assembly, Read mapping</td>
+      <td>Whole genome sequencing, Mapping, Sequence assembly</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/connor-lab/vapor</td>
+      <td>Sequence Analysis</td>
+      <td>vapor</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor</td>
+      <td>1.0.2</td>
+      <td>vapor</td>
+      <td>1.0.2</td>
+      <td>Data retrieval, De-novo assembly, Read mapping</td>
+      <td>Whole genome sequencing, Mapping, Sequence assembly</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>5936</td>
+      <td>5936</td>
+      <td>147</td>
+      <td>147</td>
+      <td>523</td>
+      <td>523</td>
+      <td>15</td>
+      <td>15</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6459</td>
+      <td>6459</td>
+      <td>162</td>
+      <td>162</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vardict</td>
+      <td>vardict_java</td>
+      <td>VarDict - calls SNVs and indels for tumour-normal pairs</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AstraZeneca-NGS/VarDictJava</td>
+      <td>Variant Analysis</td>
+      <td>vardict_java</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict</td>
+      <td>1.8.3</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>381</td>
+      <td>381</td>
+      <td>37</td>
+      <td>37</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>381</td>
+      <td>381</td>
+      <td>37</td>
+      <td>37</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>variant_analyzer</td>
+      <td>mut2read, mut2sscs, read2mut</td>
+      <td>Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>variant_analyzer</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer</td>
+      <td>2.0.0</td>
+      <td>matplotlib</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>95</td>
+      <td>95</td>
+      <td>14</td>
+      <td>14</td>
+      <td>516</td>
+      <td>516</td>
+      <td>67</td>
+      <td>67</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>611</td>
+      <td>611</td>
+      <td>81</td>
+      <td>81</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>varscan</td>
+      <td>varscan_copynumber, varscan_mpileup, varscan_somatic</td>
+      <td>VarScan is a variant caller for high-throughput sequencing data</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://dkoboldt.github.io/varscan/</td>
+      <td>Variant Analysis</td>
+      <td>varscan</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/iuc/tree/master/tools/varscan</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan</td>
+      <td>2.4.3</td>
+      <td>varscan</td>
+      <td>2.4.6</td>
+      <td></td>
+      <td></td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>10711</td>
+      <td>11502</td>
+      <td>1442</td>
+      <td>1560</td>
+      <td>16705</td>
+      <td>16705</td>
+      <td>3135</td>
+      <td>3135</td>
+      <td>1036</td>
+      <td>1036</td>
+      <td>100</td>
+      <td>100</td>
+      <td>28452</td>
+      <td>29243</td>
+      <td>4677</td>
+      <td>4795</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>varscan_vaf</td>
+      <td>varscan_vaf</td>
+      <td>Compute variant allele frequency in vcf files generated by varscan.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>Variant Analysis</td>
+      <td>varscan_vaf</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf</td>
+      <td>0.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>varscan_version_2</td>
+      <td>varscan</td>
+      <td>VarScan wrapper</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://dkoboldt.github.io/varscan/</td>
+      <td>Variant Analysis</td>
+      <td>varscan_version_2</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2</td>
+      <td>2.4.2</td>
+      <td>varscan</td>
+      <td>2.4.6</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>5058</td>
+      <td>6139</td>
+      <td>606</td>
+      <td>699</td>
+      <td>17232</td>
+      <td>53268</td>
+      <td>2965</td>
+      <td>5686</td>
+      <td>2298</td>
+      <td>2656</td>
+      <td>424</td>
+      <td>482</td>
+      <td>24588</td>
+      <td>62063</td>
+      <td>3995</td>
+      <td>6867</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>varvamp</td>
+      <td>varvamp</td>
+      <td>Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses</td>
+      <td>varvamp</td>
+      <td>varvamp</td>
+      <td></td>
+      <td>varVAMP</td>
+      <td>variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.</td>
+      <td>PCR primer design</td>
+      <td>Virology, Probes and primers</td>
+      <td>To update</td>
+      <td>https://github.com/jonas-fuchs/varVAMP/</td>
+      <td>Sequence Analysis</td>
+      <td>varvamp</td>
+      <td>iuc</td>
+      <td>https://github.com/jonas-fuchs/varVAMP</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp</td>
+      <td>1.2.0</td>
+      <td>varvamp</td>
+      <td>1.2.1</td>
+      <td>PCR primer design</td>
+      <td>Virology, Probes and primers</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>273</td>
+      <td>273</td>
+      <td>12</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>273</td>
+      <td>273</td>
+      <td>12</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf2maf</td>
+      <td>vcf2maf</td>
+      <td>vcf2maf: Convert VCF into MAF</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/mskcc/vcf2maf</td>
+      <td>Convert Formats</td>
+      <td>vcf2maf</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf</td>
+      <td>1.6.21</td>
+      <td>vcf2maf</td>
+      <td>1.6.22</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1097</td>
+      <td>1097</td>
+      <td>46</td>
+      <td>46</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>65</td>
+      <td>65</td>
+      <td>5</td>
+      <td>5</td>
+      <td>1162</td>
+      <td>1162</td>
+      <td>51</td>
+      <td>51</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf2pgsnp</td>
+      <td>vcf2pgSnp</td>
+      <td>VCF to pgSnp</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>vcf2pgsnp</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>191</td>
+      <td>221</td>
+      <td>57</td>
+      <td>65</td>
+      <td>1399</td>
+      <td>2700</td>
+      <td>209</td>
+      <td>584</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1590</td>
+      <td>2921</td>
+      <td>266</td>
+      <td>649</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf2snvalignment</td>
+      <td>vcf2snvalignment</td>
+      <td>Generates multiple alignment of variant calls</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>vcf2snvalignment</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf2tsv</td>
+      <td>vcf2tsv</td>
+      <td>Converts VCF files into tab-delimited format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis, Convert Formats</td>
+      <td>vcf2tsv</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>169090</td>
+      <td>169679</td>
+      <td>823</td>
+      <td>874</td>
+      <td>16304</td>
+      <td>42215</td>
+      <td>1141</td>
+      <td>2594</td>
+      <td>2485</td>
+      <td>2511</td>
+      <td>169</td>
+      <td>172</td>
+      <td>187879</td>
+      <td>214405</td>
+      <td>2133</td>
+      <td>3640</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf_annotate</td>
+      <td>vcf_annotate</td>
+      <td>Annotate a VCF file (dbSNP, hapmap)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>vcf_annotate</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>263</td>
+      <td>340</td>
+      <td>31</td>
+      <td>54</td>
+      <td>263</td>
+      <td>342</td>
+      <td>31</td>
+      <td>56</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf_extract</td>
+      <td>vcf_extract</td>
+      <td>Extract reads from a specified region</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>vcf_extract</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>513</td>
+      <td>569</td>
+      <td>6</td>
+      <td>9</td>
+      <td>513</td>
+      <td>569</td>
+      <td>6</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf_filter</td>
+      <td>vcf_filter</td>
+      <td>Filter a VCF file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>vcf_filter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>400</td>
+      <td>455</td>
+      <td>129</td>
+      <td>140</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>238</td>
+      <td>606</td>
+      <td>19</td>
+      <td>56</td>
+      <td>638</td>
+      <td>1061</td>
+      <td>148</td>
+      <td>196</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcf_intersect</td>
+      <td>vcf_intersect</td>
+      <td>Generate the intersection of two VCF files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Variant Analysis</td>
+      <td>vcf_intersect</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect</td>
+      <td>1.0.0</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>19</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>335</td>
+      <td>463</td>
+      <td>19</td>
+      <td>28</td>
+      <td>335</td>
+      <td>482</td>
+      <td>19</td>
+      <td>31</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfaddinfo</td>
+      <td>vcfaddinfo</td>
+      <td>Adds info fields from the second dataset which are not present in the first dataset.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfaddinfo</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>882</td>
+      <td>888</td>
+      <td>30</td>
+      <td>32</td>
+      <td>6118</td>
+      <td>8261</td>
+      <td>36</td>
+      <td>114</td>
+      <td>175</td>
+      <td>184</td>
+      <td>6</td>
+      <td>6</td>
+      <td>7175</td>
+      <td>9333</td>
+      <td>72</td>
+      <td>152</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfallelicprimitives</td>
+      <td>vcfallelicprimitives</td>
+      <td>Splits alleleic primitives (gaps or mismatches) into multiple VCF lines</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfallelicprimitives</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>6879</td>
+      <td>17157</td>
+      <td>897</td>
+      <td>1219</td>
+      <td>7585</td>
+      <td>14509</td>
+      <td>1245</td>
+      <td>1925</td>
+      <td>1648</td>
+      <td>1681</td>
+      <td>225</td>
+      <td>229</td>
+      <td>16112</td>
+      <td>33347</td>
+      <td>2367</td>
+      <td>3373</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfanno</td>
+      <td>vcfanno</td>
+      <td>Annotate VCF files</td>
+      <td>vcfanno</td>
+      <td>vcfanno</td>
+      <td></td>
+      <td>vcfanno</td>
+      <td>Fast, flexible annotation of genetic variants.</td>
+      <td>SNP annotation</td>
+      <td>Genetic variation, Data submission, annotation and curation</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/brentp/vcfanno</td>
+      <td>Variant Analysis</td>
+      <td>vcfanno</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/vcfanno/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno</td>
+      <td>0.3.5</td>
+      <td>vcfanno</td>
+      <td>0.3.5</td>
+      <td>SNP annotation</td>
+      <td>Genetic variation, Data submission, annotation and curation</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>174</td>
+      <td>174</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1139</td>
+      <td>1139</td>
+      <td>174</td>
+      <td>174</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfannotate</td>
+      <td>vcfannotate</td>
+      <td>Intersect VCF records with BED annotations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfannotate</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2797</td>
+      <td>2850</td>
+      <td>157</td>
+      <td>181</td>
+      <td>3668</td>
+      <td>14532</td>
+      <td>652</td>
+      <td>1392</td>
+      <td>494</td>
+      <td>507</td>
+      <td>61</td>
+      <td>63</td>
+      <td>6959</td>
+      <td>17889</td>
+      <td>870</td>
+      <td>1636</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfannotategenotypes</td>
+      <td>vcfannotategenotypes</td>
+      <td>Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfannotategenotypes</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>189</td>
+      <td>203</td>
+      <td>62</td>
+      <td>66</td>
+      <td>497</td>
+      <td>1828</td>
+      <td>155</td>
+      <td>387</td>
+      <td>184</td>
+      <td>197</td>
+      <td>11</td>
+      <td>11</td>
+      <td>870</td>
+      <td>2228</td>
+      <td>228</td>
+      <td>464</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfbedintersect</td>
+      <td>vcfbedintersect</td>
+      <td>Intersect VCF and BED datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfbedintersect</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>3017</td>
+      <td>4049</td>
+      <td>185</td>
+      <td>210</td>
+      <td>4709</td>
+      <td>20250</td>
+      <td>406</td>
+      <td>1147</td>
+      <td>507</td>
+      <td>527</td>
+      <td>40</td>
+      <td>42</td>
+      <td>8233</td>
+      <td>24826</td>
+      <td>631</td>
+      <td>1399</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfbreakcreatemulti</td>
+      <td>vcfbreakcreatemulti</td>
+      <td>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfbreakcreatemulti</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>416</td>
+      <td>478</td>
+      <td>35</td>
+      <td>40</td>
+      <td>3969</td>
+      <td>10457</td>
+      <td>82</td>
+      <td>309</td>
+      <td>362</td>
+      <td>378</td>
+      <td>8</td>
+      <td>8</td>
+      <td>4747</td>
+      <td>11313</td>
+      <td>125</td>
+      <td>357</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfcheck</td>
+      <td>vcfcheck</td>
+      <td>Verify that the reference allele matches the reference genome</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfcheck</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>745</td>
+      <td>767</td>
+      <td>96</td>
+      <td>106</td>
+      <td>803</td>
+      <td>1895</td>
+      <td>222</td>
+      <td>627</td>
+      <td>241</td>
+      <td>256</td>
+      <td>16</td>
+      <td>17</td>
+      <td>1789</td>
+      <td>2918</td>
+      <td>334</td>
+      <td>750</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfcombine</td>
+      <td>vcfcombine</td>
+      <td>Combine multiple VCF datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfcombine</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1422</td>
+      <td>2020</td>
+      <td>284</td>
+      <td>505</td>
+      <td>4951</td>
+      <td>19530</td>
+      <td>1021</td>
+      <td>2669</td>
+      <td>493</td>
+      <td>516</td>
+      <td>60</td>
+      <td>62</td>
+      <td>6866</td>
+      <td>22066</td>
+      <td>1365</td>
+      <td>3236</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfcommonsamples</td>
+      <td>vcfcommonsamples</td>
+      <td>Output records belonging to samples commong between two datasets.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfcommonsamples</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>233</td>
+      <td>253</td>
+      <td>37</td>
+      <td>42</td>
+      <td>234</td>
+      <td>1839</td>
+      <td>79</td>
+      <td>287</td>
+      <td>199</td>
+      <td>214</td>
+      <td>11</td>
+      <td>12</td>
+      <td>666</td>
+      <td>2306</td>
+      <td>127</td>
+      <td>341</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfdistance</td>
+      <td>vcfdistance</td>
+      <td>Calculate distance to the nearest variant.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfdistance</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>572</td>
+      <td>585</td>
+      <td>90</td>
+      <td>92</td>
+      <td>2063</td>
+      <td>2427</td>
+      <td>139</td>
+      <td>296</td>
+      <td>272</td>
+      <td>290</td>
+      <td>19</td>
+      <td>22</td>
+      <td>2907</td>
+      <td>3302</td>
+      <td>248</td>
+      <td>410</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcffilter</td>
+      <td>vcffilter2</td>
+      <td>Tool for filtering VCF files</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcffilter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>37489</td>
+      <td>47142</td>
+      <td>2113</td>
+      <td>2218</td>
+      <td>75128</td>
+      <td>162296</td>
+      <td>5730</td>
+      <td>10533</td>
+      <td>2626</td>
+      <td>2736</td>
+      <td>320</td>
+      <td>331</td>
+      <td>115243</td>
+      <td>212174</td>
+      <td>8163</td>
+      <td>13082</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcffixup</td>
+      <td>vcffixup</td>
+      <td>Count the allele frequencies across alleles present in each record in the VCF file.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcffixup</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>926</td>
+      <td>957</td>
+      <td>155</td>
+      <td>173</td>
+      <td>2291</td>
+      <td>5323</td>
+      <td>313</td>
+      <td>985</td>
+      <td>251</td>
+      <td>265</td>
+      <td>28</td>
+      <td>31</td>
+      <td>3468</td>
+      <td>6545</td>
+      <td>496</td>
+      <td>1189</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfflatten</td>
+      <td>vcfflatten2</td>
+      <td>Removes multi-allelic sites by picking the most common alternate</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfflatten</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>172</td>
+      <td>183</td>
+      <td>21</td>
+      <td>25</td>
+      <td>351</td>
+      <td>879</td>
+      <td>67</td>
+      <td>201</td>
+      <td>312</td>
+      <td>342</td>
+      <td>15</td>
+      <td>16</td>
+      <td>835</td>
+      <td>1404</td>
+      <td>103</td>
+      <td>242</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfgeno2haplo</td>
+      <td>vcfgeno2haplo</td>
+      <td>Convert genotype-based phased alleles into haplotype alleles</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfgeno2haplo</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>778</td>
+      <td>794</td>
+      <td>107</td>
+      <td>112</td>
+      <td>2414</td>
+      <td>3721</td>
+      <td>179</td>
+      <td>508</td>
+      <td>209</td>
+      <td>225</td>
+      <td>20</td>
+      <td>21</td>
+      <td>3401</td>
+      <td>4740</td>
+      <td>306</td>
+      <td>641</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfgenotypes</td>
+      <td>vcfgenotypes</td>
+      <td>Convert numerical representation of genotypes to allelic.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfgenotypes</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>502</td>
+      <td>555</td>
+      <td>134</td>
+      <td>143</td>
+      <td>3428</td>
+      <td>6338</td>
+      <td>266</td>
+      <td>858</td>
+      <td>220</td>
+      <td>235</td>
+      <td>23</td>
+      <td>24</td>
+      <td>4150</td>
+      <td>7128</td>
+      <td>423</td>
+      <td>1025</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfhethom</td>
+      <td>vcfhethom</td>
+      <td>Count the number of heterozygotes and alleles, compute het/hom ratio.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfhethom</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1964</td>
+      <td>1991</td>
+      <td>182</td>
+      <td>186</td>
+      <td>1937</td>
+      <td>3846</td>
+      <td>188</td>
+      <td>644</td>
+      <td>567</td>
+      <td>601</td>
+      <td>26</td>
+      <td>27</td>
+      <td>4468</td>
+      <td>6438</td>
+      <td>396</td>
+      <td>857</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfleftalign</td>
+      <td>vcfleftalign</td>
+      <td>Left-align indels and complex variants in VCF dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfleftalign</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>269</td>
+      <td>310</td>
+      <td>38</td>
+      <td>42</td>
+      <td>358</td>
+      <td>1071</td>
+      <td>89</td>
+      <td>287</td>
+      <td>179</td>
+      <td>213</td>
+      <td>12</td>
+      <td>14</td>
+      <td>806</td>
+      <td>1594</td>
+      <td>139</td>
+      <td>343</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfprimers</td>
+      <td>vcfprimers</td>
+      <td>Extract flanking sequences for each VCF record</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfprimers</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>590</td>
+      <td>711</td>
+      <td>28</td>
+      <td>33</td>
+      <td>403</td>
+      <td>831</td>
+      <td>75</td>
+      <td>200</td>
+      <td>190</td>
+      <td>214</td>
+      <td>10</td>
+      <td>12</td>
+      <td>1183</td>
+      <td>1756</td>
+      <td>113</td>
+      <td>245</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfrandomsample</td>
+      <td>vcfrandomsample</td>
+      <td>Randomly sample sites from VCF dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfrandomsample</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>161</td>
+      <td>168</td>
+      <td>13</td>
+      <td>15</td>
+      <td>153</td>
+      <td>350</td>
+      <td>27</td>
+      <td>75</td>
+      <td>184</td>
+      <td>192</td>
+      <td>6</td>
+      <td>6</td>
+      <td>498</td>
+      <td>710</td>
+      <td>46</td>
+      <td>96</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfselectsamples</td>
+      <td>vcfselectsamples</td>
+      <td>Select samples from a VCF file</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfselectsamples</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>830</td>
+      <td>900</td>
+      <td>69</td>
+      <td>88</td>
+      <td>1315</td>
+      <td>6257</td>
+      <td>237</td>
+      <td>959</td>
+      <td>344</td>
+      <td>363</td>
+      <td>20</td>
+      <td>21</td>
+      <td>2489</td>
+      <td>7520</td>
+      <td>326</td>
+      <td>1068</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfsort</td>
+      <td>vcfsort</td>
+      <td>Sort VCF dataset by coordinate</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfsort</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1868</td>
+      <td>1904</td>
+      <td>174</td>
+      <td>185</td>
+      <td>18378</td>
+      <td>24175</td>
+      <td>422</td>
+      <td>1279</td>
+      <td>537</td>
+      <td>674</td>
+      <td>70</td>
+      <td>73</td>
+      <td>20783</td>
+      <td>26753</td>
+      <td>666</td>
+      <td>1537</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_annotate</td>
+      <td>vcftools_annotate</td>
+      <td>Annotate VCF using custom/user-defined annotations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_annotate</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate</td>
+      <td>0.1</td>
+      <td>echo</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>155</td>
+      <td>192</td>
+      <td>81</td>
+      <td>90</td>
+      <td>1853</td>
+      <td>3943</td>
+      <td>581</td>
+      <td>1280</td>
+      <td>144</td>
+      <td>156</td>
+      <td>13</td>
+      <td>16</td>
+      <td>2152</td>
+      <td>4291</td>
+      <td>675</td>
+      <td>1386</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_compare</td>
+      <td>vcftools_compare</td>
+      <td>Compare VCF files to get overlap and uniqueness statistics</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_compare</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare</td>
+      <td>0.1</td>
+      <td>tabix</td>
+      <td>1.11</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>440</td>
+      <td>594</td>
+      <td>127</td>
+      <td>142</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>16</td>
+      <td>0</td>
+      <td>12</td>
+      <td>440</td>
+      <td>610</td>
+      <td>127</td>
+      <td>154</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_consensus</td>
+      <td>vcftools_consensus</td>
+      <td>Apply VCF variants to a fasta file to create consensus sequence</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_consensus</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus</td>
+      <td>0.1.11</td>
+      <td>samtools</td>
+      <td>1.21</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_isec</td>
+      <td>vcftools_isec</td>
+      <td>Intersect multiple VCF datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_isec</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec</td>
+      <td>0.1.1</td>
+      <td>tabix</td>
+      <td>1.11</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>379</td>
+      <td>537</td>
+      <td>104</td>
+      <td>118</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>39</td>
+      <td>496</td>
+      <td>28</td>
+      <td>48</td>
+      <td>418</td>
+      <td>1034</td>
+      <td>132</td>
+      <td>167</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_merge</td>
+      <td>vcftools_merge</td>
+      <td>Merge multiple VCF datasets into a single dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_merge</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge</td>
+      <td>0.1.11</td>
+      <td>tabix</td>
+      <td>1.11</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>817</td>
+      <td>1084</td>
+      <td>244</td>
+      <td>273</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>93</td>
+      <td>448</td>
+      <td>44</td>
+      <td>60</td>
+      <td>910</td>
+      <td>1532</td>
+      <td>288</td>
+      <td>333</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_slice</td>
+      <td>vcftools_slice</td>
+      <td>Subset VCF dataset by genomic regions</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_slice</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice</td>
+      <td>0.1</td>
+      <td>echo</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>410</td>
+      <td>423</td>
+      <td>56</td>
+      <td>60</td>
+      <td>6261</td>
+      <td>8115</td>
+      <td>133</td>
+      <td>362</td>
+      <td>127</td>
+      <td>157</td>
+      <td>10</td>
+      <td>19</td>
+      <td>6798</td>
+      <td>8695</td>
+      <td>199</td>
+      <td>441</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcftools_subset</td>
+      <td>vcftools_subset</td>
+      <td>Select samples from a VCF dataset</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://vcftools.github.io/</td>
+      <td>Variant Analysis</td>
+      <td>vcftools_subset</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset</td>
+      <td>0.1</td>
+      <td>tabix</td>
+      <td>1.11</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>134</td>
+      <td>142</td>
+      <td>46</td>
+      <td>49</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>120</td>
+      <td>142</td>
+      <td>12</td>
+      <td>19</td>
+      <td>254</td>
+      <td>284</td>
+      <td>58</td>
+      <td>68</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vcfvcfintersect</td>
+      <td>vcfvcfintersect</td>
+      <td>Intersect two VCF datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/ekg/vcflib</td>
+      <td>Variant Analysis</td>
+      <td>vcfvcfintersect</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect</td>
+      <td></td>
+      <td>vcflib</td>
+      <td>1.0.10</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>976544</td>
+      <td>977015</td>
+      <td>703</td>
+      <td>748</td>
+      <td>64155</td>
+      <td>81830</td>
+      <td>981</td>
+      <td>2103</td>
+      <td>11044</td>
+      <td>11069</td>
+      <td>225</td>
+      <td>229</td>
+      <td>1051743</td>
+      <td>1069914</td>
+      <td>1909</td>
+      <td>3080</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vegan</td>
+      <td>vegan_diversity, vegan_fisher_alpha, vegan_rarefaction</td>
+      <td>an R package fo community ecologist</td>
+      <td>vegan</td>
+      <td>vegan</td>
+      <td></td>
+      <td>vegan</td>
+      <td>Ordination methods, diversity analysis and other functions for community and vegetation ecologists</td>
+      <td>Standardisation and normalisation, Analysis</td>
+      <td>Ecology, Phylogenetics, Environmental science</td>
+      <td>To update</td>
+      <td>https://cran.r-project.org/package=vegan</td>
+      <td>Metagenomics</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan</td>
+      <td>2.4-3</td>
+      <td>r-vegan</td>
+      <td>2.3_4</td>
+      <td>Standardisation and normalisation, Analysis</td>
+      <td>Ecology, Phylogenetics, Environmental science</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>2157</td>
+      <td>2287</td>
+      <td>198</td>
+      <td>209</td>
+      <td>3930</td>
+      <td>5591</td>
+      <td>446</td>
+      <td>744</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6087</td>
+      <td>7878</td>
+      <td>644</td>
+      <td>953</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>velocyto</td>
+      <td>velocyto_cli</td>
+      <td>Velocyto is a library for the analysis of RNA velocity.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>http://velocyto.org/</td>
+      <td>Transcriptomics, Single Cell</td>
+      <td>velocyto</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto</td>
+      <td>0.17.17</td>
+      <td>velocyto.py</td>
+      <td>0.17.17</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>4</td>
+      <td>4</td>
+      <td>22</td>
+      <td>22</td>
+      <td>6</td>
+      <td>6</td>
+      <td>16</td>
+      <td>16</td>
+      <td>1</td>
+      <td>1</td>
+      <td>45</td>
+      <td>45</td>
+      <td>11</td>
+      <td>11</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>velvet</td>
+      <td>velvetg, velveth</td>
+      <td>de novo genomic assembler specially designed for short read sequencing technologies</td>
+      <td>velvet</td>
+      <td>velvet</td>
+      <td></td>
+      <td>Velvet</td>
+      <td>A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.</td>
+      <td>Formatting, De-novo assembly</td>
+      <td>Sequence assembly</td>
+      <td>To update</td>
+      <td>https://www.ebi.ac.uk/~zerbino/velvet/</td>
+      <td>Assembly</td>
+      <td>velvet</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet</td>
+      <td></td>
+      <td>velvet</td>
+      <td>1.2.10</td>
+      <td>Formatting, De-novo assembly</td>
+      <td>Sequence assembly</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>25171</td>
+      <td>27943</td>
+      <td>3899</td>
+      <td>4270</td>
+      <td>51187</td>
+      <td>51187</td>
+      <td>7557</td>
+      <td>7557</td>
+      <td>28546</td>
+      <td>28619</td>
+      <td>3585</td>
+      <td>3613</td>
+      <td>104904</td>
+      <td>107749</td>
+      <td>15041</td>
+      <td>15440</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>velvet_optimiser</td>
+      <td>velvetoptimiser</td>
+      <td>Automatically optimize Velvet assemblies</td>
+      <td>velvetoptimiser</td>
+      <td>velvetoptimiser</td>
+      <td></td>
+      <td>VelvetOptimiser</td>
+      <td>This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.</td>
+      <td>Optimisation and refinement, Sequence assembly</td>
+      <td>Genomics, Sequence assembly</td>
+      <td>To update</td>
+      <td></td>
+      <td>Assembly</td>
+      <td>velvetoptimiser</td>
+      <td>simon-gladman</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser</td>
+      <td>2.2.6+galaxy2</td>
+      <td>velvet</td>
+      <td>1.2.10</td>
+      <td>Optimisation and refinement, Sequence assembly</td>
+      <td>Genomics, Sequence assembly</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4715</td>
+      <td>5343</td>
+      <td>888</td>
+      <td>965</td>
+      <td>9575</td>
+      <td>9576</td>
+      <td>2117</td>
+      <td>2117</td>
+      <td>3271</td>
+      <td>5524</td>
+      <td>1050</td>
+      <td>1397</td>
+      <td>17561</td>
+      <td>20443</td>
+      <td>4055</td>
+      <td>4479</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>venn_list</td>
+      <td>venn_list</td>
+      <td>Draw Venn Diagram (PDF) from lists, FASTA files, etc</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list</td>
+      <td>Graphics, Sequence Analysis, Visualization</td>
+      <td>venn_list</td>
+      <td>peterjc</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list</td>
+      <td>https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list</td>
+      <td>0.1.2</td>
+      <td>galaxy_sequence_utils</td>
+      <td>1.2.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4519</td>
+      <td>5476</td>
+      <td>667</td>
+      <td>730</td>
+      <td>9858</td>
+      <td>18420</td>
+      <td>986</td>
+      <td>2010</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14377</td>
+      <td>23896</td>
+      <td>1653</td>
+      <td>2740</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>verify_map</td>
+      <td>verify_map</td>
+      <td>Checks the mapping quality of all BAM(s)</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://snvphyl.readthedocs.io/en/latest/</td>
+      <td>Sequence Analysis</td>
+      <td>verify_map</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy</td>
+      <td>https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map</td>
+      <td>1.8.2</td>
+      <td>snvphyl-tools</td>
+      <td>1.8.2</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>verkko</td>
+      <td>verkko</td>
+      <td>Telomere-to-telomere assembly pipeline</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/marbl/verkko</td>
+      <td>Assembly</td>
+      <td>verkko</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko</td>
+      <td>1.3.1</td>
+      <td>verkko</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>25</td>
+      <td>25</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>48</td>
+      <td>48</td>
+      <td>25</td>
+      <td>25</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vg</td>
+      <td>vg_convert, vg_deconstruct, vg_view</td>
+      <td>Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/vgteam/vg</td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td></td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg</td>
+      <td>1.23.0</td>
+      <td>vg</td>
+      <td>1.59.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>478</td>
+      <td>478</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>478</td>
+      <td>478</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vibrant</td>
+      <td>vibrant</td>
+      <td>Virus Identification By iteRative ANnoTation</td>
+      <td>VIBRANT</td>
+      <td>VIBRANT</td>
+      <td></td>
+      <td>VIBRANT</td>
+      <td>Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions</td>
+      <td>Sequence trimming, Scaffolding, Genome annotation</td>
+      <td>Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/AnantharamanLab/VIBRANT</td>
+      <td>Metagenomics</td>
+      <td>vibrant</td>
+      <td>ufz</td>
+      <td>https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant</td>
+      <td>1.2.1</td>
+      <td>vibrant</td>
+      <td>1.2.1</td>
+      <td>Sequence trimming, Scaffolding, Genome annotation</td>
+      <td>Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vienna_rna</td>
+      <td>viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup</td>
+      <td>ViennaRNA - Prediction and comparison of RNA secondary structures</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://www.tbi.univie.ac.at/RNA/</td>
+      <td>RNA</td>
+      <td>viennarna</td>
+      <td>rnateam</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna</td>
+      <td>2.2.10</td>
+      <td>viennarna</td>
+      <td>2.6.4</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>21</td>
+      <td>21</td>
+      <td>0</td>
+      <td>3197</td>
+      <td>8107</td>
+      <td>344</td>
+      <td>415</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3197</td>
+      <td>8107</td>
+      <td>344</td>
+      <td>415</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vigiechiro</td>
+      <td>vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid</td>
+      <td>Tools created by the vigiechiro team to analyses and identify chiro sounds files.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro</td>
+      <td>Ecology</td>
+      <td>vigiechiro</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro</td>
+      <td>0.1.1</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>14412</td>
+      <td>14590</td>
+      <td>722</td>
+      <td>732</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>14412</td>
+      <td>14590</td>
+      <td>722</td>
+      <td>732</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>virAnnot</td>
+      <td>virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv</td>
+      <td>virAnnot wrappers</td>
+      <td>virannot</td>
+      <td>virannot</td>
+      <td></td>
+      <td>virAnnot</td>
+      <td>VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project "Plant Health Bioinformatics Network". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy.</td>
+      <td>Sequence annotation, Sequence clustering, Sequence cluster visualisation</td>
+      <td>Metagenomics, Virology, Microbial ecology</td>
+      <td>To update</td>
+      <td>https://github.com/marieBvr/virAnnot</td>
+      <td>Metagenomics</td>
+      <td>virannot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot</td>
+      <td>1.1.0+galaxy0</td>
+      <td>biopython</td>
+      <td>1.70</td>
+      <td>Sequence annotation, Sequence clustering, Sequence cluster visualisation</td>
+      <td>Metagenomics, Virology, Microbial ecology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>94</td>
+      <td>94</td>
+      <td>16</td>
+      <td>16</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>94</td>
+      <td>94</td>
+      <td>16</td>
+      <td>16</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>virheat</td>
+      <td>virheat</td>
+      <td>generates a heatmap of allele frequencies from vcf files</td>
+      <td>virheat</td>
+      <td>virheat</td>
+      <td></td>
+      <td>virHEAT</td>
+      <td>VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.</td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/jonas-fuchs/virHEAT</td>
+      <td>Visualization, Variant Analysis</td>
+      <td>virheat</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat</td>
+      <td>0.7.1</td>
+      <td>virheat</td>
+      <td>0.7.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>12</td>
+      <td>12</td>
+      <td>2</td>
+      <td>2</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>virhunter</td>
+      <td>virhunter</td>
+      <td>Deep Learning method for novel virus detection in sequencing data</td>
+      <td>virhunter</td>
+      <td>virhunter</td>
+      <td></td>
+      <td>VirHunter</td>
+      <td>VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).</td>
+      <td>Sequence classification</td>
+      <td>Virology</td>
+      <td>To update</td>
+      <td>https://github.com/cbib/virhunter</td>
+      <td>Machine Learning</td>
+      <td>virhunter</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter</td>
+      <td>1.0.0</td>
+      <td>numpy</td>
+      <td></td>
+      <td>Sequence classification</td>
+      <td>Virology</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>574</td>
+      <td>574</td>
+      <td>76</td>
+      <td>76</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>574</td>
+      <td>574</td>
+      <td>76</td>
+      <td>76</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>virsorter</td>
+      <td>virsorter</td>
+      <td>VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.</td>
+      <td>virsorter</td>
+      <td>virsorter</td>
+      <td></td>
+      <td>virsorter</td>
+      <td>Identify DNA and RNA virus sequences.</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/jiarong/VirSorter2/</td>
+      <td>Metagenomics</td>
+      <td>virsorter</td>
+      <td>ufz</td>
+      <td>https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter</td>
+      <td>https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter</td>
+      <td>2.2.4</td>
+      <td>virsorter</td>
+      <td>2.2.4</td>
+      <td>Taxonomic classification</td>
+      <td>Metagenomics</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>visceral_evaluatesegmentation</td>
+      <td>ip_visceral_evaluatesegmentation</td>
+      <td>Visceral Project - Evaluate Segmentation Tool</td>
+      <td></td>
+      <td></td>
+      <td>evaluatesegmentation-tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>visceral_evaluatesegmentation</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation</td>
+      <td>0.5-2</td>
+      <td>visceral-evaluatesegmentation</td>
+      <td>2015.07.03</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>20</td>
+      <td>25</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>20</td>
+      <td>25</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vmd</td>
+      <td></td>
+      <td>vmd is a package for  visualizing and analyzing trajectories from molecular dynamics (MD) simulations</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.ks.uiuc.edu/Research/vmd/</td>
+      <td>Computational chemistry</td>
+      <td>vmd</td>
+      <td>chemteam</td>
+      <td>https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd</td>
+      <td>https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>volcanoplot</td>
+      <td>volcanoplot</td>
+      <td>Tool to create a Volcano Plot</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://ggplot2.tidyverse.org/</td>
+      <td>Visualization, Transcriptomics, Statistics</td>
+      <td>volcanoplot</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot</td>
+      <td>0.0.6</td>
+      <td>r-ggplot2</td>
+      <td>2.2.1</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>34917</td>
+      <td>36852</td>
+      <td>3670</td>
+      <td>3786</td>
+      <td>54931</td>
+      <td>54931</td>
+      <td>5597</td>
+      <td>5597</td>
+      <td>7183</td>
+      <td>7183</td>
+      <td>905</td>
+      <td>905</td>
+      <td>97031</td>
+      <td>98966</td>
+      <td>10172</td>
+      <td>10288</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>voronoi_tessellation</td>
+      <td>voronoi_tessellation</td>
+      <td>Compute Voronoi tesselation</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>scikit-image</td>
+      <td>Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.</td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>voronoi_tesselation</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation</td>
+      <td>0.22.0</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td>Image analysis, Image annotation, Visualisation, Data handling</td>
+      <td>Imaging, Software engineering, Literature and language</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>3</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vsearch</td>
+      <td>vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting</td>
+      <td>VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.</td>
+      <td>vsearch</td>
+      <td>vsearch</td>
+      <td></td>
+      <td>VSEARCH</td>
+      <td>High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.</td>
+      <td>DNA mapping, Chimera detection</td>
+      <td>Metagenomics, Sequence analysis</td>
+      <td>To update</td>
+      <td>https://github.com/torognes/vsearch</td>
+      <td>Sequence Analysis</td>
+      <td>vsearch</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch</td>
+      <td>2.8.3</td>
+      <td>vsearch</td>
+      <td>2.29.0</td>
+      <td>DNA mapping, Chimera detection</td>
+      <td>Metagenomics, Sequence analysis</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>8</td>
+      <td>8</td>
+      <td>8</td>
+      <td>0</td>
+      <td>9694</td>
+      <td>10338</td>
+      <td>559</td>
+      <td>628</td>
+      <td>12282</td>
+      <td>53546</td>
+      <td>1031</td>
+      <td>2007</td>
+      <td>5334</td>
+      <td>5672</td>
+      <td>246</td>
+      <td>277</td>
+      <td>27310</td>
+      <td>69556</td>
+      <td>1836</td>
+      <td>2912</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vsnp</td>
+      <td>vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics</td>
+      <td>The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/USDA-VS/vSNP</td>
+      <td>Sequence Analysis</td>
+      <td>vsnp</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp</td>
+      <td>3.0.6</td>
+      <td>pysam</td>
+      <td>0.22.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>vt</td>
+      <td>vt_@BINARY@, vt_@BINARY@</td>
+      <td>A tool set for short variant discovery in genetic sequence data.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>vt</td>
+      <td>bgruening</td>
+      <td>https://github.com/atks/vt</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/vt</td>
+      <td>0.2</td>
+      <td>vt</td>
+      <td>2015.11.10</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>w4mclassfilter</td>
+      <td>w4mclassfilter</td>
+      <td>Filter W4M data by values or metadata</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper</td>
+      <td>Metabolomics</td>
+      <td>w4mclassfilter</td>
+      <td>eschen42</td>
+      <td>https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master</td>
+      <td>https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter</td>
+      <td>0.98.19</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2370</td>
+      <td>2836</td>
+      <td>9</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1482</td>
+      <td>1509</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3852</td>
+      <td>4345</td>
+      <td>13</td>
+      <td>14</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>w4mconcatenate</td>
+      <td>W4Mconcatenate</td>
+      <td>[W4M][Utils] concatenate two Metadata tables</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://workflow4metabolomics.org</td>
+      <td>Metabolomics</td>
+      <td>w4mconcatenate</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate</td>
+      <td>1.0.0+galaxy0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>w4mcorcov</td>
+      <td>w4mcorcov</td>
+      <td>OPLS-DA Contrasts of Univariate Results</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper</td>
+      <td>Metabolomics</td>
+      <td>w4mcorcov</td>
+      <td>eschen42</td>
+      <td>https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master</td>
+      <td>https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov</td>
+      <td>0.98.18</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>238</td>
+      <td>375</td>
+      <td>10</td>
+      <td>10</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>10</td>
+      <td>10</td>
+      <td>2</td>
+      <td>2</td>
+      <td>248</td>
+      <td>385</td>
+      <td>12</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>w4mjoinpn</td>
+      <td>w4mjoinpn</td>
+      <td>Join positive- and negative-mode W4M datasets</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper</td>
+      <td>Metabolomics</td>
+      <td>w4mjoinpn</td>
+      <td>eschen42</td>
+      <td>https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master</td>
+      <td>https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn</td>
+      <td>0.98.2</td>
+      <td>coreutils</td>
+      <td>8.25</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>150</td>
+      <td>171</td>
+      <td>7</td>
+      <td>7</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>7</td>
+      <td>7</td>
+      <td>2</td>
+      <td>2</td>
+      <td>157</td>
+      <td>178</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>wade</td>
+      <td>wade</td>
+      <td>identify regions of interest</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/phac-nml/wade</td>
+      <td>Sequence Analysis</td>
+      <td>wade</td>
+      <td>nml</td>
+      <td>https://github.com/phac-nml/wade</td>
+      <td>https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade</td>
+      <td>0.2.5+galaxy1</td>
+      <td>wade</td>
+      <td>0.2.6</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>waveica</td>
+      <td>waveica</td>
+      <td>Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.</td>
+      <td>waveica</td>
+      <td>waveica</td>
+      <td></td>
+      <td>WaveICA</td>
+      <td>Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.</td>
+      <td>Standardisation and normalisation</td>
+      <td>Metabolomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/RECETOX/WaveICA</td>
+      <td>Metabolomics</td>
+      <td></td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/waveica</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/waveica</td>
+      <td>0.2.0</td>
+      <td>r-recetox-waveica</td>
+      <td>0.2.0</td>
+      <td>Standardisation and normalisation</td>
+      <td>Metabolomics</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>39</td>
+      <td>39</td>
+      <td>6</td>
+      <td>6</td>
+      <td>4</td>
+      <td>4</td>
+      <td>3</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>43</td>
+      <td>43</td>
+      <td>9</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>weather_app</td>
+      <td>simple_weather</td>
+      <td>provides simple weather in text format</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://wttr.in/</td>
+      <td>Visualization, Web Services</td>
+      <td>simpleweather</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app</td>
+      <td>0.1.2</td>
+      <td>curl</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>weblogo3</td>
+      <td>rgweblogo3</td>
+      <td>Sequence Logo generator for fasta</td>
+      <td>weblogo</td>
+      <td>weblogo</td>
+      <td></td>
+      <td>WebLogo</td>
+      <td>Web-based application designed to make generate sequence logos.</td>
+      <td>Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition</td>
+      <td>Nucleic acid sites, features and motifs, Sequence analysis</td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics</td>
+      <td>weblogo3</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3</td>
+      <td>3.5.0</td>
+      <td>weblogo</td>
+      <td>3.7.9</td>
+      <td>Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition</td>
+      <td>Nucleic acid sites, features and motifs, Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>2720</td>
+      <td>2818</td>
+      <td>206</td>
+      <td>228</td>
+      <td>10299</td>
+      <td>30578</td>
+      <td>1354</td>
+      <td>3657</td>
+      <td>1226</td>
+      <td>1285</td>
+      <td>50</td>
+      <td>59</td>
+      <td>14245</td>
+      <td>34681</td>
+      <td>1610</td>
+      <td>3944</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>weightedaverage</td>
+      <td>wtavg</td>
+      <td>Assign weighted-average of the values of features overlapping an interval</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>weightedaverage</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage</td>
+      <td>1.0.1</td>
+      <td>galaxy-ops</td>
+      <td>1.1.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>227</td>
+      <td>2307</td>
+      <td>17</td>
+      <td>75</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>227</td>
+      <td>2307</td>
+      <td>17</td>
+      <td>75</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>whisper</td>
+      <td>whisper</td>
+      <td>Transcribe audio or video files to text using the OpenAI Whisper.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/whisper</td>
+      <td>Machine Learning</td>
+      <td>whisper</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/whisper</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/whisper</td>
+      <td>20231117</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>96</td>
+      <td>96</td>
+      <td>13</td>
+      <td>13</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>96</td>
+      <td>96</td>
+      <td>13</td>
+      <td>13</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>wigtobigwig</td>
+      <td>ucsc_wigtobigwig</td>
+      <td>converts bedGraph (wig) files into binary bigwig</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td>UCSC_Genome_Browser_Utilities</td>
+      <td></td>
+      <td>UCSC Genome Browser Utilities</td>
+      <td>Utilities for handling sequences and assemblies from the UCSC Genome Browser project.</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>Up-to-date</td>
+      <td>https://genome.ucsc.edu/goldenPath/help/bigWig.html</td>
+      <td>Convert Formats</td>
+      <td>ucsc_wigtobigwig</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig</td>
+      <td>469</td>
+      <td>ucsc-wigtobigwig</td>
+      <td>469</td>
+      <td></td>
+      <td>Sequence analysis</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1601</td>
+      <td>1601</td>
+      <td>106</td>
+      <td>106</td>
+      <td>1108</td>
+      <td>1108</td>
+      <td>172</td>
+      <td>172</td>
+      <td>200</td>
+      <td>200</td>
+      <td>15</td>
+      <td>15</td>
+      <td>2909</td>
+      <td>2909</td>
+      <td>293</td>
+      <td>293</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>windowmasker</td>
+      <td>windowmasker_mkcounts, windowmasker_ustat</td>
+      <td>Identify repetitive regions using WindowMasker</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/</td>
+      <td>Sequence Analysis</td>
+      <td>windowmasker</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker</td>
+      <td>1.0</td>
+      <td>blast</td>
+      <td>2.16.0</td>
+      <td></td>
+      <td></td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>2</td>
+      <td>2</td>
+      <td>2</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>537</td>
+      <td>537</td>
+      <td>19</td>
+      <td>19</td>
+      <td>12</td>
+      <td>12</td>
+      <td>7</td>
+      <td>7</td>
+      <td>297</td>
+      <td>297</td>
+      <td>2</td>
+      <td>2</td>
+      <td>846</td>
+      <td>846</td>
+      <td>28</td>
+      <td>28</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>windowsplitter</td>
+      <td>winSplitter</td>
+      <td>Make windows</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Sequence Analysis, Variant Analysis</td>
+      <td>windowsplitter</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter</td>
+      <td>1.0.1</td>
+      <td>bx-python</td>
+      <td>0.13.0</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>11</td>
+      <td>0</td>
+      <td>2</td>
+      <td>171</td>
+      <td>3961</td>
+      <td>34</td>
+      <td>328</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>171</td>
+      <td>3972</td>
+      <td>34</td>
+      <td>330</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>winnowmap</td>
+      <td>winnowmap</td>
+      <td>A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/marbl/Winnowmap</td>
+      <td>Next Gen Mappers</td>
+      <td>winnowmap</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap</td>
+      <td>2.03</td>
+      <td>winnowmap</td>
+      <td>2.03</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>279</td>
+      <td>279</td>
+      <td>46</td>
+      <td>46</td>
+      <td>12</td>
+      <td>12</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>291</td>
+      <td>291</td>
+      <td>50</td>
+      <td>50</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>woundhealing</td>
+      <td>woundhealing_scratch_assay</td>
+      <td>Tool to automate quantification of wound healing in high-throughput microscopy scratch assays</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://git.embl.de/grp-cba/wound-healing-htm-screen</td>
+      <td>Imaging</td>
+      <td>Wound healing scratch assay image analysis</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing</td>
+      <td>1.6.1</td>
+      <td>fiji-morpholibj</td>
+      <td>1.6.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>31</td>
+      <td>31</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>wsi_extract_top_view</td>
+      <td>ip_wsi_extract_top_view</td>
+      <td>WSI Extract Top View</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/bmcv</td>
+      <td>Imaging</td>
+      <td>wsi_extract_top_view</td>
+      <td>imgteam</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/</td>
+      <td>https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view</td>
+      <td>0.2-2</td>
+      <td>scikit-image</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>32</td>
+      <td>38</td>
+      <td>2</td>
+      <td>3</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>32</td>
+      <td>38</td>
+      <td>2</td>
+      <td>3</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>wtdbg</td>
+      <td>wtdbg</td>
+      <td>WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.</td>
+      <td>wtdbg2</td>
+      <td>wtdbg2</td>
+      <td></td>
+      <td>wtdbg2</td>
+      <td>Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.</td>
+      <td>Genome assembly, De-novo assembly</td>
+      <td>Sequence assembly, Sequencing</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/ruanjue/wtdbg2</td>
+      <td>Assembly</td>
+      <td>wtdbg</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg</td>
+      <td>2.5</td>
+      <td>wtdbg</td>
+      <td>2.5</td>
+      <td>Genome assembly, De-novo assembly</td>
+      <td>Sequence assembly, Sequencing</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1619</td>
+      <td>1715</td>
+      <td>337</td>
+      <td>376</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1619</td>
+      <td>1715</td>
+      <td>337</td>
+      <td>376</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xarray</td>
+      <td>timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select</td>
+      <td>xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://xarray.pydata.org</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray</td>
+      <td>2022.3.0</td>
+      <td>xarray</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>5</td>
+      <td>2</td>
+      <td>6</td>
+      <td>0</td>
+      <td>5</td>
+      <td>2</td>
+      <td>6</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>2</td>
+      <td>0</td>
+      <td>5995</td>
+      <td>5995</td>
+      <td>275</td>
+      <td>275</td>
+      <td>66</td>
+      <td>66</td>
+      <td>23</td>
+      <td>23</td>
+      <td>295</td>
+      <td>295</td>
+      <td>3</td>
+      <td>3</td>
+      <td>6356</td>
+      <td>6356</td>
+      <td>301</td>
+      <td>301</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xcms</td>
+      <td>abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw</td>
+      <td></td>
+      <td>XCMS</td>
+      <td>XCMS</td>
+      <td></td>
+      <td>xcms</td>
+      <td>Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data.  The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling.</td>
+      <td>Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation</td>
+      <td>Biological imaging, Data visualisation, Metabolomics</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/sneumann/xcms</td>
+      <td>Metabolomics</td>
+      <td>xcms</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/</td>
+      <td>https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms</td>
+      <td>4.0.0</td>
+      <td>bioconductor-xcms</td>
+      <td>4.0.0</td>
+      <td>Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation</td>
+      <td>Data visualisation, Metabolomics</td>
+      <td>9</td>
+      <td>11</td>
+      <td>12</td>
+      <td>0</td>
+      <td>9</td>
+      <td>11</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>6</td>
+      <td>10</td>
+      <td>9</td>
+      <td>0</td>
+      <td>31909</td>
+      <td>35790</td>
+      <td>1357</td>
+      <td>1384</td>
+      <td>7099</td>
+      <td>7099</td>
+      <td>413</td>
+      <td>413</td>
+      <td>5333</td>
+      <td>5357</td>
+      <td>330</td>
+      <td>330</td>
+      <td>44341</td>
+      <td>48246</td>
+      <td>2100</td>
+      <td>2127</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xmlstarlet</td>
+      <td>xmlstarlet</td>
+      <td>Tool to convert a xml file from one metadata standard to another</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Convert Formats</td>
+      <td>xmlstarlet</td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet</td>
+      <td>1.6.1</td>
+      <td>xmlstarlet</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59</td>
+      <td>59</td>
+      <td>17</td>
+      <td>17</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>59</td>
+      <td>59</td>
+      <td>17</td>
+      <td>17</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xpath</td>
+      <td>xpath</td>
+      <td>XPath XML querying tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://search.cpan.org/dist/XML-XPath/</td>
+      <td>Text Manipulation</td>
+      <td>xpath</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath</td>
+      <td></td>
+      <td>perl-xml-xpath</td>
+      <td>1.47</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>128</td>
+      <td>235</td>
+      <td>7</td>
+      <td>8</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>128</td>
+      <td>236</td>
+      <td>7</td>
+      <td>9</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xpore</td>
+      <td>xpore_dataprep, xpore_diffmod</td>
+      <td>Identification and quantification of differential RNA modifications from direct RNA sequencing</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/GoekeLab/xpore</td>
+      <td>Nanopore</td>
+      <td>xpore</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore</td>
+      <td>2.1+galaxy0</td>
+      <td>xpore</td>
+      <td>2.1</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xtb</td>
+      <td>xtb_molecular_optimization</td>
+      <td>Performs semiempirical molecular optimization.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/grimme-lab/xtb</td>
+      <td>Metabolomics</td>
+      <td>xtb_molecular_optimization</td>
+      <td>recetox</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/xtb</td>
+      <td>https://github.com/RECETOX/galaxytools/tree/master/tools/xtb</td>
+      <td>6.6.1</td>
+      <td>xtb</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>143</td>
+      <td>143</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>143</td>
+      <td>143</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>xy_plot</td>
+      <td>XY_Plot_1</td>
+      <td>Plotting tool for multiple series and graph types</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td></td>
+      <td>Graphics, Statistics</td>
+      <td>xy_plot</td>
+      <td>devteam</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot</td>
+      <td>https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot</td>
+      <td>1.0.2</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>4490</td>
+      <td>6169</td>
+      <td>768</td>
+      <td>889</td>
+      <td>6120</td>
+      <td>15516</td>
+      <td>1921</td>
+      <td>3653</td>
+      <td>2033</td>
+      <td>2212</td>
+      <td>556</td>
+      <td>590</td>
+      <td>12643</td>
+      <td>23897</td>
+      <td>3245</td>
+      <td>5132</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>yac_clipper</td>
+      <td>yac</td>
+      <td>Clips 3' adapters for small RNA sequencing reads.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>http://artbio.fr</td>
+      <td>RNA, Fastq Manipulation</td>
+      <td>yac_clipper</td>
+      <td>artbio</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper</td>
+      <td>2.5.1</td>
+      <td>python</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>yahs</td>
+      <td>yahs</td>
+      <td>Yet Another Hi-C scaffolding tool</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/c-zhou/yahs</td>
+      <td>Assembly</td>
+      <td>yahs</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs</td>
+      <td>1.2a.2</td>
+      <td>yahs</td>
+      <td>1.2.2</td>
+      <td></td>
+      <td></td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>618</td>
+      <td>618</td>
+      <td>176</td>
+      <td>176</td>
+      <td>336</td>
+      <td>336</td>
+      <td>62</td>
+      <td>62</td>
+      <td>588</td>
+      <td>588</td>
+      <td>25</td>
+      <td>25</td>
+      <td>1542</td>
+      <td>1542</td>
+      <td>263</td>
+      <td>263</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>zeiss_lmd_converter</td>
+      <td>ZeissLMDconverter</td>
+      <td>Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter</td>
+      <td>Proteomics</td>
+      <td></td>
+      <td>galaxyp</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter</td>
+      <td>https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter</td>
+      <td>2.0.4</td>
+      <td>shapely</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1</td>
+      <td>1</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>zerone</td>
+      <td>zerone</td>
+      <td>ChIP-seq discretization and quality control</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/nanakiksc/zerone</td>
+      <td>ChIP-seq</td>
+      <td>zerone</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone</td>
+      <td>1.0</td>
+      <td>zerone</td>
+      <td>1.0</td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>0</td>
+      <td>83</td>
+      <td>96</td>
+      <td>9</td>
+      <td>12</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>83</td>
+      <td>96</td>
+      <td>9</td>
+      <td>12</td>
+      <td></td>
+    </tr>
+    <tr>
+      <td></td>
+      <td>zoo_project_ogc_api_processes</td>
+      <td>zoo_project_ogc_api_processes</td>
+      <td>This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/AquaINFRA/galaxy</td>
+      <td>Ecology</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper</td>
+      <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes</td>
+      <td>0.1.0</td>
+      <td>r-base</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>1</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>4</td>
+      <td>4</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>26</td>
+      <td>26</td>
+      <td>4</td>
+      <td>4</td>
+      <td></td>
+    </tr>
+  </tbody>
+</table>
+
+</div>
\ No newline at end of file
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+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+10x_bamtofastq	10x_bamtofastq	Converts 10x Genomics BAM to FASTQ								Up-to-date	https://github.com/10XGenomics/bamtofastq	Convert Formats	10x_bamtofastq	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	1.4.1	10x_bamtofastq	1.4.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	307	307	80	80	8	8	3	3	3	3	1	1	318	318	84	84	False		
+2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1434	6746	120	122	0	0	0	0	305	305	11	11	1739	7051	131	133	False		
+2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1156	13842	40	42	0	0	0	0	121	121	4	4	1277	13963	44	46	False		
+2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	591	6863	38	40	0	0	0	0	119	119	3	3	710	6982	41	43	False		
+2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	762	782	100	101	0	0	0	0	230	230	14	14	992	1012	114	115	False		
+2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	948	6261	98	100	0	0	0	0	153	153	13	13	1101	6414	111	113	False		
+AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	119	14	17	0	0	0	0	0	0	0	0	45	119	14	17	False		
+AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	189	3094	23	25	0	0	0	0	0	0	0	0	189	3094	23	25	False		
+CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25532	50045	45	57	0	0	0	0	0	0	0	0	25532	50045	45	57	False		
+CollectResults	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1119	2115	50	62	0	0	0	0	0	0	0	0	1119	2115	50	62	False		
+CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	108	1	3	0	0	0	0	0	0	0	0	37	108	1	3	False		
+EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	516	516	128	128	0	0	0	0	0	0	0	0	516	516	128	128	False		
+Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	352	352	36	36	0	0	0	0	0	0	0	0	352	352	36	36	False		
+Ensembl-REST	get_feature_info, get_genetree, get_sequences	A suite of Galaxy tools designed to work with Ensembl REST API.								To update	https://rest.ensembl.org	Data Source		earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	0.1.2	requests				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	474	2914	132	163	0	0	0	0	0	0	0	0	474	2914	132	163	False		
+GAFA	gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	47	6	6	0	0	0	0	0	0	0	0	40	47	6	6	False		
+GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	80	150	18	23	0	0	0	0	0	0	0	0	80	150	18	23	False		
+Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	53	53	18	18	0	0	0	0	0	0	0	0	53	53	18	18	False		
+LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25572	50177	45	57	0	0	0	0	0	0	0	0	25572	50177	45	57	False		
+NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	3210	62854	96	124	0	0	0	0	0	0	0	0	3210	62854	96	124	False		
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	1038	1038	146	146	0	0	0	0	849	849	38	38	1887	1887	184	184	False		
+Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	71	9	10	0	0	0	0	0	0	0	0	45	71	9	10	False		
+PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1202	2121	48	62	0	0	0	0	0	0	0	0	1202	2121	48	62	False		
+Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1116	1897	57	71	0	0	0	0	0	0	0	0	1116	1897	57	71	False		
+Structure_GSPAN	structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	991	3060	50	62	0	0	0	0	0	0	0	0	991	3060	50	62	False		
+ThermoRawFileParser	thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2467	2959	88	124	0	0	0	0	1097	1097	18	18	3564	4056	106	142	False		
+TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1003	1022	48	52	0	0	0	0	0	0	0	0	1003	1022	48	52	False		
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	43	43	20	20	0	0	0	0	0	0	0	0	43	43	20	20	False		
+ab1_fastq	ab1_fastq_converter	Tool to convert ab1 files into FASTQ files								To update		Convert Formats	ab1fastq	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq	1.20.0	bioconductor-sangerseqr	1.38.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	49465	49465	281	281	0	0	0	0	0	0	0	0	49465	49465	281	281	False		
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	619817	622353	4097	4130	320454	320454	2915	2915	496156	503743	2012	2227	1436427	1446550	9024	9272	False		
+abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1139	1139	109	109	0	0	0	0	0	0	0	0	1139	1139	109	109	False		
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5543	5543	1042	1042	1301	1305	413	414	2030	2030	299	299	8874	8878	1754	1755	False		
+adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	348	348	62	62	0	0	0	0	0	0	0	0	348	348	62	62	False		
+add_input_name_as_column	addName	Add input name as column on an existing tabular file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	Text Manipulation	add_input_name_as_column	mvdbeek	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	76834	86002	227	246	20174	20953	312	395	11	11	2	2	97019	106966	541	643	False		
+add_line_to_file	add_line_to_file	Adds a text line to the beginning or end of a file.								To update		Text Manipulation	add_line_to_file	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	0.1.0	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	15933	15933	378	378	1736	1736	214	214	380	380	28	28	18049	18049	620	620	False		
+add_value	addValue	Add a value as a new column.								To update		Text Manipulation	add_value	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value	https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value	1.0.1	perl				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	37860	374587	1293	1610	17588	293713	1243	6197	3873	4397	202	229	59321	672697	2738	8036	False		
+aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	200	200	77	77	83	83	39	39	1747	1747	44	44	2030	2030	160	160	False		
+agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	244	244	0	0	0	0	119	119	10	10	1555	1555	254	254	False		
+aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	262	36	36	0	0	0	0	0	0	0	0	262	262	36	36	False		
+align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	511	541	32	35	0	0	0	0	0	0	0	0	511	541	32	35	False		
+allegro	allegro	Linkage and haplotype analysis from deCODE	allegro	allegro		Allegro	It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	To update	http://www.decode.com/software/	Variant Analysis	allegro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro	@VER@.0	allegro	3	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ambertools	ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap	Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.								To update	http://ambermd.org/AmberTools.php	Molecular Dynamics, Computational chemistry	ambertools	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools	21.10	ambertools				7	2	7	0	7	2	7	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	5	0	41793	41881	510	511	1126	1126	159	159	1552	1552	85	85	44471	44559	754	755	False		
+amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	81	81	17	17	0	0	0	0	0	0	0	0	81	81	17	17	False		
+ampvis2	ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.9			Analysis, Visualisation	Biodiversity	0	0	19	0	0	0	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	1213	1213	155	155	0	0	0	0	0	0	0	0	1213	1213	155	155	False		
+amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5734	5734	334	334	1035	1035	106	106	0	0	0	0	6769	6769	440	440	False		
+ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	7	7	0	0	0	0	0	0	0	0	26	26	7	7	False		
+anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	41	2	2	0	0	0	0	0	0	0	0	36	41	2	2	False		
+anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	43047	43139	1826	1827	17240	17240	878	878	9309	9309	298	298	69596	69688	3002	3003	False		
+annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	29266	30655	2849	2973	59299	66180	5917	6355	5644	5644	1049	1049	94209	102479	9815	10377	False		
+antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	292	306	5	7	0	0	0	0	0	0	0	0	292	306	5	7	False		
+antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15949	16490	726	811	5113	5113	649	649	6043	6043	169	169	27105	27646	1544	1629	False		
+apoc	apoc	Large-scale structural comparison of protein pockets								To update	http://cssb.biology.gatech.edu/APoc	Computational chemistry	apoc	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc	1.0+galaxy1	apoc	1b16			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	4	4	4	1	1	1	1	0	0	0	0	5	5	5	5	False		
+apollo	create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism	Access an Apollo instance from Galaxy								To update	https://github.com/galaxy-genome-annotation/python-apollo	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo		apollo	4.2.13			0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	0	3600	3760	883	911	6	6	4	4	0	0	0	0	3606	3766	887	915	False		
+appendfdr	append_fdr									To update			appendfdr	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr	0.2.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	75	75	9	9	0	0	0	0	0	0	0	0	75	75	9	9	False		
+aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	59	74	10	12	0	0	0	0	0	0	0	0	59	74	10	12	False		
+argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3670	3670	71	71	3	3	2	2	234	234	10	10	3907	3907	83	83	False		
+art	art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/	Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	Conversion	Bioinformatics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	140	140	9	9	0	0	0	0	0	0	0	0	140	140	9	9	False		
+artbio_bam_cleaning	artbio_bam_cleaning	filter bam files before somatic-varscan or lumpy-smoove analysis								To update	http://artbio.fr	SAM, Variant Analysis	artbio_bam_cleaning	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	1.10+galaxy0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	9021	9021	238	238	0	0	0	0	0	0	0	0	9021	9021	238	238	False		
+askomics	askomics_integrate	Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/								To update	https://github.com/askomics/	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics		askocli	0.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+askor	askor_de	AskoR links EdgeR and AskOmics								To update	https://github.com/askomics/askoR	Transcriptomics	askor_de	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	0.2	bioconductor-limma	3.58.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+astral	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees								Up-to-date	https://github.com/smirarab/ASTRAL	Phylogenetics	astral	iuc	https://github.com/usegalaxy-be/galaxytools/tree/main/astral	https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral	5.7.8	astral-tree	5.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	151	151	5	5	151	151	5	5	False		
+astropytools	astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo	AstropyTools library contains Galaxy tools for elementary Astrophysical operations								To update	https://github.com/astropy/astropy	Astronomy	astropytools	volodymyrss	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	0.1.0+galaxy0	astropy				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	13	13	5	5	0	0	0	0	0	0	0	0	13	13	5	5	False		
+atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	232	279	62	72	0	0	0	0	0	0	0	0	232	279	62	72	False		
+augustus	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	12890	13988	1826	1988	14901	14901	2633	2633	6187	6187	511	511	33978	35076	4970	5132	False		
+augustus	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10109	11052	1378	1509	12573	12573	2206	2206	5274	5274	369	369	27956	28899	3953	4084	False		
+b2btools	b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.7	Protein disorder prediction, Protein secondary structure prediction		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	369	369	19	19	0	0	0	0	0	0	0	0	369	369	19	19	False		
+background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1	False		
+bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11117	11117	534	534	19	19	1	1	9601	9601	167	167	20737	20737	702	702	False		
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bam_to_scidx	bam_to_scidx	Contains a tool that converts a BAM file to an ScIdx file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx	Convert Formats	bam_to_scidx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	83	131	15	20	329	785	50	210	0	0	0	0	412	916	65	230	False		
+bamclipper	bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bamhash	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	158	181	40	44	0	0	0	0	0	0	0	0	158	181	40	44	False		
+bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	14693	15620	653	721	61872	101400	1656	5678	39	39	3	3	76604	117059	2312	6402	False		
+bamtools_filter	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115954	124795	2994	3180	95433	142254	6712	10660	5793	5793	497	497	217180	272842	10203	14337	False		
+bamtools_split	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	9073	9073	401	401	2746	2746	224	224	103	103	10	10	11922	11922	635	635	False		
+bamutil	bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	45	45	20	20	69	69	21	21	258	258	1	1	372	372	42	42	False		
+bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	55392	56095	4951	5035	47603	47603	4916	4916	18089	18089	3121	3121	121084	121787	12988	13072	False		
+barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	111	111	8	8	29	29	10	10	21	21	4	4	161	161	22	22	False		
+baric_archive	baric_archive_rennes, baric_archive_toulouse	A data source tool to fetch data from a BARIC Archive server.								To update	https://www.cesgo.org/catibaric/	Data Source		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	1.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+barrnap	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update	https://github.com/tseemann/barrnap	Sequence Analysis	barrnap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	Gene prediction	Genomics, Model organisms, Model organisms	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6041	6041	316	316	0	0	0	0	6723	7273	240	322	12764	13314	556	638	False		
+basecoverage	gops_basecoverage_1	Base Coverage of all intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	basecoverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	226	308	27	35	2615	45557	302	2284	482	522	32	36	3323	46387	361	2355	False		
+baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+basil	basil	Breakpoint detection, including large insertions								Up-to-date	https://github.com/seqan/anise_basil	Variant Analysis	basil	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil	1.2.0	anise_basil	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	306	311	82	83	467	467	99	99	0	0	0	0	773	778	181	182	False		
+batched_lastz	batched_lastz	Galaxy wrapper for the batching Lastz runs								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	batched_lastz	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	1.04.22	lastz	1.04.22			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	123	123	5	5	0	0	0	0	123	123	5	5	False		
+bax2bam	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	208	208	26	26	210	210	30	30	0	0	0	0	418	418	56	56	False		
+bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	90	90	28	28	0	0	0	0	0	0	0	0	90	90	28	28	False		
+bbgbigwig	bbgtobigwig	Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://www.encodeproject.org/software/bedgraphtobigwig/	Convert Formats	bbgbigwig	iuc	https://www.encodeproject.org/software/bedgraphtobigwig/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig	0.1	ucsc-bedgraphtobigwig	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	42	42	7	7	175	175	26	26	0	0	0	0	217	217	33	33	False		
+bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.09	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	4	0	0	11989	11989	768	768	4458	4458	652	652	2507	2507	80	80	18954	18954	1500	1500	False		
+bcftools	bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@	BCFtools toolkit wrappers	bcftools	bcftools		BCFtools	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.	Data handling, Variant calling	Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment	To update	https://samtools.github.io/bcftools/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools	1.15.1	bcftools	1.21	Data handling, Variant calling	DNA polymorphism, GWAS study, Genotyping experiment	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	7	0	2352	3092	234	265	0	0	0	0	0	0	0	0	2352	3092	234	265	False		
+beacon2	beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff	beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://github.com/EGA-archive/beacon2-ri-tools/tree/main	Variant Analysis	beacon2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2	2.0.0	beacon2-ri-tools	2.0.0	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	33	33	9	9	0	0	0	0	0	0	0	0	33	33	9	9	False		
+beacon2-import	beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence	Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants.	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://pypi.org/project/beacon2-import/	Variant Analysis	Beacon2_Import	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import	2.2.4	beacon2-import	2.2.4	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22	22	7	7	0	0	0	0	0	0	0	0	22	22	7	7	False		
+beagle	beagle	Beagle is a program for phasing and imputing missing genotypes.								To update	https://faculty.washington.edu/browning/beagle/beagle.html	Variant Analysis	beagle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle	5.2_21Apr21.304	beagle	5.4_22Jul22.46e			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	88	88	28	28	0	0	0	0	0	0	0	0	88	88	28	28	False		
+bed_to_protein_map	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	410	419	134	137	363	363	99	99	158	158	13	13	931	940	246	249	False		
+bedops	bedops-sort-bed	BEDOPS: high-performance genomic feature operations								Up-to-date	https://bedops.readthedocs.io/en/latest/	Genomic Interval Operations	bedops_sortbed	iuc	https://bedops.readthedocs.io/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops	2.4.41	bedops	2.4.41			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	93	93	36	36	181	181	62	62	0	0	0	0	274	274	98	98	False		
+bedtools	bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed	bedtools is a powerful toolset for genome arithmetic	bedtools	bedtools		BEDTools	BEDTools is an extensive suite of utilities for comparing genomic features in BED format.	Mapping	Genomics	Up-to-date	https://github.com/arq5x/bedtools2	Genomic Interval Operations, Text Manipulation	bedtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools	2.31.1	bedtools	2.31.1	Mapping	Genomics	37	37	37	0	37	37	37	0	0	0	0	0	0	0	0	0	0	37	6	37	0	0	37	0	0	0	37	0	0	0	0	0	0	37	37	37	0	916111	962278	13235	14525	407944	647621	25849	41751	84008	89233	2486	2832	1408063	1699132	41570	59108	False		
+bellerophon	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1611	1611	262	262	763	763	67	67	543	543	30	30	2917	2917	359	359	False		
+berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	617	617	63	63	617	617	63	63	False		
+best_regression_subsets	BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3	4	3	4	14	253	7	72	0	0	0	0	17	257	10	76	False		
+bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1635	1671	123	124	0	0	0	0	334	334	21	21	1969	2005	144	145	False		
+bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	2	0	0	0	0	0	0	0	0	3	3	2	2	False		
+bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	544	544	20	20	0	0	0	0	0	0	0	0	544	544	20	20	False		
+bigwig_outlier_bed	bigwig_outlier_bed	pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files	bigtools	bigtools		bigtools	Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.			To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	Sequence Analysis	bigwig_outlier_bed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed	0.2.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	218	218	5	5	0	0	0	0	0	0	0	0	218	218	5	5	False		
+bigwig_to_bedgraph	bigwig_to_bedgraph	Convert from bigWig to bedGraph format								To update		Convert Formats	bigwig_to_bedgraph	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	0.1.0	ucsc_tools				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5769	6802	567	650	0	0	0	0	0	3	0	1	5769	6805	567	651	False		
+bigwig_to_bedgraph	bigwig_to_bedgraph	Converts a bigWig file to bedGraph format								To update	http://artbio.fr	Convert Formats	bigwig_to_bedgraph	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	377+galaxy1	ucsc-bigwigtobedgraph	469			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5769	6802	567	650	0	0	0	0	0	3	0	1	5769	6805	567	651	False		
+bigwig_to_wig	bigwig_to_wig	Converts a bigWig file to Wiggle (WIG) format								To update	https://artbio.fr	Convert Formats	bigwig_to_wig	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	3+galaxy0	ucsc-bigwiginfo	469			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	401	1385	87	88	0	0	0	0	188	188	9	9	589	1573	96	97	False		
+binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	29	1	1	0	0	0	0	0	0	0	0	24	29	1	1	False		
+binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	126	126	42	42	0	0	0	0	0	0	0	0	126	126	42	42	False		
+bio3d	bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize	Bio3d is a program that can be used to analyse molecular dynamics trajectories.								To update	http://thegrantlab.org/bio3d/index.php	Computational chemistry	bio3d	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	2.4_1	r-bio3d	2.3_3			5	4	5	0	5	4	5	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	5	5	0	10600	10729	1150	1159	1042	1042	255	255	2756	2756	215	215	14398	14527	1620	1629	False		
+bioext	bioext_bam2msa, bioext_bealign	A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!								Up-to-date	https://pypi.python.org/pypi/biopython-extensions/	Next Gen Mappers		iuc	https://github.com/davebx/bioext-gx/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext	0.21.9	python-bioext	0.21.9			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	17413	17413	822	822	15349	15349	2020	2020	2	2	1	1	32764	32764	2843	2843	False		
+bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	61	61	4	4	0	0	0	0	0	0	0	0	61	61	4	4	False		
+biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+biohansel_bionumeric_converter	bionumeric_convert	Convert BioHansel output data to a Bionumerics friendly form								To update	https://github.com/phac-nml/galaxy_tools	Text Manipulation	biohansel_bionumeric_converter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter	0.2.0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	1	0	0	0	0	0	0	0	0	2	2	1	1	False		
+bioinformatics_cafe	fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1137	1137	97	97	1029	1029	71	71	0	0	0	0	2166	2166	168	168	False		
+biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12725	12725	297	297	2851	5049	450	638	2171	2371	214	239	17747	20145	961	1174	False		
+biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	25	11	11	0	0	0	0	0	0	0	0	25	25	11	11	False		
+biomoldyn	biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering	Tools for MD analysis								To update	https://github.com/moldyn/	Molecular Dynamics, Computational chemistry	biomoldyn	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn	1.5.2	scipy				4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	3	0	493	493	119	119	441	441	148	148	0	0	0	0	934	934	267	267	False		
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	151	151	143	143	43	43	596	596	22	22	1286	1286	216	216	False		
+bioperl	bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	Data handling, Service invocation	Genomics, Software engineering	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7738	7931	478	508	8301	8301	849	849	1369	1369	154	154	17408	17601	1481	1511	False		
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6243	6243	375	375	0	0	0	0	6243	6243	375	375	False		
+biotransformer	biotransformer	BioTransformer is a tool for prediction of small molecule metabolism in mammals.	biotransformer	biotransformer		BioTransformer	BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	Up-to-date	https://bitbucket.org/djoumbou/biotransformerjar/src/master/	Metabolomics	biotransformer	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	3.0.20230403	biotransformer	3.0.20230403	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	48	48	1	1	48	48	1	1	False		
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	3	1	1	0	0	0	0	0	0	0	0	3	3	1	1	False		
+bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	4	4	4	0	13715	14997	992	1099	0	0	0	0	197	197	22	22	13912	15194	1014	1121	False		
+blast	magicblast	Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome								Up-to-date	https://ncbi.github.io/magicblast/	Next Gen Mappers	magicblast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast	1.7.0	magicblast	1.7.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	738	738	151	151	0	0	0	0	2	2	1	1	740	740	152	152	False		
+blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1063	1237	257	300	0	0	0	0	0	0	0	0	1063	1237	257	300	False		
+blast_parser	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	417	438	99	104	0	0	0	0	0	0	0	0	417	438	99	104	False		
+blast_plus_remote_blastp	blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.16.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24916	27120	283	347	0	0	0	0	0	0	0	0	24916	27120	283	347	False		
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blastxml_to_gapped_gff3	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	585	585	102	102	172	172	63	63	135	135	16	16	892	892	181	181	False		
+blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	264392	265217	483	552	0	0	0	0	0	0	0	0	264392	265217	483	552	False		
+blat_coverage_report	generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blat_mapping	blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1527	1527	79	79	6	6	1	1	317	317	26	26	1850	1850	106	106	False		
+blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	768	3043	97	119	14	14	11	11	276	276	9	9	1058	3333	117	139	False		
+blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	811	1501	54	79	64	64	29	29	561	561	15	15	1436	2126	98	123	False		
+bowtie2	bowtie2	Bowtie2: Fast and sensitive read alignment	bowtie2	bowtie2		Bowtie 2	Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.	Read mapping	Mapping, Genomics, Mapping	To update	http://bowtie-bio.sourceforge.net/bowtie2	Next Gen Mappers	bowtie2	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2	2.5.3	bowtie2	2.5.4	Read mapping	Mapping, Genomics, Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	1	1	1	0	397893	427447	12133	13176	577209	903193	33086	52020	60105	67495	3779	4271	1035207	1398135	48998	69467	False		
+bowtie_wrappers	bowtie_wrapper	Galaxy wrappers for the Bowtie short read mapping tools.								To update	http://bowtie-bio.sourceforge.net/	Next Gen Mappers	bowtie_wrappers	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers	https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers	1.2.0	bowtie	1.3.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	24164	25149	1320	1480	17537	203397	1330	17491	15654	15992	291	351	57355	244538	2941	19322	False		
+bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	51378	51378	775	775	3298	3298	160	160	1660	1660	63	63	56336	56336	998	998	False		
+braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	165	165	48	48	0	0	0	0	0	0	0	0	165	165	48	48	False		
+braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1938	1938	294	294	0	0	0	0	412	412	71	71	2350	2350	365	365	False		
+breseq	breseq	Predicts mutations in microbial genomes	breseq	breseq		breseq	Runs Breseq software on a set of fastq files.	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	To update	https://github.com/barricklab/breseq	Variant Analysis	breseq	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq	0.35.5	breseq	0.39.0	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	2976	2976	98	98	0	0	0	0	884	884	70	70	3860	3860	168	168	False		
+brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template	brew3r.r	brew3r.r		BREW3R.r	This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.	Genome annotation	Transcriptomics, Genomics	To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2			Genome annotation	Transcriptomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6	6	2	2	0	0	0	0	7	7	3	3	False		
+bumbershoot	idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	1186	1356	21	32	0	0	0	0	0	0	0	0	1186	1356	21	32	False		
+bundle_collections	bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.58			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	1	1518	1526	73	76	1520	1528	74	77	False		
+busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	102717	103051	3877	3926	34251	34251	3506	3506	33192	34369	2439	2525	170160	171671	9822	9957	False		
+bwa	bwa_mem, bwa	Wrapper for bwa mem, aln, sampe, and samse	bwa	bwa		BWA	Fast, accurate, memory-efficient aligner for short and long sequencing reads	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	Up-to-date	http://bio-bwa.sourceforge.net/	Next Gen Mappers	bwa	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa	0.7.18	bwa	0.7.18	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	2	0	0	0	2	0	0	0	0	0	0	2	2	2	2	976935	1017671	13526	14401	474702	681286	32627	47624	79802	87191	4219	4954	1531439	1786148	50372	66979	False		
+bwa_mem2	bwa_mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.	bwa-mem2	bwa-mem2		Bwa-mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,  dataset and the running machine.	Sequence alignment	Mapping	Up-to-date	https://github.com/bwa-mem2/bwa-mem2	Next Gen Mappers	bwa_mem2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2	2.2.1	bwa-mem2	2.2.1	Sequence alignment	Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	56619	56619	2324	2324	36631	36631	2808	2808	18121	18121	713	713	111371	111371	5845	5845	False		
+bwameth	bwameth	Fast and accurate alignment of BS-seq reads								Up-to-date	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.7	bwameth	0.2.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7970	11724	643	826	5524	5524	611	611	1242	1242	114	114	14736	18490	1368	1551	False		
+c3s	c3s	Copernicus Climate Change Service (C3S)								To update	https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset	Climate Analysis	c3s	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	0.3.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	234	234	11	11	4	4	4	4	92	92	3	3	330	330	18	18	False		
+cactus	cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			Multiple sequence alignment, Genome alignment	Genomics, Sequence assembly, Mapping, Phylogenetics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	299	299	61	61	0	0	0	0	1339	1339	95	95	1638	1638	156	156	False		
+cads	cads	Copernicus Atmosphere Data Store (ADS)								To update	https://ads.atmosphere.copernicus.eu/#!/home	Climate Analysis	cads	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	52	52	1	1	0	0	0	0	0	0	0	0	52	52	1	1	False		
+calculate_contrast_threshold	calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+calculate_numeric_param	calculate_numeric_param	Calculate a numeric parameter value using integer and float values.								To update		Text Manipulation	calculate_numeric_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param	0.1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1393	1393	10	10	0	0	0	0	0	0	0	0	1393	1393	10	10	False		
+calisp	calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	False		
+camera	abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos									To update		Metabolomics	camera	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera	1.48.0	r-snow	0.4_1			1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	2	0	677	787	114	120	60	60	30	30	734	746	26	26	1471	1593	170	176	False		
+cami_amber	biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert	Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments								Up-to-date	https://github.com/CAMI-challenge/AMBER	Metagenomics	cami_amber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber	2.0.7	cami-amber	2.0.7			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	195	195	4	4	0	0	0	0	0	0	0	0	195	195	4	4	False		
+canonical_correlation_analysis	cca1	Canonical Correlation Analysis								To update		Statistics	canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis	1.0.0	R				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	66	75	16	18	141	505	31	147	0	0	0	0	207	580	47	165	False		
+canu	canu	Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).	canu	canu		CANU	De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.	De-novo assembly	Genomics	Up-to-date	https://github.com/marbl/canu		canu	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/canu	https://github.com/bgruening/galaxytools/tree/master/tools/canu	2.2	canu	2.2	De-novo assembly	Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13360	14618	1383	1444	0	0	0	0	3542	3542	385	385	16902	18160	1768	1829	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	9869	9869	158	158	0	0	0	0	6886	6886	146	146	16755	16755	304	304	False		
+cardinal	cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								Up-to-date	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	3.4.3	bioconductor-cardinal	3.4.3			0	9	11	0	0	9	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	0	9	11	9	0	41875	50702	663	713	12	12	1	1	7512	7512	231	231	49399	58226	895	945	False		
+cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3835	3835	597	597	1359	1359	467	467	646	646	98	98	5840	5840	1162	1162	False		
+categorize_elements_satisfying_criteria	categorize_elements_satisfying_criteria	Categorize Elements satisfying criteria.								To update		Statistics	categorize_elements_satisfying_criteria	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria	https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	41	4	5	0	0	0	0	168	186	12	14	205	227	16	19	False		
+ccat	peakcalling_ccat	Control-based ChIP-seq Analysis Tool								To update		ChIP-seq	ccat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat	0.0.2	ccat	3.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	175	28	39	0	0	0	0	0	0	0	0	88	175	28	39	False		
+cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5946	7379	407	628	0	0	0	0	5946	7379	407	628	False		
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10414	10414	510	510	2	2	1	1	2	2	1	1	10418	10418	512	512	False		
+cdo	cdo_info, cdo_operations	CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.								To update	https://code.mpimet.mpg.de/projects/cdo/	Climate Analysis		climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	2.0.0					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	218	218	17	17	0	0	0	0	0	0	0	0	218	218	17	17	False		
+cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	4	4	0	0	0	0	0	0	0	0	8	8	4	4	False		
+cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	4	4	0	0	0	0	0	0	0	0	14	14	4	4	False		
+cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	0	0	23	23	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	0	4773	4773	749	749	0	0	0	0	5688	5688	94	94	10461	10461	843	843	False		
+cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55	55	11	11	0	0	0	0	0	0	0	0	55	55	11	11	False		
+cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	225	225	32	32	271	271	61	61	0	0	0	0	496	496	93	93	False		
+cesm	cesm	Community Earth System Model (CESM)								Up-to-date	https://www.cesm.ucar.edu/	Climate Analysis	cesm	climate	https://github.com/ESCOMP/CESM	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm	2.1.3	cesm	2.1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	14	2	2	0	0	0	0	0	0	0	0	14	14	2	2	False		
+cfm	cfmid	Competitive Fragmentation Modeling (CFM)								Up-to-date	https://sourceforge.net/p/cfm-id/	Metabolomics	cfmid	computational-metabolomics	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	33	cfm	33			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+chado	analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree	Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado								To update	https://github.com/galaxy-genome-annotation/python-chado	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado		python-chado	2.3.9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	183	183	20	20	0	0	0	0	0	0	0	0	183	183	20	20	False		
+change_case	ChangeCase	Convert column case.								To update		Text Manipulation	change_case	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case	https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case	1.0.1	perl				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	0	1	1	1	1	10606	12531	2204	2547	9044	17167	1748	2394	923	938	240	245	20573	30636	4192	5186	False		
+charts	charts	Enables advanced visualization options in Galaxy Charts								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3383	4001	1576	1822	7870	13727	3823	6880	249	350	108	145	11502	18078	5507	8847	False		
+chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	62	12	12	0	0	0	0	0	0	0	0	62	62	12	12	False		
+checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	7500	7500	930	930	0	0	0	0	0	0	0	0	7500	7500	930	930	False		
+checkv	checkv_end_to_end	Assess quality of single-contig viral genomes	checkv	checkv		CheckV	CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	Up-to-date	https://bitbucket.org/berkeleylab/checkv/	Metagenomics	checkv	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv	1.0.3	checkv	1.0.3	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	207	207	1	1	0	0	0	0	0	0	0	0	207	207	1	1	False		
+cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+chewbbaca	chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema	BSR-Based Allele Calling Algorithm								To update	https://github.com/B-UMMI/chewBBACA/tree/master	Variant Analysis	chewbbaca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca		chewbbaca	3.3.10			0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	727	727	76	76	0	0	0	0	0	0	0	0	727	727	76	76	False		
+chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	16468	18344	956	991	33692	34453	2559	2625	2948	2948	104	104	53108	55745	3619	3720	False		
+chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	16542	16542	287	287	1061	1061	102	102	27	27	5	5	17630	17630	394	394	False		
+chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	6	6	0	0	0	0	14	14	6	6	False		
+chromeister	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2696	2696	398	398	0	0	0	0	1235	1235	186	186	3931	3931	584	584	False		
+chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+circexplorer	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	211	263	32	40	0	0	0	0	209	209	6	6	420	472	38	46	False		
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	524	524	32	32	0	0	0	0	0	0	0	0	524	524	32	32	False		
+circos	circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile	Build Circos Plots in Galaxy	galactic_circos	galactic_circos		Galactic Circos	Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.	Sequence visualisation		To update	http://circos.ca/	Graphics	circos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos	0.69.8	circos	0.69.9	Sequence visualisation		11	11	11	0	11	11	11	0	0	0	0	0	0	0	0	0	0	0	11	11	0	0	0	0	0	0	11	0	0	0	0	0	0	11	11	11	0	26265	26265	2483	2483	31332	31332	3535	3535	26359	26359	999	999	83956	83956	7017	7017	False		
+cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	21	4	4	9	9	5	5	18	18	1	1	48	48	10	10	False		
+clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3388	3388	187	187	1	1	1	1	1	1	1	1	3390	3390	189	189	False		
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+climate-stripes	climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	239	239	35	35	16	16	2	2	182	182	3	3	437	437	40	40	False		
+clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	548	548	18	18	0	0	0	0	548	548	18	18	False		
+clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	79867	80817	1675	1785	49493	87884	3703	7380	8797	9713	670	728	138157	178414	6048	9893	False		
+cluster	gops_cluster_1	Cluster the intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	cluster	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	513	813	18	35	2406	30579	156	1547	1353	1393	17	20	4272	32785	191	1602	False		
+clustering_from_distmat	clustering_from_distmat	Distance matrix-based hierarchical clustering using SciPy								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	Statistics	clustering_from_distmat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat	1.1.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	5	5	0	0	0	0	0	0	0	0	12	12	5	5	False		
+cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2609	2609	3	3	0	0	0	0	0	0	0	0	2609	2609	3	3	False		
+cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	90	112	11	14	0	0	0	0	0	0	0	0	90	112	11	14	False		
+cnv-phenopacket	cnv_phenopacket	cnv-phenopacket Converts TSV metadata file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv_phenopacket	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket	1.0.2	cnv-phenopacket				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	False		
+cnv-vcf2json	cnv_vcf2json	cnv-vcf2json Converts structural variants VCF file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv-vcf2json	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json	1.1.0	cnv-vcf2json				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5	False		
+cnvkit	cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target	detecting copy number variants and alterations genome-wide from high-throughput sequencing	cnvkit	cnvkit		CNVkit	CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.	Variant calling	DNA structural variation	Up-to-date	https://github.com/etal/cnvkit	Variant Analysis	cnvkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit	0.9.11	cnvkit	0.9.11	Variant calling		0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	618	618	177	177	0	0	0	0	0	0	0	0	618	618	177	177	False		
+codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	61197	61220	64	65	0	0	0	0	0	0	0	0	61197	61220	64	65	False		
+cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	316	355	25	29	0	0	0	0	0	0	0	0	316	355	25	29	False		
+cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2758	2758	22	22	20	20	10	10	0	0	0	0	2778	2778	32	32	False		
+colabfold	colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6771	6771	50	50	0	0	0	0	6771	6771	50	50	False		
+colibread	commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								Up-to-date	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14	commet	24.7.14			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	273	273	40	40	0	0	0	0	0	0	0	0	273	273	40	40	False		
+collapse_collection	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	39518	40471	3555	3629	22007	24841	3536	4045	3969	4101	814	835	65494	69413	7905	8509	False		
+collection_column_join	collection_column_join	Column Join on Collections								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	Text Manipulation	collection_column_join	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join	0.0.3	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	23979	25337	3827	4011	21671	25163	4645	5045	2939	3036	688	701	48589	53536	9160	9757	False		
+collection_element_identifiers	collection_element_identifiers	Extract element identifiers of a collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	Text Manipulation	collection_element_identifiers	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers	0.0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6905	7102	1620	1630	7761	7761	1897	1897	1157	1157	243	243	15823	16020	3760	3770	False		
+color_deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	16	2	3	0	0	0	0	0	0	0	0	15	16	2	3	False		
+colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	40	40	2	2	0	0	0	0	0	0	0	0	40	40	2	2	False		
+column_arrange_by_header	bg_column_arrange_by_header	Column arrange by header name								To update		Text Manipulation	column_arrange_by_header	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5356	5636	446	484	2026	2026	375	375	1400	1531	117	138	8782	9193	938	997	False		
+column_maker	Add_a_column1	Compute an expression on every row								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	Text Manipulation	column_maker	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker	2.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2940752	3907183	5422	6121	263254	737503	6095	13728	96478	97667	884	974	3300484	4742353	12401	20823	False		
+column_order_header_sort	column_order_header_sort	Sort Column Order by heading								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	Text Manipulation	column_order_header_sort	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort	0.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3735	3891	268	297	1923	1923	381	381	0	0	0	0	5658	5814	649	678	False		
+column_remove_by_header	column_remove_by_header	Remove columns by header								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	Text Manipulation	column_remove_by_header	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header	1.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8331	8917	613	662	5206	5206	716	716	1976	1976	27	27	15513	16099	1356	1405	False		
+combineJSON	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	530	530	65	65	8	8	6	6	0	0	0	0	538	538	71	71	False		
+combine_tabular_collection	combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	221	5	28	0	0	0	0	0	0	0	0	39	221	5	28	False		
+compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	332	28	32	0	0	0	0	0	0	0	0	306	332	28	32	False		
+compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	266	266	39	39	28	28	15	15	0	0	0	0	294	294	54	54	False		
+complement	gops_complement_1	Complement intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	complement	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	187	233	15	20	495	4810	165	836	405	451	7	7	1087	5494	187	863	False		
+compose_text_param	compose_text_param	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	compose_text_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param	0.1.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	0	0	0	45827	45831	689	691	7721	7721	303	303	1481	1481	121	121	55029	55033	1113	1115	False		
+compress_file	compress_file	Compress files.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	Text Manipulation	compress_file	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file	0.1.0	gzip				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6343	6343	290	290	3674	3674	286	286	11832	11832	59	59	21849	21849	635	635	False		
+compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	85	96	9	10	0	0	0	0	316	334	8	8	401	430	17	18	False		
+compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	55	65	2	2	0	0	0	0	317	335	5	5	372	400	7	7	False		
+compute_q_values	compute_q_values	Compute q-values based on multiple simultaneous tests p-values								To update		Statistics	compute_q_values	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values	1.0.1	R				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	35	0	3	0	0	0	0	0	0	0	0	0	35	0	3	False		
+concat	gops_concat_1	Concatenate two bed files								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	concat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat	1.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	575128	575441	694	783	43420	85345	629	3508	19330	19418	104	117	637878	680204	1427	4408	False		
+concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	76	82	11	12	0	0	0	0	0	0	0	0	76	82	11	12	False		
+concat_multi_datasets	cat_multi_datasets	Concatenate multiple datasets tail-to-head, including collection datasets.								To update	http://artbio.fr	Text Manipulation	concatenate_multiple_datasets	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	1.4.3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	4822	4824	613	614	1317	1317	204	204	3088	3795	252	289	9227	9936	1069	1107	False		
+concat_paired	concat_fastqs	Concatenate paired datasets								To update	https://github.com/phac-nml/concat	Text Manipulation	concat_paired	nml	https://github.com/phac-nml/concat	https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	2105	2105	155	155	0	0	0	0	0	0	0	0	2105	2105	155	155	False		
+condense_characters	Condense characters1	Condense consecutive characters.								To update		Text Manipulation	condense_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters	1.0.0					1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47	2173	28	368	195	205	8	8	242	2378	36	376	False		
+consensus_from_alignments	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1184	1184	154	154	0	0	0	0	0	0	0	0	1184	1184	154	154	False		
+consolidate_vcfs	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+convert_characters	Convert characters1	Convert delimiters to tab.								To update		Text Manipulation	convert_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters	1.0.1	python				1	1	1	0	1	1	1	0	1	1	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	23589	28986	1061	1200	23507	160693	2302	8699	5413	6446	251	329	52509	196125	3614	10228	False		
+convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cooler	cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify	cooler different tools to process Hi-C from mirnylab								To update	https://github.com/open2c/cooler	Epigenetics	cooler	lldelisle	https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler	0.9.3	htslib	1.21			4	0	5	0	4	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	170	170	26	26	195	195	39	39	0	0	0	0	365	365	65	65	False		
+coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16077	16547	11	11	0	0	0	0	0	0	0	0	16077	16547	11	11	False		
+coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+correlation	cor2	Correlation for numeric columns								To update		Statistics	correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation	1.0.0	rpy				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	398	876	106	134	412	5568	105	755	192	239	21	27	1002	6683	232	916	False		
+correlation_analysis	correlation_analysis	[Metabolomics][W4M] Metabolites Correlation Analysis								To update	http://workflow4metabolomics.org	Metabolomics	correlation_analysis	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis	1.0.1+galaxy0	r-batch	1.1_4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	280	307	110	124	712	1277	332	628	476	541	55	79	1468	2125	497	831	False		
+count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	314	326	73	75	0	0	0	0	129	129	6	6	443	455	79	81	False		
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage	gops_coverage_1	Coverage of a set of intervals on second set of intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	coverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1560	1725	43	58	4328	44209	193	2113	283	316	16	18	6171	46250	252	2189	False		
+coverage_report	CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1081	1081	151	151	0	0	0	0	0	0	0	0	1081	1081	151	151	False		
+cpat	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.								Up-to-date	https://github.com/liguowang/cpat	Transcriptomics	cpat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	3.0.5	cpat	3.0.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	204	204	47	47	165	165	40	40	125	125	7	7	494	494	94	94	False		
+cpm_tpm_rpk	cpm_tpm_rpk	Generate CPM,TPM or RPK from raw counts								To update	http://artbio.fr	Transcriptomics	cpm_tpm_rpk	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	0.6.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+crispr_studio	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	Visualisation	Sequence analysis, Genomics, Data visualisation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1052	1053	75	76	0	0	0	0	0	0	0	0	1052	1053	75	76	False		
+crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	276	390	61	76	131	131	42	42	0	0	0	0	407	521	103	118	False		
+crossmap	crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig	CrossMap converts genome coordinates or annotation files between genome assemblies								Up-to-date	http://crossmap.sourceforge.net/	Convert Formats, Genomic Interval Operations	crossmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap	0.7.0	crossmap	0.7.0			5	0	6	0	5	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	5	6	5	0	2182	2182	331	331	5251	5251	903	903	0	0	0	0	7433	7433	1234	1234	False		
+crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4066	4139	166	180	0	0	0	0	0	0	0	0	4066	4139	166	180	False		
+cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9942	9942	26	26	0	0	0	0	0	0	0	0	9942	9942	26	26	False		
+csvtk	csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq	Rapid data investigation and manipulation of csv/tsv files								To update	https://bioinf.shenwei.me/csvtk/	Text Manipulation	csvtk	nml	https://github.com/shenwei356/csvtk	https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk	0.20.0	csvtk	0.30.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	20	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cta	cta_astro_tool	Basic simulation of CTA telescope observations using gammapy package								To update		Astronomy	cta_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta	0.0.1+galaxy0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	196	211	41	48	1	447	1	161	0	0	0	0	197	658	42	209	False		
+cuffcompare	cuffcompare	Galaxy wrappers for the Cuffcompare tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffcompare	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1	1	0	768	1199	171	300	2205	24981	754	5750	251	493	46	98	3224	26673	971	6148	False		
+cuffdiff	cuffdiff	Galaxy wrappers for the Cuffdiff tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffdiff	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff	2.2.1	cufflinks	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	4176	6065	564	725	24284	117007	4952	20249	971	4231	193	616	29431	127303	5709	21590	False		
+cufflinks	cufflinks	Galaxy wrappers for the Cufflinks tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cufflinks	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	1	1	1	0	26122	33320	870	1213	70653	349091	6984	27076	3963	10315	440	836	100738	392726	8294	29125	False		
+cuffmerge	cuffmerge	Galaxy wrappers for the Cuffmerge tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffmerge	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1	1	0	2406	3448	351	637	20978	67769	3641	13764	1209	3057	227	573	24593	74274	4219	14974	False		
+cuffnorm	cuffnorm	The Cuffnorm tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffnorm	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	374	701	81	114	1032	13499	273	1166	262	322	53	70	1668	14522	407	1350	False		
+cuffquant	cuffquant	The Cuffquant tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffquant	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	408	732	54	71	1964	15883	267	1310	308	422	26	46	2680	17037	347	1427	False		
+cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1251	1803	98	166	3461	15159	486	2044	2425	3338	57	159	7137	20300	641	2369	False		
+cummerbund_to_tabular	cummerbund_to_cuffdiff	Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.								To update		Convert Formats, Next Gen Mappers	cummerbund_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular	1.0.1					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	888	1208	43	97	1334	2683	101	479	0	0	0	0	2222	3891	144	576	False		
+curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	12	2	2	0	0	0	0	0	0	0	0	12	12	2	2	False		
+custom_pro_db	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1729	1744	144	146	450	450	72	72	361	361	12	12	2540	2555	228	230	False		
+custom_pro_db_annotation_data_manager		CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cut_columns	Cut1	Select columns from a dataset.								To update		Text Manipulation	cut_columns	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns	1.0.2					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	0	1	1	1	1	1973168	2034965	11939	12833	352364	803522	12967	30199	128777	133584	2341	2572	2454309	2972071	27247	45604	False		
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	259754	272370	11716	12601	334550	362356	18618	20162	64377	65986	3507	3627	658681	700712	33841	36390	False		
+cutesv	cutesv	Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.	cuteSV	cuteSV		cuteSV	Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis	Split read mapping, Genotyping, Structural variation detection	DNA structural variation, Sequencing, Computer science	To update	https://github.com/tjiangHIT/cuteSV	Variant Analysis	cutesv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv	1.0.8	cutesv	2.1.1	Split read mapping, Genotyping, Structural variation detection	Sequencing, Computer science	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	260	260	43	43	0	0	0	0	119	119	8	8	379	379	51	51	False		
+cwpair2	cwpair2	Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.								To update		ChIP-seq	cwpair2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2	1.1.1	matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	173	280	41	83	0	0	0	0	173	280	41	83	False		
+dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	0	10	10	10	0	92240	92240	2716	2716	179176	179176	5317	5317	12478	12478	394	394	283894	283894	8427	8427	False		
+das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1323	1323	47	47	0	0	0	0	0	0	0	0	1323	1323	47	47	False		
+data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	441	451	83	87	3	3	2	2	0	0	0	0	444	454	85	89	False		
+data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	867	877	213	216	339	339	94	94	64	64	5	5	1270	1280	312	315	False		
+data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	967	967	308	308	0	0	0	0	0	0	0	0	967	967	308	308	False		
+data_manager_eggnog_mapper		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+data_manager_eggnog_mapper_abspath		download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+data_source_iris_tcga	data_source_iris_tcga	IRIS-TCGA Data source tool								To update		Data Source	data_source_iris_tcga	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga	https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+datamash	datamash_ops, datamash_reverse, datamash_transpose	GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.								To update	https://www.gnu.org/software/datamash/	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash	1.8	datamash	1.1.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	1	3	3	0	0	1	0	0	0	1	0	0	0	0	0	0	3	3	3	0	748586	760943	7066	7307	98089	112831	5306	6131	16235	16317	2161	2171	862910	890091	14533	15609	False		
+dbbuilder	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4813	5555	687	805	0	0	0	0	961	961	87	87	5774	6516	774	892	False		
+decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	121	121	28	28	0	0	0	0	0	0	0	0	121	121	28	28	False		
+decoupler	score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk	decoupler - Ensemble of methods to infer biological activities								To update	https://decoupler-py.readthedocs.io/en/latest/	Transcriptomics	suite_decoupler	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler	1.4.0+galaxy3	decoupler	1.5.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	54	6	6	0	0	0	0	0	0	0	0	54	54	6	6	False		
+decoyfasta		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	558	558	7	7	0	0	0	0	0	0	0	0	558	558	7	7	False		
+deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	37	37	0	0	0	0	0	0	0	0	65	65	37	37	False		
+deepvariant	deepvariant	DeepVariant is a deep learning-based variant caller								To update	https://github.com/google/deepvariant	Variant Analysis	deepvariant	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant	1.5.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2561	2561	325	325	2916	2916	460	460	0	0	0	0	5477	5477	785	785	False		
+deg_annotate	deg_annotate	Annotate DESeq2/DEXSeq output tables								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	Transcriptomics	deg_annotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate	1.1.0	bedtools	2.31.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22774	23146	4084	4155	33972	33972	5372	5372	4236	4236	846	846	60982	61354	10302	10373	False		
+delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	40	6	7	0	0	0	0	0	0	0	0	33	40	6	7	False		
+delly	delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge	Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.	delly2	delly2		Delly2	Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.	Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis	DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases	To update	https://github.com/dellytools/delly	Variant Analysis	delly	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly	https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly	0.9.1	delly	1.2.9	Indel detection, Structural variation detection, Genotyping	Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	6	0	0	0	0	0	0	6	6	0	0	1451	1451	288	288	0	0	0	0	0	0	0	0	1451	1451	288	288	False		
+deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	97434	109474	11355	12514	183905	246475	24951	31957	18551	20166	2647	2905	299890	376115	38953	47376	False		
+deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	43	48	8	8	0	0	0	0	0	0	0	0	43	48	8	8	False		
+dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	18	18	0	0	0	0	0	0	0	0	89	89	18	18	False		
+dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	14874	16927	533	837	18475	28854	1403	2568	3854	4271	141	163	37203	50052	2077	3568	False		
+dgidb_annotator	dgidb_annotate	Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)								To update		Systems Biology, Variant Analysis	dgidb_annotator	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator	0.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	69	26	30	0	304	0	133	0	0	0	0	59	373	26	163	False		
+dia_umpire	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	28	33	4	4	0	0	0	0	134	134	4	4	162	167	8	8	False		
+dialignr	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	40	2	2	0	0	0	0	0	0	0	0	40	40	2	2	False		
+diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	0	3	3	0	61376	61746	1847	1895	23164	28729	1140	1556	63034	63034	522	522	147574	153509	3509	3973	False		
+diann	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	72	72	14	14	0	0	0	0	171	171	14	14	243	243	28	28	False		
+diapysef	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	262	262	38	38	0	0	0	0	256	256	6	6	518	518	44	44	False		
+diff	diff	GNU diff tool that calculates the differences between two files.								To update	http://www.gnu.org/software/diffutils/	Text Manipulation	diff	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diff	https://github.com/bgruening/galaxytools/tree/master/tools/diff	3.7	diffutils				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	362	362	99	99	23	23	17	17	0	0	0	0	385	385	116	116	False		
+diffacto	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	11	7	7	0	0	0	0	0	0	0	0	11	11	7	7	False		
+diffbind	diffbind	Diffbind provides functions for  processing  ChIP-Seq  data.	diffbind	diffbind		DiffBind	Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.	Differential binding analysis	ChIP-seq	Up-to-date	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind	3.12.0	bioconductor-diffbind	3.12.0	Differential binding analysis	ChIP-seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7092	7663	606	652	14367	18624	1360	1916	1477	1640	69	84	22936	27927	2035	2652	False		
+diffbind		Diffbind provides functions for  processing  ChIP-Seq  data.								To update	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+digestdb	digestdb									To update			digestdb	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dimet	dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@	DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.								Up-to-date	https://github.com/cbib/DIMet	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet	0.2.4	dimet	0.2.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+directag_and_tagrecon										To update			directag_and_tagrecon	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	358	406	124	139	1361	1361	384	384	0	0	0	0	1719	1767	508	523	False		
+divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26	32	8	9	86	172	20	53	0	0	0	0	112	204	28	62	False		
+dnabot	dnabot	DNA assembly using BASIC on OpenTrons								To update	https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT	Synthetic Biology	dnabot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot	3.1.0	dnabot				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dnaweaver	dnaweaver	Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.								Up-to-date	https://github.com/Edinburgh-Genome-Foundry/DnaWeaver	Synthetic Biology	dnaweaver	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver	1.0.2	dnaweaver_synbiocad	1.0.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	921	1626	4	31	0	0	0	0	0	0	0	0	921	1626	4	31	False		
+dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	74	88	12	15	0	0	0	0	0	0	0	0	74	88	12	15	False		
+dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	7358	7358	88	88	0	0	0	0	0	0	0	0	7358	7358	88	88	False		
+draw_stacked_barplots	draw_stacked_barplots	Draw Stacked Bar Plots for different categories and different criteria								To update		Graphics, Statistics	draw_stacked_barplots	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots	https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots	1.0.0	R				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	216	47	52	0	0	0	0	183	213	22	31	372	429	69	83	False		
+drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	916	916	113	113	0	0	0	0	0	0	0	0	916	916	113	113	False		
+droplet-barcode-plot	_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1151	1151	184	184	356	356	77	77	3	3	1	1	1510	1510	262	262	False		
+dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1900	1901	412	413	609	609	131	131	0	0	0	0	2509	2510	543	544	False		
+dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4413	4442	430	431	4403	4403	255	255	1816	1816	33	33	10632	10661	718	719	False		
+dwt_cor_ava_perclass	compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Feature Occurrences								To update		Statistics	dwt_cor_ava_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	141	8	11	136	141	8	11	False		
+dwt_cor_avb_all	compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features								To update		Statistics	dwt_cor_avb_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	124	124	7	7	124	124	7	7	False		
+dwt_ivc_all	compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Second Moments for Feature Occurrences								To update		Statistics	dwt_ivc_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	121	123	5	7	121	123	5	7	False		
+dwt_var_perclass	compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom	Compute P-values and Max Variances for Feature Occurrences								To update		Statistics	dwt_var_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	131	132	7	8	131	132	7	8	False		
+dwt_var_perfeature	dwt_var1	Wavelet variance using Discrete Wavelet Transfoms								To update		Statistics	dwt_var_perfeature	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature	1.0.2	r-bitops				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	30	36	2	4	11	11	4	4	206	220	6	7	247	267	12	15	False		
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	28	28	2	2	0	0	0	0	0	0	0	0	28	28	2	2	False		
+ebi_tools	ebi_search_rest_results	Tools to query and download data from several EMBL-EBI databases								To update	http://www.ebi.ac.uk/services/all	Web Services, Data Source	ebi_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools	0.1.1	six				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	276	406	133	163	1421	1421	547	547	0	0	0	0	1697	1827	680	710	False		
+ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12996	12996	137	137	10	10	1	1	0	0	0	0	13006	13006	138	138	False		
+edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	19294	20905	2423	2618	48876	58723	6341	7527	8010	8705	846	892	76180	88333	9610	11037	False		
+edta	edta	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. 	edta	edta		The Extensive de novo TE Annotator (EDTA)	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	To update	https://github.com/oushujun/EDTA	Variant Analysis	edta	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta	https://github.com/bgruening/galaxytools/tree/master/tools/edta		edta	2.2.0	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4495	4495	111	111	0	0	0	0	0	0	0	0	4495	4495	111	111	False		
+effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	1	3	1	0	34432	34437	1149	1152	42	42	2	2	21027	21027	413	413	55501	55506	1564	1567	False		
+egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2809	3060	371	402	5179	5179	759	759	1931	1931	226	226	9919	10170	1356	1387	False		
+embl2fa	embl2fa	Converts EMBL flat format to fasta format								To update	http://artbio.fr	Text Manipulation	embl2fa	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	0	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	107	107	107	0	143762	148864	4481	5039	151989	296028	13224	31140	24955	27001	2397	2705	320706	471893	20102	38884	False		
+ena_upload	ena_upload	Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 								To update	https://github.com/usegalaxy-eu/ena-upload-cli	Data Export	ena_upload	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload	0.7.3	ena-upload-cli	0.7.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	366	366	41	41	0	0	0	0	1302	1302	14	14	1668	1668	55	55	False		
+enasearch	enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data	A Python library for interacting with ENA's API								To update	https://github.com/bebatut/enasearch	Data Source	enasearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch		enasearch	0.2.2			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	1989	2302	367	453	0	0	0	0	0	0	0	0	1989	2302	367	453	False		
+encyclopedia	encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30			2	4	7	0	2	4	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	738	738	98	98	1	1	1	1	42	42	4	4	781	781	103	103	False		
+ensembl_vep	ensembl_vep	Ensembl VEP: Annotate VCFs with variant effect predictions								Up-to-date	https://github.com/Ensembl/ensembl-vep	Variant Analysis	ensembl_vep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep	112.0	ensembl-vep	112.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3051	3051	171	171	0	0	0	0	0	0	0	0	3051	3051	171	171	False		
+eodie	eodie	Earth Observation Data Information Extractor								To update	https://eodie.readthedocs.io/	Climate Analysis	eodie	climate	https://gitlab.com/eetun-tiimi/EODIE	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie	1.0.2	eodie				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	45	45	4	4	0	0	0	0	0	0	0	0	45	45	4	4	False		
+epicseg	epicseg_segment	EpiCSeg is a tool for conducting chromatin segmentation.								To update	https://github.com/lamortenera/epicseg	Epigenetics	epicseg	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	@VERSION_STRING@	epicseg	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	160	252	17	21	0	0	0	0	0	0	0	0	160	252	17	21	False		
+episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	880	880	80	80	221	221	37	37	49	49	3	3	1150	1150	120	120	False		
+essential_climate_variables	cds_essential_variability	Get Copernicus Essential Climate Variables for assessing climate variability								To update	https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview	Climate Analysis, Data Source	cds_essential_variability	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	232	336	39	40	0	0	0	0	0	0	0	0	232	336	39	40	False		
+ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	820	966	89	106	0	0	0	0	0	0	0	0	820	966	89	106	False		
+evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+exomedepth	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	517	517	61	61	2995	2995	184	184	0	0	0	0	3512	3512	245	245	False		
+exonerate	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1030	1072	185	188	1058	1058	189	189	922	922	35	35	3010	3052	409	412	False		
+exparna	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5396	5938	580	607	628	628	168	168	519	519	107	107	6543	7085	855	882	False		
+export_to_cluster	export_to_cluster	Export datasets to cluster								To update	https://github.com/TGAC/earlham-galaxytools/	Data Export	export_to_cluster	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster	0.0.2	EXPORT_DIR_PREFIX				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+express	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	278	337	34	45	0	1184	0	117	2402	2844	23	60	2680	4365	57	222	False		
+extract_genomic_dna	Extract genomic DNA 1	Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.								To update		Genomic Interval Operations	extract_genomic_dna	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna	https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna	3.0.3+galaxy2	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	1	0	0	0	1	1	1	1	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	9409	12735	813	923	20180	259099	2072	11791	168	611	20	63	29757	272445	2905	12777	False		
+ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+falco	falco	A high throughput sequence QC analysis tool	falco	falco		Falco	A high-speed FastQC emulation for quality control of sequencing data.	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	Up-to-date	https://github.com/smithlabcode/falco/	Sequence Analysis	falco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco	https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco	1.2.4	falco	1.2.4	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4298	4298	34	34	0	0	0	0	0	0	0	0	4298	4298	34	34	False		
+fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	601	601	128	128	1165	1165	232	232	0	0	0	0	1766	1766	360	360	False		
+fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	469	ucsc-fasplit	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3278	3361	460	478	6144	6144	595	595	1139	1139	183	183	10561	10644	1238	1256	False		
+fasta2bed	fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5191	5367	104	130	5191	5367	104	130	False		
+fasta_compute_length	fasta_compute_length	Compute sequence length								To update	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.4	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	8547	9136	978	1129	17748	51150	1404	5670	4239	4404	162	190	30534	64690	2544	6989	False		
+fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39695	39742	242	255	13660	19007	600	1398	1521	1603	92	112	54876	60352	934	1765	False		
+fasta_extract	fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	10	10	1	1	0	0	0	0	1286	1827	144	181	1296	1837	145	182	False		
+fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	47494	51924	889	997	50663	101663	1488	3742	3919	5601	241	276	102076	159188	2618	5015	False		
+fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	1	5235	5486	237	288	4060	25609	480	2039	816	1093	73	89	10111	32188	790	2416	False		
+fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	30917	32191	1142	1257	36869	36869	1346	1346	5236	5236	230	230	73022	74296	2718	2833	False		
+fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	497	808	71	108	2249	5479	216	703	415	437	18	20	3161	6724	305	831	False		
+fasta_nucleotide_color_plot	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	164	179	42	47	758	905	128	170	0	0	0	0	922	1084	170	217	False		
+fasta_stats	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	43726	44512	3104	3259	19941	19941	3693	3693	16788	18589	2467	2650	80455	83042	9264	9602	False		
+fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	108876	113638	1572	1793	82527	192112	2209	8565	5711	7649	275	334	197114	313399	4056	10692	False		
+fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6685	6685	603	603	0	0	0	0	0	0	0	0	6685	6685	603	603	False		
+fastg2protlib	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	29	29	8	8	0	0	0	0	0	0	0	0	29	29	8	8	False		
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	136	11	11	0	0	0	0	0	0	0	0	136	136	11	11	False		
+fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	1	1126086	1127111	6847	6909	422259	422259	10722	10722	76462	76462	2242	2242	1624807	1625832	19811	19873	False		
+fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8604	8799	215	240	54200	75329	919	2957	1562	1680	76	85	64366	85808	1210	3282	False		
+fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15582	18350	690	771	40489	121585	2715	9239	4657	5793	214	287	60728	145728	3619	10297	False		
+fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	92594	102535	2576	2995	179461	897457	9437	44701	15434	25533	664	1073	287489	1025525	12677	48769	False		
+fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7560	7560	1266	1266	6539	6539	1581	1581	0	0	0	0	14099	14099	2847	2847	False		
+fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2488	3132	215	267	6241	14508	834	2121	4121	4592	131	158	12850	22232	1180	2546	False		
+fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	234	249	43	44	2648	8092	288	983	442	466	12	17	3324	8807	343	1044	False		
+fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5873	8936	532	657	14738	20229	1889	2366	2316	2711	225	261	22927	31876	2646	3284	False		
+fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18216	19573	2348	2492	23484	25936	3482	3851	6207	6551	1402	1442	47907	52060	7232	7785	False		
+fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15628	17130	536	679	24157	58368	1954	5716	1941	2266	172	214	41726	77764	2662	6609	False		
+fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3169	3521	459	535	19309	30747	1410	3441	807	1023	219	247	23285	35291	2088	4223	False		
+fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1271	1393	131	176	12763	58819	2073	8850	430	479	32	51	14464	60691	2236	9077	False		
+fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	335	352	44	47	1583	9696	269	2229	1131	1254	15	27	3049	11302	328	2303	False		
+fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	17279	18386	3826	4062	55268	136888	6055	12590	7685	9356	1854	2043	80232	164630	11735	18695	False		
+fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_stats	fastq_stats	FASTQ Summary Statistics by column								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3858	4595	680	815	15213	81513	3159	14109	3855	4163	184	256	22926	90271	4023	15180	False		
+fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	36069	37805	1151	1234	45213	99852	2691	6370	8457	13335	408	609	89739	150992	4250	8213	False		
+fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	12895	14110	269	297	13315	30673	612	1810	5125	5373	64	87	31335	50156	945	2194	False		
+fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10114	11383	582	665	23906	92351	1986	8818	1588	2607	108	212	35608	106341	2676	9695	False		
+fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								To update		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4881	6165	859	967	29458	99179	3455	11369	2171	2678	259	338	36510	108022	4573	12674	False		
+fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	1	0	1784056	1913280	41344	43940	2269843	3195869	90828	140008	410004	445555	14195	16026	4463903	5554704	146367	199974	False		
+fastqc_stats	FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5162	5162	2350	2350	10176	10176	4714	4714	2610	2610	991	991	17948	17948	8055	8055	False		
+fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	3	0	0	0	0	0	8	0	3	False		
+fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	208349	217568	3421	3732	131388	245005	5108	13227	18655	18655	679	679	358392	481228	9208	17638	False		
+fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	65542	65631	1049	1071	25992	25992	2147	2147	6733	7339	649	745	98267	98962	3845	3963	False		
+fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1769	2020	88	101	6948	24960	358	2424	623	998	32	50	9340	27978	478	2575	False		
+fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	16957	18124	225	260	37001	89126	919	2720	863	989	56	68	54821	108239	1200	3048	False		
+fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3140	3520	178	212	13975	117900	1198	6006	409	712	36	55	17524	122132	1412	6273	False		
+fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	64187	67981	326	349	87477	185555	781	3067	16563	17125	58	78	168227	270661	1165	3494	False		
+fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	174	272	61	92	4295	25068	1056	4180	1127	1171	70	89	5596	26511	1187	4361	False		
+fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2218	2344	168	206	20551	60032	3784	9866	2347	2460	234	256	25116	64836	4186	10328	False		
+fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2364	2526	180	214	6572	11745	303	1024	462	696	49	64	9398	14967	532	1302	False		
+fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10707	12597	356	415	21568	67304	574	1527	719	861	61	78	32994	80762	991	2020	False		
+fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	13584	14557	550	641	123676	206733	2034	8390	2819	4757	229	267	140079	226047	2813	9298	False		
+fates-emerald	ctsm_fates	EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model								To update	https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api	Climate Analysis	ctsm_fates	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	2.0	fates-emerald				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	264	264	69	69	34	34	11	11	103	103	1	1	401	401	81	81	False		
+fatovcf	fatovcf	Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_fatovcf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	448	ucsc-fatovcf	448		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	385	385	46	46	587	587	107	107	58	58	5	5	1030	1030	158	158	False		
+feature_alignment	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	18	18	1	1	0	0	0	0	0	0	0	0	18	18	1	1	False		
+featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22308	22388	16	19	350	13711	54	349	0	0	0	0	22658	36099	70	368	False		
+featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	740719	770524	11699	12547	643892	784396	23272	27598	66108	68867	2348	2463	1450719	1623787	37319	42608	False		
+feelnc	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	Annotation, Classification	Functional, regulatory and non-coding RNA	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1375	1500	95	99	797	797	116	116	59	59	3	3	2231	2356	214	218	False		
+feelnc2asko	feelnc2asko	Convert FeelNC GTF to GFF3								To update	https://github.com/tderrien/FEELnc	Convert Formats	feelnc2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+feht	feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	1	1	1	1	False		
+fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5618	5820	582	607	21673	21673	938	938	869	869	110	110	28160	28362	1630	1655	False		
+file_manipulation	bg_uniq	This tool returns all unique lines from a tab-separated file.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	Text Manipulation	unique	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	0.4	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	6690	8818	554	612	0	0	0	0	0	0	0	0	6690	8818	554	612	False		
+filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	26717	29932	1026	1072	42990	42990	1176	1176	9619	9619	230	230	79326	82541	2432	2478	False		
+filter_compounds	filter_orgmet_anorg	Tool for filtering organometallics/anorganic compounds from a list of compounds.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	filter_compounds	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	3.1.1	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_density	filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_stats	filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_transcripts_via_tracking	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23	24	9	10	62	635	26	241	2	2	2	2	87	661	37	253	False		
+filter_vcf	filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	53310	53944	1499	1575	25043	25043	726	726	10824	10824	593	593	89177	89811	2818	2894	False		
+find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	62	70	10	12	3	1787	1	204	0	0	0	0	65	1857	11	216	False		
+find_repeats	findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+find_subsequences	bg_find_subsequences									To update			find_subsequences	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences	0.3	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	554	784	69	79	2820	3047	323	361	20	20	1	1	3394	3851	393	441	False		
+fisher_test	fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	1985	1985	41	41	0	0	0	0	0	0	0	0	1985	1985	41	41	False		
+flanking_features	flanking_features_1	Fetch closest non-overlapping feature for every interval								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	flanking_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features	4.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	589	731	51	63	2445	32847	304	2549	1214	1294	15	22	4248	34872	370	2634	False		
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22017	22304	239	255	9399	14886	462	709	4	4	1	1	31420	37194	702	965	False		
+flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	661	715	52	54	0	0	0	0	167	167	15	15	828	882	67	69	False		
+flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	2	2	0	0	0	0	0	0	0	0	9	9	2	2	False		
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32514	32675	3379	3422	19434	19434	2537	2537	9843	9843	1624	1624	61791	61952	7540	7583	False		
+footprint	footprint	Find transcription factor footprints								To update	https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/	Epigenetics	footprint	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	1.0.0	footprint	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	57	5	5	0	0	0	0	0	0	0	0	57	57	5	5	False		
+format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	189	203	57	60	0	0	0	0	0	0	0	0	189	203	57	60	False		
+format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5940	6474	558	608	0	0	0	0	0	0	0	0	5940	6474	558	608	False		
+fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1257	1450	150	162	0	0	0	0	1052	1052	45	45	2309	2502	195	207	False		
+fragpipe	fragpipe	Data analysis for mass spectrometry-based proteomics.								Up-to-date	https://fragpipe.nesvilab.org/	Proteomics	fragpipe	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	20.0	fragpipe	20.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	64	64	9	9	0	0	0	0	0	0	0	0	64	64	9	9	False		
+free_energy		Free energy tools of BRIDGE.								To update		Molecular Dynamics, Computational chemistry	freeenergy	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+freebayes	freebayes, bamleftalign	Galaxy Freebayes Bayesian genetic variant detector tool	freebayes	freebayes		FreeBayes	Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	To update	https://github.com/ekg/freebayes	Variant Analysis	freebayes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes	1.3.6	freebayes	1.3.8	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	149715	171093	8158	8794	144708	256315	15996	25107	19156	21936	2251	2571	313579	449344	26405	36472	False		
+freec	control_freec	Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.	freec	freec		FREEC	A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.	Copy number estimation, Variant calling, Genome alignment	DNA structural variation, Oncology, Human genetics, Data mining	To update	http://boevalab.inf.ethz.ch/FREEC/	Variant Analysis	control_freec	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec	11.6	gawk		Copy number estimation, Variant calling, Genome alignment	Oncology, Human genetics, Data mining	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	748	748	91	91	0	0	0	0	12	12	1	1	760	760	92	92	False		
+freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	21757	21757	101	101	217	217	21	21	0	0	0	0	21974	21974	122	122	False		
+frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fromHicupToJuicebox	fromHicupToJuicebox	Convert the output of hicup (as sam or bam) to the input of juicebox.								To update		Epigenetics	from_hicup_to_juicebox	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fromgtfTobed12	fromgtfTobed12	Convert GTF files to BED12 format								To update	https://pythonhosted.org/gffutils/contents.html	Convert Formats	fromgtftobed12	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	0.11.1+galaxy1	gffutils	0.13			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fsd	fsd, fsd_beforevsafter, fsd_regions, td	Tool that plots a histogram of sizes of read families								To update		Graphics	duplex_family_size_distribution	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd	1.0.2	matplotlib				4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	578	578	34	34	0	0	0	0	578	578	34	34	False		
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	8648	8648	1408	1408	32	32	6	6	6406	6406	597	597	15086	15086	2011	2011	False		
+garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	11	11	0	0	0	0	0	0	0	0	27	27	11	11	False		
+gatk4	filtermutectcalls, mergemutectstats, mutect2	Find somatic variations								To update	http://artbio.fr	Variant Analysis	gatk4	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gatk4	gatk4_mutect2	A Galaxy wrapper for Mutect2 from GATK								To update	https://software.broadinstitute.org/gatk/gatk4	Variant Analysis	gatk4_mutect2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3463	3463	452	452	9040	9040	1639	1639	0	0	0	0	12503	12503	2091	2091	False		
+gblocks	gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	466	466	62	62	466	466	62	62	False		
+gc_derivatization	gc_derivatization	In silico derivatization for GC.								Up-to-date	https://github.com/RECETOX/gc-meox-tms	Metabolomics	gc_derivatization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	1.0.1	gc-meox-tms	1.0.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gcms2isocor	gcms2isocor	Conversion from GCMS PostRun Analysis to Isocor								To update		Metabolomics	gcms2isocor	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gcms2isocor	gcms2isocor	Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs								To update	https://github.com/p2m2/p2m2tools	Metabolomics	gcms2isocor	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor	0.2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	1409	1498	39	42	0	0	0	0	0	0	0	0	1409	1498	39	42	False		
+gdcwebapp	data_source_gdcwebapp	GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format								To update	http://bioinf.iasi.cnr.it/gdcwebapp/	Data Source, Convert Formats	gdcwebapp	iuc	https://github.com/fabio-cumbo/GDCWebApp4Galaxy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp	1.0.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gecko	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	723	723	235	235	0	0	0	0	786	786	95	95	1509	1509	330	330	False		
+gemini	gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	Sequence analysis, Genetic variation analysis	Sequence analysis	1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	4967	5475	1863	1992	992	1118	279	370	3756	3811	423	425	9715	10404	2565	2787	False		
+genebed_maf_to_fasta	GeneBed_Maf_Fasta2	Stitch gene blocks given a set of coding exon intervals								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	Genomic Interval Operations	genebed_maf_to_fasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta	1.0.1+galaxy0					1	1	1	0	1	1	1	0	0	1	0	0	0	1	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	1	0	4	4	2	2	221	2905	23	279	0	0	0	0	225	2909	25	281	False		
+genehunter_modscore	genehunter_modscore	Maximised LOD score pedigree analysis utility								To update	https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1	Variant Analysis	genehunter_modscore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore	3.0.0	ghm	3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+geneiobio	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	101	101	25	25	0	0	0	0	59	59	6	6	160	160	31	31	False		
+genenotebook	genenotebook_build	Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io								Up-to-date	https://genenotebook.github.io	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	0.4.16	genoboo	0.4.16			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+generate_pc_lda_matrix	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115	124	29	30	518	1029	102	261	184	198	14	17	817	1351	145	308	False		
+genetrack	genetrack	"Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand."								To update		ChIP-seq	genetrack	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack		numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	445	660	104	197	0	0	0	0	445	660	104	197	False		
+genform	genform	genform: generation of molecular formulas by high-resolution MS and MS/MS data								To update	https://sourceforge.net/projects/genform/	Metabolomics	genform	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform		genform	r8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	68	68	4	4	0	0	0	0	0	0	0	0	68	68	4	4	False		
+genomad	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	genomad	genomad		geNomad	geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.	Sequence annotation, Taxonomic classification	Sequence analysis	To update	https://github.com/apcamargo/genomad/	Metagenomics	genomad	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad	1.8.0	genomad	1.8.1	Sequence annotation, Taxonomic classification	Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+genomescope	genomescope	Analyze unassembled short reads								Up-to-date	https://github.com/tbenavi1/genomescope2.0	Statistics	genomescope	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope	2.0.1	genomescope2	2.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3181	3181	665	665	2112	2112	435	435	1622	1622	148	148	6915	6915	1248	1248	False		
+genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	47	47	13	13	0	0	0	0	0	0	0	0	47	47	13	13	False		
+genrich	genrich	Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).								To update	https://github.com/jsh58/Genrich	ChIP-seq	genrich	iuc	https://github.com/jsh58/Genrich	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich	0.5+galaxy2	genrich	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3534	3577	402	405	2840	2840	419	419	571	571	31	31	6945	6988	852	855	False		
+getTn5ExtendedCoverage	getTn5ExtendedCoverage	Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension								To update		Epigenetics	gettn5extendedcoverage	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+get_flanks	get_flanks1	Get flanks returns flanking region/s for every gene								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	get_flanks	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3768	325011	1462	2044	9350	242043	2201	6583	787	1070	119	146	13905	568124	3782	8773	False		
+get_hrun	get_hrun	Annotate indel variants with homopolymer context								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	Variant Analysis	get_hrun	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun	0.5.9.2	pyfaidx	0.8.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5	False		
+get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	746	746	136	136	0	0	0	0	1504	1504	244	244	2250	2250	380	380	False		
+get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+getindelrates_3way	indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	290	20	86	0	0	0	0	70	290	20	86	False		
+getindels_2way	getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	74	237	24	61	0	0	0	0	74	237	24	61	False		
+getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1542	1542	159	159	0	0	0	0	587	587	64	64	2129	2129	223	223	False		
+gfa_to_fa	gfa_to_fa	gfa_to_fa - Converting GFA format to Fasta format								To update	http://gfa-spec.github.io/GFA-spec/	Convert Formats	gfa_to_fa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa	0.1.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9664	9775	763	765	5623	5623	493	493	1000	1000	135	135	16287	16398	1391	1393	False		
+gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	To update	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.7	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11748	11748	767	767	6560	6560	397	397	2556	2556	106	106	20864	20864	1270	1270	False		
+gff3_rebase	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	806	812	68	68	197	197	37	37	132	132	12	12	1135	1141	117	117	False		
+gffcompare	gffcompare	Galaxy wrappers for Geo Pertea's GffCompare package.	gffcompare	gffcompare		gffcompare	Program for comparing, annotating, merging and tracking transcripts in GFF files.	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	https://github.com/gpertea/gffcompare/	Transcriptomics	gffcompare	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare	0.12.6	gffcompare	0.12.6	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3560	3980	916	999	5281	8000	1713	2521	1468	1642	208	225	10309	13622	2837	3745	False		
+gffcompare_to_bed	gffcompare_to_bed	Filter and convert a gffCompare GTF to BED								To update	https://github.com/gpertea/gffcompare/	Convert Formats	gffcompare_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	0.2.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1375	2230	329	347	1071	1071	362	362	492	492	64	64	2938	3793	755	773	False		
+gffread	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12828	13716	1740	1829	15217	23818	2588	3486	4423	4423	732	732	32468	41957	5060	6047	False		
+ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	0	5	5	5	0	24606	25662	3463	3630	26805	26808	5143	5144	8174	8237	1259	1279	59585	60707	9865	10053	False		
+ggupset	emc-ggupset	Create Upset Plots with ggupset								To update	https://github.com/const-ae/ggupset	Graphics	ggupset	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset	1.0	r-ggupset				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	490	682	74	109	127	14058	20	1798	0	0	0	0	617	14740	94	1907	False		
+glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	0	4343	4343	407	407	0	0	0	0	0	0	0	0	4343	4343	407	407	False		
+glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	11	6	6	85	984	29	230	10	11	7	8	106	1006	42	244	False		
+gnali	gnali	A tool to find nonessential, loss-of-function gene variants								Up-to-date	https://github.com/phac-nml/gnali/	Variant Analysis	gnali	nml	https://github.com/phac-nml/gnali/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali	1.1.0	gnali	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	5800	6212	826	871	7756	7756	1048	1048	1149	1149	215	215	14705	15117	2089	2134	False		
+goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	20207	21960	2807	3139	24488	26198	3066	3321	4155	4155	545	545	48850	52313	6418	7005	False		
+gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	72	5	7	0	0	0	0	0	0	0	0	34	72	5	7	False		
+gprofiler	gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense	functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more								To update	https://biit.cs.ut.ee/gprofiler	Statistics, Web Services	gprofiler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler	@TOOL_VERSION@+galaxy11	r-gprofiler2				5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	4001	4001	614	614	7882	7882	1238	1238	0	0	0	0	11883	11883	1852	1852	False		
+graph_converter	graph_converter	Convert between different graph formats								To update		Convert Formats	graph_converter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+graphclust	graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	1	0	0	0	0	0	0	0	0	0	6	0	1	False		
+graphembed	graphembed	Compute a 2D embedding of a data matrix given supervised class information								Up-to-date	https://github.com/fabriziocosta/GraphEmbed	Statistics, Graphics	graphembed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed	2.4	graph_embed	2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	78	78	6	6	120	120	43	43	0	0	0	0	198	198	49	49	False		
+graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1725	2708	97	99	2	2	2	2	0	0	0	0	1727	2710	99	101	False		
+graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	9816	10927	1285	1350	1273	1273	368	368	1104	1104	242	242	12193	13304	1895	1960	False		
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	7012	7344	323	338	0	0	0	0	0	0	0	0	7012	7344	323	338	False		
+graphprot	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy2	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	463	484	18	19	0	0	0	0	0	0	0	0	463	484	18	19	False		
+gromacs	gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj	GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.								To update	https://github.com/gromacs	Molecular Dynamics, Computational chemistry	gromacs	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	2022	gromacs	2021.3			14	8	15	0	14	8	15	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	15	9	0	184067	184203	3441	3451	9382	9382	1438	1438	10325	10325	648	648	203774	203910	5527	5537	False		
+gsc_center_scale	center_scale	Center or scale (standardize) data								To update	http://artbio.fr	Statistics	gsc_center_scale	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_filter_cells	filter_cells	Filter single cell RNAseq data on libray depth and number of detected genes								To update	http://artbio.fr	Transcriptomics	gsc_filter_cells	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_filter_genes	filter_genes	Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_filter_genes	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_gene_expression_correlations	single_cell_gene_expression_correlations	Compute single-cell paire-wise gene expressions correlations								To update	http://artbio.fr	Transcriptomics	gsc_gene_expression_correlations	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_mannwhitney_de	mannwhitney_de	Perform a mann-whitney differential testing between two sets of gene expression data								To update	http://artbio.fr	Transcriptomics	gsc_mannwhitney_de	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	4.1.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_scran_normalize	scran_normalize	Normalize raw counts using scran								To update	http://artbio.fr	Transcriptomics	gsc_scran_normalize	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	1.28.1+galaxy0	bioconductor-scran	1.30.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	24	24	3	3	2	2	10	10	2	2	102	102	28	28	False		
+gsc_signature_score	signature_score	Compute signature scores from single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_signature_score	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	2.3.9+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gstf_preparation	gstf_preparation	GeneSeqToFamily preparation converts data for the workflow								To update	https://github.com/TGAC/earlham-galaxytools/	Convert Formats	gstf_preparation	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	0.4.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	377	400	17	17	0	0	0	0	0	0	0	0	377	400	17	17	False		
+gtdb_to_taxdump	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	gtdb_to_taxdump	gtdb_to_taxdump		gtdb_to_taxdump	Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.	Data handling, Mapping, Generation	Computational biology	Up-to-date	https://github.com/nick-youngblut/gtdb_to_taxdump	Metagenomics	gtdb_to_taxdump	iuc	https://github.com/nick-youngblut/gtdb_to_taxdump	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	0.1.9	Data handling, Mapping, Generation	Computational biology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	Up-to-date	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.4.0	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	476	476	87	87	0	0	0	0	588	588	74	74	1064	1064	161	161	False		
+gtf-2-gene-list	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1982	1983	323	324	1040	1040	343	343	205	205	38	38	3227	3228	704	705	False		
+gtfToBed12	gtftobed12	Convert GTF files to BED12 format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README	Convert Formats	gtftobed12	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12	357	ucsc-gtftogenepred	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	8329	9363	3336	3828	8009	8009	3130	3130	1577	1577	344	344	17915	18949	6810	7302	False		
+gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3690	3811	326	336	3323	3323	235	235	1895	2429	234	258	8908	9563	795	829	False		
+guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	1	1	7	7	1	1	False		
+gvcftools	gvcftools_extract_variants	gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf.								To update	https://github.com/sequencing/gvcftools	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools	0.1	gvcftools	0.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gwastools	gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	Deposition, Analysis, Annotation	GWAS study	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	7303	7303	222	222	20	20	2	2	0	0	0	0	7323	7323	224	224	False		
+hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	349	359	32	33	364	364	53	53	0	0	0	0	713	723	85	86	False		
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	103	103	4	4	103	103	4	4	False		
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	502	502	66	66	0	0	0	0	0	0	0	0	502	502	66	66	False		
+happy	som.py	A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.	hap.py	hap.py		hap.py	This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	To update	https://github.com/Illumina/hap.py	Variant Analysis	happy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy	0.3.14	hap.py	0.3.15	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hardklor	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	98	111	5	8	0	0	0	0	0	0	0	0	98	111	5	8	False		
+hclust2	hclust2	Plots heatmaps								To update	https://bitbucket.org/nsegata/hclust2/	Data Visualization	hclust2	rnateam	https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2	https://github.com/bgruening/galaxytools/tree/master/tools/hclust2	0.99	hclust2	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hcluster_sg	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	243	263	54	57	0	0	0	0	0	0	0	0	243	263	54	57	False		
+hcluster_sg_parser	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	266	293	22	25	0	0	0	0	0	0	0	0	266	293	22	25	False		
+heatmap2	ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	0	46700	50808	4645	5114	64214	70429	5799	6830	7783	7912	704	724	118697	129149	11148	12668	False		
+heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	bionet, heinz		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	1281	1434	367	442	1559	1559	636	636	678	678	52	52	3518	3671	1055	1130	False		
+helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	267	267	39	39	0	0	0	0	80	80	7	7	347	347	46	46	False		
+hess	hess_astro_tool	Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope								To update		Astronomy	hess_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess	0.0.2+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+hgv_fundo	hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	145	1794	33	397	0	0	0	0	145	1794	33	397	False		
+hgv_hilbertvis	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	119	265	16	60	0	0	0	0	119	265	16	60	False		
+hgvsparser	hgvsparser	Parsing and building variant descriptor strings compliant with the HGVS standard								To update	https://github.com/VariantEffect/hgvsParseR/tree/master	Variant Analysis	hgvsparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6346	6346	2	2	0	0	0	0	0	0	0	0	6346	6346	2	2	False		
+hicexplorer	hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								Up-to-date	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.5	hicexplorer	3.7.5			38	38	38	0	38	38	38	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	33	36	33	0	44449	68602	3236	4177	46	46	21	21	1328	1328	67	67	45823	69976	3324	4265	False		
+hicstuff	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices								To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hictk	hictk	Convert cooler to juicebox_hic								Up-to-date	https://github.com/paulsengroup/hictk	Convert Formats, Epigenetics	hictk	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	1.0.0	hictk	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	9	9	0	0	0	0	0	0	0	0	17	17	9	9	False		
+hicup	hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater	The HiCUP-Pipeline from the Bioinformatics Babraham Institute.								To update	https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html	Epigenetics	hicup	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	0.9.2					7	0	7	0	7	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	6	0	901	1020	160	184	440	440	111	111	0	0	0	0	1341	1460	271	295	False		
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1819	1819	539	539	1334	1334	389	389	2472	2472	137	137	5625	5625	1065	1065	False		
+hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	156	156	20	20	0	0	0	0	220	220	11	11	376	376	31	31	False		
+high_dim_heatmap	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	2	2	0	0	0	0	0	0	0	0	18	18	2	2	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	0	12	0	0	0	0	0	0	0	0	0	228	0	12	False		
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	337151	353499	10046	10719	699868	896164	26656	34018	87016	94859	5302	5695	1124035	1344522	42004	50432	False		
+histogram	histogram_rpy	Histogram of a numeric column								To update		Graphics, Statistics	histogram	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram	https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram	1.0.4	rpy2	2.7.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3748	4661	866	1002	5993	48272	1507	7101	549	746	152	253	10290	53679	2525	8356	False		
+hivclustering	hivclustering	Infers transmission networks from pairwise distances inferred by tn93								To update	https://pypi.org/project/hivclustering/	Next Gen Mappers	hivclustering	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering	1.3.1	python-hivclustering	1.8.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	0	0	12	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	12	0	35919	36952	1283	1321	0	0	0	0	3023	3023	180	180	38942	39975	1463	1501	False		
+homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+homer	homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	Sequence motif discovery		0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	5	0	0	8531	8531	633	633	0	0	0	0	0	0	0	0	8531	8531	633	633	False		
+htseq-clip	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	98	98	19	19	0	0	0	0	0	0	0	0	98	98	19	19	False		
+htseq_count	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	Nucleic acid sequence analysis	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	144907	168824	3703	4366	213407	346792	10798	16485	27209	33124	2613	2854	385523	548740	17114	23705	False		
+humann	humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.9	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	10	10	0	6	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	26659	26659	2067	2067	865	865	174	174	3238	3238	351	351	30762	30762	2592	2592	False		
+hybpiper	hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.3.0	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1571	1571	3	3	0	0	0	0	144	144	4	4	1715	1715	7	7	False		
+hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	0	17	2	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	12	17	12	0	11429	11429	428	428	7751	7751	676	676	715	715	58	58	19895	19895	1162	1162	False		
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	473	473	93	93	0	0	0	0	0	0	0	0	473	473	93	93	False		
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	1200	1220	187	195	1588	1588	267	267	0	0	0	0	2788	2808	454	462	False		
+idconvert	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	241	276	24	33	0	0	0	0	0	0	0	0	241	276	24	33	False		
+idr	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2953	3027	109	114	1710	1710	199	199	0	0	0	0	4663	4737	308	313	False		
+idr_download	idr_download_by_ids	Image Data Resource downloading tool								To update	https://idr.openmicroscopy.org	Data Source	idr_download_by_ids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download	0.45	omero-py	5.11.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	404	404	37	37	0	0	0	0	24	24	1	1	428	428	38	38	False		
+iedb_api	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1539	1539	35	35	0	0	0	0	0	0	0	0	1539	1539	35	35	False		
+illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	273	659	101	102	0	0	0	0	153	153	15	15	426	812	116	117	False		
+image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	2	2	0	0	0	0	0	0	0	0	58	58	2	2	False		
+image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	5	5	0	0	0	0	0	0	0	0	16	16	5	5	False		
+imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21409	21849	10	12	0	0	0	0	0	0	0	0	21409	21849	10	12	False		
+imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20240614			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	1731	1731	109	109	0	0	0	0	0	0	0	0	1731	1731	109	109	False		
+improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	22	1	1	44	292	3	21	0	0	0	0	62	314	4	22	False		
+infercnv	infercnv	Infer Copy Number Variation from Single-Cell RNA-Seq Data								Up-to-date	https://github.com/broadinstitute/infercnv	Transcriptomics, Variant Analysis	infercnv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv	1.20.0	bioconductor-infercnv	1.20.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	2	2	0	0	0	0	0	0	0	0	10	10	2	2	False		
+infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	59700	112582	223	282	0	0	0	0	1157	1221	34	35	60857	113803	257	317	False		
+influx_data_manager	influx_data_manager	Handling influx_si data inputs in Galaxy workflows								To update	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/	Metabolomics	influx_si_data_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager	1.0.2	influx-si-data-manager	1.0.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+influx_si	influx_si	metabolic flux estimation based on [in]stationary labeling								To update	https://github.com/sgsokol/influx	Metabolomics	influx_si	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si	7.0.1	influx_si	7.0.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+inforna		INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	157	157	14	14	0	0	0	0	0	0	0	0	157	157	14	14	False		
+instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	102	102	16	16	0	0	0	0	0	0	0	0	102	102	16	16	False		
+intarna	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.1	intarna	3.4.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3071	7652	41	47	0	0	0	0	0	0	0	0	3071	7652	41	47	False		
+integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55149	55149	161	161	0	0	0	0	6085	6085	73	73	61234	61234	234	234	False		
+intermine_galaxy_exchange	galaxy_intermine_exchange	InterMine Exporter								To update	https://github.com/intermine	Convert Formats	intermine_galaxy_exchange	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange	0.0.1	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	46	6	12	72	87	13	15	108	108	1	1	217	241	20	28	False		
+interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	70	7	7	0	0	0	0	0	0	0	0	70	70	7	7	False		
+interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34689	55189	1634	1713	65	65	15	15	10897	10897	607	607	45651	66151	2256	2335	False		
+intersect	gops_intersect_1	Intersect the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	20472	349984	2351	3007	45587	778988	4359	14116	6087	7417	484	561	72146	1136389	7194	17684	False		
+interval2maf	Interval2Maf1	Extract MAF blocks given a set of intervals	bx-python	bx-python		bx-python	Tools for manipulating biological data, particularly multiple sequence alignments.		Sequence analysis	To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	interval2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf	1.0.1+galaxy1	bx-python	0.13.0		Sequence analysis	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	32	107	7	10	758	19538	87	1246	16	24	2	2	806	19669	96	1258	False		
+intervene	intervene_pairwise, intervene_upset	Create pairwise and upset plots	intervene	intervene		Intervene	Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.	Sequence comparison, Sequence visualisation	Computational biology	Up-to-date	https://intervene.readthedocs.io	Statistics	intervene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene	0.6.5	intervene	0.6.5	Sequence comparison, Sequence visualisation	Computational biology	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1557	1607	278	292	4458	4458	458	458	0	0	0	0	6015	6065	736	750	False		
+ipo	ipo4retgroup, ipo4xcmsSet	[W4M][LC-MS] IPO								To update	https://github.com/rietho/IPO	Metabolomics	ipo	lecorguille	https://github.com/rietho/IPO	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo	1.10.0	bioconductor-ipo	1.28.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	28279	28481	1623	1646	24662	24662	2093	2093	9780	10086	979	992	62721	63229	4695	4731	False		
+irissv	irissv	Refine insertion sequences								To update	https://github.com/mkirsche/Iris	Variant Analysis	irissv	iuc	https://github.com/galaxyproject/tools-iuc/tools/irissv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv	1.0.5	samtools	1.21			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	29	29	8	8	0	0	0	0	0	0	0	0	29	29	8	8	False		
+isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	59386	59386	151	151	56	56	1	1	4741	4741	59	59	64183	64183	211	211	False		
+isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1301	1301	59	59	1331	1331	60	60	507	507	9	9	3139	3139	128	128	False		
+isolib	isolib	Create an isotopic pattern library for given compounds and adducts.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	isolib	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	1.0.1+galaxy0	bioconductor-metabocoreutils	1.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+isoplot	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	4	3	3	0	0	0	0	0	0	0	0	4	4	3	3	False		
+itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1426	1426	71	71	0	0	0	0	0	0	0	0	1426	1426	71	71	False		
+ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	0	5	5	5	0	1252220	1252220	2366	2366	126027	126027	2496	2496	41901	41901	993	993	1420148	1420148	5855	5855	False		
+iwtomics	iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot	Interval-Wise Testing for Omics Data	iwtomics	iwtomics		IWTomics	"Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset."	Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison	Statistics and probability	To update	https://bioconductor.org/packages/release/bioc/html/IWTomics.html	Statistics	iwtomics	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics	1.0.0	bioconductor-iwtomics	1.26.0	Differential gene expression analysis, Peak calling, Genome annotation, Comparison	Statistics and probability	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	675	690	27	28	159	251	29	49	383	383	12	12	1217	1324	68	89	False		
+jasminesv	jasminesv	Merge structural variants across samples								To update	https://github.com/mkirsche/Jasmine/	Variant Analysis	jasminesv	iuc	https://github.com/galaxyproject/tools-iuc/jasminesv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv	1.0.11	jasminesv	1.1.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32	32	9	9	53	53	19	19	0	0	0	0	85	85	28	28	False		
+jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	21153	22174	5514	5779	17428	17428	6458	6458	15673	17267	3248	3786	54254	56869	15220	16023	False		
+jbrowse	jbrowse_to_container	A tool allowing to export a JBrowse dataset into a JBrowse docker container								To update	https://jbrowse.org	Web Services	jbrowse_to_container	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse		python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse_2	jbrowse_2		JBrowse 2	Modular genome browser with views of synteny and structural variation.	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.15.4	jbrowse2	2.15.4	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1312	1312	219	219	116	116	58	58	37	37	6	6	1465	1465	283	283	False		
+jcvi_gff_stats	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.16			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2747	2926	596	637	2311	2311	741	741	1145	1145	469	469	6203	6382	1806	1847	False		
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1825	1825	237	237	0	0	0	0	971	971	56	56	2796	2796	293	293	False		
+join	gops_join_1	Join the intervals of two datasets side-by-side								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	join	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	15624	330820	1864	2438	52317	513688	10198	39421	1329	1645	213	289	69270	846153	12275	42148	False		
+join_files_by_id	join_files_by_id	This tool will join datasets according to a column with identifier								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	Text Manipulation	join_files_by_id	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id	1.0	r-data.table	1.11.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+join_files_on_column_fuzzy	join_files_on_column_fuzzy	Join two files on a common column, allowing a certain difference.								To update		Text Manipulation	join_files_on_column_fuzzy	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	1.0.1	python				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1980	2697	345	410	0	0	0	0	1081	1081	44	44	3061	3778	389	454	False		
+jq	jq	JQ is a lightweight and flexible command-line JSON processor								To update	https://stedolan.github.io/jq/	Text Manipulation	jq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq	1.0	jq	1.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	660	2374	61	63	336	336	82	82	281	281	11	11	1277	2991	154	156	False		
+jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	30	30	2	2	0	0	0	0	0	0	0	0	30	30	2	2	False		
+justdiff	justdiff	Unix diff								To update	http://artbio.fr	Text Manipulation	justdiff	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	3.10+galaxy0	diffutils				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+justgzip	justgzip	Compress fastq sequence files								To update	http://artbio.fr	Convert Formats	justgzip	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	2.8+galaxy0	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+jvarkit	jvarkit_wgscoverageplotter	Jvarkit : Java utilities for Bioinformatics								Up-to-date	https://lindenb.github.io/jvarkit/	SAM	jvarkit	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit	20201223	jvarkit-wgscoverageplotter	20201223			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7179	7179	509	509	11138	11138	1145	1145	0	0	0	0	18317	18317	1654	1654	False		
+kallisto	kallisto_pseudo, kallisto_quant	kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.	kallisto	kallisto		kallisto	A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.	Gene expression profiling	Transcriptomics, RNA-seq, Gene expression	To update	https://pachterlab.github.io/kallisto/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto	0.48.0	kallisto	0.51.1	Gene expression profiling	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	28398	29031	932	965	73705	80087	2603	3025	5333	5567	218	230	107436	114685	3753	4220	False		
+kaptive	kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kat_sect	kat_@EXECUTABLE@	SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.								To update			kat_sect	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	379	379	53	53	8259	8259	271	271	0	0	0	0	8638	8638	324	324	False		
+kegalign	kegalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	kegalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	0.1.2.7	kegalign-full	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	5	5	1	1	False		
+kernel_canonical_correlation_analysis	kcca1	Kernel Canonical Correlation Analysis								To update		Statistics	kernel_canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis	1.0.0	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	62	70	4	4	207	334	27	71	0	0	0	0	269	404	31	75	False		
+kernel_principal_component_analysis	kpca1	Kernel Principal Component Analysis								To update		Statistics	kernel_principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis	1.0.0	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	144	157	26	30	268	707	83	248	0	0	0	0	412	864	109	278	False		
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	8	8	8	0	1995	2091	174	193	1430	1430	389	389	1580	1580	56	56	5005	5101	619	638	False		
+king	king	Kinship-based INference for Gwas								Up-to-date	http://people.virginia.edu/~wc9c/KING/	Variant Analysis	king	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/king	2.2.7	king	2.2.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	8	4	4	0	0	0	0	0	0	0	0	8	8	4	4	False		
+kinwalker		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.1.0	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	503	503	58	58	0	0	0	0	0	0	0	0	503	503	58	58	False		
+kma	kma_map	Map with KMA								To update	https://bitbucket.org/genomicepidemiology/kma	Next Gen Mappers	kma	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma	1.4.14	kma	1.4.15			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+kmd_hmdb_data_plot	kmd_hmdb_data_plot	retrieves data from KMD HMDB API and produce plot and csv file								To update	https://github.com/workflow4metabolomics/tools-metabolomics	Metabolomics	kmd_hmdb_data_plot	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1342	1342	63	63	0	0	0	0	0	0	0	0	1342	1342	63	63	False		
+kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	5	5	5	0	48136	48164	2754	2760	59952	130398	5869	8654	29008	31148	1936	2200	137096	209710	10559	13614	False		
+kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	271367	271786	6384	6409	101752	101752	4662	4662	53562	53562	1663	1663	426681	427100	12709	12734	False		
+kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23008	23014	1060	1061	16194	24490	1719	2168	14898	14898	436	436	54100	62402	3215	3665	False		
+kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3185	3185	495	495	0	0	0	0	385	385	48	48	3570	3570	543	543	False		
+kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3981	3986	769	771	4087	5610	991	1284	88	88	41	41	8156	9684	1801	2096	False		
+krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	48516	48516	2373	2373	8787	8787	943	943	4369	4369	393	393	61672	61672	3709	3709	False		
+krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	38	2	2	0	0	0	0	0	0	0	0	34	38	2	2	False		
+labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	887	927	13	15	4	4	3	3	0	0	0	0	891	931	16	18	False		
+last	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1584	Sequence alignment	Comparative genomics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	329	329	94	94	0	0	0	0	0	0	0	0	329	329	94	94	False		
+lastz	lastz_wrapper_2, lastz_d_wrapper	Galaxy wrappers for the Lastz and Lastz_d	lastz	lastz		LASTZ	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.	Sequence alignment, Read mapping	Genomics	Up-to-date	https://github.com/lastz/lastz	Next Gen Mappers	lastz	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz	1.04.22	lastz	1.04.22	Sequence alignment, Read mapping	Genomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	77409	84356	447	475	156658	193590	870	3511	38579	38780	173	203	272646	316726	1490	4189	False		
+lastz_paired_reads	lastz_paired_reads_wrapper	Galaxy wrapper for the Lastz alignment tool on paired reads								To update		Next Gen Mappers	lastz_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads	1.1.1	lastz	1.04.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	9	3	4	0	0	0	0	8	10	5	5	15	19	8	9	False		
+lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	89	137	4	20	118	6136	15	1112	0	0	0	0	207	6273	19	1132	False		
+lcrgenie	lcrgenie	Ligase Chain Reaction Genie								To update	https://github.com/neilswainston/LCRGenie	Synthetic Biology	lcrgenie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie	1.0.2	lcr_genie				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lda_analysis	lda_analy1	Perform Linear Discriminant Analysis								To update		Graphics, Statistics	lda_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis	1.0.1	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	147	159	46	48	793	1538	101	314	0	4	0	3	940	1701	147	365	False		
+legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	92	92	8	8	0	0	0	0	0	0	0	0	92	92	8	8	False		
+length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	4349	4466	666	698	2093	2286	928	998	201	201	77	77	6643	6953	1671	1773	False		
+lfq_protein_quant	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	78	116	12	19	0	0	0	0	0	0	0	0	78	116	12	19	False		
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	171	27	30	0	0	0	0	0	0	0	0	149	171	27	30	False		
+limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23442	24466	2379	2475	45734	49342	4565	5032	9327	9517	835	842	78503	83325	7779	8349	False		
+lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	39	4	4	0	0	0	0	0	0	0	0	39	39	4	4	False		
+linear_regression	LinearRegression1	Perform Linear Regression								To update		Statistics	linear_regression	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression	https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression	1.0.1	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	146	1103	31	271	0	0	0	0	146	1103	31	271	False		
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	512	512	126	126	0	0	0	0	480	480	65	65	992	992	191	191	False		
+locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								Up-to-date	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	2.0.1	locarna	2.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	314	350	36	46	0	0	0	0	0	0	0	0	314	350	36	46	False		
+lofreq	lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi	LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.								Up-to-date	https://csb5.github.io/lofreq/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq	2.1.5	lofreq	2.1.5			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	0	0	0	4	0	0	0	0	0	0	5	5	5	0	4176367	4176367	4301	4301	509615	509615	8213	8213	106342	106342	1815	1815	4792324	4792324	14329	14329	False		
+logistic_regression_vif	LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	64	173	12	48	0	0	0	0	64	173	12	48	False		
+logol	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+longorf	longORF	obtain longest ORF in six-frame translations								To update		Sequence Analysis	longorf	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf	0.3.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	822	822	14	14	0	0	0	0	0	0	0	0	822	822	14	14	False		
+lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1219	1219	182	182	0	0	0	0	37	37	4	4	1256	1256	186	186	False		
+ltq_iquant_cli										To update			ltq_iquant_cli	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lumpy_smoove	lumpy_smoove, vcf2hrdetect	Galaxy wrapper of the lumpy-using smoove workflow								To update	http://artbio.fr	Variant Analysis	lumpy_smoove	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	0.2.8+galaxy1	svtyper	0.7.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lumpy_sv	lumpy_prep, lumpy_sv	LUMPY - a general probabilistic framework for structural variant discovery								Up-to-date	http://layerlab.org/software/	Variant Analysis	lumpy_sv	iuc	https://github.com/arq5x/lumpy-sv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv	0.3.1	lumpy-sv	0.3.1			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	1534	1534	199	199	0	0	0	0	0	0	0	0	1534	1534	199	199	False		
+lumpy_sv	lumpy	Find structural variations								To update	http://artbio.fr	Variant Analysis	lumpy_sv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv	1.3	lumpy-sv	0.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	44	44	11	11	0	0	0	0	0	0	0	0	44	44	11	11	False		
+maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2835	2835	59	59	0	0	0	0	0	0	0	0	2835	2835	59	59	False		
+macs2	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	0	0	9	0	0	0	0	0	0	9	9	9	0	87810	96069	4980	5629	153500	227569	12946	18825	10988	12301	692	807	252298	335939	18618	25261	False		
+maf_cpg_filter	cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	85	356	6	28	0	0	0	0	85	356	6	28	False		
+maf_stats	maf_stats1	MAF Coverage statistics								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	maf_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats	1.0.2+galaxy0					1	1	1	0	1	1	1	0	0	1	0	0	0	1	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	1	0	15	21	7	9	227	2470	52	464	1	1	1	1	243	2492	60	474	False		
+mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	0	2	2	2	0	172433	174456	1865	1951	108640	122790	4266	5521	20027	20027	1172	1172	301100	317273	7303	8644	False		
+maftoaxt	maftoaxt	Convert dataset from MAF to axt format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_maftoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	469	ucsc-maftoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mageck	mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test	Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	mageck	mageck		MAGeCK	Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	Genetic variation analysis	Genetics, Genetic variation, Genomics	To update	https://sourceforge.net/projects/mageck/	Genome editing		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck	0.5.9.2	mageck	0.5.9.5	Genetic variation analysis	Genetics, Genetic variation, Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	11761	12093	873	889	5762	5762	473	473	5610	5610	343	343	23133	23465	1689	1705	False		
+mahotas_features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	44	6	6	0	0	0	0	0	0	0	0	39	44	6	6	False		
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6417	6861	1315	1366	7235	7235	1858	1858	4112	4112	902	902	17764	18208	4075	4126	False		
+maldiquant	maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base				0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1452	3822	61	68	0	0	0	0	1065	1065	39	39	2517	4887	100	107	False		
+malt	malt_run	Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.								To update	https://github.com/husonlab/malt	Next Gen Mappers	malt_run	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt	0.5.3	malt	0.62			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	24	9	9	0	0	0	0	0	0	0	0	24	24	9	9	False		
+manta	manta	Structural variant and indel caller for mapped sequencing data								To update	http://artbio.fr	Variant Analysis	manta	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/manta	https://github.com/ARTbio/tools-artbio/tree/main/tools/manta	1.6	manta	1.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	218	218	34	34	0	0	0	0	0	0	0	0	218	218	34	34	False		
+map_param_value	map_param_value	Map a parameter value to another value								To update		Text Manipulation	map_param_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3780	3780	67	67	1012	1012	57	57	105	105	3	3	4897	4897	127	127	False		
+map_peptides_to_bed	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	38	44	6	7	0	0	0	0	0	0	0	0	38	44	6	7	False		
+mapping_quality_stats	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mapping_to_ucsc	mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7871	7871	32	32	0	0	0	0	0	0	0	0	7871	7871	32	32	False		
+marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	51	51	4	4	0	0	0	0	0	0	0	0	51	51	4	4	False		
+mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	10119	10119	61	61	19	19	9	9	647	647	7	7	10785	10785	77	77	False		
+mashmap	mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	894	894	12	12	81	81	5	5	0	0	0	0	975	975	17	17	False		
+masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	471	582	35	40	589	589	80	80	0	0	0	0	1060	1171	115	120	False		
+matchms	matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting	Searching, filtering and converting mass spectral libraries.	matchms	matchms		Matchms	Tool to import, process, clean, and compare mass spectrometry data.	Spectral library search, Format validation, Filtering	Metabolomics	Up-to-date	https://github.com/matchms/matchms	Metabolomics	matchms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	0.27.0	matchms	0.27.0	Spectral library search, Format validation, Filtering	Metabolomics	2	14	14	0	2	14	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	1620	1620	70	70	27	27	8	8	1685	1685	12	12	3332	3332	90	90	False		
+mauve_contig_mover	mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mavedb	mavedb_importer	data source for MaveDB								To update		Data Source	mavedb_importer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb	0.9					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	2	2	0	0	0	0	0	0	0	0	8	8	2	2	False		
+maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	1	0	2798	2798	314	314	2452	2452	508	508	914	914	89	89	6164	6164	911	911	False		
+maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6863	7021	1251	1264	2798	2798	543	543	3189	3189	352	352	12850	13008	2146	2159	False		
+mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	35	13	13	0	0	0	0	0	0	0	0	35	35	13	13	False		
+mdanalysis	mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf	MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations								To update	https://github.com/MDAnalysis/mdanalysis	Computational chemistry	mdanalysis	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis	1.0.0	mdanalysis				10	5	10	0	10	5	10	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	3209	3268	318	326	182	182	51	51	397	397	39	39	3788	3847	408	416	False		
+mdfileconverter	md_converter	A tool for interconverting between different MD structure and trajectory file formats.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter	1.9.7	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26720	26762	251	253	784	784	54	54	977	977	53	53	28481	28523	358	360	False		
+mdslicer	md_slicer	A tool for slicing trajectory files using MDTraj.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer	1.9.9	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	174	174	19	19	6	6	4	4	441	441	7	7	621	621	30	30	False		
+mdtraj	traj_selections_and_merge	MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories								To update	https://github.com/mdtraj/mdtraj	Computational chemistry	mdtraj	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj	1.9.7	mdtraj				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	36	8	8	63	63	4	4	0	0	0	0	99	99	12	12	False		
+mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	73	86	5	5	0	0	0	0	0	0	0	0	73	86	5	5	False		
+mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	3	3	0	0	0	0	0	0	0	0	20	25	3	3	False		
+measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	0	3	3	3	0	117975	117975	1693	1693	55063	55063	796	796	9325	9325	639	639	182363	182363	3128	3128	False		
+medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	9	9	0	0	0	0	0	0	0	0	27	27	9	9	False		
+megablast_xml_parser	megablast_xml_parser	Parse blast XML output								To update		Next Gen Mappers, Convert Formats	megablast_xml_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	743	816	103	141	292	2868	82	459	0	0	0	0	1035	3684	185	600	False		
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	12692	13292	1349	1400	16645	16645	2140	2140	6214	6214	431	431	35551	36151	3920	3971	False		
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	513	557	152	155	74	74	35	35	10	10	4	4	597	641	191	194	False		
+megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	4130	4130	447	447	0	0	0	0	0	0	0	0	4130	4130	447	447	False		
+meme	meme_dreme, meme_fimo, meme_meme, meme_psp_gen	The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.	meme_meme	meme_fimo, meme_meme		meme_meme	An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	To update	http://meme-suite.org/	ChIP-seq	meme	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme	5.5.6	meme	5.5.7	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	3	0	4	0	3	0	4	0	0	0	0	0	0	0	0	0	0	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	4	4	0	20990	22979	762	892	10975	25929	1551	3249	0	0	0	0	31965	48908	2313	4141	False		
+meme_chip	meme_chip	Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.								To update	http://meme-suite.org/	ChIP-seq	meme_chip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip	4.11.2	graphicsmagick	1.3.26			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6413	7000	705	743	7260	7260	1171	1171	0	0	0	0	13673	14260	1876	1914	False		
+meneco	meneco	Meneco computes minimal completions to your draft network with reactions from a repair network								Up-to-date	http://bioasp.github.io/meneco/	Systems Biology	meneco	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	1.5.2	meneco	1.5.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+merge	gops_merge_1	Merge the overlapping intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	565922	566630	418	441	45844	107523	671	4353	19828	19994	100	137	631594	694147	1189	4931	False		
+merge_cols	mergeCols1	Merge columns together.								To update		Text Manipulation	merge_cols	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols	https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols	1.0.3	python				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	20905	31051	1906	2128	21780	132833	885	3172	1524	1925	122	152	44209	165809	2913	5452	False		
+mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	25	2	3	0	0	0	0	0	0	0	0	18	25	2	3	False		
+merlin	merlin	Pedigree Analysis package	merlin	merlin		Merlin	Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation	Haplotype mapping, Genetic mapping	GWAS study, Mapping	Up-to-date	http://csg.sph.umich.edu/abecasis/Merlin/	Variant Analysis	merlin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin	1.1.2	merlin	1.1.2	Haplotype mapping	GWAS study, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3150	3150	477	477	730	730	196	196	1183	1183	151	151	5063	5063	824	824	False		
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+meta_proteome_analyzer	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	126	126	20	20	0	0	0	0	0	0	0	0	126	126	20	20	False		
+metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	0	2	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	6135	6135	382	382	881	881	151	151	1094	1094	104	104	8110	8110	637	637	False		
+metabuli	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	metabuli	metabuli		metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid	Taxonomic classification	Taxonomy	To update	https://github.com/steineggerlab/Metabuli	Sequence Analysis, Metagenomics	metabuli	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli	1.0.5	metabuli	1.0.8	Taxonomic classification	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	7.bba0d80	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	312	312	40	40	0	0	0	0	0	0	0	0	312	312	40	40	False		
+metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	980	980	323	323	0	0	0	0	0	0	0	0	980	980	323	323	False		
+metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	556	756	17	21	310	514	35	55	0	0	0	0	866	1270	52	76	False		
+metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4471	4471	29	29	0	0	0	0	0	0	0	0	4471	4471	29	29	False		
+metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	0	1	2	4	0	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	16629	16648	1183	1187	3983	3983	572	572	4747	4747	278	278	25359	25378	2033	2037	False		
+metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	2730	2831	260	262	0	0	0	0	1540	1540	71	71	4270	4371	331	333	False		
+metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	142	142	32	32	0	0	0	0	379	379	47	47	521	521	79	79	False		
+metfrag	metfrag	[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity)								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag	2.4.5+galaxy3	metfrag	2.4.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	192	192	20	20	0	0	0	0	0	0	0	0	192	192	20	20	False		
+metfrag-vis	metfrag_vis	[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis	2.4.5+galaxy0	metfrag	2.4.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	50	14	14	0	0	0	0	0	0	0	0	50	50	14	14	False		
+methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	632	5461	155	453	0	0	0	0	0	0	0	0	632	5461	155	453	False		
+methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	14907	18971	638	894	2677	2677	230	230	2313	2313	83	83	19897	23961	951	1207	False		
+methylkit	methylkit	A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.								To update	http://bioconductor.org/packages/release/bioc/html/methylKit.html	Epigenetics	methylkit	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	0.99.2	bioconductor-methylkit	1.28.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3209	4572	312	442	479	479	79	79	315	315	51	51	4003	5366	442	572	False		
+mfassignr	mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot	The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements	mfassignr	mfassignr		MFAssignR	Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements.	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	Up-to-date	https://github.com/RECETOX/MFAssignR	Metabolomics	MFAssignR	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	1.1.1	r-mfassignr	1.1.1	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	8	8	0	0	0	0	0	0	0	0	10	10	8	8	False		
+mg_toolkit	mg_toolkit_bulk_download, mg_toolkit_original_metadata	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	mg-toolkit	mg-toolkit		mg-toolkit	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	Data retrieval	Metagenomics	Up-to-date	https://github.com/EBI-Metagenomics/emg-toolkit	Metagenomics	mg_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	0.10.4	mg-toolkit	0.10.4	Data retrieval	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+mgf_formatter	mgf_formatter									Up-to-date			mgf_formatter	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter	1.0.0	mgf-formatter	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	573	573	3	3	0	0	0	0	0	0	0	0	573	573	3	3	False		
+miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+microsatbed	microsatbed	Select microsatellites for a bed file								To update	https://github.com/lmdu/pytrf	Sequence Analysis	microsatbed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed	1.3.3	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	228	4	4	18	18	1	1	0	0	0	0	246	246	5	5	False		
+microsatellite_birthdeath	microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+microsats_alignment_level	microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	135	973	50	140	0	0	0	0	135	973	50	140	False		
+microsats_mutability	microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	34	312	22	87	0	0	0	0	34	312	22	87	False		
+migmap	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	Sequence analysis, Read mapping	Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1082	1229	25	33	1153	1376	70	89	0	0	0	0	2235	2605	95	122	False		
+minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1213	1309	115	124	0	0	0	0	0	0	0	0	1213	1309	115	124	False		
+mine	maximal_information_based_nonparametric_exploration	Maximal Information-based Nonparametric Exploration								To update		Variant Analysis	mine	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine	0.0.1	MINE				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	11	8	8	17	63	6	19	0	0	0	0	26	74	14	27	False		
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7116	7116	256	256	0	0	0	0	278	278	60	60	7394	7394	316	316	False		
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13357	13479	554	562	8416	8416	448	448	898	898	85	85	22671	22793	1087	1095	False		
+minimap2	minimap2	A fast pairwise aligner for genomic and spliced nucleotide sequences	minimap2	minimap2		Minimap2	Pairwise aligner for genomic and spliced nucleotide sequences	Pairwise sequence alignment	Mapping	Up-to-date	https://github.com/lh3/minimap2	Next Gen Mappers	minimap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2	2.28	minimap2	2.28	Pairwise sequence alignment	Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	346530	349075	4323	4419	108535	108535	4075	4075	22331	22331	1166	1166	477396	479941	9564	9660	False		
+minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	229	229	32	32	0	0	0	0	0	0	0	0	229	229	32	32	False		
+miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1244	1244	86	86	24	24	15	15	0	0	0	0	1268	1268	101	101	False		
+miranda	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6408	6514	94	99	0	0	0	0	0	0	0	0	6408	6514	94	99	False		
+miranda2asko	miranda2asko	Converts miRanda output into AskOmics format								To update		Convert Formats	miranda2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	0.2	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1458	1458	36	36	1458	1458	36	36	False		
+mirmachine	mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	False		
+mirnature	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	18	18	9	9	0	0	0	0	0	0	0	0	18	18	9	9	False		
+misc	target_screen, use_theoretical_mz_annotations									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	1.0.0	pandas				0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	2	2	0	0	0	0	0	0	0	0	6	6	2	2	False		
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1117	1117	116	116	0	0	0	0	295	295	25	25	1412	1412	141	141	False		
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1020	1020	176	176	414	414	73	73	277	277	20	20	1711	1711	269	269	False		
+mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	0	191295	191295	1111	1111	42265	42265	320	320	10904	10904	83	83	244464	244464	1514	1514	False		
+mixmodel4repeated_measures	mixmodel4repeated_measures	[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model								To update	http://workflow4metabolomics.org	Metabolomics	mixmodel4repeated_measures	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures	3.1.0	r-lme4				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	13300	13471	1480	1501	6532	6532	1167	1167	10334	11841	1083	1300	30166	31844	3730	3968	False		
+moFF	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	331	762	20	34	0	0	0	0	137	137	4	4	468	899	24	38	False		
+moabs	moabs	MOABS for differential methylation analysis on Bisulfite sequencing data.								To update	https://github.com/sunnyisgalaxy/moabs	Epigenetics	moabs	iuc	https://github.com/sunnyisgalaxy/moabs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs	1.3.4.6	moabs	1.3.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	339	339	56	56	0	0	0	0	0	0	0	0	339	339	56	56	False		
+mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	119024	119024	628	628	42	42	2	2	36310	36310	191	191	155376	155376	821	821	False		
+molecule2gspan	bg_mol2gspan	converter								To update	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	Convert Formats	molecule_to_gspan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	0.2	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3610	3610	559	559	1728	1728	434	434	0	0	0	0	5338	5338	993	993	False		
+morpheus	morpheus	Morpheus MS Search Application	morpheus	morpheus		Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.	Peptide database search	Proteomics	To update	https://cwenger.github.io/Morpheus	Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	288	morpheus	290	Peptide database search	Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	105	153	12	19	0	0	0	0	833	833	93	93	938	986	105	112	False		
+morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mosdepth	mosdepth	fast and flexible BAM/CRAM depth calculation								Up-to-date	https://github.com/brentp/mosdepth	SAM	mosdepth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth	0.3.8	mosdepth	0.3.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1278	1278	87	87	168	168	24	24	102	102	5	5	1548	1548	116	116	False		
+mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	0	129	129	129	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	126	129	129	0	297546	326056	37506	41763	565218	682083	72163	89926	167400	182490	26963	28404	1030164	1190629	136632	160093	False		
+motus	mereg_mOTUs_tables, motus_profiler	Tool for profiling the abundance of microbial taxa.	mOTUs	mOTUs		Metagenomic operational taxonomic units (mOTUs)	Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/motu-tool/mOTUs	Metagenomics	motus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs	https://github.com/bgruening/galaxytools/tree/master/tools/motus	3.1.0	motus	3.1.0	Taxonomic classification	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	76	9	9	0	0	0	0	0	0	0	0	71	76	9	9	False		
+mqppep	mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	13	13	3	3	0	0	0	0	0	0	0	0	13	13	3	3	False		
+mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ms2deepscore	ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training	Mass spectra similarity scoring using a trained ms2deepscore model.	ms2deepscore	ms2deepscore		MS2DeepScore	MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	To update	https://github.com/matchms/ms2deepscore	Metabolomics	ms2deepscore	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	2.0.0	ms2deepscore	2.1.0	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ms2snoop	ms2snoop	[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.								To update	http://workflow4metabolomics.org	Metabolomics	ms2snoop	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop	2.2.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+msPurity	mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								Up-to-date	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity	1.28.0	bioconductor-mspurity	1.28.0			0	0	10	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	848	848	91	91	0	0	0	0	0	0	0	0	848	848	91	91	False		
+msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	864	929	91	101	1100	1100	175	175	0	0	0	0	1964	2029	266	276	False		
+msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20749	22184	455	469	1239	1239	71	71	2666	2666	53	53	24654	26089	579	593	False		
+msgfplus	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	473	529	33	43	0	0	0	0	0	0	0	0	473	529	33	43	False		
+msmetaenhancer	msmetaenhancer		msmetaenhancer	msmetaenhancer		MSMetaEnhancer	Tool for mass spectra metadata annotation.	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/MSMetaEnhancer	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	0.4.0	msmetaenhancer	0.4.0	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	10	10	0	0	0	0	48	48	1	1	251	251	11	11	False		
+msms_extractor	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	110	110	11	11	0	0	0	0	0	0	0	0	110	110	11	11	False		
+msp_merge	msp_merge									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	0.1.0	matchms	0.27.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+msp_split	msp_split	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								To update	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		tomnl	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split	0.0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+msstats	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2353	2353	559	559	1122	1122	211	211	1091	1091	35	35	4566	4566	805	805	False		
+msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	795	795	104	104	0	0	0	0	461	461	12	12	1256	1256	116	116	False		
+mt2mq	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	275	275	38	38	0	0	0	0	0	0	0	0	275	275	38	38	False		
+multigps	multigps	Analyzes collections of multi-condition ChIP-seq data.								To update	http://mahonylab.org/software/multigps/	ChIP-seq	multigps	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps	0.74.0	fonts-conda-ecosystem				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	485	871	159	298	0	0	0	0	485	871	159	298	False		
+multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	106	106	25	25	0	0	0	0	0	0	0	0	106	106	25	25	False		
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	182221	192389	19343	20494	163961	182413	26449	29758	40663	41855	5974	6157	386845	416657	51766	56409	False		
+multispecies_orthologous_microsats	multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mummer	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	883	921	199	211	730	730	199	199	136	202	34	49	1749	1853	432	459	False		
+mummer4	mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1			6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	6	3	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	21587	22119	1940	2033	29284	29284	3626	3626	8194	8194	545	545	59065	59597	6111	6204	False		
+music_deconvolution	music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)								Up-to-date	https://github.com/xuranw/MuSiC	Transcriptomics	music	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/	https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution	0.1.1	music-deconvolution	0.1.1			5	5	4	0	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	2801	2801	289	289	364	364	80	80	1357	1357	21	21	4522	4522	390	390	False		
+mutate_snp_codon	mutate_snp_codon_1	Mutate Codons with SNPs								To update		Variant Analysis	mutate_snp_codon	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	44	49	5	5	81	417	23	118	0	0	0	0	125	466	28	123	False		
+mutational_patterns	mutational_patterns	Mutational patterns and signatures in base substitution catalogs								Up-to-date	http://artbio.fr	Variant Analysis	mutational_patterns	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	3.12.0	bioconductor-mutationalpatterns	3.12.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	854	860	110	111	79	79	15	15	274	274	13	13	1207	1213	138	139	False		
+mzmine	mzmine_batch	mass-spectrometry data processing, with the main focus on LC-MS data	mzmine	mzmine		MZmine	Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	Up-to-date	http://mzmine.github.io/	Metabolomics	mzmine_batch	iuc	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine	3.9.0	mzmine	3.9.0	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5	False		
+mzml_validator	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mzxmlshaper	mzxmlshaper	Convert mzML, mzXML or netCDF files to mzML or mzXML								To update	https://rdrr.io/bioc/mzR/	Metabolomics	mzxmlshaper	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper	1.0.0+galaxy0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+naltorfs	bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2			3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	204	204	75	75	0	0	0	0	204	204	75	75	False		
+nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	839	839	12	12	0	0	0	0	269	269	5	5	1108	1108	17	17	False		
+nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	99052	100009	5671	5755	40386	40386	3371	3371	17919	17919	2188	2188	157357	158314	11230	11314	False		
+nanopolish	nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants	Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.								Up-to-date	https://github.com/jts/nanopolish		nanopolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	0.14.0	nanopolish	0.14.0			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	9284	9694	215	229	0	0	0	0	2358	2358	49	49	11642	12052	264	278	False		
+nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1091	1091	44	44	0	0	0	0	0	0	0	0	1091	1091	44	44	False		
+nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	40	1	1	0	0	0	0	0	0	0	0	36	40	1	1	False		
+ncbi_acc_download	ncbi_acc_download	Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API								Up-to-date	https://github.com/kblin/ncbi-acc-download	Data Source	ncbi_acc_download	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download	0.2.8	ncbi-acc-download	0.2.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6873	6873	1664	1664	17651	17651	4513	4513	6228	6228	972	972	30752	30752	7149	7149	False		
+ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	15	16	16	15	0	391141	443752	9760	10546	306361	350178	11767	13684	227235	244814	3192	3617	924737	1038744	24719	27847	False		
+ncbi_datasets	datasets_download_gene, datasets_download_genome	NCBI datasets downloads biological sequence data across all domains of life from NCBI.	ncbi_datasets	ncbi_datasets		NCBI Datasets	NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.	Data handling, Sequence database search, Data retrieval	Biological databases	To update	https://github.com/ncbi/datasets	Data Source	ncbi_datasets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets	16.20.0	ncbi-datasets-cli		Data handling, Sequence database search, Data retrieval	Biological databases	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	1	2	2	0	4417	4417	1024	1024	6940	6940	2275	2275	1	1	1	1	11358	11358	3300	3300	False		
+ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	6	6	0	0	0	0	15	15	6	6	False		
+ncbi_entrez_direct	ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch	NCBI Entrez Direct allow fetching data from NCBI Databases								Up-to-date	http://www.ncbi.nlm.nih.gov/books/NBK179288/	Data Source	ncbi_entrez_direct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct	22.4	entrez-direct	22.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	2	0	0	0	0	0	3	0	2	False		
+ncbi_entrez_eutils	ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary	NCBI Entrez E-Utilties allow fetching data from NCBI Databases								To update	https://www.ncbi.nlm.nih.gov/books/NBK25501/	Data Source	ncbi_entrez_eutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils	1.70	python				0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	4	0	0	0	2	0	0	0	0	0	0	0	7	7	0	2794	3191	533	664	0	0	0	0	0	0	0	0	2794	3191	533	664	False		
+ncbi_fcs_adaptor	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	842	842	93	93	0	0	0	0	842	842	93	93	False		
+ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	125	125	26	26	2489	2489	139	139	0	0	0	0	2614	2614	165	165	False		
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	790	790	160	160	0	0	0	0	0	0	0	0	790	790	160	160	False		
+netboxr	netboxr	netboxr enables automated discovery of biological process modules by network analysis								To update		Systems Biology	netboxr	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/netboxr	1.6.0	bioconductor-netboxr	1.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	12	6	6	0	0	0	0	0	0	0	0	12	12	6	6	False		
+newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33637	34195	1113	1172	16257	16257	1816	1816	7582	7582	899	899	57476	58034	3828	3887	False		
+nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	0	2	0	0	4411	4411	396	396	9708	9708	279	279	2099	2099	212	212	16218	16218	887	887	False		
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	391	391	158	158	0	0	0	0	0	0	0	0	391	391	158	158	False		
+ngmlr	ngmlr	CoNvex Gap-cost alignMents for Long Reads	ngmlr	ngmlr		NGMLR	An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping, DNA structural variation	Up-to-date	https://github.com/philres/ngmlr	Next Gen Mappers	ngmlr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr	0.2.7	ngmlr	0.2.7	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1403	1403	49	49	0	0	0	0	0	0	0	0	1403	1403	49	49	False		
+ngsutils	ngsutils_bam_filter	NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.	ngsutils	ngsutils		NGSUtils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets	Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering	Genomics, Transcriptomics	To update	https://github.com/ngsutils/ngsutils	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils		ngsutils	0.5.9	Read pre-processing, Variant calling, Formatting, Sequence contamination filtering	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	24611	29662	633	716	15523	21395	740	1128	7751	8972	125	145	47885	60029	1498	1989	False		
+nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+nmr_annotation	NmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation								To update	http://workflow4metabolomics.org	Metabolomics	nmr_annotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_annotation	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation	3.0.0	r-batch	1.1_4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	49	49	5	5	0	0	0	0	0	0	0	0	49	49	5	5	False		
+nmr_annotation2d	2DNmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra								To update	http://workflow4metabolomics.org	Metabolomics	2dnmrannotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d	2.0.0	r-batch	1.1_4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+nmr_preprocessing	NMR_Preprocessing, NMR_Read	[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction								To update	http://workflow4metabolomics.org	Metabolomics	nmr_preprocessing	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_preprocessing	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing		r-batch	1.1_4			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	142	142	8	8	0	0	0	0	335	341	9	9	477	483	17	17	False		
+nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	107	143	13	15	148	148	20	20	0	0	0	0	255	291	33	35	False		
+normalization	normalization	[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data								To update	http://workflow4metabolomics.org	Metabolomics	normalization	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/normalization	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization	1.0.7	r-batch	1.1_4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	152	162	39	40	0	0	0	0	233	236	12	12	385	398	51	52	False		
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	7780	7780	337	337	1	1	1	1	2323	2323	99	99	10104	10104	437	437	False		
+nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	118	863	19	26	0	0	0	0	0	0	0	0	118	863	19	26	False		
+nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+numeric_clustering	numeric_clustering	Clustering tool for numberic values								To update	http://scikit-learn.org/stable/index.html	Statistics	numeric_clustering	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	0.9	anaconda				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	391	486	5	11	0	0	0	0	0	0	0	0	391	486	5	11	False		
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	352	352	42	42	8	8	6	6	0	0	0	0	360	360	48	48	False		
+obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	37598	37598	1277	1277	0	0	0	0	3862	3862	280	280	41460	41460	1557	1557	False		
+ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	54	6	6	0	0	0	0	0	0	0	0	54	54	6	6	False		
+ococo	ococo	Variant detection of SNVs								To update	https://github.com/karel-brinda/ococo	Variant Analysis	ococo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo	0.1.2.6	ococo	0.1.2.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1850	1963	79	93	1370	1370	194	194	0	0	0	0	3220	3333	273	287	False		
+odgi	odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	26	26	6	6	0	0	0	0	0	0	0	0	26	26	6	6	False		
+ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	98	6	6	0	0	0	0	0	0	0	0	98	98	6	6	False		
+ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	57	57	4	4	0	0	0	0	0	0	0	0	57	57	4	4	False		
+omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	158	158	12	12	0	0	0	0	0	0	0	0	158	158	12	12	False		
+omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	3051	3051	87	87	0	0	0	0	0	0	0	0	3051	3051	87	87	False		
+onto_toolkit	onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def	ONTO-Toolkit is a collection of tools for managing ontologies.								Up-to-date	http://search.cpan.org/~easr/ONTO-PERL-1.45/	Ontology Manipulation	onto_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit	1.45	perl-onto-perl	1.45			0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	0	582	663	68	69	0	0	0	0	0	0	0	0	582	663	68	69	False		
+openlabcds2csv	openlabcds2csv	"Creates a summary of several ""Internal Standard Report"" OpenLabCDS results."								To update		Metabolomics	openlabcds2csv	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+openmm	pdbfixer	OpenMM is a toolkit for molecular simulation using high performance GPU code.								To update	https://github.com/openmm	Molecular Dynamics, Computational chemistry	openmm	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	1.8.1	pdbfixer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	491	491	52	52	0	0	0	0	0	0	0	0	491	491	52	52	False		
+openms	AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	3.1	openms	3.2.0			8	34	144	0	8	34	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	141	124	0	32169	108654	3316	4889	50	50	15	15	940	940	245	245	33159	109644	3576	5149	False		
+openms	AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.2.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	135	134	0	31121	108907	3369	5029	50	50	15	15	933	933	242	242	32104	109890	3626	5286	False		
+optdoe	optdoe	Optimal Design Of Experiment								To update	https://github.com/pablocarb/doebase	Synthetic Biology	optdoe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe	v2.0.2	doebase				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+optitype	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	500	500	45	45	0	0	0	0	0	0	0	0	500	500	45	45	False		
+orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	897	897	99	99	1792	1792	239	239	0	0	0	0	2689	2689	338	338	False		
+orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	To update	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	3.0.1b1	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2018	2018	419	419	0	0	0	0	438	438	58	58	2456	2456	477	477	False		
+overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	149	149	31	31	0	0	0	0	18	18	1	1	167	167	32	32	False		
+packaged_annotation_loader	packaged_annotation_loader	Tool to make cached genome annotation data available as a list of datasets collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	Data Source	packaged_annotation_loader	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+packmol	packmol	PACKMOL is a package for creating starting structures for Molecular Dynamics simulations								To update	http://m3g.iqm.unicamp.br/packmol/home.shtml	Molecular Dynamics, Computational chemistry	packmol	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol	18.169.1	packmol				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	282	295	32	33	420	420	8	8	0	0	0	0	702	715	40	41	False		
+pacu	pacu_map, pacu_snp	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.	pacu	pacu		PACU	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).	Clustering	Phylogenetics, Sequence analysis	Up-to-date	https://github.com/BioinformaticsPlatformWIV-ISP/PACU	Sequence Analysis, Phylogenetics	pacu	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu	0.0.5	pacu_snp	0.0.5	Clustering	Phylogenetics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pairtools	pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0			5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	196	196	16	16	19	19	14	14	0	0	0	0	215	215	30	30	False		
+pandas_rolling_window	pandas_rolling_window	Rolling window calculations								To update	https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html	Statistics	pandas_rolling_window	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	0.1	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	261	275	12	12	63	63	22	22	0	0	0	0	324	338	34	34	False		
+pangolin	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	0	0	7457	7457	508	508	8518	8518	377	377	2760	2760	259	259	18735	18735	1144	1144	False		
+pangolin	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	Tree-based sequence alignment, Variant classification	Virology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	0	0	7457	7457	508	508	8518	8518	377	377	2760	2760	259	259	18735	18735	1144	1144	False		
+paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	322	349	24	29	0	0	0	0	0	0	0	0	322	349	24	29	False		
+parse_mito_blast	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	65	65	288	288	62	62	110	110	20	20	601	601	147	147	False		
+partialr_square	partialRsq	Compute partial R square								To update		Statistics	partialr_square	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square	https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	55	142	8	42	0	0	0	0	55	142	8	42	False		
+pathifier	pathifier	pathifier								Up-to-date	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	1.40.0	bioconductor-pathifier	1.40.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	245	245	10	10	0	0	0	0	0	0	0	0	245	245	10	10	False		
+pathview	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6204	6211	1261	1261	6667	6667	1143	1143	1160	1160	189	189	14031	14038	2593	2593	False		
+pathwaymatcher	reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	174	244	65	76	0	0	0	0	0	0	0	0	174	244	65	76	False		
+patrist	patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pbgcpp	pbgcpp	Compute genomic consensus and call variants using PacBio reads mapped to a reference	genomicconsensus	genomicconsensus		GenomicConsensus	The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.	Variant calling	Mapping	Up-to-date	https://github.com/PacificBiosciences/gcpp	Variant Analysis	pbgcpp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp	2.0.2	pbgcpp	2.0.2	Variant calling	Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pbmm2	pbmm2	A minimap2 SMRT wrapper for PacBio data.	pbmm2	pbmm2		pbmm2	pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.	Pairwise sequence alignment, Sorting	Mapping	Up-to-date	https://github.com/PacificBiosciences/pbmm2	Next Gen Mappers	pbmm2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2	1.14.99	pbmm2	1.14.99	Pairwise sequence alignment, Sorting	Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	70	17	17	0	0	0	0	0	0	0	0	70	70	17	17	False		
+pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	22	22	109	109	19	19	0	0	0	0	167	167	41	41	False		
+pe_histogram	pe_histogram	Contains a tool that produces an insert size histogram for a paired-end BAM file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram	Graphics	pe_histogram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram	1.0.2	openjdk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	5505	5505	510	510	7932	8582	811	909	736	736	119	119	14173	14823	1440	1538	False		
+peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2807	3337	178	196	0	0	0	0	0	0	0	0	2807	3337	178	196	False		
+peakzilla	peakzilla	Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.								To update	https://github.com/steinmann/peakzilla	ChIP-seq	peakzilla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla	1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	9	9	0	0	0	0	0	0	0	0	18	18	9	9	False		
+pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	6269	6866	260	292	5530	20068	467	1664	5647	8471	198	300	17446	35405	925	2256	False		
+pearson_correlation	Pearson_and_apos_Correlation1	Pearson and apos Correlation between any two numeric columns								To update		Statistics	pearson_correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	2	0	2	False		
+pep_pointer	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	506	511	54	55	21	21	12	12	163	163	8	8	690	695	74	75	False		
+pepquery	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7047	7047	76	76	0	0	0	0	0	0	0	0	7047	7047	76	76	False		
+pepquery2	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2			0	1	3	0	0	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1222	1222	28	28	0	0	0	0	0	0	0	0	1222	1222	28	28	False		
+peptide_genomic_coordinate	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	472	472	56	56	16	16	10	10	149	149	5	5	637	637	71	71	False		
+peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.11			4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	2	0	11986	17898	1046	1153	1314	1314	389	389	3034	3034	118	118	16334	22246	1553	1660	False		
+peptimapper	peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pepxml_to_xls		Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+percolator	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.7.1			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	338	378	15	16	0	0	0	0	1059	1059	13	13	1397	1437	28	29	False		
+perf	stats_perf_tool	suitable for boolean classification problems								To update	http://osmot.cs.cornell.edu/kddcup/software.html		stats_perf_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/perf	https://github.com/bgruening/galaxytools/tree/master/tools/perf	5.11.0	perf				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	42	1	2	0	0	0	0	0	0	0	0	36	42	1	2	False		
+pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	773	773	60	60	495	495	72	72	246	246	17	17	1514	1514	149	149	False		
+pg_tools	pg_dump, pg_import, pg_query	tool suite for dealing with Postgresql databases from Galaxy's history								To update	https://www.postgresql.org	Data Export, Data Source	pgtools	bgruening	https://github.com/bgruening/galaxytools/tools/pgtools	https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools		postgresql				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pgsnp2gd_snp	pgSnp2gd_snp	Convert from pgSnp to gd_snp								To update		Variant Analysis	pgsnp2gd_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pharmcat	pharmcat	Pharmacogenomics Clinical Annotation Tool								To update	https://pharmcat.org/	Variant Analysis	pharmcat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat						1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	109	109	29	29	250	250	84	84	0	0	0	0	359	359	113	113	False		
+pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
+                pharokka
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	5462	5462	334	334	0	0	0	0	309	309	52	52	5771	5771	386	386	False		
+phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	0	0	1	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	1199	1199	193	193	0	0	0	0	6	6	1	1	1205	1205	194	194	False		
+phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1975	2034	246	258	0	0	0	0	553	564	140	144	2528	2598	386	402	False		
+physiofit	physiofit	PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit	workflow4metabolomics	https://github.com/MetaSys-LISBP/PhysioFit	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit	3.4.0	physiofit	3.4.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+physiofit_manager	physiofit_data_manager	Handling of physiofit input files								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager	1.0.1	physiofit_data_manager	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pi_db_tools	calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+picard	picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile	Picard SAM/BAM manipulation tools.	picard_samtofastq	picard_samtofastq, picard_replacesamheader, picard_fastqtosam, picard_reordersam		picard_samtofastq	Create a FASTQ file.	Formatting	Sequencing	To update	http://broadinstitute.github.io/picard/	SAM	picard	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard	3.1.1	picard	3.2.0	Formatting	Sequencing	31	31	31	0	31	31	31	0	0	0	0	0	0	0	0	0	0	31	4	31	0	0	31	0	0	0	31	0	0	0	0	0	0	31	31	31	0	386934	399039	11024	11956	366646	589980	32000	57111	56622	62258	2845	3398	810202	1051277	45869	72465	False		
+pick_value	pick_value	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	pick_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1607	1607	41	41	490	490	53	53	127	127	4	4	2224	2224	98	98	False		
+picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	867	1128	144	165	0	0	0	0	2106	2106	121	121	2973	3234	265	286	False		
+picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	2532	2532	382	382	1	1	1	1	1311	1311	83	83	3844	3844	466	466	False		
+pileup_interval	pileup_interval	Pileup-to-Interval condenses pileup format into ranges of bases								To update		SAM	pileup_interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval	1.0.3	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	613	640	48	54	1381	7804	201	1552	756	815	22	30	2750	9259	271	1636	False		
+pileup_parser	pileup_parser	Filter pileup on coverage and SNPs								To update	https://github.com/galaxyproject/tools-devteam/	SAM	pileup_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser	1.0.2	perl				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3639	3774	414	461	9754	52522	1247	4531	1893	2433	191	318	15286	58729	1852	5310	False		
+pilon	pilon	pilon is a tool for assembly improvement and variant analysis in bacteria	pilon	pilon		pilon	Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.	Sequence assembly, Analysis, Read alignment	Assembly	To update	https://github.com/broadinstitute/pilon/wiki	Variant Analysis	pilon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon	1.20.1	pilon	1.24	Sequence assembly, Analysis	Assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9045	9458	1115	1144	7989	7989	1070	1070	3945	4137	726	741	20979	21584	2911	2955	False		
+pindel	pindel	Pindel detects genome-wide structural variation.								Up-to-date	http://artbio.fr	Variant Analysis	pindel	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel	https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel	0.2.5b9	pindel	0.2.5b9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pipelign	pipelign	Multipe sequence alignment								Up-to-date	https://github.com/asmmhossain/pipelign/	Next Gen Mappers	pipelign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign	0.2	pipelign	0.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1245	1245	231	231	9046	9046	630	630	0	0	0	0	10291	10291	861	861	False		
+pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	238	283	42	45	0	0	0	0	0	0	0	0	238	283	42	45	False		
+piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1408	2068	94	119	0	0	0	0	0	0	0	0	1408	2068	94	119	False		
+pizzly	pizzly	Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.								To update	https://github.com/pmelsted/pizzly/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly	0.37.3.1	pizzly	0.37.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	201	210	23	24	998	998	76	76	0	0	0	0	1199	1208	99	100	False		
+plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37086	37272	711	734	6346	6346	583	583	3065	3065	61	61	46497	46683	1355	1378	False		
+plasmid_profiler	plasmid_profiler	Explores plasmid content in WGS data								To update			plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler	0.1.6	r				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plasmid_profiler_suite		Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14652	14652	251	251	0	0	0	0	101	101	18	18	14753	14753	269	269	False		
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plink	plink	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	plink	plink		PLINK	Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	Genetic variation analysis	GWAS study	Up-to-date	https://www.cog-genomics.org/plink	Genome-Wide Association Study	plink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink	1.90b6.21	plink	1.90b6.21	Genetic variation analysis	GWAS study	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	851	851	127	127	249	249	43	43	0	0	0	0	1100	1100	170	170	False		
+plot_from_lda	plot_for_lda_output1	"Draw ROC plot on ""Perform LDA"" output"								To update		Graphics, Statistics	plot_from_lda	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda	https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda	1.0.1	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	65	77	19	25	153	886	38	343	142	155	8	10	360	1118	65	378	False		
+plotheatmap	plotheatmap	This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output.								To update		Computational chemistry	plotheatmap	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	1.0	bioconductor-preprocesscore	1.64.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.4	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1342	1472	184	197	902	902	156	156	630	630	24	24	2874	3004	364	377	False		
+plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	408	664	91	122	627	627	118	118	605	605	26	26	1640	1896	235	266	False		
+plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	764	879	213	237	304	304	95	95	193	193	26	26	1261	1376	334	358	False		
+pmd_fdr	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pneumocat	pneumocat	Pneumococcal Capsular Typing of illumina fastq reads								Up-to-date	https://github.com/phe-bioinformatics/PneumoCaT	Variant Analysis	pneumocat	nml	https://github.com/phe-bioinformatics/PneumoCaT	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat	1.2.1	pneumocat	1.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	33	33	2	2	0	0	0	0	0	0	0	0	33	33	2	2	False		
+points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	4	4	0	0	0	0	0	0	0	0	29	29	4	4	False		
+poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	112	120	16	16	4	562	1	140	320	347	7	8	436	1029	24	164	False		
+polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	731	731	86	86	0	0	0	0	42	42	4	4	773	773	90	90	False		
+porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	262015	262852	2627	2711	83623	83623	1918	1918	52558	52558	1037	1037	398196	399033	5582	5666	False		
+poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	13	0	19942	20587	1055	1245	33619	40808	2183	2594	9261	9261	365	365	62822	70656	3603	4204	False		
+positions2snv_alignment	positions2snv_alignment	Generate alignment of SNVs from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+positions2snv_invariant_alignment	positions2snv_invariant_alignment	Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_invariant_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+presto	presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	63244	65177	1392	1599	0	0	0	0	63244	65177	1392	1599	False		
+pretext	pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6			3	2	3	0	3	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	3463	3463	538	538	1853	1853	256	256	1097	1097	70	70	6413	6413	864	864	False		
+principal_component_analysis	pca1	Principal Component Analysis								To update		Statistics	principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis	1.0.2	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9788	10032	207	244	3072	8054	607	1488	0	0	0	0	12860	18086	814	1732	False		
+prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10152	10626	253	281	10581	10581	1240	1240	0	0	0	0	20733	21207	1493	1521	False		
+probecoverage	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1902	1902	167	167	0	0	0	0	0	0	0	0	1902	1902	167	167	False		
+progressivemauve	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update	http://darlinglab.org/mauve/user-guide/progressivemauve.html	Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2064	2173	678	695	2900	2900	1034	1034	0	0	0	0	4964	5073	1712	1729	False		
+projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	86	4	6	0	0	0	0	0	0	0	0	40	86	4	6	False		
+projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20858	21444	14	18	0	0	0	0	0	0	0	0	20858	21444	14	18	False		
+prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	464359	476554	7475	7721	313285	331256	11243	12384	131211	141875	4358	4947	908855	949685	23076	25052	False		
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+prot-scriber	prot_scriber	Protein annotation of short human readable descriptions								Up-to-date	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.6	prot-scriber	0.1.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	10	7	7	0	0	0	0	0	0	0	0	10	10	7	7	False		
+protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	129	155	15	21	0	0	0	0	0	0	0	0	129	155	15	21	False		
+protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	11743	12752	1137	1278	2	2	1	1	0	0	0	0	11745	12754	1138	1279	False		
+protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	465	638	81	100	0	0	0	0	0	0	0	0	465	638	81	100	False		
+proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3962	3962	501	501	0	0	0	0	0	0	0	0	3962	3962	501	501	False		
+proteinpilot	convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml									To update			proteinpilot	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+proteomiqon_joinquantpepionswithproteins	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	366	366	4	4	0	0	0	0	0	0	0	0	366	366	4	4	False		
+proteomiqon_labeledproteinquantification	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	8	8	0	0	0	0	0	0	0	0	16	16	8	8	False		
+proteomiqon_labelfreeproteinquantification	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	6	4	4	0	0	0	0	0	0	0	0	6	6	4	4	False		
+proteomiqon_mzmltomzlite	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	721	721	8	8	0	0	0	0	0	0	0	0	721	721	8	8	False		
+proteomiqon_peptidedb	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	96	96	12	12	0	0	0	0	0	0	0	0	96	96	12	12	False		
+proteomiqon_peptidespectrummatching	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	686	686	5	5	0	0	0	0	0	0	0	0	686	686	5	5	False		
+proteomiqon_proteininference	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	6	6	0	0	0	0	0	0	0	0	89	89	6	6	False		
+proteomiqon_psmbasedquantification	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	604	604	4	4	0	0	0	0	0	0	0	0	604	604	4	4	False		
+proteomiqon_psmstatistics	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	694	694	6	6	0	0	0	0	0	0	0	0	694	694	6	6	False		
+proteore_venn_diagram	proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	1	1	0	0	0	0	0	0	0	0	15	15	1	1	False		
+protxml_to_xls	protxml_to_xls									To update			protxml_to_xls	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pseudogenome	pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+psiclass	psiclass	PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.	psiclass	psiclass		PsiCLASS	Reference-based transcriptome assembler for single or multiple RNA-seq samples	Transcriptome assembly	Sequence assembly	Up-to-date	https://github.com/splicebox/PsiCLASS	Transcriptomics	psiclass	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass	https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass	1.0.3	psiclass	1.0.3	Transcriptome assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	24	5	5	0	0	0	0	0	0	0	0	24	24	5	5	False		
+psm2sam	PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+psm_eval	psm_eval									To update			psm_eval	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval	0.1.0	binaries_for_psm_eval				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+psm_validation	psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	20	20	4	4	0	0	0	0	0	0	0	0	20	20	4	4	False		
+psy-maps	psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.3.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	333	502	62	62	0	0	0	0	0	0	0	0	333	502	62	62	False		
+pureclip	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1319	1507	81	92	0	0	0	0	0	0	0	0	1319	1507	81	92	False		
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17782	17782	287	287	853	853	65	65	2224	2224	65	65	20859	20859	417	417	False		
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22742	22742	557	557	2159	2159	716	716	776	776	448	448	25677	25677	1721	1721	False		
+pyega3	pyega3	EGA python client uses the EGA REST API to download authorized datasets and files.								To update	https://github.com/EGA-archive/ega-download-client	Data Source	ega_download_client	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3	5.0.2	pyega3	5.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2716	2716	104	104	134	134	43	43	40	40	1	1	2890	2890	148	148	False		
+pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12858	13232	986	996	8092	8092	943	943	3238	3238	124	124	24188	24562	2053	2063	False		
+pyprophet	pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5			0	5	6	0	0	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	6	6	0	2626	2626	150	150	0	0	0	0	609	609	9	9	3235	3235	159	159	False		
+pyscenic	pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/								To update		Transcriptomics, RNA, Sequence Analysis	suite_pyscenic	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic	0.12.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pysradb	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.2	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	163	163	35	35	0	0	0	0	0	0	0	0	163	163	35	35	False		
+pyteomics	mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.4	Protein identification	Proteomics, Proteomics experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	92	92	4	4	0	0	0	0	0	0	0	0	92	92	4	4	False		
+pyvo_integration	astronomical_archives	Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy								To update		Data Source	astronomicalarchivestool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration	0.10.0	astropy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	53	6	6	0	0	0	0	0	0	0	0	53	53	6	6	False		
+qcxms	qcxms_getres, qcxms_neutral_run, qcxms_production_run	QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).								To update	https://github.com/grimme-lab/QCxMS	Computational chemistry, Molecular Dynamics	QCxMS	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	5.2.1					0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11246	11246	13	13	0	0	0	0	0	0	0	0	11246	11246	13	13	False		
+qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2092	2342	209	238	0	0	0	0	2	2	1	1	2094	2344	210	239	False		
+qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	0	0	0	32	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	31825	34677	3375	3785	1	1	1	1	14	14	4	4	31840	34692	3380	3790	False		
+qiime_extract_viz	qiime_extract_viz	Extract vizualization from QIIME artifacts								To update	http://www.qiime.org	Metagenomics	qiime_extract_viz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz	0.1.0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	8	8	0	0	0	0	0	0	0	0	17	17	8	8	False		
+qq_tools	qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	0	4	4	4	0	684820	684820	3239	3239	90503	90503	3881	3881	29018	29018	826	826	804341	804341	7946	7946	False		
+quality_filter	qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.13.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	724	35	62	0	0	0	0	98	724	35	62	False		
+quantp	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	197	241	17	22	0	0	0	0	0	0	0	0	197	241	17	22	False		
+quantwiz_iq	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	32	3	3	0	0	0	0	0	0	0	0	32	32	3	3	False		
+quasitools	aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0			0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13483	13483	434	434	13483	13483	434	434	False		
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	67737	69738	7787	7971	51925	56602	9692	10646	32003	34145	3890	4127	151665	160485	21369	22744	False		
+query	query	Execute an SQL statement on a set of tables								To update		Text Manipulation	query	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/query	https://github.com/RECETOX/galaxytools/tree/master/tools/query	0.2	click				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+query_impc	query_impc	Contains a tool to query the IMPC database.								To update	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	Convert Formats, Web Services	query_impc	iuc	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc	0.9.0	requests				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	2	0	0	0	0	0	0	0	0	3	3	2	2	False		
+query_tabular	filter_tabular, query_tabular, sqlite_to_tabular	Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular	3.3.1	python				3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	3	2	0	0	0	0	0	0	1	0	0	0	0	0	0	3	3	3	0	130124	135361	1265	1305	11135	11135	922	922	5939	5939	153	153	147198	152435	2340	2380	False		
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	172	172	9	9	0	0	0	0	0	0	0	0	172	172	9	9	False		
+rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3077	4581	395	518	2856	2856	1093	1093	1977	1977	19	19	7910	9414	1507	1630	False		
+racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	27113	27315	839	850	9089	9089	475	475	5452	5452	171	171	41654	41856	1485	1496	False		
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4844	4844	480	480	0	0	0	0	7	7	3	3	4851	4851	483	483	False		
+ramclustr	ramclustr, ramclustr_define_experiment		ramclustr	ramclustr		RAMClustR	A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	To update	https://rdrr.io/cran/RAMClustR/	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	1.3.0	r-ramclustr	1.3.1	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	58	58	22	22	29	29	14	14	344	344	4	4	431	431	40	40	False		
+rapidnj	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2		Phylogeny	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	339	339	30	30	1737	1737	256	256	6	6	1	1	2082	2082	287	287	False		
+rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	42	42	9	9	0	0	0	0	0	0	0	0	42	42	9	9	False		
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9477	9477	438	438	0	0	0	0	10585	10585	182	182	20062	20062	620	620	False		
+rawtools	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	166	179	32	33	0	0	0	0	414	414	13	13	580	593	45	46	False		
+raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10905	10905	966	966	5100	5114	587	587	4955	6094	765	892	20960	22113	2318	2445	False		
+rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	1.0		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	90	90	6	6	0	0	0	0	0	0	0	0	90	90	6	6	False		
+rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	860	1257	88	98	0	0	0	0	0	0	0	0	860	1257	88	98	False		
+rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	655	655	57	57	0	0	0	0	0	0	0	0	655	655	57	57	False		
+rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	49	191	5	46	0	0	0	0	49	191	5	46	False		
+rcx-tk	rcx-tk	Tools to process metadata or alkane files.								To update	https://github.com/RECETOX/rcx-tk	Metabolomics	rcx_tk	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk	0.1.0+galaxy0	rcx-tk	0.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rdock	rdock	Docking ligands to proteins and nucleic acids								To update	http://rdock.sourceforge.net/	Computational chemistry	rdock	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock	1.0	rDock	2013.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3710	3710	80	80	7	7	6	6	0	0	0	0	3717	3717	86	86	False		
+reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.15.0	recentrifuge	1.15.0	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	472	472	92	92	32	32	13	13	6	6	4	4	510	510	109	109	False		
+recetox_aplcms	recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise	Peak detection tool for HRMS profile data.	recetox-aplcms	recetox-aplcms		recetox-aplcms	recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	Up-to-date	https://github.com/RECETOX/recetox-aplcms	Metabolomics	recetox-aplcms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	0.13.3	r-recetox-aplcms	0.13.3	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	862	862	12	12	0	0	0	0	48	48	1	1	910	910	13	13	False		
+recetox_msfinder	recetox_msfinder		recetox-msfinder	recetox-msfinder		recetox-msfinder	This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.	Annotation	Metabolomics	To update	https://github.com/RECETOX/recetox-msfinder	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	v3.5.2			Annotation	Metabolomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47	47	4	4	0	0	0	0	0	0	0	0	47	47	4	4	False		
+recetox_xmsannotator	recetox_xmsannotator_advanced		recetox-xmsannotator	recetox-xmsannotator		recetox-xMSannotator	Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		Up-to-date	https://github.com/RECETOX/recetox-xMSannotator	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator	0.10.0	r-recetox-xmsannotator	0.10.0	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	93	93	2	2	93	93	2	2	False		
+red	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	859	859	203	203	305	305	142	142	227	227	58	58	1391	1391	403	403	False		
+refseq_masher	refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	428	428	35	35	141	141	42	42	0	0	0	0	569	569	77	77	False		
+regex_find_replace	regex1, regexColumn1	Use python regular expressions to find and replace text								To update		Text Manipulation	regex_find_replace	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	1.0.3	python				2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	78648	78834	1144	1156	18063	18063	870	870	4455	6051	194	289	101166	102948	2208	2315	False		
+regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	438	542	128	157	0	0	0	0	0	0	0	0	438	542	128	157	False		
+rem_complex	rem_complex	Removes molecular coordination complexes.								To update	https://github.com/RECETOX/galaxytools	Metabolomics	rem_complex	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	2	2	0	0	0	0	0	0	0	0	18	18	2	2	False		
+remove_beginning	Remove beginning1	Remove lines from the beginning of a file.								To update		Text Manipulation	remove_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	148572	169964	3525	3682	36694	113826	3910	8163	9713	10577	1475	1598	194979	294367	8910	13443	False		
+remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	44	6	7	0	0	0	0	0	0	0	0	39	44	6	7	False		
+rename_annotated_feature	rename_annotated_feature	Update column names in an abundance table using a annotation table with spectral matching results								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	rename_annotated_feature	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1	False		
+repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.0.9_p2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5998	5998	810	810	7618	7618	803	803	3135	3135	292	292	16751	16751	1905	1905	False		
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	95	38	38	0	0	0	0	0	0	0	0	95	95	38	38	False		
+repeatmasker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.0.9_p2	Genome annotation	Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5998	5998	810	810	7618	7618	803	803	3135	3135	292	292	16751	16751	1905	1905	False		
+repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7963	7963	413	413	1485	1485	220	220	8402	8402	168	168	17850	17850	801	801	False		
+repenrich	edger-repenrich, repenrich	Repeat element profiling								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	Transcriptomics	repenrich	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	2.31.1					0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1725	1790	56	57	1725	1790	56	57	False		
+repenrich2	edger-repenrich2, repenrich2	Repeat element profiling using bowtie2 aligner								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	Transcriptomics	repenrich2	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	2.31.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+replaceColumn	replace_column_with_key_value_file	A tool to replace all column entries of a file given by values of a key-value file.								To update		Text Manipulation	replace_column_by_key_value_file	bgruening	https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn	https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn	0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	577184	577312	463	492	43900	44233	283	373	2190	2190	112	112	623274	623735	858	977	False		
+replace_chromosome_names	replace_chromosome_names	Replace chromosome names								To update		Text Manipulation	replace_chromosome_names	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names	0.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	514	573	69	83	0	0	0	0	0	0	0	0	514	573	69	83	False		
+repmatch_gff3	repmatch_gff3	Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.								To update		ChIP-seq	repmatch_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3		matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	415	721	128	219	0	0	0	0	415	721	128	219	False		
+reshape2	cast, melt	Flexibly restructure and aggregate data using just the two functions melt and dcast								To update	https://cran.r-project.org/web/packages/reshape2/index.html	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2	1.4.2	r-reshape2				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	3543	3619	108	111	536	536	157	157	0	0	0	0	4079	4155	265	268	False		
+resize_coordinate_window	resize_coordinate_window	Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.								To update		Genomic Interval Operations	resize_coordinate_window	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window	https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window	1.0.2	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	75	86	8	9	138	216	30	57	0	0	0	0	213	302	38	66	False		
+rest_tool	pubchem_rest_tool	This tool fetches data from pubchem via the PubChem REST API.								To update	https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html	Data Source	pubchem_rest_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+retip	retip_apply, retip_descriptors, retip_filter_rt, retip_train		retip	retip		Retip	Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.	Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	To update	https://github.com/PaoloBnn/Retip	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	0.5.4			Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+retrieve_ensembl_bed	retrieve_ensembl_bed	Retrieve cDNA features from Ensembl REST API in BED format								To update	http://rest.ensembl.org/	Data Source	retrieve_ensembl_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+revertR2orientationInBam	revertR2orientationInBam	Revert the mapped orientation of R2 mates in a bam.								To update		SAM	revertr2orientationinbam	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	0.0.2	samtools	1.21			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	40	11	11	520	520	31	31	0	0	0	0	560	560	42	42	False		
+revoluzer	revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	Structural variation detection	Molecular evolution, Phylogeny	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2444	2444	52	52	0	0	0	0	0	0	0	0	2444	2444	52	52	False		
+rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	7	7	0	0	0	0	0	0	0	0	15	15	7	7	False		
+rgcca	rgcca	multi-block analysis								To update	https://github.com/rgcca-factory/RGCCA	Statistics	rgcca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca	3.0.2	rgccacmd	3.0.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	44	44	6	6	77	77	35	35	0	0	0	0	121	121	41	41	False		
+rgrnastar	rna_star, rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	star	star		STAR	Ultrafast universal RNA-seq data aligner	Sequence alignment	RNA-Seq, Transcriptomics	To update	https://github.com/alexdobin/STAR	Next Gen Mappers, Transcriptomics	rgrnastar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar	2.7.11a	star	2.7.11b	Sequence alignment	RNA-Seq, Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	2	0	0	0	2	0	0	0	0	0	1	2	2	2	0	438078	473957	10142	10900	325474	403925	15284	18791	49662	53138	1359	1449	813214	931020	26785	31140	False		
+riassigner	riassigner, riassigner_from_comment		riassigner	riassigner		RIAssigner	RIAssigner is a python tool for retention index (RI) computation for GC-MS data.	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/RIAssigner	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	0.4.1	riassigner	0.4.1	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	46	46	19	19	15	15	4	4	1	1	1	1	62	62	24	24	False		
+ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	661	681	78	78	0	0	0	0	0	0	0	0	661	681	78	78	False		
+ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	171	171	20	20	0	0	0	0	0	0	0	0	171	171	20	20	False		
+rmap	rmap_wrapper	RMAP for Solexa Short Reads Alignment								To update		Next Gen Mappers	rmap	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rmapq	rmapq_wrapper	RMAPQ for Solexa Short Reads Alignment with Quality Scores								To update		Next Gen Mappers	rmapq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rmassbank	rmassbank	RMassBank is an R package for processing tandem MS files and building of MassBank records.								To update	https://github.com/MassBank/RMassBank	Metabolomics	rmassbank	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	3.0.0	python				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	48	48	1	1	48	48	1	1	False		
+rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	137	173	40	49	0	0	0	0	0	0	0	0	137	173	40	49	False		
+rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	90	196	9	11	0	0	0	0	0	0	0	0	90	196	9	11	False		
+rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	878	1363	29	35	0	0	0	0	0	0	0	0	878	1363	29	35	False		
+rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1024	1077	18	21	0	0	0	0	0	0	0	0	1024	1077	18	21	False		
+rnaformer	infer_rnaformer	RNAformer: RNA secondary structure prediction								To update	https://github.com/automl/RNAformer	RNA	rnaformer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	1.0.0	rnaformer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	6	6	0	0	0	0	0	0	0	0	26	26	6	6	False		
+rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	33	10	14	0	0	0	0	0	0	0	0	23	33	10	14	False		
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1522	1522	254	254	372	372	75	75	5	5	1	1	1899	1899	330	330	False		
+rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	65	89	14	18	0	0	0	0	0	0	0	0	65	89	14	18	False		
+rnaz	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	1156	43309	93	121	0	0	0	0	0	0	0	0	1156	43309	93	121	False		
+roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15196	15685	1459	1501	12188	12188	1768	1768	4881	5539	518	555	32265	33412	3745	3824	False		
+rp2biosensor	rp2biosensor	Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output								To update	https://github.com/brsynth/rp2biosensor	Synthetic Biology	rp2biosensor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor	3.2.1	rp2biosensor				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rp2paths	rp2paths	Enumerate and seperate the different pathways generated by RetroPath2.0								To update	https://github.com/brsynth/rp2paths	Synthetic Biology	rp2paths	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths	1.5.1	rp2paths				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rpbasicdesign	rpbasicdesign	Extracting enzyme IDs from rpSBML files								To update	https://github.com/brsynth/rpbasicdesign	Synthetic Biology	rpbasicdesign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign	1.2.2	rpbasicdesign				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rpfba	rpfba	Perform FBA for the RetroPath2.0 heterologous pathways								To update	https://github.com/brsynth/rptools/releases	Synthetic Biology	rpfba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba	5.12.3	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rptools	rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz	Suite of tools that work on rpSBML format								To update	https://github.com/brsynth/rptools	Synthetic Biology	rptools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools	5.13.1	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rrparser	rrparser	Reaction Rules Parser								To update	https://github.com/brsynth/RRParser	Synthetic Biology	rrparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser	2.5.2	rrparser				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rsat_filter_snps	rsat_filter_snps	Filter SNPs in RSAT Matrix Scan output								To update	https://github.com/TGAC/earlham-galaxytools/	ChIP-seq, Systems Biology	rsat_filter_snps	earlham	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	1	1	0	363	430	158	183	0	0	0	0	67	146	13	39	430	576	171	222	False		
+rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	0	22	22	22	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	0	22	22	22	0	136315	147595	8341	9385	138707	161046	10696	12789	22718	23767	1593	1695	297740	332408	20630	23869	False		
+ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1286	1364	178	193	2220	2220	299	299	0	0	0	0	3506	3584	477	492	False		
+sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3628	4168	165	199	8399	14473	573	1147	2710	3000	151	175	14737	21641	889	1521	False		
+salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	0	2	2	3	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	0	3	3	3	0	73085	77081	2243	2319	90634	122835	3402	4726	13371	15818	513	586	177090	215734	6158	7631	False		
+salmon-kallisto-mtx-to-10x	_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	682	682	172	172	322	322	74	74	3	3	3	3	1007	1007	249	249	False		
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	463	463	119	119	1038	1038	87	87	410	410	24	24	1911	1911	230	230	False		
+sam2interval	sam2interval	Convert SAM to interval.								To update		SAM	sam2interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1155	1251	57	63	2264	18187	189	1748	525	590	10	17	3944	20028	256	1828	False		
+sam_bitwise_flag_filter	sam_bw_filter	Filter SAM on bitwise flag values								To update		SAM	sam_bitwise_flag_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter	1.0.1	python				1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	96	278	12	26	3554	76029	450	6346	229	345	16	29	3879	76652	478	6401	False		
+sambamba	sambamba_sample_or_filter	filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM								To update	http://artbio.fr	SAM	sambamba	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba	https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba	0.7.1+galaxy1	sambamba	1.0.1			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	684	684	17	17	684	684	17	17	False		
+sambamba	sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort	Sambamba: process your BAM data faster!								Up-to-date	https://github.com/biod/sambamba	SAM	sambamba	bgruening	https://github.com/biod/sambamba	https://github.com/bgruening/galaxytools/tree/master/tools/sambamba	1.0.1	sambamba	1.0.1			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	297	297	51	51	0	0	0	0	0	0	0	0	297	297	51	51	False		
+samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	Up-to-date	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.26	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3421	3859	340	382	883	883	109	109	1138	1138	15	15	5442	5880	464	506	False		
+samtools										To update	https://github.com/samtools/samtools	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools	1.20	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6485	6549	720	726	10127	10127	1518	1518	238	238	37	37	16850	16914	2275	2281	False		
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	52099	55110	4053	4497	73194	108684	6930	9936	14771	15714	1222	1419	140064	179508	12205	15852	False		
+sansa	sansa_annotate	Sansa is a tool for structural variant annotation.								To update	https://github.com/dellytools/sansa	Variant Analysis	sansa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa	0.2.1	sansa	0.2.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	138	138	36	36	0	0	0	0	0	0	0	0	138	138	36	36	False		
+sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	174	174	16	16	399	399	29	29	0	0	0	0	573	573	45	45	False		
+sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	140	140	5	5	253	253	6	6	0	0	0	0	393	393	11	11	False		
+sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sbml2sbol	sbml2sbol	Convert SBML to SBOL format								To update	https://github.com/neilswainston/SbmlToSbol	Synthetic Biology	sbml2sbol	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol	0.1.13	sbml2sbol				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	10	10	0	0	0	0	0	0	0	0	13	13	10	10	False		
+scaffold	scaffold, scaffold_export									To update			scaffold	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold	0.1.0	scaffold				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	477	520	13	16	0	0	0	0	0	0	0	0	477	520	13	16	False		
+scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			27	27	27	0	27	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	0	45501	45666	4832	4868	7304	7304	1846	1846	3106	3106	457	457	55911	56076	7135	7171	False		
+scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	63789	64034	2543	2547	29962	29962	1185	1185	18028	18028	379	379	111779	112024	4107	4111	False		
+scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			1	2	6	0	1	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	381	388	99	100	0	0	0	0	297	297	9	9	678	685	108	109	False		
+scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	1345	1371	350	351	0	0	0	0	903	903	29	29	2248	2274	379	380	False		
+scatterplot	scatterplot_rpy	Scatterplot of two numeric columns								To update		Graphics, Statistics	scatterplot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot	1.0.3	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1234	1752	179	261	680	9223	231	1927	0	49	0	18	1914	11024	410	2206	False		
+sccaf	run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out	SCCAF: Single Cell Clustering Assessment Framework.								To update	https://github.com/sccaf/sccaf	Transcriptomics	SCCAF	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf	0.0.9	sccaf	0.0.10			4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	110	110	19	19	0	0	0	0	0	0	0	0	110	110	19	19	False		
+sceasy	sceasy_convert	Convert scRNA data object between popular formats								To update		Transcriptomics	sceasy	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy	0.0.5	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1059	1059	222	222	426	426	71	71	1	1	1	1	1486	1486	294	294	False		
+sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1059	1059	222	222	426	426	71	71	1	1	1	1	1486	1486	294	294	False		
+schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	809	809	78	78	3	3	2	2	105	105	16	16	917	917	96	96	False		
+scikit-bio	scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1503	1955	283	402	0	0	0	0	1504	1956	284	403	False		
+scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	97	97	41	41	0	0	0	0	0	0	0	0	97	97	41	41	False		
+scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	901	901	90	90	0	0	0	0	0	0	0	0	901	901	90	90	False		
+scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	284	632	34	38	786	786	61	61	1	1	1	1	1071	1419	96	100	False		
+scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	25	5	5	0	0	0	0	0	0	0	0	25	25	5	5	False		
+scripting	singularity_scriptrunner	suite_scripting								To update	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	Text Manipulation	scripting tools	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+seacr	seacr	SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.								Up-to-date	https://github.com/FredHutch/SEACR	Epigenetics, ChIP-seq	seacr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr	1.3	seacr	1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5106	5106	116	116	6419	6419	241	241	0	0	0	0	11525	11525	357	357	False		
+sed	sed_stream_editor	Manipulate your data with the sed command line tool.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/sed	Text Manipulation	sed_wrapper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sed	https://github.com/bgruening/galaxytools/tree/master/tools/sed	0.0.1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	281	2284	10	53	0	0	0	0	0	0	0	0	281	2284	10	53	False		
+segalign	segalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/gsneha26/SegAlign	Next Gen Mappers	segalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	0.1.2.7	segalign-galaxy	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	252	252	47	47	0	0	0	0	252	252	47	47	False		
+segemehl	segemehl	segemehl - short read mapping with gaps								To update	http://www.bioinf.uni-leipzig.de/Software/segemehl/	Next Gen Mappers	segemehl	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	0.2.0.4	segemehl	0.3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1095	1306	98	113	0	0	0	0	0	0	0	0	1095	1306	98	113	False		
+segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	2	2	0	0	0	0	0	0	0	0	7	7	2	2	False		
+selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	305	463	43	50	0	0	0	0	0	0	0	0	305	463	43	50	False		
+selenzy_wrapper	selenzy_wrapper	Performs enzyme selection from a reaction query.								Up-to-date	https://github.com/brsynth/selenzy-wrapper	Synthetic Biology	selenzy_wrapper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper	0.3.0	selenzy_wrapper	0.3.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	931	931	93	93	0	0	0	0	0	0	0	0	931	931	93	93	False		
+seq2hla	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	342	342	40	40	0	0	0	0	0	0	0	0	342	342	40	40	False		
+seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1053	1186	137	195	680	680	206	206	0	0	0	0	1733	1866	343	401	False		
+seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30300	32553	732	799	21726	31891	619	621	2886	2886	144	144	54912	67330	1495	1564	False		
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4322	4714	180	205	0	0	0	0	0	0	0	0	4322	4714	180	205	False		
+seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2196	3529	260	289	2196	3529	260	289	False		
+seqcomplexity	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	70	70	19	19	109	109	47	47	0	0	0	0	179	179	66	66	False		
+seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	0	0	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3364	3364	247	247	0	0	0	0	244	244	33	33	3608	3608	280	280	False		
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2424	2424	102	102	0	0	0	0	0	0	0	0	2424	2424	102	102	False		
+seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4182	4182	42	42	0	0	0	0	0	0	0	0	4182	4182	42	42	False		
+seqtk	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	Data handling, Sequence file editing		15	15	15	0	15	15	15	0	0	0	0	0	0	0	0	0	0	14	0	14	0	0	14	0	0	0	15	0	0	0	0	0	0	14	14	14	14	72816	73514	2210	2300	102777	107831	2313	2669	154613	154613	682	682	330206	335958	5205	5651	False		
+seqtk_nml	seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seqwish	seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	271	271	2	2	0	0	0	0	0	0	0	0	271	271	2	2	False		
+seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	0	1	1	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	121	121	11	11	32	32	5	5	0	0	0	0	153	153	16	16	False		
+seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.4.0			14	14	14	0	14	14	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	0	2296	2328	673	676	141	141	39	39	0	0	0	0	2437	2469	712	715	False		
+sgwb	sgwb_astro_tool	SGWB								To update		Astronomy	sgwb_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb	0.0.1+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	2	2	0	0	0	0	0	0	0	0	5	5	2	2	False		
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	913	913	308	308	0	0	0	0	568	568	73	73	1481	1481	381	381	False		
+shift-longitudes	shyft_longitudes	Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/	Climate Analysis	shift_longitudes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	54	64	4	4	0	0	0	0	0	0	0	0	54	64	4	4	False		
+shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+short_reads_figure_score	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	145	163	25	30	196	3360	23	711	0	0	0	0	341	3523	48	741	False		
+short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	175	220	51	60	350	6657	85	1602	0	0	0	0	525	6877	136	1662	False		
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46125	47376	2273	2356	40577	40577	3971	3971	19960	21130	1085	1199	106662	109083	7329	7526	False		
+show_beginning	Show beginning1	Select lines from the beginning of a file.								To update		Text Manipulation	show_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	27232	36366	2184	2789	16648	84460	4191	18767	2785	3276	373	452	46665	124102	6748	22008	False		
+show_tail	Show tail1	Select lines from the end of a file.								To update		Text Manipulation	show_tail	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	1620	2660	378	589	10551	24579	682	1851	284	398	67	83	12455	27637	1127	2523	False		
+sicer	peakcalling_sicer	Statistical approach for the Identification of ChIP-Enriched Regions								Up-to-date	https://home.gwu.edu/~wpeng/Software.htm	ChIP-seq	sicer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer	1.1	SICER	1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	276	379	30	42	972	9053	146	1008	644	689	5	7	1892	10121	181	1057	False		
+sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	0	18184	18937	555	608	10514	10514	1063	1063	0	0	0	0	28698	29451	1618	1671	False		
+simtext	abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix	A text mining framework for interactive analysis and visualization of similarities among biomedical entities.								To update	https://github.com/dlal-group/simtext	Text Manipulation	simtext	iuc	https://github.com/galaxyproject/tools-iuc/tools/simtext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext	0.0.2	r-argparse	1.0.1			0	2	4	0	0	2	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	220	220	68	68	0	0	0	0	416	416	10	10	636	636	78	78	False		
+sina	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1369	1369	125	125	2398	2398	420	420	0	0	0	0	3767	3767	545	545	False		
+sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								Up-to-date	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.10.1	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	284	284	70	70	165	165	38	38	14	14	2	2	463	463	110	110	False		
+sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3457	3457	301	301	0	0	0	0	556	556	65	65	4013	4013	366	366	False		
+sixgill	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	312	312	71	71	0	0	0	0	0	0	0	0	312	312	71	71	False		
+sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	0	30	14	31	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	0	82169	116810	2402	2666	18101	18101	2375	2375	17549	17549	321	321	117819	152460	5098	5362	False		
+skyline2isocor	skyline2isocor	Converting skyline output to IsoCor input								Up-to-date	https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor	Metabolomics	skyline2isocor	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor	1.0.0	skyline2isocor	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	346	362	16	16	872	872	67	67	0	0	0	0	1218	1234	83	83	False		
+sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	141	141	26	26	0	0	0	0	0	0	0	0	141	141	26	26	False		
+slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	96	103	4	5	0	0	0	0	4	4	1	1	100	107	5	6	False		
+small_rna_clusters	small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+small_rna_maps	small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+small_rna_signatures	overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	158	158	8	8	0	0	0	0	0	0	0	0	158	158	8	8	False		
+smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smart_domains	smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smina	smina	smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization								To update	https://sourceforge.net/projects/smina/	Computational chemistry	smina	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina	1.0	smina	2017.11.9			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	499	499	16	16	44	44	10	10	0	0	0	0	543	543	26	26	False		
+smithsonian-volcanoes	smithsonian_volcanoes	Retrieve data from Volcanoes of the World (VOTW) Database								To update	https://volcano.si.edu/gvp_votw.cfm	Retrieve Data	smithsonian_volcanoes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	0.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	325	325	61	61	137	137	54	54	843	843	63	63	1305	1305	178	178	False		
+snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	1638	331	358	779	779	244	244	467	467	83	83	2745	2884	658	685	False		
+snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1817	1817	14	14	4	4	2	2	136	136	4	4	1957	1957	20	20	False		
+sniffles	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	Up-to-date	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	2.4	sniffles	2.4	Sequence analysis, Structural variation detection	Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1141	1141	134	134	606	606	156	156	2267	2267	80	80	4014	4014	370	370	False		
+snipit	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	Base position variability plotting	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	905	905	44	44	0	0	0	0	0	0	0	0	905	905	44	44	False		
+snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	0	121363	124773	3448	3602	92504	92504	3945	3945	48068	52034	2705	3073	261935	269311	10098	10620	False		
+snp-dists	snp_dists	Compute pairwise SNP distance matrix from a FASTA sequence alignment								Up-to-date	https://github.com/tseemann/snp-dists	Variant Analysis	snp_dists	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists	0.8.2	snp-dists	0.8.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6555	6555	807	807	5336	5336	171	171	1143	1143	182	182	13034	13034	1160	1160	False		
+snp-sites	snp_sites	Finds SNP sites from a multi-FASTA alignment file								Up-to-date	https://github.com/sanger-pathogens/snp-sites	Variant Analysis	snp_sites	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites	2.5.1	snp-sites	2.5.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6597	6597	663	663	1467	1467	256	256	1279	1279	114	114	9343	9343	1033	1033	False		
+snpeff	snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names	SnpEff is a genetic variant annotation and effect prediction toolbox								To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff		biopython	1.70			5	5	5	0	5	5	5	0	0	0	0	0	0	0	1	0	0	0	5	5	0	0	5	0	0	0	5	0	0	0	0	0	0	5	5	5	0	103826	108296	7181	7908	115727	178110	15871	22769	11817	13155	2148	2321	231370	299561	25200	32998	False		
+snpeff-covid19	snpeff_sars_cov_2	SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox	snpeff	snpeff		snpEff	Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).	SNP detection	DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs	To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff_sars_cov_2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19				SNP detection	DNA polymorphism, Nucleic acid sites, features and motifs	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	764895	764895	1276	1276	94572	94572	1636	1636	26990	26990	561	561	886457	886457	3473	3473	False		
+snpfreq	hgv_snpFreq	snpFreq significant SNPs in case-control data								To update		Variant Analysis, Statistics	snpfreq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	44	10	12	307	649	68	181	227	260	16	23	569	953	94	216	False		
+snpfreqplot	snpfreqplot	A plotting app to visualise the SNPs across a region								To update	https://github.com/BrownfieldPlantLab/SNPFreqPlot	Variant Analysis	snpfreqplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot	1.0	r-base				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	3683	3683	338	338	1401	1401	433	433	1029	1029	95	95	6113	6113	866	866	False		
+snpsift	snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck	snpEff SnpSift tools from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html	Variant Analysis	snpsift	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift		snpsift	5.2			8	8	8	0	8	8	8	0	0	0	0	0	0	0	8	0	0	0	0	8	0	0	8	0	0	0	8	0	0	0	0	0	0	8	8	8	0	5142904	5146618	3602	4283	382391	421190	7013	9678	104030	105024	960	1184	5629325	5672832	11575	15145	False		
+snpsift_dbnsfp	snpSift_dbnsfp	snpEff SnpSift dbnsfp tool from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html#dbNSFP	Variant Analysis	snpsift_dbnsfp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	52	55	23	24	421	421	75	75	0	0	0	0	473	476	98	99	False		
+snpsift_genesets	snpSift_geneSets	Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome								To update	http://snpeff.sourceforge.net/SnpSift.html#geneSets	Variant Analysis	snpsift_genesets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	509	554	107	128	474	474	190	190	0	0	0	0	983	1028	297	318	False		
+snv_matrix	snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+snvtocnv	sequenzaindex, snvtocnv	infer copy number variations from a vcf file with SNVs using R sequenza								To update	http://artbio.fr	Variant Analysis	snvtocnv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv	https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv	3.0.0+galaxy1	sequenza-utils	3.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+socru	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	659	659	42	42	296	296	92	92	0	0	0	0	955	955	134	134	False		
+sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19865	21034	1047	1126	3141	3141	328	328	3304	3304	189	189	26310	27479	1564	1643	False		
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	3	9	3	0	82716	87113	8209	8526	120471	120475	14787	14790	54067	61541	5817	6653	257254	269129	28813	29969	False		
+spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	450	491	91	100	4270	4270	288	288	0	0	0	0	4720	4761	379	388	False		
+spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spatyper	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spec2vec	spec2vec_similarity, spec2vec_training	Mass spectra similarity scoring using a trained Spec2Vec model.	spec2vec	spec2vec		Spec2Vec	Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	Up-to-date	https://github.com/iomega/spec2vec	Metabolomics	spec2vec	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	0.8.0	spec2vec	0.8.0	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+spectrast2spectrast_irt	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spectrast2tsv	gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+split_file_on_column	tp_split_on_column	Split a file on a specific column.								To update		Text Manipulation	split_file_on_column	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	0.6	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5995	6261	408	453	2150	2150	311	311	26	26	2	2	8171	8437	721	766	False		
+split_file_to_collection	split_file_to_collection	Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	Text Manipulation	split_file_to_collection	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	0.5.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	16415	16623	968	984	9133	9133	672	672	4140	4140	148	148	29688	29896	1788	1804	False		
+split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	44	51	2	3	0	0	0	0	0	0	0	0	44	51	2	3	False		
+split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	3	200	384	31	66	200	397	31	69	False		
+splitfasta	rbc_splitfasta	Split a multi-sequence fasta file into files containing single sequences								To update		Text Manipulation	splitfasta	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	0.4.0	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1772	1811	278	294	3012	3012	564	564	0	0	0	0	4784	4823	842	858	False		
+spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	789	840	130	134	0	0	0	0	0	0	0	0	789	840	130	134	False		
+spolpred	spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.1	giatools	0.3.1	Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	4	4	0	0	0	0	0	0	0	0	16	16	4	4	False		
+spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	23	23	0	0	0	0	0	0	0	0	1436	1436	23	23	False		
+spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	142	142	5	5	0	0	0	0	0	0	0	0	142	142	5	5	False		
+sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	80	80	1	1	0	0	0	0	80	80	1	1	False		
+sr_bowtie_dataset_annotation	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	0	3	3	3	0	364871	376580	16710	17342	583675	678448	53271	59638	48131	50455	5910	6181	996677	1105483	75891	83161	False		
+srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	0	4	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	239	239	34	34	44	44	13	13	0	0	0	0	283	283	47	47	False		
+srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41	False		
+srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41	False		
+sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	214	225	17	18	0	0	0	0	0	0	0	0	214	225	17	18	False		
+stacks	stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	Data handling	Mapping, Population genetics	0	13	13	0	0	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	13	0	6440	11998	465	593	0	0	0	0	4070	4070	76	76	10510	16068	541	669	False		
+stacks2	stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65			0	12	12	0	0	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	8437	8592	626	646	0	0	0	0	18016	18016	270	270	26453	26608	896	916	False		
+star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update	https://github.com/STAR-Fusion/STAR-Fusion	Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1312	1383	82	95	2198	3076	234	303	173	173	3	3	3683	4632	319	401	False		
+staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20778	20891	2030	2045	9520	9520	1424	1424	6753	6753	864	864	37051	37164	4318	4333	False		
+statistics	bg_statistical_hypothesis_testing	Tool for computing statistical tests.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	Statistics	bg_statistical_hypothesis_testing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	0.3	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	169	346	46	61	0	0	0	0	0	0	0	0	169	346	46	61	False		
+stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	328	328	38	38	0	0	0	0	0	0	0	0	328	328	38	38	False		
+straindesign	straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion	Toolbox to optimize biological model								To update	https://github.com/brsynth/straindesign	Systems Biology, Synthetic Biology	straindesign	iuc	https://github.com/brsynth/straindesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign	3.2.2	straindesign	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+strelka	strelka_germline, strelka_somatic	Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision.								Up-to-date	https://github.com/Illumina/strelka/	Variant Analysis	strelka	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka	2.9.10	strelka	2.9.10			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	669	669	112	112	1261	1261	417	417	0	0	0	0	1930	1930	529	529	False		
+stress_ng	stress_ng	stress test a computer system in various selectable ways								To update		Web Services	stress_ng	bgruening-util	https://github.com/ColinIanKing/stress-ng	https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng	0.12.04	stress-ng				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	62	3	3	0	0	0	0	0	0	0	0	62	62	3	3	False		
+stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+stringtie	stringtie, stringtie_merge	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	stringtie	stringtie		StringTie	Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.	Transcriptome assembly, RNA-Seq analysis	Transcriptomics, RNA-seq	Up-to-date	http://ccb.jhu.edu/software/stringtie/	Transcriptomics	stringtie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie	2.2.3	stringtie	2.2.3	Transcriptome assembly, RNA-Seq analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	178677	187728	4972	5347	320780	407379	10825	15171	26375	28921	1032	1167	525832	624028	16829	21685	False		
+structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2858	3001	118	123	0	0	0	0	0	0	0	0	2858	3001	118	123	False		
+structureharvester	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date	http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/	Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+substitution_rates	subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	121	3901	34	747	105	114	4	4	226	4015	38	751	False		
+substitutions	substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	93	901	13	84	0	0	0	0	93	901	13	84	False		
+subtract	gops_subtract_1	Subtract the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	566512	567199	410	470	49985	184650	1473	7631	20648	20897	155	188	637145	772746	2038	8289	False		
+subtract_query	subtract_query1	Subtract Whole Dataset from another dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract_query	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query	0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1178	1450	124	141	3169	40539	636	3435	799	950	26	38	5146	42939	786	3614	False		
+suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	249	249	32	32	16	16	10	10	102	102	16	16	367	367	58	58	False		
+suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	117	117	41	41	84	84	24	24	161	161	13	13	362	362	78	78	False		
+suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	217	217	47	47	42	42	20	20	96	96	12	12	355	355	79	79	False		
+suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	721	721	160	160	350	350	91	91	214	214	35	35	1285	1285	286	286	False		
+suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	125	125	30	30	13	13	9	9	83	83	8	8	221	221	47	47	False		
+suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	396	396	134	134	121	121	57	57	144	144	39	39	661	661	230	230	False		
+suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	22	0	21	21	22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	964	964	318	318	249	249	118	118	475	475	108	108	1688	1688	544	544	False		
+suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	8	8	8	8	13	13	11	11	1302	1302	19	19	1323	1323	38	38	False		
+suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	58	58	23	23	24	24	11	11	92	92	11	11	174	174	45	45	False		
+suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	863	863	220	220	237	237	98	98	181	181	41	41	1281	1281	359	359	False		
+suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	0	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	983	983	287	287	375	375	144	144	907	907	106	106	2265	2265	537	537	False		
+suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	46	46	13	13	9	9	5	5	0	0	0	0	55	55	18	18	False		
+suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	0	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	37	37	16	16	22	22	7	7	89	89	14	14	148	148	37	37	False		
+suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	615	615	143	143	246	246	75	75	115	115	27	27	976	976	245	245	False		
+suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	330	330	83	83	64	64	40	40	195	195	49	49	589	589	172	172	False		
+suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	4	4	4	4	5	5	5	5	1	1	1	1	10	10	10	10	False		
+suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	14	14	16	16	6	6	37	37	2	2	82	82	22	22	False		
+suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	0	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	10	10	3	3	14	14	10	10	5	5	5	5	29	29	18	18	False		
+suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	664	664	145	145	113	113	43	43	255	255	50	50	1032	1032	238	238	False		
+suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	84	84	52	52	25	25	16	16	9	9	5	5	118	118	73	73	False		
+suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14941	14941	383	383	25941	25941	255	255	2856	2856	112	112	43738	43738	750	750	False		
+suite_snvphyl		SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	5	5	0	0	0	0	0	0	0	0	26	26	5	5	False		
+swift	swiftlink	Parallel MCMC Linkage Analysis								Up-to-date	https://github.com/ajm/swiftlink	Variant Analysis	swiftlink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift	1.0	swiftlink	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+syndiva	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	30	30	2	2	0	0	0	0	0	0	0	0	30	30	2	2	False		
+t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	411	472	68	90	102	7952	13	1240	0	0	0	0	513	8424	81	1330	False		
+t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	927	959	65	78	130	7194	18	1143	0	0	0	0	1057	8153	83	1221	False		
+t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3783	9125	211	229	1	1	1	1	0	0	0	0	3784	9126	212	230	False		
+t_test_two_samples	t_test_two_samples	T Test for Two Samples								To update		Statistics	t_test_two_samples	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples	https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	141	215	20	31	520	1166	79	274	1025	1118	11	12	1686	2499	110	317	False		
+table_annovar	table_annovar	Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered								To update		Variant Analysis	table_annovar	devteam	Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar	https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar	0.2	annovar				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16526	64515	2803	7456	0	0	0	0	16526	64515	2803	7456	False		
+table_compute	table_compute	Perform general-purpose table operations								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	Text Manipulation	table_compute	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute	1.2.4	pandas				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	216072	216115	1811	1814	12326	12326	1558	1558	16136	16136	256	256	244534	244577	3625	3628	False		
+tables_arithmetic_operations	tables_arithmetic_operations	Arithmetic Operations on tables								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	tables_arithmetic_operations	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations	1.0.0	perl				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2188	2220	33	38	0	0	0	0	0	0	0	0	2188	2220	33	38	False		
+tabular_to_fasta	tab2fasta	Tabular-to-FASTA								To update		Convert Formats	tabular_to_fasta	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta	1.1.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	329032	333057	1489	1702	79033	215770	2441	8587	27876	33727	296	360	435941	582554	4226	10649	False		
+tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7011	8135	449	482	9473	28494	626	2183	850	1090	80	104	17334	37719	1155	2769	False		
+tag_pileup_frequency	tag_pileup_frequency	Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup	Statistics, SAM, Genomic Interval Operations	tag_pileup_frequency	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency	1.0.2	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	158	164	15	16	722	865	40	73	0	0	0	0	880	1029	55	89	False		
+tapscan	tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	19	6	6	0	0	0	0	0	0	0	0	19	19	6	6	False		
+tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	827	838	89	92	114	114	41	41	900	900	29	29	1841	1852	159	162	False		
+tasmanian_mismatch	tasmanian_mismatch	Analysis of positional mismatches								Up-to-date	https://github.com/nebiolabs/tasmanian-mismatch	Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	4	61	61	7	7	0	0	0	0	65	65	11	11	False		
+taxonkit	name2taxid, profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	taxonkit	taxonkit		TaxonKit	TaxonKit is a practical and efficient NCBI taxonomy toolkit.	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	Up-to-date	https://bioinf.shenwei.me/taxonkit/	Metagenomics	taxonkit	iuc	https://github.com/shenwei356/taxonkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit	0.17.0	taxonkit	0.17.0	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	36069	36922	5257	5431	25255	30822	5066	5826	7949	7949	1584	1584	69273	75693	11907	12841	False		
+taxpasta	taxpasta	standardise taxonomic profiles	taxpasta	taxpasta		taxpasta	TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	Up-to-date	https://taxpasta.readthedocs.io/en/latest/	Sequence Analysis	taxpasta	iuc	https://github.com/taxprofiler/taxpasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta	0.7.0	taxpasta	0.7.0	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	34	34	5	5	0	0	0	0	0	0	0	0	34	34	5	5	False		
+tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6372	6395	372	379	7339	7339	378	378	6966	6966	154	154	20677	20700	904	911	False		
+tb_variant_filter	tb_variant_filter	M. tuberculosis H37Rv VCF filter								Up-to-date	https://github.com/COMBAT-TB/tb_variant_filter	Variant Analysis	tb_variant_filter	iuc	https://github.com/COMBAT-TB/tb_variant_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter	0.4.0	tb_variant_filter	0.4.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22977	22977	461	461	3888	3888	274	274	3611	3611	80	80	30476	30476	815	815	False		
+tbl2gff3	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1941	1941	466	466	0	0	0	0	463	463	112	112	2404	2404	578	578	False		
+tbvcfreport	tbvcfreport	Generate HTML report from SnpEff M.tuberculosis VCF(s)								Up-to-date	https://github.com/COMBAT-TB/tbvcfreport	Variant Analysis	tbvcfreport	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport	1.0.1	tbvcfreport	1.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2955	2955	335	335	6090	6090	348	348	2347	2347	72	72	11392	11392	755	755	False		
+te_finder	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.21	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	20	20	0	0	0	0	0	0	0	0	203	203	20	20	False		
+telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+tetoolkit	tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1013	1013	74	74	0	0	0	0	70	70	4	4	1083	1083	78	78	False		
+tetyper	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	106	106	16	16	155	155	47	47	0	0	0	0	261	261	63	63	False		
+text_processing	tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq	High performance text processing tools using the GNU coreutils, sed, awk and friends.								To update	https://www.gnu.org/software/	Text Manipulation	text_processing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	9.3	coreutils	8.25			20	20	20	0	20	20	20	0	0	0	0	0	0	0	0	0	0	19	1	19	0	0	19	0	0	0	20	0	0	0	0	0	0	19	19	19	0	3898014	4015573	37698	42095	648268	915282	47636	69828	103365	105214	7778	7953	4649647	5036069	93112	119876	False		
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	51	51	0	0	0	0	0	0	0	0	547	547	51	51	False		
+tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	8	8	0	0	0	0	0	0	0	0	15	15	8	8	False		
+tn93	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								Up-to-date	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.14	tn93	1.0.14			4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1915	1915	42	42	1972	1972	225	225	0	0	0	0	3887	3887	267	267	False		
+tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	445	445	25	25	71	71	32	32	0	0	0	0	516	516	57	57	False		
+tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9.1	tooldistillator	0.9.1	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	9	9	6	6	5	5	0	0	0	0	71	71	14	14	False		
+tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	158	66524	28	7228	0	0	0	0	158	66525	28	7229	False		
+tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	15496	26623	1076	1664	83063	343017	8372	27829	5388	14057	508	1012	103947	383697	9956	30505	False		
+tophat_fusion_post	tophat_fusion_post	Wrapper for Tophat-Fusion post step								To update		Transcriptomics	tophat_fusion_post	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post	0.1	blast+				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	220	242	41	46	6	814	2	191	100	120	8	12	326	1176	51	249	False		
+topologyeditors	gromacs_modify_topology, gromacs_extract_topology	Set of python scripts and associated tool files that can be used to modify topology files.								To update	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	Molecular Dynamics, Computational chemistry	topologyeditors	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	0	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	57	57	10	10	20	20	8	8	0	0	0	0	77	77	18	18	False		
+tracegroomer	tracegroomer	TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.								Up-to-date	https://github.com/cbib/TraceGroomer	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer	0.1.4	tracegroomer	0.1.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	1	1	0	0	0	0	0	0	0	0	7	7	1	1	False		
+tracy	tracy_align, tracy_assemble, tracy_basecall, tracy_decompose									To update				iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy	0.6.1	tracy	0.7.8			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	3314	3314	124	124	0	0	0	0	0	0	0	0	3314	3314	124	124	False		
+transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5964	6418	944	970	5450	5450	1066	1066	2610	2796	317	344	14024	14664	2327	2380	False		
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	1039	1039	189	189	2672	3349	467	485	358	358	47	47	4069	4746	703	721	False		
+translate_bed	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	649	685	138	142	473	473	105	105	761	761	18	18	1883	1919	261	265	False		
+translate_bed_sequences	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	69	16	21	0	0	0	0	0	0	0	0	57	69	16	21	False		
+transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	250	254	31	31	174	174	45	45	0	0	0	0	424	428	76	76	False		
+tree_relabeler	tree_relabel	Relabels the tips of a newick formatted tree.								To update		Text Manipulation	tree_relabeler	nml	https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler	https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	229489	275008	5733	6500	228708	324716	11708	16638	22644	23869	1439	1527	480841	623593	18880	24665	False		
+trimmer	trimmer	Trim leading or trailing characters.								To update		Text Manipulation	trimmer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer	0.0.1					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	5304	7438	447	512	15698	108672	658	2946	266	822	53	81	21268	116932	1158	3539	False		
+trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	1	1	1	0	352353	383014	14547	15408	632385	839058	39323	49850	125340	139097	5268	5975	1110078	1361169	59138	71233	False		
+trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	To update	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.2	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	0	9	13	13	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	0	11	13	12	0	35698	39132	4376	4632	44509	44509	6714	6714	21883	23889	1924	2070	102090	107530	13014	13416	False		
+trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1968	2080	374	390	1825	1825	527	527	862	1060	161	195	4655	4965	1062	1112	False		
+tripal	analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync	Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal								To update	https://github.com/galaxy-genome-annotation/python-tripal	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal		python-tripal	3.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	4361	4601	741	807	0	0	0	0	2469	2469	190	190	6830	7070	931	997	False		
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	14681	14681	265	265	0	0	0	0	4488	4488	147	147	19169	19169	412	412	False		
+tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	7	7	0	0	0	0	0	0	0	0	17	17	7	7	False		
+tsne	tsne	T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation								To update	https://cran.r-project.org/web/packages/Rtsne/	Text Manipulation	tsne	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne	0.0.2	r-rtsne	0.13			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	379	31	37	281	281	64	64	0	0	0	0	536	660	95	101	False		
+twobittofa	ucsc-twobittofa	twoBitToFa is a tool to convert all or part of .2bit file to FASTA	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenpath/help/twoBit.html	Convert Formats	ucsc_twobittofa	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	469	ucsc-twobittofa	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	413	511	84	118	441	441	123	123	21	21	2	2	875	973	209	243	False		
+tximport	tximport	Wrapper for the Bioconductor package tximport	tximport	tximport		tximport	An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	Up-to-date	http://bioconductor.org/packages/tximport/	Transcriptomics	tximport	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport	1.30.0	bioconductor-tximport	1.30.0	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1802	1802	225	225	6963	6963	904	904	0	0	0	0	8765	8765	1129	1129	False		
+ucsc-cell-browser	ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets								To update	https://cells.ucsc.edu/	Transcriptomics	ucsc_cell_browser	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser	1.0.0+galaxy1	ucsc-cell-browser	1.2.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	965	975	178	181	0	0	0	0	0	0	0	0	965	975	178	181	False		
+ucsc_axtchain	ucsc_axtchain	Chain together genome alignments	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_axtchain	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain	469	ucsc-axtchain	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_axttomaf	ucsc_axtomaf	Convert dataset from axt to MAF format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_axttomaf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf	469	ucsc-axttomaf	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_blat	ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	Up-to-date	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	469	ucsc-blat	469	Sequence alignment	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainnet	ucsc_chainnet	Make alignment nets out of chains	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainnet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	469	ucsc-chainnet	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainprenet	ucsc_chainprenet	Remove chains that don't have a chance of being netted	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainprenet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet	469	ucsc-chainprenet	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainsort	ucsc_chainsort	Sort chains. By default sorts by score.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainsort	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort	469	ucsc-chainsort	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	373	463	134	151	2249	18611	638	4080	0	0	0	0	2622	19074	772	4231	False		
+ucsc_netfilter	ucsc_netfilter	Filter out parts of net	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netfilter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter	469	ucsc-netfilter	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_netsyntenic	ucsc_netsyntenic	Add synteny info to a net dataset	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netsyntenic	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic	469	ucsc-netsyntenic	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_nettoaxt	ucsc_nettoaxt	Convert net (and chain) to axt format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_nettoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt	469	ucsc-nettoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	0	3	5	5	0	55050	68123	1090	1223	9001	9001	906	906	12444	12444	187	187	76495	89568	2183	2316	False		
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	74120	77648	3798	3963	64946	90075	5451	7380	19516	20422	2010	2080	158582	188145	11259	13423	False		
+unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4900	5146	257	270	251	251	81	81	1069	1069	29	29	6220	6466	367	380	False		
+uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.6	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2117	2725	341	412	3111	5779	594	1011	806	806	50	50	6034	9310	985	1473	False		
+uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1488	1596	230	266	0	0	0	0	743	743	35	35	2231	2339	265	301	False		
+unzip	unzip	Unzip file								To update	https://github.com/bmcv	Convert Formats	unzip	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip	6.0	unzip				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6942	7024	1345	1356	1	1	1	1	2461	2461	266	266	9404	9486	1612	1623	False		
+upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1060	1060	5	5	0	0	0	0	0	0	0	0	1060	1060	5	5	False		
+valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	518	677	75	87	234	234	65	65	0	0	0	0	752	911	140	152	False		
+validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	112	38	38	0	0	0	0	0	0	0	0	112	112	38	38	False		
+vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5936	5936	147	147	523	523	15	15	0	0	0	0	6459	6459	162	162	False		
+vardict	vardict_java	VarDict - calls SNVs and indels for tumour-normal pairs								To update	https://github.com/AstraZeneca-NGS/VarDictJava	Variant Analysis	vardict_java	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict	1.8.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	381	381	37	37	0	0	0	0	0	0	0	0	381	381	37	37	False		
+variant_analyzer	mut2read, mut2sscs, read2mut	Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data								To update		Variant Analysis	variant_analyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer	2.0.0	matplotlib				3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	95	95	14	14	516	516	67	67	0	0	0	0	611	611	81	81	False		
+varscan	varscan_copynumber, varscan_mpileup, varscan_somatic	VarScan is a variant caller for high-throughput sequencing data								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/varscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan	2.4.3	varscan	2.4.6			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	10711	11502	1442	1560	16705	16705	3135	3135	1036	1036	100	100	28452	29243	4677	4795	False		
+varscan_vaf	varscan_vaf	Compute variant allele frequency in vcf files generated by varscan.								To update	http://artbio.fr	Variant Analysis	varscan_vaf	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf	https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+varscan_version_2	varscan	VarScan wrapper								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan_version_2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2	2.4.2	varscan	2.4.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5058	6139	606	699	17232	53268	2965	5686	2298	2656	424	482	24588	62063	3995	6867	False		
+varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	273	273	12	12	0	0	0	0	0	0	0	0	273	273	12	12	False		
+vcf2maf	vcf2maf	vcf2maf: Convert VCF into MAF								To update	https://github.com/mskcc/vcf2maf	Convert Formats	vcf2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf	1.6.21	vcf2maf	1.6.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1097	1097	46	46	0	0	0	0	65	65	5	5	1162	1162	51	51	False		
+vcf2pgsnp	vcf2pgSnp	VCF to pgSnp								To update		Variant Analysis	vcf2pgsnp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	191	221	57	65	1399	2700	209	584	0	0	0	0	1590	2921	266	649	False		
+vcf2snvalignment	vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vcf2tsv	vcf2tsv	Converts VCF files into tab-delimited format								To update	https://github.com/ekg/vcflib	Variant Analysis, Convert Formats	vcf2tsv	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	169090	169679	823	874	16304	42215	1141	2594	2485	2511	169	172	187879	214405	2133	3640	False		
+vcf_annotate	vcf_annotate	Annotate a VCF file (dbSNP, hapmap)								To update		Variant Analysis	vcf_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	1	0	1	263	340	31	54	263	342	31	56	False		
+vcf_extract	vcf_extract	Extract reads from a specified region								To update		Variant Analysis	vcf_extract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	513	569	6	9	513	569	6	9	False		
+vcf_filter	vcf_filter	Filter a VCF file								To update		Variant Analysis	vcf_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	400	455	129	140	0	0	0	0	238	606	19	56	638	1061	148	196	False		
+vcf_intersect	vcf_intersect	Generate the intersection of two VCF files								To update		Variant Analysis	vcf_intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	3	0	0	0	0	335	463	19	28	335	482	19	31	False		
+vcfaddinfo	vcfaddinfo	Adds info fields from the second dataset which are not present in the first dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfaddinfo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	882	888	30	32	6118	8261	36	114	175	184	6	6	7175	9333	72	152	False		
+vcfallelicprimitives	vcfallelicprimitives	Splits alleleic primitives (gaps or mismatches) into multiple VCF lines								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfallelicprimitives	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6879	17157	897	1219	7585	14509	1245	1925	1648	1681	225	229	16112	33347	2367	3373	False		
+vcfanno	vcfanno	Annotate VCF files	vcfanno	vcfanno		vcfanno	Fast, flexible annotation of genetic variants.	SNP annotation	Genetic variation, Data submission, annotation and curation	Up-to-date	https://github.com/brentp/vcfanno	Variant Analysis	vcfanno	iuc	https://github.com/galaxyproject/tools-iuc/vcfanno/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno	0.3.5	vcfanno	0.3.5	SNP annotation	Genetic variation, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1139	1139	174	174	0	0	0	0	0	0	0	0	1139	1139	174	174	False		
+vcfannotate	vcfannotate	Intersect VCF records with BED annotations								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotate	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2797	2850	157	181	3668	14532	652	1392	494	507	61	63	6959	17889	870	1636	False		
+vcfannotategenotypes	vcfannotategenotypes	Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotategenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	203	62	66	497	1828	155	387	184	197	11	11	870	2228	228	464	False		
+vcfbedintersect	vcfbedintersect	Intersect VCF and BED datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbedintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3017	4049	185	210	4709	20250	406	1147	507	527	40	42	8233	24826	631	1399	False		
+vcfbreakcreatemulti	vcfbreakcreatemulti	Break multiple alleles into multiple records, or combine overallpoing alleles into a single record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbreakcreatemulti	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	416	478	35	40	3969	10457	82	309	362	378	8	8	4747	11313	125	357	False		
+vcfcheck	vcfcheck	Verify that the reference allele matches the reference genome								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcheck	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	745	767	96	106	803	1895	222	627	241	256	16	17	1789	2918	334	750	False		
+vcfcombine	vcfcombine	Combine multiple VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcombine	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1422	2020	284	505	4951	19530	1021	2669	493	516	60	62	6866	22066	1365	3236	False		
+vcfcommonsamples	vcfcommonsamples	Output records belonging to samples commong between two datasets.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcommonsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	233	253	37	42	234	1839	79	287	199	214	11	12	666	2306	127	341	False		
+vcfdistance	vcfdistance	Calculate distance to the nearest variant.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfdistance	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	572	585	90	92	2063	2427	139	296	272	290	19	22	2907	3302	248	410	False		
+vcffilter	vcffilter2	Tool for filtering VCF files								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffilter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37489	47142	2113	2218	75128	162296	5730	10533	2626	2736	320	331	115243	212174	8163	13082	False		
+vcffixup	vcffixup	Count the allele frequencies across alleles present in each record in the VCF file.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffixup	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	926	957	155	173	2291	5323	313	985	251	265	28	31	3468	6545	496	1189	False		
+vcfflatten	vcfflatten2	Removes multi-allelic sites by picking the most common alternate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfflatten	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	172	183	21	25	351	879	67	201	312	342	15	16	835	1404	103	242	False		
+vcfgeno2haplo	vcfgeno2haplo	Convert genotype-based phased alleles into haplotype alleles								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgeno2haplo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	778	794	107	112	2414	3721	179	508	209	225	20	21	3401	4740	306	641	False		
+vcfgenotypes	vcfgenotypes	Convert numerical representation of genotypes to allelic.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	502	555	134	143	3428	6338	266	858	220	235	23	24	4150	7128	423	1025	False		
+vcfhethom	vcfhethom	Count the number of heterozygotes and alleles, compute het/hom ratio.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfhethom	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1964	1991	182	186	1937	3846	188	644	567	601	26	27	4468	6438	396	857	False		
+vcfleftalign	vcfleftalign	Left-align indels and complex variants in VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfleftalign	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	269	310	38	42	358	1071	89	287	179	213	12	14	806	1594	139	343	False		
+vcfprimers	vcfprimers	Extract flanking sequences for each VCF record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfprimers	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	590	711	28	33	403	831	75	200	190	214	10	12	1183	1756	113	245	False		
+vcfrandomsample	vcfrandomsample	Randomly sample sites from VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfrandomsample	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	161	168	13	15	153	350	27	75	184	192	6	6	498	710	46	96	False		
+vcfselectsamples	vcfselectsamples	Select samples from a VCF file								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfselectsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	830	900	69	88	1315	6257	237	959	344	363	20	21	2489	7520	326	1068	False		
+vcfsort	vcfsort	Sort VCF dataset by coordinate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfsort	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1868	1904	174	185	18378	24175	422	1279	537	674	70	73	20783	26753	666	1537	False		
+vcftools_annotate	vcftools_annotate	Annotate VCF using custom/user-defined annotations								To update	https://vcftools.github.io/	Variant Analysis	vcftools_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate	0.1	echo				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	155	192	81	90	1853	3943	581	1280	144	156	13	16	2152	4291	675	1386	False		
+vcftools_compare	vcftools_compare	Compare VCF files to get overlap and uniqueness statistics								To update	https://vcftools.github.io/	Variant Analysis	vcftools_compare	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	440	594	127	142	0	0	0	0	0	16	0	12	440	610	127	154	False		
+vcftools_consensus	vcftools_consensus	Apply VCF variants to a fasta file to create consensus sequence								To update	https://vcftools.github.io/	Variant Analysis	vcftools_consensus	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus	0.1.11	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vcftools_isec	vcftools_isec	Intersect multiple VCF datasets								To update	https://vcftools.github.io/	Variant Analysis	vcftools_isec	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec	0.1.1	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	379	537	104	118	0	1	0	1	39	496	28	48	418	1034	132	167	False		
+vcftools_merge	vcftools_merge	Merge multiple VCF datasets into a single dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge	0.1.11	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	817	1084	244	273	0	0	0	0	93	448	44	60	910	1532	288	333	False		
+vcftools_slice	vcftools_slice	Subset VCF dataset by genomic regions								To update	https://vcftools.github.io/	Variant Analysis	vcftools_slice	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice	0.1	echo				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	410	423	56	60	6261	8115	133	362	127	157	10	19	6798	8695	199	441	False		
+vcftools_subset	vcftools_subset	Select samples from a VCF dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_subset	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	134	142	46	49	0	0	0	0	120	142	12	19	254	284	58	68	False		
+vcfvcfintersect	vcfvcfintersect	Intersect two VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfvcfintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	976544	977015	703	748	64155	81830	981	2103	11044	11069	225	229	1051743	1069914	1909	3080	False		
+vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	2157	2287	198	209	3930	5591	446	744	0	0	0	0	6087	7878	644	953	False		
+velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	4	4	22	22	6	6	16	16	1	1	45	45	11	11	False		
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	25171	27943	3899	4270	51187	51187	7557	7557	28546	28619	3585	3613	104904	107749	15041	15440	False		
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4715	5343	888	965	9575	9576	2117	2117	3271	5524	1050	1397	17561	20443	4055	4479	False		
+venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4519	5476	667	730	9858	18420	986	2010	0	0	0	0	14377	23896	1653	2740	False		
+verify_map	verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	48	25	25	0	0	0	0	0	0	0	0	48	48	25	25	False		
+vg	vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.59.0			0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	478	478	17	17	0	0	0	0	0	0	0	0	478	478	17	17	False		
+vibrant	vibrant	Virus Identification By iteRative ANnoTation	VIBRANT	VIBRANT		VIBRANT	Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	Up-to-date	https://github.com/AnantharamanLab/VIBRANT	Metagenomics	vibrant	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant	1.2.1	vibrant	1.2.1	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vienna_rna	viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	0	3197	8107	344	415	0	0	0	0	0	0	0	0	3197	8107	344	415	False		
+vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	14412	14590	722	732	0	0	0	0	0	0	0	0	14412	14590	722	732	False		
+virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	94	94	16	16	0	0	0	0	0	0	0	0	94	94	16	16	False		
+virheat	virheat	generates a heatmap of allele frequencies from vcf files	virheat	virheat		virHEAT	VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.			Up-to-date	https://github.com/jonas-fuchs/virHEAT	Visualization, Variant Analysis	virheat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat	0.7.1	virheat	0.7.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	2	2	0	0	0	0	0	0	0	0	12	12	2	2	False		
+virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	574	574	76	76	0	0	0	0	0	0	0	0	574	574	76	76	False		
+virsorter	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	virsorter	virsorter		virsorter	Identify DNA and RNA virus sequences.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/jiarong/VirSorter2/	Metagenomics	virsorter	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter	2.2.4	virsorter	2.2.4	Taxonomic classification	Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+visceral_evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	1	1	0	0	0	0	0	0	0	0	20	25	1	1	False		
+vmd		vmd is a package for  visualizing and analyzing trajectories from molecular dynamics (MD) simulations								To update	https://www.ks.uiuc.edu/Research/vmd/	Computational chemistry	vmd	chemteam	https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	34917	36852	3670	3786	54931	54931	5597	5597	7183	7183	905	905	97031	98966	10172	10288	False		
+voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	43	43	3	3	0	0	0	0	0	0	0	0	43	43	3	3	False		
+vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.29.0	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	0	8	8	8	0	9694	10338	559	628	12282	53546	1031	2007	5334	5672	246	277	27310	69556	1836	2912	False		
+vsnp	vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+w4mclassfilter	w4mclassfilter	Filter W4M data by values or metadata								To update	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper	Metabolomics	w4mclassfilter	eschen42	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter	0.98.19	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2370	2836	9	10	0	0	0	0	1482	1509	4	4	3852	4345	13	14	False		
+w4mconcatenate	W4Mconcatenate	[W4M][Utils] concatenate two Metadata tables								To update	http://workflow4metabolomics.org	Metabolomics	w4mconcatenate	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate	1.0.0+galaxy0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+w4mcorcov	w4mcorcov	OPLS-DA Contrasts of Univariate Results								To update	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper	Metabolomics	w4mcorcov	eschen42	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov	0.98.18	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	238	375	10	10	0	0	0	0	10	10	2	2	248	385	12	12	False		
+w4mjoinpn	w4mjoinpn	Join positive- and negative-mode W4M datasets								To update	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper	Metabolomics	w4mjoinpn	eschen42	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn	0.98.2	coreutils	8.25			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	150	171	7	7	0	0	0	0	7	7	2	2	157	178	9	9	False		
+wade	wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+waveica	waveica	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.	waveica	waveica		WaveICA	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.	Standardisation and normalisation	Metabolomics	Up-to-date	https://github.com/RECETOX/WaveICA	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	0.2.0	r-recetox-waveica	0.2.0	Standardisation and normalisation	Metabolomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	39	6	6	4	4	3	3	0	0	0	0	43	43	9	9	False		
+weather_app	simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+weblogo3	rgweblogo3	Sequence Logo generator for fasta	weblogo	weblogo		WebLogo	Web-based application designed to make generate sequence logos.	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	To update		Graphics	weblogo3	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3	3.5.0	weblogo	3.7.9	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2720	2818	206	228	10299	30578	1354	3657	1226	1285	50	59	14245	34681	1610	3944	False		
+weightedaverage	wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	227	2307	17	75	0	0	0	0	227	2307	17	75	False		
+whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	96	96	13	13	0	0	0	0	0	0	0	0	96	96	13	13	False		
+wigtobigwig	ucsc_wigtobigwig	converts bedGraph (wig) files into binary bigwig	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenPath/help/bigWig.html	Convert Formats	ucsc_wigtobigwig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig	469	ucsc-wigtobigwig	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1601	1601	106	106	1108	1108	172	172	200	200	15	15	2909	2909	293	293	False		
+windowmasker	windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.16.0			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	537	537	19	19	12	12	7	7	297	297	2	2	846	846	28	28	False		
+windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	2	171	3961	34	328	0	0	0	0	171	3972	34	330	False		
+winnowmap	winnowmap	A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.								Up-to-date	https://github.com/marbl/Winnowmap	Next Gen Mappers	winnowmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap	2.03	winnowmap	2.03			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	279	279	46	46	12	12	4	4	0	0	0	0	291	291	50	50	False		
+woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	1	1	0	0	0	0	0	0	0	0	31	31	1	1	False		
+wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	38	2	3	0	0	0	0	0	0	0	0	32	38	2	3	False		
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1619	1715	337	376	0	0	0	0	0	0	0	0	1619	1715	337	376	False		
+xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	0	5	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	5995	5995	275	275	66	66	23	23	295	295	3	3	6356	6356	301	301	False		
+xcms	abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw		XCMS	XCMS		xcms	Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data.  The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling.	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Biological imaging, Data visualisation, Metabolomics	Up-to-date	https://github.com/sneumann/xcms	Metabolomics	xcms	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms	4.0.0	bioconductor-xcms	4.0.0	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Data visualisation, Metabolomics	9	11	12	0	9	11	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	10	9	0	31909	35790	1357	1384	7099	7099	413	413	5333	5357	330	330	44341	48246	2100	2127	False		
+xmlstarlet	xmlstarlet	Tool to convert a xml file from one metadata standard to another								To update		Convert Formats	xmlstarlet	ecology	https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet	https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet	1.6.1	xmlstarlet				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	59	59	17	17	0	0	0	0	0	0	0	0	59	59	17	17	False		
+xpath	xpath	XPath XML querying tool								To update	http://search.cpan.org/dist/XML-XPath/	Text Manipulation	xpath	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath	https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath		perl-xml-xpath	1.47			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	128	235	7	8	0	1	0	1	0	0	0	0	128	236	7	9	False		
+xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+xtb	xtb_molecular_optimization	Performs semiempirical molecular optimization.								To update	https://github.com/grimme-lab/xtb	Metabolomics	xtb_molecular_optimization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	6.6.1	xtb				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	143	143	4	4	0	0	0	0	0	0	0	0	143	143	4	4	False		
+xy_plot	XY_Plot_1	Plotting tool for multiple series and graph types								To update		Graphics, Statistics	xy_plot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot	1.0.2	r-base				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4490	6169	768	889	6120	15516	1921	3653	2033	2212	556	590	12643	23897	3245	5132	False		
+yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	618	618	176	176	336	336	62	62	588	588	25	25	1542	1542	263	263	False		
+zeiss_lmd_converter	ZeissLMDconverter	Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	2.0.4	shapely				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	1	1	0	0	0	0	0	0	0	0	4	4	1	1	False		
+zerone	zerone	ChIP-seq discretization and quality control								Up-to-date	https://github.com/nanakiksc/zerone	ChIP-seq	zerone	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone	https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone	1.0	zerone	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	83	96	9	12	0	0	0	0	0	0	0	0	83	96	9	12	False		
+zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	4	4	0	0	0	0	0	0	0	0	26	26	4	4	False		
diff --git a/communities/proteomics/resources/tools_filtered_by_ts_categories.tsv b/communities/proteomics/resources/tools_filtered_by_ts_categories.tsv
new file mode 100644
index 00000000..e8073b86
--- /dev/null
+++ b/communities/proteomics/resources/tools_filtered_by_ts_categories.tsv
@@ -0,0 +1,1470 @@
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+10x_bamtofastq	10x_bamtofastq	Converts 10x Genomics BAM to FASTQ								Up-to-date	https://github.com/10XGenomics/bamtofastq	Convert Formats	10x_bamtofastq	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	1.4.1	10x_bamtofastq	1.4.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	307	307	80	80	8	8	3	3	3	3	1	1	318	318	84	84	False		
+2d_auto_threshold	ip_threshold	Automatic thresholding	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_auto_threshold	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1434	6746	120	122	0	0	0	0	305	305	11	11	1739	7051	131	133	False		
+2d_feature_extraction	ip_2d_feature_extraction	2D feature extraction	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_feature_extraction	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1156	13842	40	42	0	0	0	0	121	121	4	4	1277	13963	44	46	False		
+2d_filter_segmentation_by_features	ip_2d_filter_segmentation_by_features	filter segmentation by rules	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	2d_filter_segmentation_by_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features	0.0.1-4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	591	6863	38	40	0	0	0	0	119	119	3	3	710	6982	41	43	False		
+2d_histogram_equalization	ip_histogram_equalization	2d histogram equalization	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	2d_histogram_equalization	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_histogram_equalization	0.18.1	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	762	782	100	101	0	0	0	0	230	230	14	14	992	1012	114	115	False		
+2d_simple_filter	ip_filter_standard	2d simple filter			scipy					To update	https://github.com/bmcv	Imaging	2d_simple_filter	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter	1.12.0	scipy				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	948	6261	98	100	0	0	0	0	153	153	13	13	1101	6414	111	113	False		
+AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	119	14	17	0	0	0	0	0	0	0	0	45	119	14	17	False		
+AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	189	3094	23	25	0	0	0	0	0	0	0	0	189	3094	23	25	False		
+CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25532	50045	45	57	0	0	0	0	0	0	0	0	25532	50045	45	57	False		
+CollectResults	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1119	2115	50	62	0	0	0	0	0	0	0	0	1119	2115	50	62	False		
+CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	37	108	1	3	0	0	0	0	0	0	0	0	37	108	1	3	False		
+EMLassemblyline	annotations_template, eal_table_template, eal_templates, eml2eal, eml_validate, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.0+galaxy0	r-base				0	0	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	516	516	128	128	0	0	0	0	0	0	0	0	516	516	128	128	False		
+Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	352	352	36	36	0	0	0	0	0	0	0	0	352	352	36	36	False		
+Ensembl-REST	get_feature_info, get_genetree, get_sequences	A suite of Galaxy tools designed to work with Ensembl REST API.								To update	https://rest.ensembl.org	Data Source		earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST	0.1.2	requests				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	474	2914	132	163	0	0	0	0	0	0	0	0	474	2914	132	163	False		
+GAFA	gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	47	6	6	0	0	0	0	0	0	0	0	40	47	6	6	False		
+GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	80	150	18	23	0	0	0	0	0	0	0	0	80	150	18	23	False		
+Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	53	53	18	18	0	0	0	0	0	0	0	0	53	53	18	18	False		
+LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	25572	50177	45	57	0	0	0	0	0	0	0	0	25572	50177	45	57	False		
+NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	3210	62854	96	124	0	0	0	0	0	0	0	0	3210	62854	96	124	False		
+PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2					0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	4	0	1038	1038	146	146	0	0	0	0	849	849	38	38	1887	1887	184	184	False		
+Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	45	71	9	10	0	0	0	0	0	0	0	0	45	71	9	10	False		
+PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1202	2121	48	62	0	0	0	0	0	0	0	0	1202	2121	48	62	False		
+Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1116	1897	57	71	0	0	0	0	0	0	0	0	1116	1897	57	71	False		
+Structure_GSPAN	structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	991	3060	50	62	0	0	0	0	0	0	0	0	991	3060	50	62	False		
+ThermoRawFileParser	thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2467	2959	88	124	0	0	0	0	1097	1097	18	18	3564	4056	106	142	False		
+TreeBest	treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1003	1022	48	52	0	0	0	0	0	0	0	0	1003	1022	48	52	False		
+TrimNs	trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	43	43	20	20	0	0	0	0	0	0	0	0	43	43	20	20	False		
+ab1_fastq	ab1_fastq_converter	Tool to convert ab1 files into FASTQ files								To update		Convert Formats	ab1fastq	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/ab1_fastq	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ab1_fastq	1.20.0	bioconductor-sangerseqr	1.38.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	49465	49465	281	281	0	0	0	0	0	0	0	0	49465	49465	281	281	False		
+abacas	abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+abricate	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	2	3	3	0	619817	622353	4097	4130	320454	320454	2915	2915	496156	503743	2012	2227	1436427	1446550	9024	9272	False		
+abritamr	abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1139	1139	109	109	0	0	0	0	0	0	0	0	1139	1139	109	109	False		
+abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5543	5543	1042	1042	1301	1305	413	414	2030	2030	299	299	8874	8878	1754	1755	False		
+adapter_removal	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.4	adapterremoval	2.3.4	Sequence trimming, Sequence merging, Primer removal		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	348	348	62	62	0	0	0	0	0	0	0	0	348	348	62	62	False		
+add_input_name_as_column	addName	Add input name as column on an existing tabular file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	Text Manipulation	add_input_name_as_column	mvdbeek	https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column	https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	76834	86002	227	246	20174	20953	312	395	11	11	2	2	97019	106966	541	643	False		
+add_line_to_file	add_line_to_file	Adds a text line to the beginning or end of a file.								To update		Text Manipulation	add_line_to_file	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	0.1.0	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	15933	15933	378	378	1736	1736	214	214	380	380	28	28	18049	18049	620	620	False		
+add_value	addValue	Add a value as a new column.								To update		Text Manipulation	add_value	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value	https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value	1.0.1	perl				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	37860	374587	1293	1610	17588	293713	1243	6197	3873	4397	202	229	59321	672697	2738	8036	False		
+aegean	aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	Sequence annotation	Sequence analysis, Gene structure	1	4	4	0	1	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	200	200	77	77	83	83	39	39	1747	1747	44	44	2030	2030	160	160	False		
+agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.4.0	agat	1.4.1	Data handling, Genome annotation	Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	244	244	0	0	0	0	119	119	10	10	1555	1555	254	254	False		
+aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	262	262	36	36	0	0	0	0	0	0	0	0	262	262	36	36	False		
+align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	511	541	32	35	0	0	0	0	0	0	0	0	511	541	32	35	False		
+allegro	allegro	Linkage and haplotype analysis from deCODE	allegro	allegro		Allegro	It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	To update	http://www.decode.com/software/	Variant Analysis	allegro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro	@VER@.0	allegro	3	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ambertools	ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap	Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.								To update	http://ambermd.org/AmberTools.php	Molecular Dynamics, Computational chemistry	ambertools	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/ambertools	21.10	ambertools				7	2	7	0	7	2	7	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	5	0	41793	41881	510	511	1126	1126	159	159	1552	1552	85	85	44471	44559	754	755	False		
+amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	81	81	17	17	0	0	0	0	0	0	0	0	81	81	17	17	False		
+ampvis2	ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.9			Analysis, Visualisation	Biodiversity	0	0	19	0	0	0	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	1213	1213	155	155	0	0	0	0	0	0	0	0	1213	1213	155	155	False		
+amrfinderplus	amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5734	5734	334	334	1035	1035	106	106	0	0	0	0	6769	6769	440	440	False		
+ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	7	7	0	0	0	0	0	0	0	0	26	26	7	7	False		
+anisotropic_diffusion	ip_anisotropic_diffusion	Anisotropic image diffusion								Up-to-date	https://github.com/bmcv	Imaging	anisotropic_diffusion	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic_diffusion	0.4.0	medpy	0.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	41	2	2	0	0	0	0	0	0	0	0	36	41	2	2	False		
+anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	43047	43139	1826	1827	17240	17240	878	878	9309	9309	298	298	69596	69688	3002	3003	False		
+annotatemyids	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	Annotation		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	29266	30655	2849	2973	59299	66180	5917	6355	5644	5644	1049	1049	94209	102479	9815	10377	False		
+antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	292	306	5	7	0	0	0	0	0	0	0	0	292	306	5	7	False		
+antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15949	16490	726	811	5113	5113	649	649	6043	6043	169	169	27105	27646	1544	1629	False		
+apoc	apoc	Large-scale structural comparison of protein pockets								To update	http://cssb.biology.gatech.edu/APoc	Computational chemistry	apoc	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc	1.0+galaxy1	apoc	1b16			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4	4	4	4	1	1	1	1	0	0	0	0	5	5	5	5	False		
+apollo	create_account, feat_from_gff3, create_or_update, delete_features, delete_organism, export, fetch_jbrowse, iframe, list_organism	Access an Apollo instance from Galaxy								To update	https://github.com/galaxy-genome-annotation/python-apollo	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo		apollo	4.2.13			0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	0	3600	3760	883	911	6	6	4	4	0	0	0	0	3606	3766	887	915	False		
+appendfdr	append_fdr									To update			appendfdr	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/appendfdr	0.2.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+aquainfra_importer	aquainfra_importer	A data source tool for downloading datasets via the AquaINFRA Interaction Platform.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/AquaINFRA/tools-ecology/tree/aquainfra_importer	https://github.com/galaxyecology/tools-ecology/tree/master/tools/aquainfra_importer	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	75	75	9	9	0	0	0	0	0	0	0	0	75	75	9	9	False		
+aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	59	74	10	12	0	0	0	0	0	0	0	0	59	74	10	12	False		
+argnorm	argnorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database	argnorm	argnorm		argNorm	argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to.	Gene functional annotation		Up-to-date	https://github.com/BigDataBiology/argNorm	Genome annotation	argnorm	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm	0.6.0	argnorm	0.6.0	Gene functional annotation		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+arriba	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3670	3670	71	71	3	3	2	2	234	234	10	10	3907	3907	83	83	False		
+art	art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update	http://www.niehs.nih.gov/research/resources/software/biostatistics/art/	Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	Conversion	Bioinformatics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	140	140	9	9	0	0	0	0	0	0	0	0	140	140	9	9	False		
+artbio_bam_cleaning	artbio_bam_cleaning	filter bam files before somatic-varscan or lumpy-smoove analysis								To update	http://artbio.fr	SAM, Variant Analysis	artbio_bam_cleaning	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	https://github.com/ARTbio/tools-artbio/tree/main/tools/artbio_bam_cleaning	1.10+galaxy0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	1	0	9021	9021	238	238	0	0	0	0	0	0	0	0	9021	9021	238	238	False		
+askomics	askomics_integrate	Galaxy tools allowing to interact with a remote AskOmics server.AskOmics is a visual SPARQL query builder for RDF database.https://github.com/askomics/								To update	https://github.com/askomics/	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics		askocli	0.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+askor	askor_de	AskoR links EdgeR and AskOmics								To update	https://github.com/askomics/askoR	Transcriptomics	askor_de	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	https://github.com/genouest/galaxy-tools/tree/master/tools/askor	0.2	bioconductor-limma	3.58.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assembly-stats	assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+astral	astral	Tool for estimating an unrooted species tree given a set of unrooted gene trees								Up-to-date	https://github.com/smirarab/ASTRAL	Phylogenetics	astral	iuc	https://github.com/usegalaxy-be/galaxytools/tree/main/astral	https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral	5.7.8	astral-tree	5.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	151	151	5	5	151	151	5	5	False		
+astropytools	astropy_fits2bitmap, astropy_fits2csv, astropy_fitsinfo	AstropyTools library contains Galaxy tools for elementary Astrophysical operations								To update	https://github.com/astropy/astropy	Astronomy	astropytools	volodymyrss	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/astropytools	0.1.0+galaxy0	astropy				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	13	13	5	5	0	0	0	0	0	0	0	0	13	13	5	5	False		
+atactk_trim_adapters	atactk_trim_adapters	Trim adapters from paired-end HTS reads.								To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	232	279	62	72	0	0	0	0	0	0	0	0	232	279	62	72	False		
+augustus	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	12890	13988	1826	1988	14901	14901	2633	2633	6187	6187	511	511	33978	35076	4970	5132	False		
+augustus	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10109	11052	1378	1509	12573	12573	2206	2206	5274	5274	369	369	27956	28899	3953	4084	False		
+b2btools	b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/b2tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.7	Protein disorder prediction, Protein secondary structure prediction		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	369	369	19	19	0	0	0	0	0	0	0	0	369	369	19	19	False		
+background_removal	background_removal	Background removal filters using scikit-image								To update	https://github.com/bmcv	Imaging	background_removal	imgteam	https://github.com/BMCV/galaxy-image-analysis/tools/background_removal	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/background_removal	0.24.0	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1	False		
+bakta	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	bakta	bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	11117	11117	534	534	19	19	1	1	9601	9601	167	167	20737	20737	702	702	False		
+bam2mappingstats	bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bam_to_scidx	bam_to_scidx	Contains a tool that converts a BAM file to an ScIdx file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx	Convert Formats	bam_to_scidx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	83	131	15	20	329	785	50	210	0	0	0	0	412	916	65	230	False		
+bamclipper	bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bamhash	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	158	181	40	44	0	0	0	0	0	0	0	0	158	181	40	44	False		
+bamparse	bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bamtools	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	14693	15620	653	721	61872	101400	1656	5678	39	39	3	3	76604	117059	2312	6402	False		
+bamtools_filter	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115954	124795	2994	3180	95433	142254	6712	10660	5793	5793	497	497	217180	272842	10203	14337	False		
+bamtools_split	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	9073	9073	401	401	2746	2746	224	224	103	103	10	10	11922	11922	635	635	False		
+bamutil	bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	45	45	20	20	69	69	21	21	258	258	1	1	372	372	42	42	False		
+bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	55392	56095	4951	5035	47603	47603	4916	4916	18089	18089	3121	3121	121084	121787	12988	13072	False		
+barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+barcode_splitter	barcode_splitter	A utility to split sequence files using multiple sets of barcodes								To update	https://bitbucket.org/princeton_genomics/barcode_splitter/	Fastq Manipulation	barcode_splitter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter	0.18.4.0	barcode_splitter	0.18.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	111	111	8	8	29	29	10	10	21	21	4	4	161	161	22	22	False		
+baric_archive	baric_archive_rennes, baric_archive_toulouse	A data source tool to fetch data from a BARIC Archive server.								To update	https://www.cesgo.org/catibaric/	Data Source		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	https://github.com/genouest/galaxy-tools/tree/master/tools/baric_archive	1.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+barrnap	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update	https://github.com/tseemann/barrnap	Sequence Analysis	barrnap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/barrnap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	Gene prediction	Genomics, Model organisms, Model organisms	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6041	6041	316	316	0	0	0	0	6723	7273	240	322	12764	13314	556	638	False		
+basecoverage	gops_basecoverage_1	Base Coverage of all intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	basecoverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	226	308	27	35	2615	45557	302	2284	482	522	32	36	3323	46387	361	2355	False		
+baseline_calculator	tt_baseline	Toxicity prediction using QSAR models								To update	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology, Text Manipulation	baseline_toxicity_calculator	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/baseline_calculator	0.1.0+galaxy0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+basil	basil	Breakpoint detection, including large insertions								Up-to-date	https://github.com/seqan/anise_basil	Variant Analysis	basil	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil	1.2.0	anise_basil	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	306	311	82	83	467	467	99	99	0	0	0	0	773	778	181	182	False		
+batched_lastz	batched_lastz	Galaxy wrapper for the batching Lastz runs								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	batched_lastz	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz	1.04.22	lastz	1.04.22			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	123	123	5	5	0	0	0	0	123	123	5	5	False		
+bax2bam	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	208	208	26	26	210	210	30	30	0	0	0	0	418	418	56	56	False		
+bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	90	90	28	28	0	0	0	0	0	0	0	0	90	90	28	28	False		
+bbgbigwig	bbgtobigwig	Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://www.encodeproject.org/software/bedgraphtobigwig/	Convert Formats	bbgbigwig	iuc	https://www.encodeproject.org/software/bedgraphtobigwig/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig	0.1	ucsc-bedgraphtobigwig	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	42	42	7	7	175	175	26	26	0	0	0	0	217	217	33	33	False		
+bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbtools, bbmap		BBMap	BBMap is a fast splice-aware aligner for RNA and DNA.  It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.09	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	4	0	0	11989	11989	768	768	4458	4458	652	652	2507	2507	80	80	18954	18954	1500	1500	False		
+bcftools	bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@	BCFtools toolkit wrappers	bcftools	bcftools		BCFtools	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.	Data handling, Variant calling	Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment	To update	https://samtools.github.io/bcftools/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools	1.15.1	bcftools	1.21	Data handling, Variant calling	DNA polymorphism, GWAS study, Genotyping experiment	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bctools	bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	7	7	0	2352	3092	234	265	0	0	0	0	0	0	0	0	2352	3092	234	265	False		
+beacon2	beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff	beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://github.com/EGA-archive/beacon2-ri-tools/tree/main	Variant Analysis	beacon2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2	2.0.0	beacon2-ri-tools	2.0.0	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	33	33	9	9	0	0	0	0	0	0	0	0	33	33	9	9	False		
+beacon2-import	beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence	Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants.	ga4gh_beacon	ga4gh_beacon		GA4GH Beacon	A global search engine for genetic mutations.	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	Up-to-date	https://pypi.org/project/beacon2-import/	Variant Analysis	Beacon2_Import	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import	2.2.4	beacon2-import	2.2.4	Service discovery, Database search, Genetic variation analysis	Genetic variation, Population genetics, Data security, Rare diseases	0	0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	22	22	7	7	0	0	0	0	0	0	0	0	22	22	7	7	False		
+beagle	beagle	Beagle is a program for phasing and imputing missing genotypes.								To update	https://faculty.washington.edu/browning/beagle/beagle.html	Variant Analysis	beagle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle	5.2_21Apr21.304	beagle	5.4_22Jul22.46e			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	88	88	28	28	0	0	0	0	0	0	0	0	88	88	28	28	False		
+bed_to_protein_map	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	410	419	134	137	363	363	99	99	158	158	13	13	931	940	246	249	False		
+bedops	bedops-sort-bed	BEDOPS: high-performance genomic feature operations								Up-to-date	https://bedops.readthedocs.io/en/latest/	Genomic Interval Operations	bedops_sortbed	iuc	https://bedops.readthedocs.io/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops	2.4.41	bedops	2.4.41			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	93	93	36	36	181	181	62	62	0	0	0	0	274	274	98	98	False		
+bedtools	bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed	bedtools is a powerful toolset for genome arithmetic	bedtools	bedtools		BEDTools	BEDTools is an extensive suite of utilities for comparing genomic features in BED format.	Mapping	Genomics	Up-to-date	https://github.com/arq5x/bedtools2	Genomic Interval Operations, Text Manipulation	bedtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools	2.31.1	bedtools	2.31.1	Mapping	Genomics	37	37	37	0	37	37	37	0	0	0	0	0	0	0	0	0	0	37	6	37	0	0	37	0	0	0	37	0	0	0	0	0	0	37	37	37	0	916111	962278	13235	14525	407944	647621	25849	41751	84008	89233	2486	2832	1408063	1699132	41570	59108	False		
+bellerophon	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1611	1611	262	262	763	763	67	67	543	543	30	30	2917	2917	359	359	False		
+berokka	berokka	Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies.								Up-to-date	https://github.com/tseemann/berokka	Fasta Manipulation	berokka	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka	0.2.3	berokka	0.2.3			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	617	617	63	63	617	617	63	63	False		
+best_regression_subsets	BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3	4	3	4	14	253	7	72	0	0	0	0	17	257	10	76	False		
+bfconvert	ip_convertimage	Convert image			python-bioformats					Up-to-date	https://github.com/bmcv	Imaging, Convert Formats	bfconvert	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert	6.7.0	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1635	1671	123	124	0	0	0	0	334	334	21	21	1969	2005	144	145	False		
+bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	2	0	0	0	0	0	0	0	0	3	3	2	2	False		
+bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE		BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	544	544	20	20	0	0	0	0	0	0	0	0	544	544	20	20	False		
+bigwig_outlier_bed	bigwig_outlier_bed	pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files	bigtools	bigtools		bigtools	Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust.			To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	Sequence Analysis	bigwig_outlier_bed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed	0.2.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	218	218	5	5	0	0	0	0	0	0	0	0	218	218	5	5	False		
+bigwig_to_bedgraph	bigwig_to_bedgraph	Convert from bigWig to bedGraph format								To update		Convert Formats	bigwig_to_bedgraph	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	0.1.0	ucsc_tools				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5769	6802	567	650	0	0	0	0	0	3	0	1	5769	6805	567	651	False		
+bigwig_to_bedgraph	bigwig_to_bedgraph	Converts a bigWig file to bedGraph format								To update	http://artbio.fr	Convert Formats	bigwig_to_bedgraph	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_bedgraph	377+galaxy1	ucsc-bigwigtobedgraph	469			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5769	6802	567	650	0	0	0	0	0	3	0	1	5769	6805	567	651	False		
+bigwig_to_wig	bigwig_to_wig	Converts a bigWig file to Wiggle (WIG) format								To update	https://artbio.fr	Convert Formats	bigwig_to_wig	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig	3+galaxy0	ucsc-bigwiginfo	469			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+binary2labelimage	ip_binary_to_labelimage	Binary 2 label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binary2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binary2labelimage	0.5	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	401	1385	87	88	0	0	0	0	188	188	9	9	589	1573	96	97	False		
+binaryimage2points	ip_binaryimage_to_points	Binary Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	binaryimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points	0.1-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24	29	1	1	0	0	0	0	0	0	0	0	24	29	1	1	False		
+binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	126	126	42	42	0	0	0	0	0	0	0	0	126	126	42	42	False		
+bio3d	bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize	Bio3d is a program that can be used to analyse molecular dynamics trajectories.								To update	http://thegrantlab.org/bio3d/index.php	Computational chemistry	bio3d	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	2.4_1	r-bio3d	2.3_3			5	4	5	0	5	4	5	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	5	5	0	10600	10729	1150	1159	1042	1042	255	255	2756	2756	215	215	14398	14527	1620	1629	False		
+bioext	bioext_bam2msa, bioext_bealign	A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!								Up-to-date	https://pypi.python.org/pypi/biopython-extensions/	Next Gen Mappers		iuc	https://github.com/davebx/bioext-gx/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext	0.21.9	python-bioext	0.21.9			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	17413	17413	822	822	15349	15349	2020	2020	2	2	1	1	32764	32764	2843	2843	False		
+bioformats2raw	bf2raw	Convert image to OME-Zarr								To update	https://github.com/Euro-BioImaging	Imaging, Convert Formats	bioformats2raw	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw	0.7.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	61	61	4	4	0	0	0	0	0	0	0	0	61	61	4	4	False		
+biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+biohansel_bionumeric_converter	bionumeric_convert	Convert BioHansel output data to a Bionumerics friendly form								To update	https://github.com/phac-nml/galaxy_tools	Text Manipulation	biohansel_bionumeric_converter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel_bionumeric_converter	0.2.0	pandas				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+bioimaging	bioimage_inference	Load model from BioImage.IO and make inferences	pytorch	pytorch	pytorch	PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		Machine learning, Computer science	To update	https://github.com/bgruening/galaxytools	Imaging	bioimage_inference	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/bioimaging	https://github.com/bgruening/galaxytools/tree/master/tools/bioimaging	2.4.0	python			Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	1	0	0	0	0	0	0	0	0	2	2	1	1	False		
+bioinformatics_cafe	fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1137	1137	97	97	1029	1029	71	71	0	0	0	0	2166	2166	168	168	False		
+biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12725	12725	297	297	2851	5049	450	638	2171	2371	214	239	17747	20145	961	1174	False		
+biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	25	11	11	0	0	0	0	0	0	0	0	25	25	11	11	False		
+biomoldyn	biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering	Tools for MD analysis								To update	https://github.com/moldyn/	Molecular Dynamics, Computational chemistry	biomoldyn	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/biomoldyn	1.5.2	scipy				4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	3	0	493	493	119	119	441	441	148	148	0	0	0	0	934	934	267	267	False		
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	151	151	143	143	43	43	596	596	22	22	1286	1286	216	216	False		
+bioperl	bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	Data handling, Service invocation	Genomics, Software engineering	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7738	7931	478	508	8301	8301	849	849	1369	1369	154	154	17408	17601	1481	1511	False		
+biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6243	6243	375	375	0	0	0	0	6243	6243	375	375	False		
+biotransformer	biotransformer	BioTransformer is a tool for prediction of small molecule metabolism in mammals.	biotransformer	biotransformer		BioTransformer	BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	Up-to-date	https://bitbucket.org/djoumbou/biotransformerjar/src/master/	Metabolomics	biotransformer	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	3.0.20230403	biotransformer	3.0.20230403	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	48	48	1	1	48	48	1	1	False		
+biscot	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	3	1	1	0	0	0	0	0	0	0	0	3	3	1	1	False		
+bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	4	4	4	0	13715	14997	992	1099	0	0	0	0	197	197	22	22	13912	15194	1014	1121	False		
+blast	magicblast	Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome								Up-to-date	https://ncbi.github.io/magicblast/	Next Gen Mappers	magicblast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast	1.7.0	magicblast	1.7.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	738	738	151	151	0	0	0	0	2	2	1	1	740	740	152	152	False		
+blast2go	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1063	1237	257	300	0	0	0	0	0	0	0	0	1063	1237	257	300	False		
+blast_parser	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	417	438	99	104	0	0	0	0	0	0	0	0	417	438	99	104	False		
+blast_plus_remote_blastp	blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.16.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	24916	27120	283	347	0	0	0	0	0	0	0	0	24916	27120	283	347	False		
+blast_to_scaffold	blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blast_unmatched	blast_unmatched	Extract unmatched query sequences from blast								To update	http://artbio.fr	Fasta Manipulation	blast_unmatched	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_unmatched	1.0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blastparser_and_hits	BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	1	1	0	0	0	0	8	8	1	1	False		
+blastx_to_scaffold	blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blastxml_to_gapped_gff3	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	585	585	102	102	172	172	63	63	135	135	16	16	892	892	181	181	False		
+blastxml_to_top_descr	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	264392	265217	483	552	0	0	0	0	0	0	0	0	264392	265217	483	552	False		
+blat_coverage_report	generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blat_mapping	blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1527	1527	79	79	6	6	1	1	317	317	26	26	1850	1850	106	106	False		
+blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	768	3043	97	119	14	14	11	11	276	276	9	9	1058	3333	117	139	False		
+blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	811	1501	54	79	64	64	29	29	561	561	15	15	1436	2126	98	123	False		
+bowtie2	bowtie2	Bowtie2: Fast and sensitive read alignment	bowtie2	bowtie2		Bowtie 2	Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.	Read mapping	Mapping, Genomics, Mapping	To update	http://bowtie-bio.sourceforge.net/bowtie2	Next Gen Mappers	bowtie2	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2	2.5.3	bowtie2	2.5.4	Read mapping	Mapping, Genomics, Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	1	1	1	0	397893	427447	12133	13176	577209	903193	33086	52020	60105	67495	3779	4271	1035207	1398135	48998	69467	False		
+bowtie_wrappers	bowtie_wrapper	Galaxy wrappers for the Bowtie short read mapping tools.								To update	http://bowtie-bio.sourceforge.net/	Next Gen Mappers	bowtie_wrappers	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers	https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers	1.2.0	bowtie	1.3.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	24164	25149	1320	1480	17537	203397	1330	17491	15654	15992	291	351	57355	244538	2941	19322	False		
+bracken	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	51378	51378	775	775	3298	3298	160	160	1660	1660	63	63	56336	56336	998	998	False		
+braker	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	165	165	48	48	0	0	0	0	0	0	0	0	165	165	48	48	False		
+braker3	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1938	1938	294	294	0	0	0	0	412	412	71	71	2350	2350	365	365	False		
+breseq	breseq	Predicts mutations in microbial genomes	breseq	breseq		breseq	Runs Breseq software on a set of fastq files.	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	To update	https://github.com/barricklab/breseq	Variant Analysis	breseq	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq	0.35.5	breseq	0.39.0	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	2976	2976	98	98	0	0	0	0	884	884	70	70	3860	3860	168	168	False		
+brew3r_r	brew3r_r	Extend 3' end of a GTF using another GTF as a template	brew3r.r	brew3r.r		BREW3R.r	This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids.	Genome annotation	Transcriptomics, Genomics	To update	https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html	Transcriptomics, RNA	brew3r_r	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r	https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r	1.0.2			Genome annotation	Transcriptomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6	6	2	2	0	0	0	0	7	7	3	3	False		
+bumbershoot	idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	1186	1356	21	32	0	0	0	0	0	0	0	0	1186	1356	21	32	False		
+bundle_collections	bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.58			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	1	1518	1526	73	76	1520	1528	74	77	False		
+busco	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	102717	103051	3877	3926	34251	34251	3506	3506	33192	34369	2439	2525	170160	171671	9822	9957	False		
+bwa	bwa_mem, bwa	Wrapper for bwa mem, aln, sampe, and samse	bwa	bwa		BWA	Fast, accurate, memory-efficient aligner for short and long sequencing reads	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	Up-to-date	http://bio-bwa.sourceforge.net/	Next Gen Mappers	bwa	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa	0.7.18	bwa	0.7.18	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	2	0	0	0	2	0	0	0	0	0	0	2	2	2	2	976935	1017671	13526	14401	474702	681286	32627	47624	79802	87191	4219	4954	1531439	1786148	50372	66979	False		
+bwa_mem2	bwa_mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.	bwa-mem2	bwa-mem2		Bwa-mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,  dataset and the running machine.	Sequence alignment	Mapping	Up-to-date	https://github.com/bwa-mem2/bwa-mem2	Next Gen Mappers	bwa_mem2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2	2.2.1	bwa-mem2	2.2.1	Sequence alignment	Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	56619	56619	2324	2324	36631	36631	2808	2808	18121	18121	713	713	111371	111371	5845	5845	False		
+bwameth	bwameth	Fast and accurate alignment of BS-seq reads								Up-to-date	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.7	bwameth	0.2.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7970	11724	643	826	5524	5524	611	611	1242	1242	114	114	14736	18490	1368	1551	False		
+c3s	c3s	Copernicus Climate Change Service (C3S)								To update	https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset	Climate Analysis	c3s	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	0.3.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	234	234	11	11	4	4	4	4	92	92	3	3	330	330	18	18	False		
+cactus	cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			Multiple sequence alignment, Genome alignment	Genomics, Sequence assembly, Mapping, Phylogenetics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	299	299	61	61	0	0	0	0	1339	1339	95	95	1638	1638	156	156	False		
+cads	cads	Copernicus Atmosphere Data Store (ADS)								To update	https://ads.atmosphere.copernicus.eu/#!/home	Climate Analysis	cads	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	52	52	1	1	0	0	0	0	0	0	0	0	52	52	1	1	False		
+calculate_contrast_threshold	calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+calculate_numeric_param	calculate_numeric_param	Calculate a numeric parameter value using integer and float values.								To update		Text Manipulation	calculate_numeric_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param	0.1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1393	1393	10	10	0	0	0	0	0	0	0	0	1393	1393	10	10	False		
+calisp	calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	False		
+camera	abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos									To update		Metabolomics	camera	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/camera	1.48.0	r-snow	0.4_1			1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	2	0	677	787	114	120	60	60	30	30	734	746	26	26	1471	1593	170	176	False		
+cami_amber	biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert	Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments								Up-to-date	https://github.com/CAMI-challenge/AMBER	Metagenomics	cami_amber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amber/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber	2.0.7	cami-amber	2.0.7			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	195	195	4	4	0	0	0	0	0	0	0	0	195	195	4	4	False		
+canonical_correlation_analysis	cca1	Canonical Correlation Analysis								To update		Statistics	canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis	1.0.0	R				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	66	75	16	18	141	505	31	147	0	0	0	0	207	580	47	165	False		
+canu	canu	Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).	canu	canu		CANU	De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.	De-novo assembly	Genomics	Up-to-date	https://github.com/marbl/canu		canu	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/canu	https://github.com/bgruening/galaxytools/tree/master/tools/canu	2.2	canu	2.2	De-novo assembly	Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	13360	14618	1383	1444	0	0	0	0	3542	3542	385	385	16902	18160	1768	1829	False		
+cap3	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	9869	9869	158	158	0	0	0	0	6886	6886	146	146	16755	16755	304	304	False		
+cardinal	cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								Up-to-date	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	3.4.3	bioconductor-cardinal	3.4.3			0	9	11	0	0	9	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	0	0	0	0	0	0	9	11	9	0	41875	50702	663	713	12	12	1	1	7512	7512	231	231	49399	58226	895	945	False		
+cat	cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3835	3835	597	597	1359	1359	467	467	646	646	98	98	5840	5840	1162	1162	False		
+categorize_elements_satisfying_criteria	categorize_elements_satisfying_criteria	Categorize Elements satisfying criteria.								To update		Statistics	categorize_elements_satisfying_criteria	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria	https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	41	4	5	0	0	0	0	168	186	12	14	205	227	16	19	False		
+ccat	peakcalling_ccat	Control-based ChIP-seq Analysis Tool								To update		ChIP-seq	ccat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat	0.0.2	ccat	3.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	88	175	28	39	0	0	0	0	0	0	0	0	88	175	28	39	False		
+cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5946	7379	407	628	0	0	0	0	5946	7379	407	628	False		
+cdhit	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	Sequence clustering	Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10414	10414	510	510	2	2	1	1	2	2	1	1	10418	10418	512	512	False		
+cdo	cdo_info, cdo_operations	CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.								To update	https://code.mpimet.mpg.de/projects/cdo/	Climate Analysis		climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	2.0.0					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	218	218	17	17	0	0	0	0	0	0	0	0	218	218	17	17	False		
+cell-types-analysis	ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	4	4	0	0	0	0	0	0	0	0	8	8	4	4	False		
+cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.10	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	4	4	0	0	0	0	0	0	0	0	14	14	4	4	False		
+cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	0	0	23	23	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	0	4773	4773	749	749	0	0	0	0	5688	5688	94	94	10461	10461	843	843	False		
+cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update	https://github.com/CellProfiler/CellProfiler	Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.7					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55	55	11	11	0	0	0	0	0	0	0	0	55	55	11	11	False		
+cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	225	225	32	32	271	271	61	61	0	0	0	0	496	496	93	93	False		
+cesm	cesm	Community Earth System Model (CESM)								Up-to-date	https://www.cesm.ucar.edu/	Climate Analysis	cesm	climate	https://github.com/ESCOMP/CESM	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cesm	2.1.3	cesm	2.1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14	14	2	2	0	0	0	0	0	0	0	0	14	14	2	2	False		
+cfm	cfmid	Competitive Fragmentation Modeling (CFM)								Up-to-date	https://sourceforge.net/p/cfm-id/	Metabolomics	cfmid	computational-metabolomics	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	https://github.com/computational-metabolomics/cfm-galaxy/tree/master/tools/cfm	33	cfm	33			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+chado	analysis_add_analysis, analysis_delete_analyses, analysis_get_analyses, export_export_fasta, export_export_gbk, export_export_gff3, expression_add_biomaterial, expression_add_expression, expression_delete_all_biomaterials, expression_delete_biomaterials, expression_get_biomaterials, feature_delete_features, feature_get_features, feature_load_fasta, feature_load_featureprops, feature_load_gff, feature_load_go, load_blast, load_interpro, organism_add_organism, organism_delete_all_organisms, organism_delete_organisms, organism_get_organisms, phylogeny_gene_families, phylogeny_gene_order, phylogeny_load_tree	Galaxy tools allowing to load data into a remote Chado database.Chado is a member of the GMOD family of tools.https://github.com/galaxy-genome-annotation/python-chado								To update	https://github.com/galaxy-genome-annotation/python-chado	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado		python-chado	2.3.9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+champ_blocs	cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base				0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	183	183	20	20	0	0	0	0	0	0	0	0	183	183	20	20	False		
+change_case	ChangeCase	Convert column case.								To update		Text Manipulation	change_case	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case	https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case	1.0.1	perl				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	0	1	1	1	1	10606	12531	2204	2547	9044	17167	1748	2394	923	938	240	245	20573	30636	4192	5186	False		
+charts	charts	Enables advanced visualization options in Galaxy Charts								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3383	4001	1576	1822	7870	13727	3823	6880	249	350	108	145	11502	18078	5507	8847	False		
+chatgpt	chatgpt_openai_api	Using the OpenAI GPT models to generate text based on user input.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	Machine Learning	chatgpt_openai_api	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	https://github.com/bgruening/galaxytools/tree/master/tools/chatgpt	2024	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	62	12	12	0	0	0	0	0	0	0	0	62	62	12	12	False		
+checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	7500	7500	930	930	0	0	0	0	0	0	0	0	7500	7500	930	930	False		
+checkv	checkv_end_to_end	Assess quality of single-contig viral genomes	checkv	checkv		CheckV	CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	Up-to-date	https://bitbucket.org/berkeleylab/checkv/	Metagenomics	checkv	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/checkv	1.0.3	checkv	1.0.3	Sequence assembly, Validation, Read mapping	Metagenomics, Sequence assembly, Metagenomic sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cherri	cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8		Molecular interactions, pathways and networks, Structure analysis, Machine learning	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	207	207	1	1	0	0	0	0	0	0	0	0	207	207	1	1	False		
+cherry_pick_fasta	cherry_pick_fasta	Pick fasta sequence with specific header content								To update	http://artbio.fr	Fasta Manipulation	cherry_pick_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/cherry_pick_fasta	4.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+chewbbaca	chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema	BSR-Based Allele Calling Algorithm								To update	https://github.com/B-UMMI/chewBBACA/tree/master	Variant Analysis	chewbbaca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca		chewbbaca	3.3.10			0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	727	727	76	76	0	0	0	0	0	0	0	0	727	727	76	76	False		
+chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	16468	18344	956	991	33692	34453	2559	2625	2948	2948	104	104	53108	55745	3619	3720	False		
+chira	chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3		Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	16542	16542	287	287	1061	1061	102	102	27	27	5	5	17630	17630	394	394	False		
+chopin2	chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing								To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2	1.0.9.post1	chopin2				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	14	6	6	0	0	0	0	14	14	6	6	False		
+chromeister	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2696	2696	398	398	0	0	0	0	1235	1235	186	186	3931	3931	584	584	False		
+chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+circexplorer	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	211	263	32	40	0	0	0	0	209	209	6	6	420	472	38	46	False		
+circexplorer2	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8		RNA splicing, Gene transcripts, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	524	524	32	32	0	0	0	0	0	0	0	0	524	524	32	32	False		
+circos	circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile	Build Circos Plots in Galaxy	galactic_circos	galactic_circos		Galactic Circos	Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format.	Sequence visualisation		To update	http://circos.ca/	Graphics	circos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos	0.69.8	circos	0.69.9	Sequence visualisation		11	11	11	0	11	11	11	0	0	0	0	0	0	0	0	0	0	0	11	11	0	0	0	0	0	0	11	0	0	0	0	0	0	11	11	11	0	26265	26265	2483	2483	31332	31332	3535	3535	26359	26359	999	999	83956	83956	7017	7017	False		
+cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	21	4	4	9	9	5	5	18	18	1	1	48	48	10	10	False		
+clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3388	3388	187	187	1	1	1	1	1	1	1	1	3390	3390	189	189	False		
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+climate-stripes	climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	239	239	35	35	16	16	2	2	182	182	3	3	437	437	40	40	False		
+clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	548	548	18	18	0	0	0	0	548	548	18	18	False		
+clustalw	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	79867	80817	1675	1785	49493	87884	3703	7380	8797	9713	670	728	138157	178414	6048	9893	False		
+cluster	gops_cluster_1	Cluster the intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	cluster	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	513	813	18	35	2406	30579	156	1547	1353	1393	17	20	4272	32785	191	1602	False		
+clustering_from_distmat	clustering_from_distmat	Distance matrix-based hierarchical clustering using SciPy								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	Statistics	clustering_from_distmat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat	1.1.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	5	5	0	0	0	0	0	0	0	0	12	12	5	5	False		
+cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2609	2609	3	3	0	0	0	0	0	0	0	0	2609	2609	3	3	False		
+cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	90	112	11	14	0	0	0	0	0	0	0	0	90	112	11	14	False		
+cnv-phenopacket	cnv_phenopacket	cnv-phenopacket Converts TSV metadata file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv_phenopacket	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket	1.0.2	cnv-phenopacket				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	False		
+cnv-vcf2json	cnv_vcf2json	cnv-vcf2json Converts structural variants VCF file to JSON.								To update	https://pypi.org/project/cnv-phenopacket/	Variant Analysis	cnv-vcf2json	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json	1.1.0	cnv-vcf2json				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5	False		
+cnvkit	cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target	detecting copy number variants and alterations genome-wide from high-throughput sequencing	cnvkit	cnvkit		CNVkit	CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.	Variant calling	DNA structural variation	Up-to-date	https://github.com/etal/cnvkit	Variant Analysis	cnvkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit	0.9.11	cnvkit	0.9.11	Variant calling		0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	618	618	177	177	0	0	0	0	0	0	0	0	618	618	177	177	False		
+codeml	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	61197	61220	64	65	0	0	0	0	0	0	0	0	61197	61220	64	65	False		
+cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	316	355	25	29	0	0	0	0	0	0	0	0	316	355	25	29	False		
+cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	2758	2758	22	22	20	20	10	10	0	0	0	0	2778	2778	32	32	False		
+colabfold	colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6771	6771	50	50	0	0	0	0	6771	6771	50	50	False		
+colibread	commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								Up-to-date	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14	commet	24.7.14			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	273	273	40	40	0	0	0	0	0	0	0	0	273	273	40	40	False		
+collapse_collection	collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	39518	40471	3555	3629	22007	24841	3536	4045	3969	4101	814	835	65494	69413	7905	8509	False		
+collection_column_join	collection_column_join	Column Join on Collections								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	Text Manipulation	collection_column_join	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join	0.0.3	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	23979	25337	3827	4011	21671	25163	4645	5045	2939	3036	688	701	48589	53536	9160	9757	False		
+collection_element_identifiers	collection_element_identifiers	Extract element identifiers of a collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	Text Manipulation	collection_element_identifiers	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_element_identifiers	https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers	0.0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6905	7102	1620	1630	7761	7761	1897	1897	1157	1157	243	243	15823	16020	3760	3770	False		
+color_deconvolution	ip_color_deconvolution	Color-deconvolution methods	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	color_deconvolution	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color-deconvolution/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution	0.8-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	15	16	2	3	0	0	0	0	0	0	0	0	15	16	2	3	False		
+colorize_labels	colorize_labels	Colorize label map								To update	https://github.com/bmcv	Imaging	colorize_labels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/colorize_labels	3.2.1	networkx				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	40	40	2	2	0	0	0	0	0	0	0	0	40	40	2	2	False		
+column_arrange_by_header	bg_column_arrange_by_header	Column arrange by header name								To update		Text Manipulation	column_arrange_by_header	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5356	5636	446	484	2026	2026	375	375	1400	1531	117	138	8782	9193	938	997	False		
+column_maker	Add_a_column1	Compute an expression on every row								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	Text Manipulation	column_maker	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker	2.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2940752	3907183	5422	6121	263254	737503	6095	13728	96478	97667	884	974	3300484	4742353	12401	20823	False		
+column_order_header_sort	column_order_header_sort	Sort Column Order by heading								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	Text Manipulation	column_order_header_sort	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort	0.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3735	3891	268	297	1923	1923	381	381	0	0	0	0	5658	5814	649	678	False		
+column_remove_by_header	column_remove_by_header	Remove columns by header								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	Text Manipulation	column_remove_by_header	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header	1.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8331	8917	613	662	5206	5206	716	716	1976	1976	27	27	15513	16099	1356	1405	False		
+combineJSON	combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	530	530	65	65	8	8	6	6	0	0	0	0	538	538	71	71	False		
+combine_tabular_collection	combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	221	5	28	0	0	0	0	0	0	0	0	39	221	5	28	False		
+compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	306	332	28	32	0	0	0	0	0	0	0	0	306	332	28	32	False		
+compleasm	compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	266	266	39	39	28	28	15	15	0	0	0	0	294	294	54	54	False		
+complement	gops_complement_1	Complement intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	complement	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	187	233	15	20	495	4810	165	836	405	451	7	7	1087	5494	187	863	False		
+compose_text_param	compose_text_param	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	compose_text_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param	0.1.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	0	0	0	45827	45831	689	691	7721	7721	303	303	1481	1481	121	121	55029	55033	1113	1115	False		
+compress_file	compress_file	Compress files.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	Text Manipulation	compress_file	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file	0.1.0	gzip				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6343	6343	290	290	3674	3674	286	286	11832	11832	59	59	21849	21849	635	635	False		
+compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	85	96	9	10	0	0	0	0	316	334	8	8	401	430	17	18	False		
+compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	55	65	2	2	0	0	0	0	317	335	5	5	372	400	7	7	False		
+compute_q_values	compute_q_values	Compute q-values based on multiple simultaneous tests p-values								To update		Statistics	compute_q_values	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values	1.0.1	R				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	35	0	3	0	0	0	0	0	0	0	0	0	35	0	3	False		
+concat	gops_concat_1	Concatenate two bed files								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	concat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat	1.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	575128	575441	694	783	43420	85345	629	3508	19330	19418	104	117	637878	680204	1427	4408	False		
+concat_channels	ip_concat_channels	Concatenate images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	concat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels	0.3-1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	76	82	11	12	0	0	0	0	0	0	0	0	76	82	11	12	False		
+concat_multi_datasets	cat_multi_datasets	Concatenate multiple datasets tail-to-head, including collection datasets.								To update	http://artbio.fr	Text Manipulation	concatenate_multiple_datasets	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	https://github.com/ARTbio/tools-artbio/tree/main/tools/concat_multi_datasets	1.4.3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	4822	4824	613	614	1317	1317	204	204	3088	3795	252	289	9227	9936	1069	1107	False		
+concat_paired	concat_fastqs	Concatenate paired datasets								To update	https://github.com/phac-nml/concat	Text Manipulation	concat_paired	nml	https://github.com/phac-nml/concat	https://github.com/phac-nml/galaxy_tools/tree/master/tools/concat_paired	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+concoct	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	Sequence clustering, Read binning	Metagenomics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	2105	2105	155	155	0	0	0	0	0	0	0	0	2105	2105	155	155	False		
+condense_characters	Condense characters1	Condense consecutive characters.								To update		Text Manipulation	condense_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters	1.0.0					1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47	2173	28	368	195	205	8	8	242	2378	36	376	False		
+consensus_from_alignments	aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1184	1184	154	154	0	0	0	0	0	0	0	0	1184	1184	154	154	False		
+consolidate_vcfs	consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+convert_characters	Convert characters1	Convert delimiters to tab.								To update		Text Manipulation	convert_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters	1.0.1	python				1	1	1	0	1	1	1	0	1	1	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	23589	28986	1061	1200	23507	160693	2302	8699	5413	6446	251	329	52509	196125	3614	10228	False		
+convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cooler	cooler_balance, cooler_cload_tabix, cooler_csort_tabix, cooler_makebins, cooler_zoomify	cooler different tools to process Hi-C from mirnylab								To update	https://github.com/open2c/cooler	Epigenetics	cooler	lldelisle	https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/cooler	0.9.3	htslib	1.21			4	0	5	0	4	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	170	170	26	26	195	195	39	39	0	0	0	0	365	365	65	65	False		
+coordinates_of_roi	ip_coordinates_of_roi	Coordinates of ROI	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	coordinates_of_roi	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/coordinates_of_roi	0.0.4-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	16077	16547	11	11	0	0	0	0	0	0	0	0	16077	16547	11	11	False		
+coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+correlation	cor2	Correlation for numeric columns								To update		Statistics	correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation	1.0.0	rpy				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	398	876	106	134	412	5568	105	755	192	239	21	27	1002	6683	232	916	False		
+correlation_analysis	correlation_analysis	[Metabolomics][W4M] Metabolites Correlation Analysis								To update	http://workflow4metabolomics.org	Metabolomics	correlation_analysis	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/correlation_analysis	1.0.1+galaxy0	r-batch	1.1_4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	280	307	110	124	712	1277	332	628	476	541	55	79	1468	2125	497	831	False		
+count_objects	ip_count_objects	Count Objects	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	count_objects	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/count_objects	0.0.5-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	314	326	73	75	0	0	0	0	129	129	6	6	443	455	79	81	False		
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage	gops_coverage_1	Coverage of a set of intervals on second set of intervals								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	coverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1560	1725	43	58	4328	44209	193	2113	283	316	16	18	6171	46250	252	2189	False		
+coverage_report	CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1081	1081	151	151	0	0	0	0	0	0	0	0	1081	1081	151	151	False		
+cpat	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.								Up-to-date	https://github.com/liguowang/cpat	Transcriptomics	cpat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	3.0.5	cpat	3.0.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	204	204	47	47	165	165	40	40	125	125	7	7	494	494	94	94	False		
+cpm_tpm_rpk	cpm_tpm_rpk	Generate CPM,TPM or RPK from raw counts								To update	http://artbio.fr	Transcriptomics	cpm_tpm_rpk	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	0.6.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+crispr_studio	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	Visualisation	Sequence analysis, Genomics, Data visualisation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1052	1053	75	76	0	0	0	0	0	0	0	0	1052	1053	75	76	False		
+crosscontamination_barcode_filter	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	276	390	61	76	131	131	42	42	0	0	0	0	407	521	103	118	False		
+crossmap	crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig	CrossMap converts genome coordinates or annotation files between genome assemblies								Up-to-date	http://crossmap.sourceforge.net/	Convert Formats, Genomic Interval Operations	crossmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap	0.7.0	crossmap	0.7.0			5	0	6	0	5	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	5	6	5	0	2182	2182	331	331	5251	5251	903	903	0	0	0	0	7433	7433	1234	1234	False		
+crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4066	4139	166	180	0	0	0	0	0	0	0	0	4066	4139	166	180	False		
+cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	9942	9942	26	26	0	0	0	0	0	0	0	0	9942	9942	26	26	False		
+csvtk	csvtk_awklike_filter, csvtk_awklike_mutate, csvtk_collapse, csvtk_concat, csvtk_convert, csvtk_correlation, csvtk_cut, csvtk_filter, csvtk_freq, csvtk_gather, csvtk_join, csvtk_mutate, csvtk_plot, csvtk_replace, csvtk_sample, csvtk_separate, csvtk_sort, csvtk_split, csvtk_summary, csvtk_uniq	Rapid data investigation and manipulation of csv/tsv files								To update	https://bioinf.shenwei.me/csvtk/	Text Manipulation	csvtk	nml	https://github.com/shenwei356/csvtk	https://github.com/phac-nml/galaxy_tools/tree/master/tools/csvtk	0.20.0	csvtk	0.30.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	20	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cta	cta_astro_tool	Basic simulation of CTA telescope observations using gammapy package								To update		Astronomy	cta_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/cta	0.0.1+galaxy0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	196	211	41	48	1	447	1	161	0	0	0	0	197	658	42	209	False		
+cuffcompare	cuffcompare	Galaxy wrappers for the Cuffcompare tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffcompare	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1	1	0	768	1199	171	300	2205	24981	754	5750	251	493	46	98	3224	26673	971	6148	False		
+cuffdiff	cuffdiff	Galaxy wrappers for the Cuffdiff tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffdiff	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff	2.2.1	cufflinks	2.2.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	4176	6065	564	725	24284	117007	4952	20249	971	4231	193	616	29431	127303	5709	21590	False		
+cufflinks	cufflinks	Galaxy wrappers for the Cufflinks tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cufflinks	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	1	0	0	0	1	1	1	0	26122	33320	870	1213	70653	349091	6984	27076	3963	10315	440	836	100738	392726	8294	29125	False		
+cuffmerge	cuffmerge	Galaxy wrappers for the Cuffmerge tool.								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffmerge	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1	1	0	2406	3448	351	637	20978	67769	3641	13764	1209	3057	227	573	24593	74274	4219	14974	False		
+cuffnorm	cuffnorm	The Cuffnorm tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffnorm	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	374	701	81	114	1032	13499	273	1166	262	322	53	70	1668	14522	407	1350	False		
+cuffquant	cuffquant	The Cuffquant tool								Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffquant	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant	2.2.1	cufflinks	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	408	732	54	71	1964	15883	267	1310	308	422	26	46	2680	17037	347	1427	False		
+cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1251	1803	98	166	3461	15159	486	2044	2425	3338	57	159	7137	20300	641	2369	False		
+cummerbund_to_tabular	cummerbund_to_cuffdiff	Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.								To update		Convert Formats, Next Gen Mappers	cummerbund_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular	1.0.1					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	888	1208	43	97	1334	2683	101	479	0	0	0	0	2222	3891	144	576	False		
+curve_fitting	ip_curve_fitting	Polynomial curve fitting to data points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	curve_fitting	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/curve_fitting	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	12	2	2	0	0	0	0	0	0	0	0	12	12	2	2	False		
+custom_pro_db	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1729	1744	144	146	450	450	72	72	361	361	12	12	2540	2555	228	230	False		
+custom_pro_db_annotation_data_manager		CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+cut_columns	Cut1	Select columns from a dataset.								To update		Text Manipulation	cut_columns	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns	1.0.2					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	0	1	1	1	1	1973168	2034965	11939	12833	352364	803522	12967	30199	128777	133584	2341	2572	2454309	2972071	27247	45604	False		
+cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	259754	272370	11716	12601	334550	362356	18618	20162	64377	65986	3507	3627	658681	700712	33841	36390	False		
+cutesv	cutesv	Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.	cuteSV	cuteSV		cuteSV	Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis	Split read mapping, Genotyping, Structural variation detection	DNA structural variation, Sequencing, Computer science	To update	https://github.com/tjiangHIT/cuteSV	Variant Analysis	cutesv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv	1.0.8	cutesv	2.1.1	Split read mapping, Genotyping, Structural variation detection	Sequencing, Computer science	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	260	260	43	43	0	0	0	0	119	119	8	8	379	379	51	51	False		
+cwpair2	cwpair2	Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans.								To update		ChIP-seq	cwpair2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2	1.1.1	matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	173	280	41	83	0	0	0	0	173	280	41	83	False		
+dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	10	0	10	0	0	1	0	0	0	0	0	0	0	0	0	0	10	10	10	0	92240	92240	2716	2716	179176	179176	5317	5317	12478	12478	394	394	283894	283894	8427	8427	False		
+das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1323	1323	47	47	0	0	0	0	0	0	0	0	1323	1323	47	47	False		
+data-hca	hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	441	451	83	87	3	3	2	2	0	0	0	0	444	454	85	89	False		
+data-scxa	retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	867	877	213	216	339	339	94	94	64	64	5	5	1270	1280	312	315	False		
+data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	967	967	308	308	0	0	0	0	0	0	0	0	967	967	308	308	False		
+data_manager_eggnog_mapper		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+data_manager_eggnog_mapper_abspath		download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+data_source_iris_tcga	data_source_iris_tcga	IRIS-TCGA Data source tool								To update		Data Source	data_source_iris_tcga	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/data_source_iris_tcga	https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+datamash	datamash_ops, datamash_reverse, datamash_transpose	GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon.								To update	https://www.gnu.org/software/datamash/	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/datamash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash	1.8	datamash	1.1.0			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	1	3	3	0	0	1	0	0	0	1	0	0	0	0	0	0	3	3	3	0	748586	760943	7066	7307	98089	112831	5306	6131	16235	16317	2161	2171	862910	890091	14533	15609	False		
+dbbuilder	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4813	5555	687	805	0	0	0	0	961	961	87	87	5774	6516	774	892	False		
+decontaminator	decontaminator	Deep Learning method for novel virus detection in sequencing data	decontaminator	decontaminator		decontaminator	Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies.	Filtering	Metagenomics	To update	https://github.com/cbib/decontaminator	Machine Learning	decontaminator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator	1.0.0	numpy		Filtering	Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	121	121	28	28	0	0	0	0	0	0	0	0	121	121	28	28	False		
+decoupler	score_genes_aucell, decoupler_pathway_inference, decoupler_pseudobulk	decoupler - Ensemble of methods to infer biological activities								To update	https://decoupler-py.readthedocs.io/en/latest/	Transcriptomics	suite_decoupler	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/decoupler	1.4.0+galaxy3	decoupler	1.5.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	54	6	6	0	0	0	0	0	0	0	0	54	54	6	6	False		
+decoyfasta		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+deepmicro	deepmicro	Representation learning and classification framework	DeepMicro	DeepMicro		DeepMicro	Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.	Essential dynamics, Splitting, Community profiling	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	Up-to-date	https://github.com/paulzierep/DeepMicro	Machine Learning	deepmicro	iuc	https://github.com/paulzierep/DeepMicro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro	1.4	deepmicro	1.4	Essential dynamics, Splitting	Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	558	558	7	7	0	0	0	0	0	0	0	0	558	558	7	7	False		
+deepsig	deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	37	37	0	0	0	0	0	0	0	0	65	65	37	37	False		
+deepvariant	deepvariant	DeepVariant is a deep learning-based variant caller								To update	https://github.com/google/deepvariant	Variant Analysis	deepvariant	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant	1.5.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2561	2561	325	325	2916	2916	460	460	0	0	0	0	5477	5477	785	785	False		
+deg_annotate	deg_annotate	Annotate DESeq2/DEXSeq output tables								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	Transcriptomics	deg_annotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate	1.1.0	bedtools	2.31.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22774	23146	4084	4155	33972	33972	5372	5372	4236	4236	846	846	60982	61354	10302	10373	False		
+delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33	40	6	7	0	0	0	0	0	0	0	0	33	40	6	7	False		
+delly	delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge	Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.	delly2	delly2		Delly2	Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.	Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis	DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases	To update	https://github.com/dellytools/delly	Variant Analysis	delly	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly	https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly	0.9.1	delly	1.2.9	Indel detection, Structural variation detection, Genotyping	Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	6	0	0	0	0	0	0	6	6	0	0	1451	1451	288	288	0	0	0	0	0	0	0	0	1451	1451	288	288	False		
+deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	97434	109474	11355	12514	183905	246475	24951	31957	18551	20166	2647	2905	299890	376115	38953	47376	False		
+deseq2_normalization	deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+detection_viz	ip_detection_viz	Detection Visualization	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	detection_viz	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	43	48	8	8	0	0	0	0	0	0	0	0	43	48	8	8	False		
+dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	18	18	0	0	0	0	0	0	0	0	89	89	18	18	False		
+dexseq	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	14874	16927	533	837	18475	28854	1403	2568	3854	4271	141	163	37203	50052	2077	3568	False		
+dgidb_annotator	dgidb_annotate	Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)								To update		Systems Biology, Variant Analysis	dgidb_annotator	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator	0.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	59	69	26	30	0	304	0	133	0	0	0	0	59	373	26	163	False		
+dia_umpire	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	28	33	4	4	0	0	0	0	134	134	4	4	162	167	8	8	False		
+dialignr	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	40	2	2	0	0	0	0	0	0	0	0	40	40	2	2	False		
+diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	3	3	3	0	0	0	1	0	0	0	0	0	0	0	0	0	0	3	3	0	61376	61746	1847	1895	23164	28729	1140	1556	63034	63034	522	522	147574	153509	3509	3973	False		
+diann	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	72	72	14	14	0	0	0	0	171	171	14	14	243	243	28	28	False		
+diapysef	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	262	262	38	38	0	0	0	0	256	256	6	6	518	518	44	44	False		
+diff	diff	GNU diff tool that calculates the differences between two files.								To update	http://www.gnu.org/software/diffutils/	Text Manipulation	diff	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diff	https://github.com/bgruening/galaxytools/tree/master/tools/diff	3.7	diffutils				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	362	362	99	99	23	23	17	17	0	0	0	0	385	385	116	116	False		
+diffacto	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11	11	7	7	0	0	0	0	0	0	0	0	11	11	7	7	False		
+diffbind	diffbind	Diffbind provides functions for  processing  ChIP-Seq  data.	diffbind	diffbind		DiffBind	Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.	Differential binding analysis	ChIP-seq	Up-to-date	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind	3.12.0	bioconductor-diffbind	3.12.0	Differential binding analysis	ChIP-seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7092	7663	606	652	14367	18624	1360	1916	1477	1640	69	84	22936	27927	2035	2652	False		
+diffbind		Diffbind provides functions for  processing  ChIP-Seq  data.								To update	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+digestdb	digestdb									To update			digestdb	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/digestdb	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dimet	dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@	DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.								Up-to-date	https://github.com/cbib/DIMet	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet	0.2.4	dimet	0.2.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+directag_and_tagrecon										To update			directag_and_tagrecon	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/directag_and_tagrecon						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	358	406	124	139	1361	1361	384	384	0	0	0	0	1719	1767	508	523	False		
+divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26	32	8	9	86	172	20	53	0	0	0	0	112	204	28	62	False		
+dnabot	dnabot	DNA assembly using BASIC on OpenTrons								To update	https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT	Synthetic Biology	dnabot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot	3.1.0	dnabot				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dnaweaver	dnaweaver	Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.								Up-to-date	https://github.com/Edinburgh-Genome-Foundry/DnaWeaver	Synthetic Biology	dnaweaver	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver	1.0.2	dnaweaver_synbiocad	1.0.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	921	1626	4	31	0	0	0	0	0	0	0	0	921	1626	4	31	False		
+dose_responses	dr_curve	A  tool for analyzing and visualizing the relationship between various doses and their corresponding biological responses								Up-to-date	https://github.com/bernt-matthias/mb-galaxy-tools	Ecology	dose_response_analysis_tool	ufz	https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses	3.0_1	r-drc	3.0_1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	74	88	12	15	0	0	0	0	0	0	0	0	74	88	12	15	False		
+dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	7358	7358	88	88	0	0	0	0	0	0	0	0	7358	7358	88	88	False		
+draw_stacked_barplots	draw_stacked_barplots	Draw Stacked Bar Plots for different categories and different criteria								To update		Graphics, Statistics	draw_stacked_barplots	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots	https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots	1.0.0	R				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	216	47	52	0	0	0	0	183	213	22	31	372	429	69	83	False		
+drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	916	916	113	113	0	0	0	0	0	0	0	0	916	916	113	113	False		
+droplet-barcode-plot	_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1151	1151	184	184	356	356	77	77	3	3	1	1	1510	1510	262	262	False		
+dropletutils	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1900	1901	412	413	609	609	131	131	0	0	0	0	2509	2510	543	544	False		
+dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4413	4442	430	431	4403	4403	255	255	1816	1816	33	33	10632	10661	718	719	False		
+dwt_cor_ava_perclass	compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Feature Occurrences								To update		Statistics	dwt_cor_ava_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	141	8	11	136	141	8	11	False		
+dwt_cor_avb_all	compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features								To update		Statistics	dwt_cor_avb_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	124	124	7	7	124	124	7	7	False		
+dwt_ivc_all	compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Second Moments for Feature Occurrences								To update		Statistics	dwt_ivc_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	121	123	5	7	121	123	5	7	False		
+dwt_var_perclass	compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom	Compute P-values and Max Variances for Feature Occurrences								To update		Statistics	dwt_var_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	131	132	7	8	131	132	7	8	False		
+dwt_var_perfeature	dwt_var1	Wavelet variance using Discrete Wavelet Transfoms								To update		Statistics	dwt_var_perfeature	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature	1.0.2	r-bitops				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	30	36	2	4	11	11	4	4	206	220	6	7	247	267	12	15	False		
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	bgruening	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	24.08.26	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	28	28	2	2	0	0	0	0	0	0	0	0	28	28	2	2	False		
+ebi_tools	ebi_search_rest_results	Tools to query and download data from several EMBL-EBI databases								To update	http://www.ebi.ac.uk/services/all	Web Services, Data Source	ebi_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools	0.1.1	six				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	276	406	133	163	1421	1421	547	547	0	0	0	0	1697	1827	680	710	False		
+ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12996	12996	137	137	10	10	1	1	0	0	0	0	13006	13006	138	138	False		
+edger	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	19294	20905	2423	2618	48876	58723	6341	7527	8010	8705	846	892	76180	88333	9610	11037	False		
+edta	edta	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. 	edta	edta		The Extensive de novo TE Annotator (EDTA)	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	To update	https://github.com/oushujun/EDTA	Variant Analysis	edta	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta	https://github.com/bgruening/galaxytools/tree/master/tools/edta		edta	2.2.0	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4495	4495	111	111	0	0	0	0	0	0	0	0	4495	4495	111	111	False		
+effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	1	3	1	0	34432	34437	1149	1152	42	42	2	2	21027	21027	413	413	55501	55506	1564	1567	False		
+egsea	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	Gene set testing	Systems biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2809	3060	371	402	5179	5179	759	759	1931	1931	226	226	9919	10170	1356	1387	False		
+embl2fa	embl2fa	Converts EMBL flat format to fasta format								To update	http://artbio.fr	Text Manipulation	embl2fa	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	0	107	107	107	0	0	0	0	0	0	0	0	0	0	0	0	107	0	0	107	0	0	0	107	0	0	0	0	0	0	107	107	107	0	143762	148864	4481	5039	151989	296028	13224	31140	24955	27001	2397	2705	320706	471893	20102	38884	False		
+ena_upload	ena_upload	Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 								To update	https://github.com/usegalaxy-eu/ena-upload-cli	Data Export	ena_upload	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload	0.7.3	ena-upload-cli	0.7.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	366	366	41	41	0	0	0	0	1302	1302	14	14	1668	1668	55	55	False		
+enasearch	enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data	A Python library for interacting with ENA's API								To update	https://github.com/bebatut/enasearch	Data Source	enasearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch		enasearch	0.2.2			0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	1989	2302	367	453	0	0	0	0	0	0	0	0	1989	2302	367	453	False		
+encyclopedia	encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30			2	4	7	0	2	4	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	738	738	98	98	1	1	1	1	42	42	4	4	781	781	103	103	False		
+ensembl_vep	ensembl_vep	Ensembl VEP: Annotate VCFs with variant effect predictions								Up-to-date	https://github.com/Ensembl/ensembl-vep	Variant Analysis	ensembl_vep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep	112.0	ensembl-vep	112.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3051	3051	171	171	0	0	0	0	0	0	0	0	3051	3051	171	171	False		
+eodie	eodie	Earth Observation Data Information Extractor								To update	https://eodie.readthedocs.io/	Climate Analysis	eodie	climate	https://gitlab.com/eetun-tiimi/EODIE	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/eodie	1.0.2	eodie				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	45	45	4	4	0	0	0	0	0	0	0	0	45	45	4	4	False		
+epicseg	epicseg_segment	EpiCSeg is a tool for conducting chromatin segmentation.								To update	https://github.com/lamortenera/epicseg	Epigenetics	epicseg	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	@VERSION_STRING@	epicseg	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	160	252	17	21	0	0	0	0	0	0	0	0	160	252	17	21	False		
+episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	880	880	80	80	221	221	37	37	49	49	3	3	1150	1150	120	120	False		
+essential_climate_variables	cds_essential_variability	Get Copernicus Essential Climate Variables for assessing climate variability								To update	https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview	Climate Analysis, Data Source	cds_essential_variability	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	232	336	39	40	0	0	0	0	0	0	0	0	232	336	39	40	False		
+ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	0	820	966	89	106	0	0	0	0	0	0	0	0	820	966	89	106	False		
+evidencemodeler	evidencemodeler	EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures.	EvidenceModeler	EvidenceModeler		EvidenceModeler	The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.	Gene prediction	Gene expression, Gene structure	Up-to-date	https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file	Genome annotation	evidencemodeler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/evidencemodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler	2.1.0	evidencemodeler	2.1.0	Gene prediction	Gene expression, Gene structure	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+exomedepth	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	517	517	61	61	2995	2995	184	184	0	0	0	0	3512	3512	245	245	False		
+exonerate	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1030	1072	185	188	1058	1058	189	189	922	922	35	35	3010	3052	409	412	False		
+exparna	exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5396	5938	580	607	628	628	168	168	519	519	107	107	6543	7085	855	882	False		
+export_to_cluster	export_to_cluster	Export datasets to cluster								To update	https://github.com/TGAC/earlham-galaxytools/	Data Export	export_to_cluster	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster	0.0.2	EXPORT_DIR_PREFIX				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+express	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	278	337	34	45	0	1184	0	117	2402	2844	23	60	2680	4365	57	222	False		
+extract_genomic_dna	Extract genomic DNA 1	Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.								To update		Genomic Interval Operations	extract_genomic_dna	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna	https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna	3.0.3+galaxy2	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	1	0	0	0	1	1	1	1	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	9409	12735	813	923	20180	259099	2072	11791	168	611	20	63	29757	272445	2905	12777	False		
+ez_histograms	ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+falco	falco	A high throughput sequence QC analysis tool	falco	falco		Falco	A high-speed FastQC emulation for quality control of sequencing data.	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	Up-to-date	https://github.com/smithlabcode/falco/	Sequence Analysis	falco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco	https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco	1.2.4	falco	1.2.4	Sequencing quality control, Visualisation, Read mapping	Workflows, Mapping, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4298	4298	34	34	0	0	0	0	0	0	0	0	4298	4298	34	34	False		
+fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	601	601	128	128	1165	1165	232	232	0	0	0	0	1766	1766	360	360	False		
+fasplit	fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit	469	ucsc-fasplit	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3278	3361	460	478	6144	6144	595	595	1139	1139	183	183	10561	10644	1238	1256	False		
+fasta2bed	fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_clipping_histogram	cshl_fasta_clipping_histogram	Length Distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Graphics, Statistics	fasta_clipping_histogram	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram	0.0.14	fastx_toolkit	0.0.14			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5191	5367	104	130	5191	5367	104	130	False		
+fasta_compute_length	fasta_compute_length	Compute sequence length								To update	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.4	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	8547	9136	978	1129	17748	51150	1404	5670	4239	4404	162	190	30534	64690	2544	6989	False		
+fasta_concatenate_by_species	fasta_concatenate0	Concatenate FASTA alignment by species								To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	39695	39742	242	255	13660	19007	600	1398	1521	1603	92	112	54876	60352	934	1765	False		
+fasta_extract	fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	10	10	1	1	0	0	0	0	1286	1827	144	181	1296	1837	145	182	False		
+fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fasta_filter_by_length	fasta_filter_by_length	Filter sequences by length								To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	47494	51924	889	997	50663	101663	1488	3742	3919	5601	241	276	102076	159188	2618	5015	False		
+fasta_formatter	cshl_fasta_formatter	FASTA Width formatter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_formatter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	1	5235	5486	237	288	4060	25609	480	2039	816	1093	73	89	10111	32188	790	2416	False		
+fasta_merge_files_and_filter_unique_sequences	fasta_merge_files_and_filter_unique_sequences	Concatenate FASTA database files together								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Fasta Manipulation	fasta_merge_files_and_filter_unique_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fasta_merge_files_and_filter_unique_sequences	1.2.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	30917	32191	1142	1257	36869	36869	1346	1346	5236	5236	230	230	73022	74296	2718	2833	False		
+fasta_nucleotide_changer	cshl_fasta_nucleotides_changer	RNA/DNA converter.								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fasta_nucleotide_changer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	497	808	71	108	2249	5479	216	703	415	437	18	20	3161	6724	305	831	False		
+fasta_nucleotide_color_plot	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	164	179	42	47	758	905	128	170	0	0	0	0	922	1084	170	217	False		
+fasta_stats	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	43726	44512	3104	3259	19941	19941	3693	3693	16788	18589	2467	2650	80455	83042	9264	9602	False		
+fasta_to_tabular	fasta2tab	FASTA-to-Tabular converter								To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	108876	113638	1572	1793	82527	192112	2209	8565	5711	7649	275	334	197114	313399	4056	10692	False		
+fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani		FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6685	6685	603	603	0	0	0	0	0	0	0	0	6685	6685	603	603	False		
+fastg2protlib	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	29	29	8	8	0	0	0	0	0	0	0	0	29	29	8	8	False		
+fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	136	136	11	11	0	0	0	0	0	0	0	0	136	136	11	11	False		
+fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	1	1126086	1127111	6847	6909	422259	422259	10722	10722	76462	76462	2242	2242	1624807	1625832	19811	19873	False		
+fastq_combiner	fastq_combiner	Combine FASTA and QUAL into FASTQ								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation, Fasta Manipulation	fastq_combiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	8604	8799	215	240	54200	75329	919	2957	1562	1680	76	85	64366	85808	1210	3282	False		
+fastq_filter	fastq_filter	Filter FASTQ reads by quality score and length								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15582	18350	690	771	40489	121585	2715	9239	4657	5793	214	287	60728	145728	3619	10297	False		
+fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_groomer	fastq_groomer	Convert between various FASTQ quality formats.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_groomer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	92594	102535	2576	2995	179461	897457	9437	44701	15434	25533	664	1073	287489	1025525	12677	48769	False		
+fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7560	7560	1266	1266	6539	6539	1581	1581	0	0	0	0	14099	14099	2847	2847	False		
+fastq_manipulation	fastq_manipulation	Manipulate FASTQ reads on various attributes.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_manipulation	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2488	3132	215	267	6241	14508	834	2121	4121	4592	131	158	12850	22232	1180	2546	False		
+fastq_masker_by_quality	fastq_masker_by_quality	FASTQ Masker by quality score								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_masker_by_quality	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	234	249	43	44	2648	8092	288	983	442	466	12	17	3324	8807	343	1044	False		
+fastq_pair	fastq_pair	Paired-end fastq pairer								To update	https://github.com/linsalrob/fastq-pair	Fastq Manipulation	fastq_pair	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_pair	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_pair	1.0+galaxy0	fastq-pair	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_paired_end_deinterlacer	fastq_paired_end_deinterlacer	FASTQ de-interlacer on paired end reads.								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_deinterlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	5873	8936	532	657	14738	20229	1889	2366	2316	2711	225	261	22927	31876	2646	3284	False		
+fastq_paired_end_interlacer	fastq_paired_end_interlacer	FASTQ interlacer on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_interlacer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18216	19573	2348	2492	23484	25936	3482	3851	6207	6551	1402	1442	47907	52060	7232	7785	False		
+fastq_paired_end_joiner	fastq_paired_end_joiner	FASTQ joiner on paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_joiner	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15628	17130	536	679	24157	58368	1954	5716	1941	2266	172	214	41726	77764	2662	6609	False		
+fastq_paired_end_splitter	fastq_paired_end_splitter	FASTQ splitter on joined paired end reads								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_paired_end_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3169	3521	459	535	19309	30747	1410	3441	807	1023	219	247	23285	35291	2088	4223	False		
+fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_provider	fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_quality_boxplot	cshl_fastq_quality_boxplot	Draw quality score boxplot								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics, Statistics	fastq_quality_boxplot	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1271	1393	131	176	12763	58819	2073	8850	430	479	32	51	14464	60691	2236	9077	False		
+fastq_quality_converter	cshl_fastq_quality_converter	Quality format converter (ASCII-Numeric)								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_converter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	335	352	44	47	1583	9696	269	2229	1131	1254	15	27	3049	11302	328	2303	False		
+fastq_quality_filter	cshl_fastq_quality_filter	Filter by quality								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation	fastq_quality_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	17279	18386	3826	4062	55268	136888	6055	12590	7685	9356	1854	2043	80232	164630	11735	18695	False		
+fastq_quality_trimmer	cshl_fastq_quality_trimmer	FASTQ trimmer based on quality								To update	https://github.com/agordon/fastx_toolkit	Fastq Manipulation	fastq_quality_trimmer	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_quality_trimmer	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_quality_trimmer	0.0.14+galaxy0	fastx_toolkit	0.0.14			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastq_stats	fastq_stats	FASTQ Summary Statistics by column								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_stats	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3858	4595	680	815	15213	81513	3159	14109	3855	4163	184	256	22926	90271	4023	15180	False		
+fastq_to_fasta	cshl_fastq_to_fasta	FASTQ to FASTA converter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Convert Formats	fastq_to_fasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	36069	37805	1151	1234	45213	99852	2691	6370	8457	13335	408	609	89739	150992	4250	8213	False		
+fastq_to_tabular	fastq_to_tabular	FASTQ to Tabular converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_to_tabular	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	12895	14110	269	297	13315	30673	612	1810	5125	5373	64	87	31335	50156	945	2194	False		
+fastq_trimmer	fastq_trimmer	FASTQ Trimmer by quality								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastq_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10114	11383	582	665	23906	92351	1986	8818	1588	2607	108	212	35608	106341	2676	9695	False		
+fastq_trimmer_by_quality	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window								To update		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4881	6165	859	967	29458	99179	3455	11369	2171	2678	259	338	36510	108022	4573	12674	False		
+fastq_utils	fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastqc	fastqc	Read QC reports using FastQC	fastqc	fastqc		FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc	0.74+galaxy1	fastqc	0.12.1	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	1	0	1784056	1913280	41344	43940	2269843	3195869	90828	140008	410004	445555	14195	16026	4463903	5554704	146367	199974	False		
+fastqc_stats	FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fastqe	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5162	5162	2350	2350	10176	10176	4714	4714	2610	2610	991	991	17948	17948	8055	8055	False		
+fastqsolexa_to_fasta_qual	fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data								To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	3	0	0	0	0	0	8	0	3	False		
+fastqtofasta	fastq_to_fasta_python	FASTQ to FASTA converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	208349	217568	3421	3732	131388	245005	5108	13227	18655	18655	679	679	358392	481228	9208	17638	False		
+fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	65542	65631	1049	1071	25992	25992	2147	2147	6733	7339	649	745	98267	98962	3845	3963	False		
+fastx_artifacts_filter	cshl_fastx_artifacts_filter	Remove sequencing artifacts								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_artifacts_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_artifacts_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1769	2020	88	101	6948	24960	358	2424	623	998	32	50	9340	27978	478	2575	False		
+fastx_barcode_splitter	cshl_fastx_barcode_splitter	Barcode Splitter								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_barcode_splitter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	16957	18124	225	260	37001	89126	919	2720	863	989	56	68	54821	108239	1200	3048	False		
+fastx_clipper	cshl_fastx_clipper	Clip adapter sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_clipper	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3140	3520	178	212	13975	117900	1198	6006	409	712	36	55	17524	122132	1412	6273	False		
+fastx_collapser	cshl_fastx_collapser	Collapse sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation	fastx_collapser	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	64187	67981	326	349	87477	185555	781	3067	16563	17125	58	78	168227	270661	1165	3494	False		
+fastx_nucleotides_distribution	cshl_fastx_nucleotides_distribution	Draw nucleotides distribution chart								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Graphics	fastx_nucleotides_distribution	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	174	272	61	92	4295	25068	1056	4180	1127	1171	70	89	5596	26511	1187	4361	False		
+fastx_quality_statistics	cshl_fastx_quality_statistics	Compute quality statistics								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Statistics	fastx_quality_statistics	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2218	2344	168	206	20551	60032	3784	9866	2347	2460	234	256	25116	64836	4186	10328	False		
+fastx_renamer	cshl_fastx_renamer	Rename sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_renamer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2364	2526	180	214	6572	11745	303	1024	462	696	49	64	9398	14967	532	1302	False		
+fastx_reverse_complement	cshl_fastx_reverse_complement	Reverse-Complement								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fastq Manipulation, Fasta Manipulation	fastx_reverse_complement	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	10707	12597	356	415	21568	67304	574	1527	719	861	61	78	32994	80762	991	2020	False		
+fastx_trimmer	cshl_fastx_trimmer	Trim sequences								Up-to-date	http://hannonlab.cshl.edu/fastx_toolkit/	Fasta Manipulation, Fastq Manipulation	fastx_trimmer	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_trimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer	0.0.14	fastx_toolkit	0.0.14			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	13584	14557	550	641	123676	206733	2034	8390	2819	4757	229	267	140079	226047	2813	9298	False		
+fates-emerald	ctsm_fates	EMERALD version of the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Community Terrestrial Systems Model as host model								To update	https://github.com/NordicESMhub/ctsm/blob/fates_emerald_api/README_fates_emerald_api	Climate Analysis	ctsm_fates	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/fates-emerald	2.0	fates-emerald				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	264	264	69	69	34	34	11	11	103	103	1	1	401	401	81	81	False		
+fatovcf	fatovcf	Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_fatovcf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf	448	ucsc-fatovcf	448		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	385	385	46	46	587	587	107	107	58	58	5	5	1030	1030	158	158	False		
+feature_alignment	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	18	18	1	1	0	0	0	0	0	0	0	0	18	18	1	1	False		
+featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.13.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22308	22388	16	19	350	13711	54	349	0	0	0	0	22658	36099	70	368	False		
+featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	740719	770524	11699	12547	643892	784396	23272	27598	66108	68867	2348	2463	1450719	1623787	37319	42608	False		
+feelnc	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	Annotation, Classification	Functional, regulatory and non-coding RNA	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1375	1500	95	99	797	797	116	116	59	59	3	3	2231	2356	214	218	False		
+feelnc2asko	feelnc2asko	Convert FeelNC GTF to GFF3								To update	https://github.com/tderrien/FEELnc	Convert Formats	feelnc2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko	0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+feht	feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fermikit	fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fetch_fasta_from_ncbi	retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers								To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	1	1	1	1	False		
+fgsea	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	Gene-set enrichment analysis	Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5618	5820	582	607	21673	21673	938	938	869	869	110	110	28160	28362	1630	1655	False		
+file_manipulation	bg_uniq	This tool returns all unique lines from a tab-separated file.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	Text Manipulation	unique	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	0.4	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	6690	8818	554	612	0	0	0	0	0	0	0	0	6690	8818	554	612	False		
+filter_by_fasta_ids	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	26717	29932	1026	1072	42990	42990	1176	1176	9619	9619	230	230	79326	82541	2432	2478	False		
+filter_compounds	filter_orgmet_anorg	Tool for filtering organometallics/anorganic compounds from a list of compounds.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	filter_compounds	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	3.1.1	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_density	filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_stats	filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filter_transcripts_via_tracking	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23	24	9	10	62	635	26	241	2	2	2	2	87	661	37	253	False		
+filter_vcf	filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	53310	53944	1499	1575	25043	25043	726	726	10824	10824	593	593	89177	89811	2818	2894	False		
+find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	62	70	10	12	3	1787	1	204	0	0	0	0	65	1857	11	216	False		
+find_repeats	findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+find_subsequences	bg_find_subsequences									To update			find_subsequences	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences	0.3	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	554	784	69	79	2820	3047	323	361	20	20	1	1	3394	3851	393	441	False		
+fisher_test	fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+flair	flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	1985	1985	41	41	0	0	0	0	0	0	0	0	1985	1985	41	41	False		
+flanking_features	flanking_features_1	Fetch closest non-overlapping feature for every interval								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	flanking_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features	4.0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	589	731	51	63	2445	32847	304	2549	1214	1294	15	22	4248	34872	370	2634	False		
+flash	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22017	22304	239	255	9399	14886	462	709	4	4	1	1	31420	37194	702	965	False		
+flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	661	715	52	54	0	0	0	0	167	167	15	15	828	882	67	69	False		
+flexynesis	flexynesis	This is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.								Up-to-date	https://github.com/BIMSBbioinfo/flexynesis/tree/main	Machine Learning, Statistics, Systems Biology	flexynesis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis	https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis	0.2.10	flexynesis	0.2.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	2	2	0	0	0	0	0	0	0	0	9	9	2	2	False		
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32514	32675	3379	3422	19434	19434	2537	2537	9843	9843	1624	1624	61791	61952	7540	7583	False		
+footprint	footprint	Find transcription factor footprints								To update	https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/	Epigenetics	footprint	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	1.0.0	footprint	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	57	5	5	0	0	0	0	0	0	0	0	57	57	5	5	False		
+format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	189	203	57	60	0	0	0	0	0	0	0	0	189	203	57	60	False		
+format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5940	6474	558	608	0	0	0	0	0	0	0	0	5940	6474	558	608	False		
+fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1257	1450	150	162	0	0	0	0	1052	1052	45	45	2309	2502	195	207	False		
+fragpipe	fragpipe	Data analysis for mass spectrometry-based proteomics.								Up-to-date	https://fragpipe.nesvilab.org/	Proteomics	fragpipe	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe	20.0	fragpipe	20.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	64	64	9	9	0	0	0	0	0	0	0	0	64	64	9	9	False		
+free_energy		Free energy tools of BRIDGE.								To update		Molecular Dynamics, Computational chemistry	freeenergy	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/free_energy						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+freebayes	freebayes, bamleftalign	Galaxy Freebayes Bayesian genetic variant detector tool	freebayes	freebayes		FreeBayes	Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	To update	https://github.com/ekg/freebayes	Variant Analysis	freebayes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes	1.3.6	freebayes	1.3.8	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	149715	171093	8158	8794	144708	256315	15996	25107	19156	21936	2251	2571	313579	449344	26405	36472	False		
+freec	control_freec	Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.	freec	freec		FREEC	A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.	Copy number estimation, Variant calling, Genome alignment	DNA structural variation, Oncology, Human genetics, Data mining	To update	http://boevalab.inf.ethz.ch/FREEC/	Variant Analysis	control_freec	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec	11.6	gawk		Copy number estimation, Variant calling, Genome alignment	Oncology, Human genetics, Data mining	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	748	748	91	91	0	0	0	0	12	12	1	1	760	760	92	92	False		
+freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja		Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	21757	21757	101	101	217	217	21	21	0	0	0	0	21974	21974	122	122	False		
+frogs	FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis	frogs	frogs		FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fromHicupToJuicebox	fromHicupToJuicebox	Convert the output of hicup (as sam or bam) to the input of juicebox.								To update		Epigenetics	from_hicup_to_juicebox	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromHicupToJuicebox	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fromgtfTobed12	fromgtfTobed12	Convert GTF files to BED12 format								To update	https://pythonhosted.org/gffutils/contents.html	Convert Formats	fromgtftobed12	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12	0.11.1+galaxy1	gffutils	0.13			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+fsd	fsd, fsd_beforevsafter, fsd_regions, td	Tool that plots a histogram of sizes of read families								To update		Graphics	duplex_family_size_distribution	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd	1.0.2	matplotlib				4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	578	578	34	34	0	0	0	0	578	578	34	34	False		
+funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	0	8648	8648	1408	1408	32	32	6	6	6406	6406	597	597	15086	15086	2011	2011	False		
+garnett	garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	11	11	0	0	0	0	0	0	0	0	27	27	11	11	False		
+gatk4	filtermutectcalls, mergemutectstats, mutect2	Find somatic variations								To update	http://artbio.fr	Variant Analysis	gatk4	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gatk4	gatk4_mutect2	A Galaxy wrapper for Mutect2 from GATK								To update	https://software.broadinstitute.org/gatk/gatk4	Variant Analysis	gatk4_mutect2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3463	3463	452	452	9040	9040	1639	1639	0	0	0	0	12503	12503	2091	2091	False		
+gblocks	gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	466	466	62	62	466	466	62	62	False		
+gc_derivatization	gc_derivatization	In silico derivatization for GC.								Up-to-date	https://github.com/RECETOX/gc-meox-tms	Metabolomics	gc_derivatization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	https://github.com/RECETOX/galaxytools/tree/master/tools/gc_derivatization	1.0.1	gc-meox-tms	1.0.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gcms2isocor	gcms2isocor	Conversion from GCMS PostRun Analysis to Isocor								To update		Metabolomics	gcms2isocor	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/gcms2isocor	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gcms2isocor	gcms2isocor	Corrective method dedicated to Isocor for calculating carbon isotopologue distribution from GCMS runs								To update	https://github.com/p2m2/p2m2tools	Metabolomics	gcms2isocor	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/gcms2isocor	0.2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0					0	0	8	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	0	1409	1498	39	42	0	0	0	0	0	0	0	0	1409	1498	39	42	False		
+gdcwebapp	data_source_gdcwebapp	GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format								To update	http://bioinf.iasi.cnr.it/gdcwebapp/	Data Source, Convert Formats	gdcwebapp	iuc	https://github.com/fabio-cumbo/GDCWebApp4Galaxy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp	1.0.0	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gecko	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	723	723	235	235	0	0	0	0	786	786	95	95	1509	1509	330	330	False		
+gemini	gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	Sequence analysis, Genetic variation analysis	Sequence analysis	1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	4967	5475	1863	1992	992	1118	279	370	3756	3811	423	425	9715	10404	2565	2787	False		
+genebed_maf_to_fasta	GeneBed_Maf_Fasta2	Stitch gene blocks given a set of coding exon intervals								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	Genomic Interval Operations	genebed_maf_to_fasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta	1.0.1+galaxy0					1	1	1	0	1	1	1	0	0	1	0	0	0	1	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	1	0	4	4	2	2	221	2905	23	279	0	0	0	0	225	2909	25	281	False		
+genehunter_modscore	genehunter_modscore	Maximised LOD score pedigree analysis utility								To update	https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1	Variant Analysis	genehunter_modscore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genehunter_modscore/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore	3.0.0	ghm	3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+geneiobio	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	101	101	25	25	0	0	0	0	59	59	6	6	160	160	31	31	False		
+genenotebook	genenotebook_build	Galaxy tools allowing to load data into a GeneNoteBook database.https://genenotebook.github.io								Up-to-date	https://genenotebook.github.io	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook	0.4.16	genoboo	0.4.16			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+generate_pc_lda_matrix	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	115	124	29	30	518	1029	102	261	184	198	14	17	817	1351	145	308	False		
+genetrack	genetrack	"Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand."								To update		ChIP-seq	genetrack	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genetrack	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack		numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	445	660	104	197	0	0	0	0	445	660	104	197	False		
+genform	genform	genform: generation of molecular formulas by high-resolution MS and MS/MS data								To update	https://sourceforge.net/projects/genform/	Metabolomics	genform	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/genform		genform	r8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	68	68	4	4	0	0	0	0	0	0	0	0	68	68	4	4	False		
+genomad	genomad_end_to_end	Identify virus and plasmid genomes from nucleotide sequences	genomad	genomad		geNomad	geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.	Sequence annotation, Taxonomic classification	Sequence analysis	To update	https://github.com/apcamargo/genomad/	Metagenomics	genomad	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/genomad	1.8.0	genomad	1.8.1	Sequence annotation, Taxonomic classification	Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+genomescope	genomescope	Analyze unassembled short reads								Up-to-date	https://github.com/tbenavi1/genomescope2.0	Statistics	genomescope	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope	2.0.1	genomescope2	2.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3181	3181	665	665	2112	2112	435	435	1622	1622	148	148	6915	6915	1248	1248	False		
+genomic_super_signature	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	47	47	13	13	0	0	0	0	0	0	0	0	47	47	13	13	False		
+genrich	genrich	Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).								To update	https://github.com/jsh58/Genrich	ChIP-seq	genrich	iuc	https://github.com/jsh58/Genrich	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich	0.5+galaxy2	genrich	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3534	3577	402	405	2840	2840	419	419	571	571	31	31	6945	6988	852	855	False		
+getTn5ExtendedCoverage	getTn5ExtendedCoverage	Take an input bam from ATAC-seq and generate a bedgraph using the center of the Tn5 insertion with an extension								To update		Epigenetics	gettn5extendedcoverage	lldelisle		https://github.com/lldelisle/tools-lldelisle/tree/master/tools/getTn5ExtendedCoverage	0.0.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+get_flanks	get_flanks1	Get flanks returns flanking region/s for every gene								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	get_flanks	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3768	325011	1462	2044	9350	242043	2201	6583	787	1070	119	146	13905	568124	3782	8773	False		
+get_hrun	get_hrun	Annotate indel variants with homopolymer context								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	Variant Analysis	get_hrun	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun	https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun	0.5.9.2	pyfaidx	0.8.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5	False		
+get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	746	746	136	136	0	0	0	0	1504	1504	244	244	2250	2250	380	380	False		
+get_pairs	get_pairs	Separate paired and unpaired reads from two fastq files								To update		Fastq Manipulation	get_pairs	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs	0.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+get_reference_fasta	get_fasta_reference	Obtain reference genome sequence.								To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+getindelrates_3way	indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	290	20	86	0	0	0	0	70	290	20	86	False		
+getindels_2way	getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	74	237	24	61	0	0	0	0	74	237	24	61	False		
+getmlst	getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1542	1542	159	159	0	0	0	0	587	587	64	64	2129	2129	223	223	False		
+gfa_to_fa	gfa_to_fa	gfa_to_fa - Converting GFA format to Fasta format								To update	http://gfa-spec.github.io/GFA-spec/	Convert Formats	gfa_to_fa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gfa_to_fa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa	0.1.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9664	9775	763	765	5623	5623	493	493	1000	1000	135	135	16287	16398	1391	1393	False		
+gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	To update	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.7	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	11748	11748	767	767	6560	6560	397	397	2556	2556	106	106	20864	20864	1270	1270	False		
+gff3_rebase	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	806	812	68	68	197	197	37	37	132	132	12	12	1135	1141	117	117	False		
+gffcompare	gffcompare	Galaxy wrappers for Geo Pertea's GffCompare package.	gffcompare	gffcompare		gffcompare	Program for comparing, annotating, merging and tracking transcripts in GFF files.	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	https://github.com/gpertea/gffcompare/	Transcriptomics	gffcompare	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare	0.12.6	gffcompare	0.12.6	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3560	3980	916	999	5281	8000	1713	2521	1468	1642	208	225	10309	13622	2837	3745	False		
+gffcompare_to_bed	gffcompare_to_bed	Filter and convert a gffCompare GTF to BED								To update	https://github.com/gpertea/gffcompare/	Convert Formats	gffcompare_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed	0.2.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1375	2230	329	347	1071	1071	362	362	492	492	64	64	2938	3793	755	773	False		
+gffread	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	Sequence annotation	Nucleic acids, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12828	13716	1740	1829	15217	23818	2588	3486	4423	4423	732	732	32468	41957	5060	6047	False		
+ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	5	0	0	0	0	0	0	3	0	0	0	0	0	0	5	5	5	0	24606	25662	3463	3630	26805	26808	5143	5144	8174	8237	1259	1279	59585	60707	9865	10053	False		
+ggupset	emc-ggupset	Create Upset Plots with ggupset								To update	https://github.com/const-ae/ggupset	Graphics	ggupset	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset	1.0	r-ggupset				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	490	682	74	109	127	14058	20	1798	0	0	0	0	617	14740	94	1907	False		
+glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	0	4343	4343	407	407	0	0	0	0	0	0	0	0	4343	4343	407	407	False		
+glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	11	6	6	85	984	29	230	10	11	7	8	106	1006	42	244	False		
+gnali	gnali	A tool to find nonessential, loss-of-function gene variants								Up-to-date	https://github.com/phac-nml/gnali/	Variant Analysis	gnali	nml	https://github.com/phac-nml/gnali/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/gnali	1.1.0	gnali	1.1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	5800	6212	826	871	7756	7756	1048	1048	1149	1149	215	215	14705	15117	2089	2134	False		
+goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	20207	21960	2807	3139	24488	26198	3066	3321	4155	4155	545	545	48850	52313	6418	7005	False		
+gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	72	5	7	0	0	0	0	0	0	0	0	34	72	5	7	False		
+gprofiler	gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense	functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more								To update	https://biit.cs.ut.ee/gprofiler	Statistics, Web Services	gprofiler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler	@TOOL_VERSION@+galaxy11	r-gprofiler2				5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	4001	4001	614	614	7882	7882	1238	1238	0	0	0	0	11883	11883	1852	1852	False		
+graph_converter	graph_converter	Convert between different graph formats								To update		Convert Formats	graph_converter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+graphclust	graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	1	0	0	0	0	0	0	0	0	0	6	0	1	False		
+graphembed	graphembed	Compute a 2D embedding of a data matrix given supervised class information								Up-to-date	https://github.com/fabriziocosta/GraphEmbed	Statistics, Graphics	graphembed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed	2.4	graph_embed	2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	78	78	6	6	120	120	43	43	0	0	0	0	198	198	49	49	False		
+graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.45	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1725	2708	97	99	2	2	2	2	0	0	0	0	1727	2710	99	101	False		
+graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	9816	10927	1285	1350	1273	1273	368	368	1104	1104	242	242	12193	13304	1895	1960	False		
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	7012	7344	323	338	0	0	0	0	0	0	0	0	7012	7344	323	338	False		
+graphprot	graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy2	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	463	484	18	19	0	0	0	0	0	0	0	0	463	484	18	19	False		
+gromacs	gmx_check, gmx_editconf, gmx_energy, gmx_get_builtin_file, gmx_rg, gmx_makendx, gmx_merge_topology_files, gmx_em, gmx_restraints, gmx_rmsd, gmx_rmsf, gmx_setup, gmx_sim, gmx_solvate, gmx_trj	GROMACS is a package for performing molecular dynamics, primarily designed for biochemical molecules such as proteins, lipids and nucleic acids.								To update	https://github.com/gromacs	Molecular Dynamics, Computational chemistry	gromacs	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs	2022	gromacs	2021.3			14	8	15	0	14	8	15	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	15	9	0	184067	184203	3441	3451	9382	9382	1438	1438	10325	10325	648	648	203774	203910	5527	5537	False		
+gsc_center_scale	center_scale	Center or scale (standardize) data								To update	http://artbio.fr	Statistics	gsc_center_scale	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_filter_cells	filter_cells	Filter single cell RNAseq data on libray depth and number of detected genes								To update	http://artbio.fr	Transcriptomics	gsc_filter_cells	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_filter_genes	filter_genes	Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_filter_genes	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_genes	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_gene_expression_correlations	single_cell_gene_expression_correlations	Compute single-cell paire-wise gene expressions correlations								To update	http://artbio.fr	Transcriptomics	gsc_gene_expression_correlations	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_gene_expression_correlations	4.3.1+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_high_dimensions_visualisation	high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_mannwhitney_de	mannwhitney_de	Perform a mann-whitney differential testing between two sets of gene expression data								To update	http://artbio.fr	Transcriptomics	gsc_mannwhitney_de	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de	4.1.3+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gsc_scran_normalize	scran_normalize	Normalize raw counts using scran								To update	http://artbio.fr	Transcriptomics	gsc_scran_normalize	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize	1.28.1+galaxy0	bioconductor-scran	1.30.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	24	24	3	3	2	2	10	10	2	2	102	102	28	28	False		
+gsc_signature_score	signature_score	Compute signature scores from single cell RNAseq data								To update	http://artbio.fr	Transcriptomics	gsc_signature_score	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_signature_score	2.3.9+galaxy0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gstf_preparation	gstf_preparation	GeneSeqToFamily preparation converts data for the workflow								To update	https://github.com/TGAC/earlham-galaxytools/	Convert Formats	gstf_preparation	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation	0.4.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	377	400	17	17	0	0	0	0	0	0	0	0	377	400	17	17	False		
+gtdb_to_taxdump	gtdb_to_taxdump	Convert GTDB taxonomy to NCBI taxdump format	gtdb_to_taxdump	gtdb_to_taxdump		gtdb_to_taxdump	Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI.	Data handling, Mapping, Generation	Computational biology	Up-to-date	https://github.com/nick-youngblut/gtdb_to_taxdump	Metagenomics	gtdb_to_taxdump	iuc	https://github.com/nick-youngblut/gtdb_to_taxdump	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump	0.1.9	gtdb_to_taxdump	0.1.9	Data handling, Mapping, Generation	Computational biology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	Up-to-date	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.4.0	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	476	476	87	87	0	0	0	0	588	588	74	74	1064	1064	161	161	False		
+gtf-2-gene-list	_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1982	1983	323	324	1040	1040	343	343	205	205	38	38	3227	3228	704	705	False		
+gtfToBed12	gtftobed12	Convert GTF files to BED12 format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README	Convert Formats	gtftobed12	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12	357	ucsc-gtftogenepred	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	8329	9363	3336	3828	8009	8009	3130	3130	1577	1577	344	344	17915	18949	6810	7302	False		
+gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3690	3811	326	336	3323	3323	235	235	1895	2429	234	258	8908	9563	795	829	False		
+guppy	guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	6.5.7+galaxy0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	1	1	7	7	1	1	False		
+gvcftools	gvcftools_extract_variants	gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf.								To update	https://github.com/sequencing/gvcftools	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools	0.1	gvcftools	0.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+gwastools	gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	Deposition, Analysis, Annotation	GWAS study	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	7303	7303	222	222	20	20	2	2	0	0	0	0	7323	7323	224	224	False		
+hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	349	359	32	33	364	364	53	53	0	0	0	0	713	723	85	86	False		
+hapcut2	hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	Haplotype mapping, Variant classification		0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	103	103	4	4	103	103	4	4	False		
+hapog	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	502	502	66	66	0	0	0	0	0	0	0	0	502	502	66	66	False		
+happy	som.py	A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets.	hap.py	hap.py		hap.py	This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison.	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	To update	https://github.com/Illumina/hap.py	Variant Analysis	happy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy	0.3.14	hap.py	0.3.15	Variant calling, Sequence analysis, Genotyping	Genomics, DNA polymorphism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hardklor	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	98	111	5	8	0	0	0	0	0	0	0	0	98	111	5	8	False		
+hclust2	hclust2	Plots heatmaps								To update	https://bitbucket.org/nsegata/hclust2/	Data Visualization	hclust2	rnateam	https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2	https://github.com/bgruening/galaxytools/tree/master/tools/hclust2	0.99	hclust2	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hcluster_sg	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	243	263	54	57	0	0	0	0	0	0	0	0	243	263	54	57	False		
+hcluster_sg_parser	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	266	293	22	25	0	0	0	0	0	0	0	0	266	293	22	25	False		
+heatmap2	ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	1	0	46700	50808	4645	5114	64214	70429	5799	6830	7783	7912	704	724	118697	129149	11148	12668	False		
+heinz	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	bionet, heinz		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	1281	1434	367	442	1559	1559	636	636	678	678	52	52	3518	3671	1055	1130	False		
+helixer	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	267	267	39	39	0	0	0	0	80	80	7	7	347	347	46	46	False		
+hess	hess_astro_tool	Basic analysis of Data Level 3 public data sample of HESS gamma-ray telescope								To update		Astronomy	hess_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/hess	0.0.2+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+hgv_fundo	hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	145	1794	33	397	0	0	0	0	145	1794	33	397	False		
+hgv_hilbertvis	hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	119	265	16	60	0	0	0	0	119	265	16	60	False		
+hgvsparser	hgvsparser	Parsing and building variant descriptor strings compliant with the HGVS standard								To update	https://github.com/VariantEffect/hgvsParseR/tree/master	Variant Analysis	hgvsparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6346	6346	2	2	0	0	0	0	0	0	0	0	6346	6346	2	2	False		
+hicexplorer	hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								Up-to-date	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.5	hicexplorer	3.7.5			38	38	38	0	38	38	38	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	33	36	33	0	44449	68602	3236	4177	46	46	21	21	1328	1328	67	67	45823	69976	3324	4265	False		
+hicstuff	hicstuff_pipeline	A toolkit to generate and manipulate Hi-C matrices								To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hictk	hictk	Convert cooler to juicebox_hic								Up-to-date	https://github.com/paulsengroup/hictk	Convert Formats, Epigenetics	hictk	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	1.0.0	hictk	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	9	9	0	0	0	0	0	0	0	0	17	17	9	9	False		
+hicup	hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater	The HiCUP-Pipeline from the Bioinformatics Babraham Institute.								To update	https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html	Epigenetics	hicup	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	0.9.2					7	0	7	0	7	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	6	0	901	1020	160	184	440	440	111	111	0	0	0	0	1341	1460	271	295	False		
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm	0.19.9	hifiasm	0.19.9			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1819	1819	539	539	1334	1334	389	389	2472	2472	137	137	5625	5625	1065	1065	False		
+hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	156	156	20	20	0	0	0	0	220	220	11	11	376	376	31	31	False		
+high_dim_heatmap	high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hirondelle_crim_ogc_api_processes	hirondelle_crim	This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/hirondelle_crim_ogc_api_processes	0.2.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	2	2	0	0	0	0	0	0	0	0	18	18	2	2	False		
+hisat	hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	0	12	0	0	0	0	0	0	0	0	0	228	0	12	False		
+hisat2	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	Sequence alignment		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	337151	353499	10046	10719	699868	896164	26656	34018	87016	94859	5302	5695	1124035	1344522	42004	50432	False		
+histogram	histogram_rpy	Histogram of a numeric column								To update		Graphics, Statistics	histogram	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram	https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram	1.0.4	rpy2	2.7.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3748	4661	866	1002	5993	48272	1507	7101	549	746	152	253	10290	53679	2525	8356	False		
+hivclustering	hivclustering	Infers transmission networks from pairwise distances inferred by tn93								To update	https://pypi.org/project/hivclustering/	Next Gen Mappers	hivclustering	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering	1.3.1	python-hivclustering	1.8.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	0	0	12	12	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	12	0	35919	36952	1283	1321	0	0	0	0	3023	3023	180	180	38942	39975	1463	1501	False		
+homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+homer	homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	Sequence motif discovery		0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	5	0	0	8531	8531	633	633	0	0	0	0	0	0	0	0	8531	8531	633	633	False		
+htseq-clip	htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	98	98	19	19	0	0	0	0	0	0	0	0	98	98	19	19	False		
+htseq_count	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	Nucleic acid sequence analysis	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	144907	168824	3703	4366	213407	346792	10798	16485	27209	33124	2613	2854	385523	548740	17114	23705	False		
+humann	humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.9	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	10	10	0	6	10	10	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	26659	26659	2067	2067	865	865	174	174	3238	3238	351	351	30762	30762	2592	2592	False		
+hybpiper	hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.3.0	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1571	1571	3	3	0	0	0	0	144	144	4	4	1715	1715	7	7	False		
+hyperstack_to_bleach_corrected_movie	hyperstack_to_bleach_corrected_movie	Generate blach corrected movie from hyperstack								To update		Imaging	hyperstack_to_bleach_corrected_movie	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/hyperstack_to_bleach_corrected_movie	20230328	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	0	17	2	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	12	17	12	0	11429	11429	428	428	7751	7751	676	676	715	715	58	58	19895	19895	1162	1162	False		
+hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	473	473	93	93	0	0	0	0	0	0	0	0	473	473	93	93	False		
+icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	1200	1220	187	195	1588	1588	267	267	0	0	0	0	2788	2808	454	462	False		
+idconvert	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	241	276	24	33	0	0	0	0	0	0	0	0	241	276	24	33	False		
+idr	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2953	3027	109	114	1710	1710	199	199	0	0	0	0	4663	4737	308	313	False		
+idr_download	idr_download_by_ids	Image Data Resource downloading tool								To update	https://idr.openmicroscopy.org	Data Source	idr_download_by_ids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download	0.45	omero-py	5.11.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	404	404	37	37	0	0	0	0	24	24	1	1	428	428	38	38	False		
+iedb_api	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1539	1539	35	35	0	0	0	0	0	0	0	0	1539	1539	35	35	False		
+illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+image_info	ip_imageinfo	Extracts image metadata			python-bioformats					To update	https://github.com/bmcv	Imaging	image_info	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_info	5.7.1	bftools	6.7.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	273	659	101	102	0	0	0	0	153	153	15	15	426	812	116	117	False		
+image_math	image_math	Process images using arithmetic expressions								To update	https://github.com/bmcv	Imaging	image_math	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math	1.26.4	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	2	2	0	0	0	0	0	0	0	0	58	58	2	2	False		
+image_registration_affine	ip_image_registration	Intensity-based Image Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	image_registration_affine	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_registration_affine	0.0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	5	5	0	0	0	0	0	0	0	0	16	16	5	5	False		
+imagecoordinates_flipaxis	imagecoordinates_flipaxis	Flip coordinate axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	imagecoordinates_flipaxis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/imagecoordinates_flipaxis	0.1-2	pandas		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	21409	21849	10	12	0	0	0	0	0	0	0	0	21409	21849	10	12	False		
+imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_crop, imagej2_enhance_contrast, imagej2_filter, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	20240614			Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	0	1731	1731	109	109	0	0	0	0	0	0	0	0	1731	1731	109	109	False		
+improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+incucyte_stack_and_upload_omero	incucyte_stack_and_upload_omero	Combine images to stack and upload to the omero server								To update		Imaging	incucyte_stack_and_upload_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/incucyte_stack_and_upload_omero	20231221	Fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	18	22	1	1	44	292	3	21	0	0	0	0	62	314	4	22	False		
+infercnv	infercnv	Infer Copy Number Variation from Single-Cell RNA-Seq Data								Up-to-date	https://github.com/broadinstitute/infercnv	Transcriptomics, Variant Analysis	infercnv	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv	1.20.0	bioconductor-infercnv	1.20.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	2	2	0	0	0	0	0	0	0	0	10	10	2	2	False		
+infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	59700	112582	223	282	0	0	0	0	1157	1221	34	35	60857	113803	257	317	False		
+influx_data_manager	influx_data_manager	Handling influx_si data inputs in Galaxy workflows								To update	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/	Metabolomics	influx_si_data_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_data_manager	1.0.2	influx-si-data-manager	1.0.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+influx_si	influx_si	metabolic flux estimation based on [in]stationary labeling								To update	https://github.com/sgsokol/influx	Metabolomics	influx_si	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/influx_si	7.0.1	influx_si	7.0.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+inforna		INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	157	157	14	14	0	0	0	0	0	0	0	0	157	157	14	14	False		
+instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	102	102	16	16	0	0	0	0	0	0	0	0	102	102	16	16	False		
+intarna	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.1	intarna	3.4.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3071	7652	41	47	0	0	0	0	0	0	0	0	3071	7652	41	47	False		
+integron_finder	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	55149	55149	161	161	0	0	0	0	6085	6085	73	73	61234	61234	234	234	False		
+intermine_galaxy_exchange	galaxy_intermine_exchange	InterMine Exporter								To update	https://github.com/intermine	Convert Formats	intermine_galaxy_exchange	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange	0.0.1	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37	46	6	12	72	87	13	15	108	108	1	1	217	241	20	28	False		
+interpolation	interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	70	7	7	0	0	0	0	0	0	0	0	70	70	7	7	False		
+interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	34689	55189	1634	1713	65	65	15	15	10897	10897	607	607	45651	66151	2256	2335	False		
+intersect	gops_intersect_1	Intersect the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	20472	349984	2351	3007	45587	778988	4359	14116	6087	7417	484	561	72146	1136389	7194	17684	False		
+interval2maf	Interval2Maf1	Extract MAF blocks given a set of intervals	bx-python	bx-python		bx-python	Tools for manipulating biological data, particularly multiple sequence alignments.		Sequence analysis	To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	interval2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf	1.0.1+galaxy1	bx-python	0.13.0		Sequence analysis	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	32	107	7	10	758	19538	87	1246	16	24	2	2	806	19669	96	1258	False		
+intervene	intervene_pairwise, intervene_upset	Create pairwise and upset plots	intervene	intervene		Intervene	Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.	Sequence comparison, Sequence visualisation	Computational biology	Up-to-date	https://intervene.readthedocs.io	Statistics	intervene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene	0.6.5	intervene	0.6.5	Sequence comparison, Sequence visualisation	Computational biology	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1557	1607	278	292	4458	4458	458	458	0	0	0	0	6015	6065	736	750	False		
+ipo	ipo4retgroup, ipo4xcmsSet	[W4M][LC-MS] IPO								To update	https://github.com/rietho/IPO	Metabolomics	ipo	lecorguille	https://github.com/rietho/IPO	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ipo	1.10.0	bioconductor-ipo	1.28.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	28279	28481	1623	1646	24662	24662	2093	2093	9780	10086	979	992	62721	63229	4695	4731	False		
+irissv	irissv	Refine insertion sequences								To update	https://github.com/mkirsche/Iris	Variant Analysis	irissv	iuc	https://github.com/galaxyproject/tools-iuc/tools/irissv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv	1.0.5	samtools	1.21			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	29	29	8	8	0	0	0	0	0	0	0	0	29	29	8	8	False		
+isescan	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	59386	59386	151	151	56	56	1	1	4741	4741	59	59	64183	64183	211	211	False		
+isoformswitchanalyzer	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1301	1301	59	59	1331	1331	60	60	507	507	9	9	3139	3139	128	128	False		
+isolib	isolib	Create an isotopic pattern library for given compounds and adducts.								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	isolib	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	https://github.com/RECETOX/galaxytools/tree/master/tools/isolib	1.0.1+galaxy0	bioconductor-metabocoreutils	1.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+isoplot	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	4	3	3	0	0	0	0	0	0	0	0	4	4	3	3	False		
+itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1426	1426	71	71	0	0	0	0	0	0	0	0	1426	1426	71	71	False		
+ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	4	0	0	0	4	0	0	0	0	0	0	5	5	5	0	1252220	1252220	2366	2366	126027	126027	2496	2496	41901	41901	993	993	1420148	1420148	5855	5855	False		
+iwtomics	iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot	Interval-Wise Testing for Omics Data	iwtomics	iwtomics		IWTomics	"Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset."	Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison	Statistics and probability	To update	https://bioconductor.org/packages/release/bioc/html/IWTomics.html	Statistics	iwtomics	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iwtomics	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics	1.0.0	bioconductor-iwtomics	1.26.0	Differential gene expression analysis, Peak calling, Genome annotation, Comparison	Statistics and probability	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	675	690	27	28	159	251	29	49	383	383	12	12	1217	1324	68	89	False		
+jasminesv	jasminesv	Merge structural variants across samples								To update	https://github.com/mkirsche/Jasmine/	Variant Analysis	jasminesv	iuc	https://github.com/galaxyproject/tools-iuc/jasminesv/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv	1.0.11	jasminesv	1.1.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32	32	9	9	53	53	19	19	0	0	0	0	85	85	28	28	False		
+jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	21153	22174	5514	5779	17428	17428	6458	6458	15673	17267	3248	3786	54254	56869	15220	16023	False		
+jbrowse	jbrowse_to_container	A tool allowing to export a JBrowse dataset into a JBrowse docker container								To update	https://jbrowse.org	Web Services	jbrowse_to_container	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/jbrowse		python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse_2	jbrowse_2		JBrowse 2	Modular genome browser with views of synteny and structural variation.	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.15.4	jbrowse2	2.15.4	Genome visualisation, Structure visualisation, Pathway visualisation	Mapping, Structural variation, Genomics, Gene structure, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1312	1312	219	219	116	116	58	58	37	37	6	6	1465	1465	283	283	False		
+jcvi_gff_stats	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.16			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2747	2926	596	637	2311	2311	741	741	1145	1145	469	469	6203	6382	1806	1847	False		
+jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1825	1825	237	237	0	0	0	0	971	971	56	56	2796	2796	293	293	False		
+join	gops_join_1	Join the intervals of two datasets side-by-side								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	join	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	15624	330820	1864	2438	52317	513688	10198	39421	1329	1645	213	289	69270	846153	12275	42148	False		
+join_files_by_id	join_files_by_id	This tool will join datasets according to a column with identifier								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	Text Manipulation	join_files_by_id	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id	1.0	r-data.table	1.11.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+join_files_on_column_fuzzy	join_files_on_column_fuzzy	Join two files on a common column, allowing a certain difference.								To update		Text Manipulation	join_files_on_column_fuzzy	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	1.0.1	python				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1980	2697	345	410	0	0	0	0	1081	1081	44	44	3061	3778	389	454	False		
+jq	jq	JQ is a lightweight and flexible command-line JSON processor								To update	https://stedolan.github.io/jq/	Text Manipulation	jq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq	1.0	jq	1.5			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	660	2374	61	63	336	336	82	82	281	281	11	11	1277	2991	154	156	False		
+jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	30	30	2	2	0	0	0	0	0	0	0	0	30	30	2	2	False		
+justdiff	justdiff	Unix diff								To update	http://artbio.fr	Text Manipulation	justdiff	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	3.10+galaxy0	diffutils				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+justgzip	justgzip	Compress fastq sequence files								To update	http://artbio.fr	Convert Formats	justgzip	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	2.8+galaxy0	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+jvarkit	jvarkit_wgscoverageplotter	Jvarkit : Java utilities for Bioinformatics								Up-to-date	https://lindenb.github.io/jvarkit/	SAM	jvarkit	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit	20201223	jvarkit-wgscoverageplotter	20201223			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7179	7179	509	509	11138	11138	1145	1145	0	0	0	0	18317	18317	1654	1654	False		
+kallisto	kallisto_pseudo, kallisto_quant	kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment.	kallisto	kallisto		kallisto	A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.	Gene expression profiling	Transcriptomics, RNA-seq, Gene expression	To update	https://pachterlab.github.io/kallisto/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto	0.48.0	kallisto	0.51.1	Gene expression profiling	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	28398	29031	932	965	73705	80087	2603	3025	5333	5567	218	230	107436	114685	3753	4220	False		
+kaptive	kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kat_sect	kat_@EXECUTABLE@	SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.								To update			kat_sect	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_sect	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	379	379	53	53	8259	8259	271	271	0	0	0	0	8638	8638	324	324	False		
+kegalign	kegalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/galaxyproject/KegAlign	Next Gen Mappers	kegalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/kegalign	0.1.2.7	kegalign-full	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	5	5	1	1	False		
+kernel_canonical_correlation_analysis	kcca1	Kernel Canonical Correlation Analysis								To update		Statistics	kernel_canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis	1.0.0	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	62	70	4	4	207	334	27	71	0	0	0	0	269	404	31	75	False		
+kernel_principal_component_analysis	kpca1	Kernel Principal Component Analysis								To update		Statistics	kernel_principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis	1.0.0	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	144	157	26	30	268	707	83	248	0	0	0	0	412	864	109	278	False		
+khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	8	8	8	0	1995	2091	174	193	1430	1430	389	389	1580	1580	56	56	5005	5101	619	638	False		
+king	king	Kinship-based INference for Gwas								Up-to-date	http://people.virginia.edu/~wc9c/KING/	Variant Analysis	king	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/king	2.2.7	king	2.2.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	8	8	4	4	0	0	0	0	0	0	0	0	8	8	4	4	False		
+kinwalker		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.1.0	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	503	503	58	58	0	0	0	0	0	0	0	0	503	503	58	58	False		
+kma	kma_map	Map with KMA								To update	https://bitbucket.org/genomicepidemiology/kma	Next Gen Mappers	kma	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma	1.4.14	kma	1.4.15			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+kmd_hmdb_data_plot	kmd_hmdb_data_plot	retrieves data from KMD HMDB API and produce plot and csv file								To update	https://github.com/workflow4metabolomics/tools-metabolomics	Metabolomics	kmd_hmdb_data_plot	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/kmd_hmdb_data_plot	1.0.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1342	1342	63	63	0	0	0	0	0	0	0	0	1342	1342	63	63	False		
+kraken	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	5	5	5	0	48136	48164	2754	2760	59952	130398	5869	8654	29008	31148	1936	2200	137096	209710	10559	13614	False		
+kraken2	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	Up-to-date	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	271367	271786	6384	6409	101752	101752	4662	4662	53562	53562	1663	1663	426681	427100	12709	12734	False		
+kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23008	23014	1060	1061	16194	24490	1719	2168	14898	14898	436	436	54100	62402	3215	3665	False		
+kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3185	3185	495	495	0	0	0	0	385	385	48	48	3570	3570	543	543	False		
+kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3981	3986	769	771	4087	5610	991	1284	88	88	41	41	8156	9684	1801	2096	False		
+krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	1	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	48516	48516	2373	2373	8787	8787	943	943	4369	4369	393	393	61672	61672	3709	3709	False		
+krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+label_to_binary	label_to_binary	Convert label map to binary image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	label_to_binary	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/label_to_binary	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+labelimage2points	ip_labelimage_to_points	Label Image to Points	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	labelimage2points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/labelimage2points	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	34	38	2	2	0	0	0	0	0	0	0	0	34	38	2	2	False		
+labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+landmark_registration	ip_landmark_registration	Landmark Registration	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	landmark_registration	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/landmark_registration	0.1.0-2	scikit-image		Image analysis	Imaging, Bioinformatics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	887	927	13	15	4	4	3	3	0	0	0	0	891	931	16	18	False		
+last	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1584	Sequence alignment	Comparative genomics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	329	329	94	94	0	0	0	0	0	0	0	0	329	329	94	94	False		
+lastz	lastz_wrapper_2, lastz_d_wrapper	Galaxy wrappers for the Lastz and Lastz_d	lastz	lastz		LASTZ	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.	Sequence alignment, Read mapping	Genomics	Up-to-date	https://github.com/lastz/lastz	Next Gen Mappers	lastz	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz	1.04.22	lastz	1.04.22	Sequence alignment, Read mapping	Genomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	77409	84356	447	475	156658	193590	870	3511	38579	38780	173	203	272646	316726	1490	4189	False		
+lastz_paired_reads	lastz_paired_reads_wrapper	Galaxy wrapper for the Lastz alignment tool on paired reads								To update		Next Gen Mappers	lastz_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads	1.1.1	lastz	1.04.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7	9	3	4	0	0	0	0	8	10	5	5	15	19	8	9	False		
+lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	89	137	4	20	118	6136	15	1112	0	0	0	0	207	6273	19	1132	False		
+lcrgenie	lcrgenie	Ligase Chain Reaction Genie								To update	https://github.com/neilswainston/LCRGenie	Synthetic Biology	lcrgenie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie	1.0.2	lcr_genie				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lda_analysis	lda_analy1	Perform Linear Discriminant Analysis								To update		Graphics, Statistics	lda_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis	1.0.1	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	147	159	46	48	793	1538	101	314	0	4	0	3	940	1701	147	365	False		
+legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	92	92	8	8	0	0	0	0	0	0	0	0	92	92	8	8	False		
+length_and_gc_content	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	4349	4466	666	698	2093	2286	928	998	201	201	77	77	6643	6953	1671	1773	False		
+lfq_protein_quant	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	78	116	12	19	0	0	0	0	0	0	0	0	78	116	12	19	False		
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	149	171	27	30	0	0	0	0	0	0	0	0	149	171	27	30	False		
+limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	23442	24466	2379	2475	45734	49342	4565	5032	9327	9517	835	842	78503	83325	7779	8349	False		
+lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	39	4	4	0	0	0	0	0	0	0	0	39	39	4	4	False		
+linear_regression	LinearRegression1	Perform Linear Regression								To update		Statistics	linear_regression	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression	https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression	1.0.1	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	146	1103	31	271	0	0	0	0	146	1103	31	271	False		
+links	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	512	512	126	126	0	0	0	0	480	480	65	65	992	992	191	191	False		
+locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								Up-to-date	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	2.0.1	locarna	2.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	314	350	36	46	0	0	0	0	0	0	0	0	314	350	36	46	False		
+lofreq	lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi	LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.								Up-to-date	https://csb5.github.io/lofreq/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq	2.1.5	lofreq	2.1.5			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	0	0	0	4	0	0	0	0	0	0	5	5	5	0	4176367	4176367	4301	4301	509615	509615	8213	8213	106342	106342	1815	1815	4792324	4792324	14329	14329	False		
+logistic_regression_vif	LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	64	173	12	48	0	0	0	0	64	173	12	48	False		
+logol	logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+longorf	longORF	obtain longest ORF in six-frame translations								To update		Sequence Analysis	longorf	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/longorf	0.3.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	822	822	14	14	0	0	0	0	0	0	0	0	822	822	14	14	False		
+lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1219	1219	182	182	0	0	0	0	37	37	4	4	1256	1256	186	186	False		
+ltq_iquant_cli										To update			ltq_iquant_cli	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ltq_iquant_cli						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lumpy_smoove	lumpy_smoove, vcf2hrdetect	Galaxy wrapper of the lumpy-using smoove workflow								To update	http://artbio.fr	Variant Analysis	lumpy_smoove	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	0.2.8+galaxy1	svtyper	0.7.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+lumpy_sv	lumpy_prep, lumpy_sv	LUMPY - a general probabilistic framework for structural variant discovery								Up-to-date	http://layerlab.org/software/	Variant Analysis	lumpy_sv	iuc	https://github.com/arq5x/lumpy-sv	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv	0.3.1	lumpy-sv	0.3.1			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	1534	1534	199	199	0	0	0	0	0	0	0	0	1534	1534	199	199	False		
+lumpy_sv	lumpy	Find structural variations								To update	http://artbio.fr	Variant Analysis	lumpy_sv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_sv	1.3	lumpy-sv	0.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	44	44	11	11	0	0	0	0	0	0	0	0	44	44	11	11	False		
+maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2835	2835	59	59	0	0	0	0	0	0	0	0	2835	2835	59	59	False		
+macs2	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	0	0	9	0	0	0	0	0	0	9	9	9	0	87810	96069	4980	5629	153500	227569	12946	18825	10988	12301	692	807	252298	335939	18618	25261	False		
+maf_cpg_filter	cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	85	356	6	28	0	0	0	0	85	356	6	28	False		
+maf_stats	maf_stats1	MAF Coverage statistics								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	maf_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats	1.0.2+galaxy0					1	1	1	0	1	1	1	0	0	1	0	0	0	1	0	0	1	1	1	0	1	0	0	0	0	0	1	0	0	0	0	1	1	1	1	1	0	15	21	7	9	227	2470	52	464	1	1	1	1	243	2492	60	474	False		
+mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	0	2	2	2	0	172433	174456	1865	1951	108640	122790	4266	5521	20027	20027	1172	1172	301100	317273	7303	8644	False		
+maftoaxt	maftoaxt	Convert dataset from MAF to axt format	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_maftoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt	469	ucsc-maftoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mageck	mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test	Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	mageck	mageck		MAGeCK	Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.	Genetic variation analysis	Genetics, Genetic variation, Genomics	To update	https://sourceforge.net/projects/mageck/	Genome editing		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck	0.5.9.2	mageck	0.5.9.5	Genetic variation analysis	Genetics, Genetic variation, Genomics	3	5	5	0	3	5	5	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	11761	12093	873	889	5762	5762	473	473	5610	5610	343	343	23133	23465	1689	1705	False		
+mahotas_features	ip_mahotas_features	Compute image features using mahotas.			mahotas-feature-computation					To update	https://github.com/luispedro/mahotas	Imaging	mahotas_features	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas_features	0.7-2	mahotas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	44	6	6	0	0	0	0	0	0	0	0	39	44	6	6	False		
+make_nr	make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+maker	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6417	6861	1315	1366	7235	7235	1858	1858	4112	4112	902	902	17764	18208	4075	4126	False		
+maldiquant	maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base				0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1452	3822	61	68	0	0	0	0	1065	1065	39	39	2517	4887	100	107	False		
+malt	malt_run	Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences.								To update	https://github.com/husonlab/malt	Next Gen Mappers	malt_run	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt	0.5.3	malt	0.62			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	24	9	9	0	0	0	0	0	0	0	0	24	24	9	9	False		
+manta	manta	Structural variant and indel caller for mapped sequencing data								To update	http://artbio.fr	Variant Analysis	manta	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/manta	https://github.com/ARTbio/tools-artbio/tree/main/tools/manta	1.6	manta	1.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	218	218	34	34	0	0	0	0	0	0	0	0	218	218	34	34	False		
+map_param_value	map_param_value	Map a parameter value to another value								To update		Text Manipulation	map_param_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3780	3780	67	67	1012	1012	57	57	105	105	3	3	4897	4897	127	127	False		
+map_peptides_to_bed	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	38	44	6	7	0	0	0	0	0	0	0	0	38	44	6	7	False		
+mapping_quality_stats	mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mapping_to_ucsc	mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mapseq	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7871	7871	32	32	0	0	0	0	0	0	0	0	7871	7871	32	32	False		
+marine_omics	sanntis_marine	The Sanntis tool identify biosynthetic gene clusters (BGCs) in genomic & metagenomic data								Up-to-date	https://github.com/Finn-Lab/SanntiS	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics	0.9.3.5	sanntis	0.9.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	51	51	4	4	0	0	0	0	0	0	0	0	51	51	4	4	False		
+mash	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	10119	10119	61	61	19	19	9	9	647	647	7	7	10785	10785	77	77	False		
+mashmap	mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	894	894	12	12	81	81	5	5	0	0	0	0	975	975	17	17	False		
+masigpro	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	Regression analysis	Gene expression, Microarray experiment, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	471	582	35	40	589	589	80	80	0	0	0	0	1060	1171	115	120	False		
+matchms	matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_remove_spectra, matchms_spectral_similarity, matchms_split, matchms_subsetting	Searching, filtering and converting mass spectral libraries.	matchms	matchms		Matchms	Tool to import, process, clean, and compare mass spectrometry data.	Spectral library search, Format validation, Filtering	Metabolomics	Up-to-date	https://github.com/matchms/matchms	Metabolomics	matchms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	0.27.0	matchms	0.27.0	Spectral library search, Format validation, Filtering	Metabolomics	2	14	14	0	2	14	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	1620	1620	70	70	27	27	8	8	1685	1685	12	12	3332	3332	90	90	False		
+mauve_contig_mover	mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mavedb	mavedb_importer	data source for MaveDB								To update		Data Source	mavedb_importer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb	0.9					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	8	2	2	0	0	0	0	0	0	0	0	8	8	2	2	False		
+maxbin2	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	1	0	2798	2798	314	314	2452	2452	508	508	914	914	89	89	6164	6164	911	911	False		
+maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	6863	7021	1251	1264	2798	2798	543	543	3189	3189	352	352	12850	13008	2146	2159	False		
+mcl	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	35	35	13	13	0	0	0	0	0	0	0	0	35	35	13	13	False		
+mdanalysis	mdanalysis_angle, mdanalysis_dihedral, mdanalysis_distance, mdanalysis_endtoend, mdanalysis_extract_rmsd, mdanalysis_hbonds, mdanalysis_cosine_analysis, mdanalysis_ramachandran_protein, mdanalysis_ramachandran_plot, mdanalysis_rdf	MDAnalysis is a package for analyzing trajectories from molecular dynamics (MD) simulations								To update	https://github.com/MDAnalysis/mdanalysis	Computational chemistry	mdanalysis	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdanalysis	1.0.0	mdanalysis				10	5	10	0	10	5	10	0	0	0	0	0	0	0	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	10	0	3209	3268	318	326	182	182	51	51	397	397	39	39	3788	3847	408	416	False		
+mdfileconverter	md_converter	A tool for interconverting between different MD structure and trajectory file formats.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdfileconverter	1.9.7	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	26720	26762	251	253	784	784	54	54	977	977	53	53	28481	28523	358	360	False		
+mdslicer	md_slicer	A tool for slicing trajectory files using MDTraj.								To update		Molecular Dynamics, Computational chemistry	md_converter	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdslicer	1.9.9	mdtraj				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	174	174	19	19	6	6	4	4	441	441	7	7	621	621	30	30	False		
+mdtraj	traj_selections_and_merge	MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories								To update	https://github.com/mdtraj/mdtraj	Computational chemistry	mdtraj	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/mdtraj	1.9.7	mdtraj				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	36	36	8	8	63	63	4	4	0	0	0	0	99	99	12	12	False		
+mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	73	86	5	5	0	0	0	0	0	0	0	0	73	86	5	5	False		
+mean-per-zone	mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	3	3	0	0	0	0	0	0	0	0	20	25	3	3	False		
+measure_gastruloids	measureGastruloids	Get the ROI coordinates around the gastruloids as well as measurements like Area, elongation index								To update		Imaging	measure_gastruloids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/measure_gastruloids	20221216	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	2	0	0	0	0	0	0	3	3	3	0	117975	117975	1693	1693	55063	55063	796	796	9325	9325	639	639	182363	182363	3128	3128	False		
+medenv	iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	9	9	0	0	0	0	0	0	0	0	27	27	9	9	False		
+megablast_xml_parser	megablast_xml_parser	Parse blast XML output								To update		Next Gen Mappers, Convert Formats	megablast_xml_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	743	816	103	141	292	2868	82	459	0	0	0	0	1035	3684	185	600	False		
+megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	12692	13292	1349	1400	16645	16645	2140	2140	6214	6214	431	431	35551	36151	3920	3971	False		
+megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	513	557	152	155	74	74	35	35	10	10	4	4	597	641	191	194	False		
+megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	4130	4130	447	447	0	0	0	0	0	0	0	0	4130	4130	447	447	False		
+meme	meme_dreme, meme_fimo, meme_meme, meme_psp_gen	The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses.	meme_meme	meme_fimo, meme_meme		meme_meme	An algorithm that discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	To update	http://meme-suite.org/	ChIP-seq	meme	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme	5.5.6	meme	5.5.7	Nucleic acid feature detection, Protein feature detection, Statistical calculation	Data mining, Sequence analysis, Genetic variation, Statistics and probability	3	0	4	0	3	0	4	0	0	0	0	0	0	0	0	0	0	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	4	4	0	20990	22979	762	892	10975	25929	1551	3249	0	0	0	0	31965	48908	2313	4141	False		
+meme_chip	meme_chip	Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.								To update	http://meme-suite.org/	ChIP-seq	meme_chip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip	4.11.2	graphicsmagick	1.3.26			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6413	7000	705	743	7260	7260	1171	1171	0	0	0	0	13673	14260	1876	1914	False		
+meneco	meneco	Meneco computes minimal completions to your draft network with reactions from a repair network								Up-to-date	http://bioasp.github.io/meneco/	Systems Biology	meneco	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	https://github.com/genouest/galaxy-tools/tree/master/tools/meneco	1.5.2	meneco	1.5.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+merge	gops_merge_1	Merge the overlapping intervals of a dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	565922	566630	418	441	45844	107523	671	4353	19828	19994	100	137	631594	694147	1189	4931	False		
+merge_cols	mergeCols1	Merge columns together.								To update		Text Manipulation	merge_cols	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols	https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols	1.0.3	python				1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	20905	31051	1906	2128	21780	132833	885	3172	1524	1925	122	152	44209	165809	2913	5452	False		
+mergeneighboursinlabelimage	ip_merge_neighbours_in_label	Merge Neighbours in Label Image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	mergeneighboursinlabelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/\mergeneighboursinlabelimage	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mergeneighboursinlabelimage	0.3-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	18	25	2	3	0	0	0	0	0	0	0	0	18	25	2	3	False		
+merlin	merlin	Pedigree Analysis package	merlin	merlin		Merlin	Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation	Haplotype mapping, Genetic mapping	GWAS study, Mapping	Up-to-date	http://csg.sph.umich.edu/abecasis/Merlin/	Variant Analysis	merlin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin	1.1.2	merlin	1.1.2	Haplotype mapping	GWAS study, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3150	3150	477	477	730	730	196	196	1183	1183	151	151	5063	5063	824	824	False		
+meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+meta_proteome_analyzer	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	126	126	20	20	0	0	0	0	0	0	0	0	126	126	20	20	False		
+metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	0	2	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	6135	6135	382	382	881	881	151	151	1094	1094	104	104	8110	8110	637	637	False		
+metabuli	metabuli_classify	Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences	metabuli	metabuli		metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid	Taxonomic classification	Taxonomy	To update	https://github.com/steineggerlab/Metabuli	Sequence Analysis, Metagenomics	metabuli	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli	1.0.5	metabuli	1.0.8	Taxonomic classification	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metaeuk	metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	7.bba0d80	metaeuk	6.a5d39d9	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	312	312	40	40	0	0	0	0	0	0	0	0	312	312	40	40	False		
+metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	980	980	323	323	0	0	0	0	0	0	0	0	980	980	323	323	False		
+metagenomeseq	metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	556	756	17	21	310	514	35	55	0	0	0	0	866	1270	52	76	False		
+metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4471	4471	29	29	0	0	0	0	0	0	0	0	4471	4471	29	29	False		
+metaphlan	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	Up-to-date	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	0	1	2	4	0	0	0	0	0	0	0	0	0	0	2	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	16629	16648	1183	1187	3983	3983	572	572	4747	4747	278	278	25359	25378	2033	2037	False		
+metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	2730	2831	260	262	0	0	0	0	1540	1540	71	71	4270	4371	331	333	False		
+metawrapmg	metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	142	142	32	32	0	0	0	0	379	379	47	47	521	521	79	79	False		
+metfrag	metfrag	[Metabolomics][LC-MS][MS/MS] MetFrag - Perform metfrag analysis (can work with the output from msPurity)								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag	2.4.5+galaxy3	metfrag	2.4.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	192	192	20	20	0	0	0	0	0	0	0	0	192	192	20	20	False		
+metfrag-vis	metfrag_vis	[Metabolomics][LC-MS][MS/MS] This tool summarises the results generated by MetFrag								To update	https://github.com/computational-metabolomics/metfrag-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/metfrag-galaxy	https://github.com/computational-metabolomics/metfrag-galaxy/tree/master/tools/metfrag-vis	2.4.5+galaxy0	metfrag	2.4.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	50	50	14	14	0	0	0	0	0	0	0	0	50	50	14	14	False		
+methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	632	5461	155	453	0	0	0	0	0	0	0	0	632	5461	155	453	False		
+methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	14907	18971	638	894	2677	2677	230	230	2313	2313	83	83	19897	23961	951	1207	False		
+methylkit	methylkit	A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.								To update	http://bioconductor.org/packages/release/bioc/html/methylKit.html	Epigenetics	methylkit	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	0.99.2	bioconductor-methylkit	1.28.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3209	4572	312	442	479	479	79	79	315	315	51	51	4003	5366	442	572	False		
+mfassignr	mfassignr_findRecalSeries, mfassignr_histnoise, mfassignr_isofiltr, mfassignr_kmdnoise, mfassignr_mfassign, mfassignr_mfassignCHO, mfassignr_recal, mfassignr_recallist, mfassignr_snplot	The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements	mfassignr	mfassignr		MFAssignR	Molecular formula assignment software for ultrahigh resolution mass spectrometry analysis of environmental complex mixtures.Ultrahigh resolution mass spectrometry is widely used for nontargeted analysis of complex environmental and biological mixtures, such as dissolved organic matter, due to its unparalleled ability to provide accurate mass measurements.	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	Up-to-date	https://github.com/RECETOX/MFAssignR	Metabolomics	MFAssignR	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr	1.1.1	r-mfassignr	1.1.1	Visualisation	Proteomics experiment, Molecular interactions, pathways and networks, Workflows	0	0	9	0	0	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	8	8	0	0	0	0	0	0	0	0	10	10	8	8	False		
+mg_toolkit	mg_toolkit_bulk_download, mg_toolkit_original_metadata	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	mg-toolkit	mg-toolkit		mg-toolkit	Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.	Data retrieval	Metagenomics	Up-to-date	https://github.com/EBI-Metagenomics/emg-toolkit	Metagenomics	mg_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit	0.10.4	mg-toolkit	0.10.4	Data retrieval	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+mgf_formatter	mgf_formatter									Up-to-date			mgf_formatter	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mgf_formatter	1.0.0	mgf-formatter	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	573	573	3	3	0	0	0	0	0	0	0	0	573	573	3	3	False		
+miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+microsatbed	microsatbed	Select microsatellites for a bed file								To update	https://github.com/lmdu/pytrf	Sequence Analysis	microsatbed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed	https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed	1.3.3	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228	228	4	4	18	18	1	1	0	0	0	0	246	246	5	5	False		
+microsatellite_birthdeath	microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+microsats_alignment_level	microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	135	973	50	140	0	0	0	0	135	973	50	140	False		
+microsats_mutability	microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	34	312	22	87	0	0	0	0	34	312	22	87	False		
+migmap	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	Sequence analysis, Read mapping	Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1082	1229	25	33	1153	1376	70	89	0	0	0	0	2235	2605	95	122	False		
+minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1213	1309	115	124	0	0	0	0	0	0	0	0	1213	1309	115	124	False		
+mine	maximal_information_based_nonparametric_exploration	Maximal Information-based Nonparametric Exploration								To update		Variant Analysis	mine	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine	0.0.1	MINE				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9	11	8	8	17	63	6	19	0	0	0	0	26	74	14	27	False		
+minia	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7116	7116	256	256	0	0	0	0	278	278	60	60	7394	7394	316	316	False		
+miniasm	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	De-novo assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	13357	13479	554	562	8416	8416	448	448	898	898	85	85	22671	22793	1087	1095	False		
+minimap2	minimap2	A fast pairwise aligner for genomic and spliced nucleotide sequences	minimap2	minimap2		Minimap2	Pairwise aligner for genomic and spliced nucleotide sequences	Pairwise sequence alignment	Mapping	Up-to-date	https://github.com/lh3/minimap2	Next Gen Mappers	minimap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2	2.28	minimap2	2.28	Pairwise sequence alignment	Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	346530	349075	4323	4419	108535	108535	4075	4075	22331	22331	1166	1166	477396	479941	9564	9660	False		
+minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	229	229	32	32	0	0	0	0	0	0	0	0	229	229	32	32	False		
+miniprot	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1244	1244	86	86	24	24	15	15	0	0	0	0	1268	1268	101	101	False		
+miranda	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6408	6514	94	99	0	0	0	0	0	0	0	0	6408	6514	94	99	False		
+miranda2asko	miranda2asko	Converts miRanda output into AskOmics format								To update		Convert Formats	miranda2asko	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	https://github.com/genouest/galaxy-tools/tree/master/tools/miranda2asko	0.2	perl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mircounts	mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar				0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1458	1458	36	36	1458	1458	36	36	False		
+mirmachine	mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	0	0	0	0	0	0	0	2	2	2	2	False		
+mirnature	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	18	18	9	9	0	0	0	0	0	0	0	0	18	18	9	9	False		
+misc	target_screen, use_theoretical_mz_annotations									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	https://github.com/RECETOX/galaxytools/tree/master/tools/misc	1.0.0	pandas				0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	2	2	0	0	0	0	0	0	0	0	6	6	2	2	False		
+mitobim	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1117	1117	116	116	0	0	0	0	295	295	25	25	1412	1412	141	141	False		
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1020	1020	176	176	414	414	73	73	277	277	20	20	1711	1711	269	269	False		
+mitos	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	0	191295	191295	1111	1111	42265	42265	320	320	10904	10904	83	83	244464	244464	1514	1514	False		
+mixmodel4repeated_measures	mixmodel4repeated_measures	[Metabolomics][W4M][Statistics] Mixed models - Analysis of variance for repeated measures using mixed model								To update	http://workflow4metabolomics.org	Metabolomics	mixmodel4repeated_measures	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mixmodel4repeated_measures	3.1.0	r-lme4				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	13300	13471	1480	1501	6532	6532	1167	1167	10334	11841	1083	1300	30166	31844	3730	3968	False		
+moFF	proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	331	762	20	34	0	0	0	0	137	137	4	4	468	899	24	38	False		
+moabs	moabs	MOABS for differential methylation analysis on Bisulfite sequencing data.								To update	https://github.com/sunnyisgalaxy/moabs	Epigenetics	moabs	iuc	https://github.com/sunnyisgalaxy/moabs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs	1.3.4.6	moabs	1.3.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	339	339	56	56	0	0	0	0	0	0	0	0	339	339	56	56	False		
+mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	119024	119024	628	628	42	42	2	2	36310	36310	191	191	155376	155376	821	821	False		
+molecule2gspan	bg_mol2gspan	converter								To update	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	Convert Formats	molecule_to_gspan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	0.2	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+monocle3	monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9			9	0	9	0	9	0	9	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3610	3610	559	559	1728	1728	434	434	0	0	0	0	5338	5338	993	993	False		
+morpheus	morpheus	Morpheus MS Search Application	morpheus	morpheus		Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.	Peptide database search	Proteomics	To update	https://cwenger.github.io/Morpheus	Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	288	morpheus	290	Peptide database search	Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	105	153	12	19	0	0	0	0	833	833	93	93	938	986	105	112	False		
+morphological_operations	morphological_operations	Apply morphological operations to images			scipy					To update	https://github.com/bmcv	Imaging	morphological_operations	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/morphological_operations	1.12.0	scipy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mosdepth	mosdepth	fast and flexible BAM/CRAM depth calculation								Up-to-date	https://github.com/brentp/mosdepth	SAM	mosdepth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mosdepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth	0.3.8	mosdepth	0.3.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1278	1278	87	87	168	168	24	24	102	102	5	5	1548	1548	116	116	False		
+mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	0	129	129	129	0	0	0	0	0	0	0	0	0	0	128	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	126	129	129	0	297546	326056	37506	41763	565218	682083	72163	89926	167400	182490	26963	28404	1030164	1190629	136632	160093	False		
+motus	mereg_mOTUs_tables, motus_profiler	Tool for profiling the abundance of microbial taxa.	mOTUs	mOTUs		Metagenomic operational taxonomic units (mOTUs)	Metagenomic operational taxonomic units (mOTUs) enable high-accuracy taxonomic profiling of known (sequenced) and unknown microorganisms at species-level resolution from shotgun metagenomic or metatranscriptomic data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to quantify their abundances in meta-omics data with very high precision and recall.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/motu-tool/mOTUs	Metagenomics	motus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs	https://github.com/bgruening/galaxytools/tree/master/tools/motus	3.1.0	motus	3.1.0	Taxonomic classification	Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	71	76	9	9	0	0	0	0	0	0	0	0	71	76	9	9	False		
+mqppep	mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	13	13	3	3	0	0	0	0	0	0	0	0	13	13	3	3	False		
+mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ms2deepscore	ms2deepscore_config_generator, ms2deepscore_similarity, ms2deepscore_training	Mass spectra similarity scoring using a trained ms2deepscore model.	ms2deepscore	ms2deepscore		MS2DeepScore	MS2DeepScore is a deep learning similarity measure for mass fragmentation spectrum comparisons. MS2DeepScore provides a Siamese neural network that is trained to predict molecular structural similarities (Tanimoto scores) from pairs of mass spectrometry spectra.	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	To update	https://github.com/matchms/ms2deepscore	Metabolomics	ms2deepscore	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	https://github.com/RECETOX/galaxytools/tree/master/tools/ms2deepscore	2.0.0	ms2deepscore	2.1.0	Spectrum calculation, Spectral library search, Network analysis	Proteomics experiment, Machine learning, Metabolomics, Small molecules, Compound libraries and screening	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ms2snoop	ms2snoop	[W4M][Utils] Extraction et nettoyage des spectre MS1/2 post-traitement MSPurity.								To update	http://workflow4metabolomics.org	Metabolomics	ms2snoop	workflow4metabolomics		https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/ms2snoop	2.2.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+msPurity	mspurity_averagefragspectra, mspurity_combineannotations, mspurity_createdatabase, mspurity_createmsp, mspurity_dimspredictpuritysingle, mspurity_filterfragspectra, mspurity_flagremove, mspurity_frag4feature, mspurity_puritya, mspurity_purityx, mspurity_spectralmatching	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								Up-to-date	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		computational-metabolomics	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/msPurity	1.28.0	bioconductor-mspurity	1.28.0			0	0	10	0	0	0	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	848	848	91	91	0	0	0	0	0	0	0	0	848	848	91	91	False		
+msaboot	msaboot	A multiple sequences alignment bootstrapping tool.								Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot	0.1.2	msaboot	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	864	929	91	101	1100	1100	175	175	0	0	0	0	1964	2029	266	276	False		
+msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20749	22184	455	469	1239	1239	71	71	2666	2666	53	53	24654	26089	579	593	False		
+msgfplus	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	473	529	33	43	0	0	0	0	0	0	0	0	473	529	33	43	False		
+msmetaenhancer	msmetaenhancer		msmetaenhancer	msmetaenhancer		MSMetaEnhancer	Tool for mass spectra metadata annotation.	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/MSMetaEnhancer	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer	0.4.0	msmetaenhancer	0.4.0	Annotation, Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	10	10	0	0	0	0	48	48	1	1	251	251	11	11	False		
+msms_extractor	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	110	110	11	11	0	0	0	0	0	0	0	0	110	110	11	11	False		
+msp_merge	msp_merge									To update	https://github.com/RECETOX/galaxytools	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge	0.1.0	matchms	0.27.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+msp_split	msp_split	[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data								To update	https://github.com/computational-metabolomics/mspurity-galaxy	Metabolomics		tomnl	https://github.com/computational-metabolomics/mspurity-galaxy	https://github.com/computational-metabolomics/mspurity-galaxy/tree/master/tools/utils/msp_split	0.0.2					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+msstats	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2353	2353	559	559	1122	1122	211	211	1091	1091	35	35	4566	4566	805	805	False		
+msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	795	795	104	104	0	0	0	0	461	461	12	12	1256	1256	116	116	False		
+mt2mq	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	275	275	38	38	0	0	0	0	0	0	0	0	275	275	38	38	False		
+multigps	multigps	Analyzes collections of multi-condition ChIP-seq data.								To update	http://mahonylab.org/software/multigps/	ChIP-seq	multigps	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigps	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps	0.74.0	fonts-conda-ecosystem				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	485	871	159	298	0	0	0	0	485	871	159	298	False		
+multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	106	106	25	25	0	0	0	0	0	0	0	0	106	106	25	25	False		
+multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25.1	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	1	1	1	1	0	182221	192389	19343	20494	163961	182413	26449	29758	40663	41855	5974	6157	386845	416657	51766	56409	False		
+multispecies_orthologous_microsats	multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mummer	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	883	921	199	211	730	730	199	199	136	202	34	49	1749	1853	432	459	False		
+mummer4	mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1			6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	6	3	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	21587	22119	1940	2033	29284	29284	3626	3626	8194	8194	545	545	59065	59597	6111	6204	False		
+music_deconvolution	music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)								Up-to-date	https://github.com/xuranw/MuSiC	Transcriptomics	music	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/	https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution	0.1.1	music-deconvolution	0.1.1			5	5	4	0	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	2801	2801	289	289	364	364	80	80	1357	1357	21	21	4522	4522	390	390	False		
+mutate_snp_codon	mutate_snp_codon_1	Mutate Codons with SNPs								To update		Variant Analysis	mutate_snp_codon	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	44	49	5	5	81	417	23	118	0	0	0	0	125	466	28	123	False		
+mutational_patterns	mutational_patterns	Mutational patterns and signatures in base substitution catalogs								Up-to-date	http://artbio.fr	Variant Analysis	mutational_patterns	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	3.12.0	bioconductor-mutationalpatterns	3.12.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	854	860	110	111	79	79	15	15	274	274	13	13	1207	1213	138	139	False		
+mzmine	mzmine_batch	mass-spectrometry data processing, with the main focus on LC-MS data	mzmine	mzmine		MZmine	Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	Up-to-date	http://mzmine.github.io/	Metabolomics	mzmine_batch	iuc	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine	3.9.0	mzmine	3.9.0	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	9	9	5	5	0	0	0	0	0	0	0	0	9	9	5	5	False		
+mzml_validator	mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+mzxmlshaper	mzxmlshaper	Convert mzML, mzXML or netCDF files to mzML or mzXML								To update	https://rdrr.io/bioc/mzR/	Metabolomics	mzxmlshaper	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/mzxmlshaper	1.0.0+galaxy0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+naltorfs	bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2			3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	204	204	75	75	0	0	0	0	204	204	75	75	False		
+nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	839	839	12	12	0	0	0	0	269	269	5	5	1108	1108	17	17	False		
+nanoplot	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	99052	100009	5671	5755	40386	40386	3371	3371	17919	17919	2188	2188	157357	158314	11230	11314	False		
+nanopolish	nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants	Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.								Up-to-date	https://github.com/jts/nanopolish		nanopolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	0.14.0	nanopolish	0.14.0			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	9284	9694	215	229	0	0	0	0	2358	2358	49	49	11642	12052	264	278	False		
+nanopolishcomp	nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	1091	1091	44	44	0	0	0	0	0	0	0	0	1091	1091	44	44	False		
+nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	40	1	1	0	0	0	0	0	0	0	0	36	40	1	1	False		
+ncbi_acc_download	ncbi_acc_download	Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API								Up-to-date	https://github.com/kblin/ncbi-acc-download	Data Source	ncbi_acc_download	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download	0.2.8	ncbi-acc-download	0.2.8			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6873	6873	1664	1664	17651	17651	4513	4513	6228	6228	972	972	30752	30752	7149	7149	False		
+ncbi_blast_plus	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python				16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	16	15	16	0	0	0	0	0	0	16	0	0	0	0	16	15	16	16	15	0	391141	443752	9760	10546	306361	350178	11767	13684	227235	244814	3192	3617	924737	1038744	24719	27847	False		
+ncbi_datasets	datasets_download_gene, datasets_download_genome	NCBI datasets downloads biological sequence data across all domains of life from NCBI.	ncbi_datasets	ncbi_datasets		NCBI Datasets	NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.	Data handling, Sequence database search, Data retrieval	Biological databases	To update	https://github.com/ncbi/datasets	Data Source	ncbi_datasets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets	16.20.0	ncbi-datasets-cli		Data handling, Sequence database search, Data retrieval	Biological databases	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	1	2	2	0	4417	4417	1024	1024	6940	6940	2275	2275	1	1	1	1	11358	11358	3300	3300	False		
+ncbi_egapx	ncbi_egapx	Eukaryotic Genome Annotation Pipeline - External (EGAPx)								To update	https://github.com/ncbi/egapx	Genome annotation	ncbi_egapx	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx	0.2-alpha					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	6	6	0	0	0	0	15	15	6	6	False		
+ncbi_entrez_direct	ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch	NCBI Entrez Direct allow fetching data from NCBI Databases								Up-to-date	http://www.ncbi.nlm.nih.gov/books/NBK179288/	Data Source	ncbi_entrez_direct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct	22.4	entrez-direct	22.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	2	0	0	0	0	0	3	0	2	False		
+ncbi_entrez_eutils	ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary	NCBI Entrez E-Utilties allow fetching data from NCBI Databases								To update	https://www.ncbi.nlm.nih.gov/books/NBK25501/	Data Source	ncbi_entrez_eutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils	1.70	python				0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	4	0	0	0	2	0	0	0	0	0	0	0	7	7	0	2794	3191	533	664	0	0	0	0	0	0	0	0	2794	3191	533	664	False		
+ncbi_fcs_adaptor	ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0					1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	842	842	93	93	0	0	0	0	842	842	93	93	False		
+ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs		NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	125	125	26	26	2489	2489	139	139	0	0	0	0	2614	2614	165	165	False		
+necat	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	De-novo assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	790	790	160	160	0	0	0	0	0	0	0	0	790	790	160	160	False		
+netboxr	netboxr	netboxr enables automated discovery of biological process modules by network analysis								To update		Systems Biology	netboxr	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/netboxr	1.6.0	bioconductor-netboxr	1.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	12	12	6	6	0	0	0	0	0	0	0	0	12	12	6	6	False		
+newick_utils	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6		Phylogeny, Genomics, Computer science	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	33637	34195	1113	1172	16257	16257	1816	1816	7582	7582	899	899	57476	58034	3828	3887	False		
+nextclade	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	0	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1	0	0	0	1	0	0	0	0	0	0	0	2	0	0	4411	4411	396	396	9708	9708	279	279	2099	2099	212	212	16218	16218	887	887	False		
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	391	391	158	158	0	0	0	0	0	0	0	0	391	391	158	158	False		
+ngmlr	ngmlr	CoNvex Gap-cost alignMents for Long Reads	ngmlr	ngmlr		NGMLR	An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping, DNA structural variation	Up-to-date	https://github.com/philres/ngmlr	Next Gen Mappers	ngmlr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr	0.2.7	ngmlr	0.2.7	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1403	1403	49	49	0	0	0	0	0	0	0	0	1403	1403	49	49	False		
+ngsutils	ngsutils_bam_filter	NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.	ngsutils	ngsutils		NGSUtils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets	Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering	Genomics, Transcriptomics	To update	https://github.com/ngsutils/ngsutils	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils		ngsutils	0.5.9	Read pre-processing, Variant calling, Formatting, Sequence contamination filtering	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	24611	29662	633	716	15523	21395	740	1128	7751	8972	125	145	47885	60029	1498	1989	False		
+nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+nmr_annotation	NmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation - Annotation of complex mixture NMR spectra and metabolite proportion estimation								To update	http://workflow4metabolomics.org	Metabolomics	nmr_annotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_annotation	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation	3.0.0	r-batch	1.1_4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	49	49	5	5	0	0	0	0	0	0	0	0	49	49	5	5	False		
+nmr_annotation2d	2DNmrAnnotation	[Metabolomics][W4M][NMR] NMR Annotation2D - Automatic annotation of bi-dimensional NMR spectra								To update	http://workflow4metabolomics.org	Metabolomics	2dnmrannotation	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_annotation2d	2.0.0	r-batch	1.1_4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+nmr_preprocessing	NMR_Preprocessing, NMR_Read	[Metabolomics][W4M][NMR] NMR Preprocessing - Preprocessing of 1D NMR spectra from FID to baseline correction								To update	http://workflow4metabolomics.org	Metabolomics	nmr_preprocessing	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/nmr_preprocessing	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/nmr_preprocessing		r-batch	1.1_4			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	142	142	8	8	0	0	0	0	335	341	9	9	477	483	17	17	False		
+nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	107	143	13	15	148	148	20	20	0	0	0	0	255	291	33	35	False		
+normalization	normalization	[Metabolomics][W4M][ALL] Normalization (operation applied on each individual spectrum) of preprocessed data								To update	http://workflow4metabolomics.org	Metabolomics	normalization	marie-tremblay-metatoul	https://github.com/workflow4metabolomics/normalization	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/normalization	1.0.7	r-batch	1.1_4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	152	162	39	40	0	0	0	0	233	236	12	12	385	398	51	52	False		
+novoplasty	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	7780	7780	337	337	1	1	1	1	2323	2323	99	99	10104	10104	437	437	False		
+nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	118	863	19	26	0	0	0	0	0	0	0	0	118	863	19	26	False		
+nugen_nudup	nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+numeric_clustering	numeric_clustering	Clustering tool for numberic values								To update	http://scikit-learn.org/stable/index.html	Statistics	numeric_clustering	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	0.9	anaconda				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	391	486	5	11	0	0	0	0	0	0	0	0	391	486	5	11	False		
+oases	oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+obisindicators	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base				1	0	2	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	352	352	42	42	8	8	6	6	0	0	0	0	360	360	48	48	False		
+obitools	obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	0	0	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	10	0	37598	37598	1277	1277	0	0	0	0	3862	3862	280	280	41460	41460	1557	1557	False		
+ocean	argo_getdata, divand_full_analysis	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15	julia				0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	54	54	6	6	0	0	0	0	0	0	0	0	54	54	6	6	False		
+ococo	ococo	Variant detection of SNVs								To update	https://github.com/karel-brinda/ococo	Variant Analysis	ococo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo	0.1.2.6	ococo	0.1.2.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1850	1963	79	93	1370	1370	194	194	0	0	0	0	3220	3333	273	287	False		
+odgi	odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	26	26	6	6	0	0	0	0	0	0	0	0	26	26	6	6	False		
+ogcProcess_otb_bandmath	otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	98	6	6	0	0	0	0	0	0	0	0	98	98	6	6	False		
+ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	57	57	4	4	0	0	0	0	0	0	0	0	57	57	4	4	False		
+omark	omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	158	158	12	12	0	0	0	0	0	0	0	0	158	158	12	12	False		
+omero	omero_import, omero_metadata_import, omero_roi_import	Import images, region of interest, metadata into an OMERO.server using omero-py	omero	omero		OMERO	Client-server Java software for visualisation, management and analysis of biological microscope images.	Image analysis	Imaging, Data visualisation	To update	https://github.com/ome/omero-py/	Imaging	omero_upload	ufz	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero	5.18.0	omero-py	5.11.1	Image analysis	Imaging, Data visualisation	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_clean_rois_tables	omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down								To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_children_ids	omero_get_children_ids	Get omero id of children of an omero object id								To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.2.0	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_get_full_images	omero_get_full_images	Get full images from omero								To update		Imaging	omero_get_full_images	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_full_images	20240521	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_fluo_measurements_on_gastruloid	omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels								To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+omero_hyperstack_to_gastruloid_measurements	omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements								To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20240614			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ont_fast5_api	ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	0	3051	3051	87	87	0	0	0	0	0	0	0	0	3051	3051	87	87	False		
+onto_toolkit	onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def	ONTO-Toolkit is a collection of tools for managing ontologies.								Up-to-date	http://search.cpan.org/~easr/ONTO-PERL-1.45/	Ontology Manipulation	onto_toolkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/onto-toolkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit	1.45	perl-onto-perl	1.45			0	0	17	0	0	0	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	0	582	663	68	69	0	0	0	0	0	0	0	0	582	663	68	69	False		
+openlabcds2csv	openlabcds2csv	"Creates a summary of several ""Internal Standard Report"" OpenLabCDS results."								To update		Metabolomics	openlabcds2csv	genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/openlabcds2csv	0.1.0	openjdk				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+openmm	pdbfixer	OpenMM is a toolkit for molecular simulation using high performance GPU code.								To update	https://github.com/openmm	Molecular Dynamics, Computational chemistry	openmm	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm	1.8.1	pdbfixer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	491	491	52	52	0	0	0	0	0	0	0	0	491	491	52	52	False		
+openms	AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, ConsensusID, ConsensusMapNormalizer, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, JSONExporter, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSstatsConverter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OpenMSDatabasesInfo, OpenMSInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, SageAdapter, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	3.1	openms	3.2.0			8	34	144	0	8	34	144	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	141	124	0	32169	108654	3316	4889	50	50	15	15	940	940	245	245	33159	109644	3576	5149	False		
+openms	AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.2.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	135	134	0	31121	108907	3369	5029	50	50	15	15	933	933	242	242	32104	109890	3626	5286	False		
+optdoe	optdoe	Optimal Design Of Experiment								To update	https://github.com/pablocarb/doebase	Synthetic Biology	optdoe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optdoe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe	v2.0.2	doebase				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+optitype	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	500	500	45	45	0	0	0	0	0	0	0	0	500	500	45	45	False		
+orfipy	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	897	897	99	99	1792	1792	239	239	0	0	0	0	2689	2689	338	338	False		
+orientationpy	orientationpy	Compute image orientation			orientationj					Up-to-date	https://github.com/bmcv	Imaging	orientationpy	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy	0.2.0.4	orientationpy	0.2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+orthofinder	orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	To update	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	3.0.1b1	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	2018	2018	419	419	0	0	0	0	438	438	58	58	2456	2456	477	477	False		
+overlay_images	ip_overlay_images	Overlay two images	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	overlay_images	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images	0.0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	149	149	31	31	0	0	0	0	18	18	1	1	167	167	32	32	False		
+packaged_annotation_loader	packaged_annotation_loader	Tool to make cached genome annotation data available as a list of datasets collection								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	Data Source	packaged_annotation_loader	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader	https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+packmol	packmol	PACKMOL is a package for creating starting structures for Molecular Dynamics simulations								To update	http://m3g.iqm.unicamp.br/packmol/home.shtml	Molecular Dynamics, Computational chemistry	packmol	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/packmol	18.169.1	packmol				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	282	295	32	33	420	420	8	8	0	0	0	0	702	715	40	41	False		
+pacu	pacu_map, pacu_snp	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.	pacu	pacu		PACU	PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads).	Clustering	Phylogenetics, Sequence analysis	Up-to-date	https://github.com/BioinformaticsPlatformWIV-ISP/PACU	Sequence Analysis, Phylogenetics	pacu	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu	0.0.5	pacu_snp	0.0.5	Clustering	Phylogenetics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pairtools	pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0			5	0	5	0	5	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	196	196	16	16	19	19	14	14	0	0	0	0	215	215	30	30	False		
+pandas_rolling_window	pandas_rolling_window	Rolling window calculations								To update	https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html	Statistics	pandas_rolling_window	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	0.1	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	261	275	12	12	63	63	22	22	0	0	0	0	324	338	34	34	False		
+pangolin	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	0	0	7457	7457	508	508	8518	8518	377	377	2760	2760	259	259	18735	18735	1144	1144	False		
+pangolin	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	Tree-based sequence alignment, Variant classification	Virology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	0	0	7457	7457	508	508	8518	8518	377	377	2760	2760	259	259	18735	18735	1144	1144	False		
+paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	322	349	24	29	0	0	0	0	0	0	0	0	322	349	24	29	False		
+parse_mito_blast	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	65	65	288	288	62	62	110	110	20	20	601	601	147	147	False		
+partialr_square	partialRsq	Compute partial R square								To update		Statistics	partialr_square	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square	https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	55	142	8	42	0	0	0	0	55	142	8	42	False		
+pathifier	pathifier	pathifier								Up-to-date	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	1.40.0	bioconductor-pathifier	1.40.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	245	245	10	10	0	0	0	0	0	0	0	0	245	245	10	10	False		
+pathview	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6204	6211	1261	1261	6667	6667	1143	1143	1160	1160	189	189	14031	14038	2593	2593	False		
+pathwaymatcher	reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	174	244	65	76	0	0	0	0	0	0	0	0	174	244	65	76	False		
+patrist	patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pbgcpp	pbgcpp	Compute genomic consensus and call variants using PacBio reads mapped to a reference	genomicconsensus	genomicconsensus		GenomicConsensus	The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.	Variant calling	Mapping	Up-to-date	https://github.com/PacificBiosciences/gcpp	Variant Analysis	pbgcpp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbgcpp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp	2.0.2	pbgcpp	2.0.2	Variant calling	Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pbmm2	pbmm2	A minimap2 SMRT wrapper for PacBio data.	pbmm2	pbmm2		pbmm2	pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.	Pairwise sequence alignment, Sorting	Mapping	Up-to-date	https://github.com/PacificBiosciences/pbmm2	Next Gen Mappers	pbmm2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbmm2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2	1.14.99	pbmm2	1.14.99	Pairwise sequence alignment, Sorting	Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	70	70	17	17	0	0	0	0	0	0	0	0	70	70	17	17	False		
+pbtk	bam2fastx	Convert PacBio Bam File to fasta or fastq file								Up-to-date	https://github.com/PacificBiosciences/pbtk	Convert Formats, Fasta Manipulation, Fastq Manipulation	bam2fastx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk	3.1.1	pbtk	3.1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	58	58	22	22	109	109	19	19	0	0	0	0	167	167	41	41	False		
+pe_histogram	pe_histogram	Contains a tool that produces an insert size histogram for a paired-end BAM file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram	Graphics	pe_histogram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pe_histogram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram	1.0.2	openjdk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	5505	5505	510	510	7932	8582	811	909	736	736	119	119	14173	14823	1440	1538	False		
+peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2807	3337	178	196	0	0	0	0	0	0	0	0	2807	3337	178	196	False		
+peakzilla	peakzilla	Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments.								To update	https://github.com/steinmann/peakzilla	ChIP-seq	peakzilla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/peakzilla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla	1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	9	9	0	0	0	0	0	0	0	0	18	18	9	9	False		
+pear	iuc_pear	PEAR evaluates all possible paired-end read overlaps	pear	pear		PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.	Sequence merging	Sequence assembly	Up-to-date	https://cme.h-its.org/exelixis/web/software/pear/	Fastq Manipulation	pear	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear	0.9.6	pear	0.9.6	Sequence merging	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	6269	6866	260	292	5530	20068	467	1664	5647	8471	198	300	17446	35405	925	2256	False		
+pearson_correlation	Pearson_and_apos_Correlation1	Pearson and apos Correlation between any two numeric columns								To update		Statistics	pearson_correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	2	0	2	False		
+pep_pointer	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	506	511	54	55	21	21	12	12	163	163	8	8	690	695	74	75	False		
+pepquery	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	7047	7047	76	76	0	0	0	0	0	0	0	0	7047	7047	76	76	False		
+pepquery2	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2			0	1	3	0	0	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	1222	1222	28	28	0	0	0	0	0	0	0	0	1222	1222	28	28	False		
+peptide_genomic_coordinate	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	472	472	56	56	16	16	10	10	149	149	5	5	637	637	71	71	False		
+peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.11			4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	2	0	11986	17898	1046	1153	1314	1314	389	389	3034	3034	118	118	16334	22246	1553	1660	False		
+peptimapper	peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pepxml_to_xls		Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+percolator	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.7.1			0	4	4	0	0	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	338	378	15	16	0	0	0	0	1059	1059	13	13	1397	1437	28	29	False		
+perf	stats_perf_tool	suitable for boolean classification problems								To update	http://osmot.cs.cornell.edu/kddcup/software.html		stats_perf_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/perf	https://github.com/bgruening/galaxytools/tree/master/tools/perf	5.11.0	perf				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+permutate_axis	ip_permutate_axis	Permutates axes	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	permutate_axis	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/permutate_axis	0.2-2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	36	42	1	2	0	0	0	0	0	0	0	0	36	42	1	2	False		
+pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	773	773	60	60	495	495	72	72	246	246	17	17	1514	1514	149	149	False		
+pg_tools	pg_dump, pg_import, pg_query	tool suite for dealing with Postgresql databases from Galaxy's history								To update	https://www.postgresql.org	Data Export, Data Source	pgtools	bgruening	https://github.com/bgruening/galaxytools/tools/pgtools	https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools		postgresql				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pgsnp2gd_snp	pgSnp2gd_snp	Convert from pgSnp to gd_snp								To update		Variant Analysis	pgsnp2gd_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pharmcat	pharmcat	Pharmacogenomics Clinical Annotation Tool								To update	https://pharmcat.org/	Variant Analysis	pharmcat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat						1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	109	109	29	29	250	250	84	84	0	0	0	0	359	359	113	113	False		
+pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
+                pharokka
+            "		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	5462	5462	334	334	0	0	0	0	309	309	52	52	5771	5771	386	386	False		
+phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	0	0	1	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	1199	1199	193	193	0	0	0	0	6	6	1	1	1205	1205	194	194	False		
+phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1975	2034	246	258	0	0	0	0	553	564	140	144	2528	2598	386	402	False		
+physiofit	physiofit	PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake & production fluxes								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit	workflow4metabolomics	https://github.com/MetaSys-LISBP/PhysioFit	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit	3.4.0	physiofit	3.4.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+physiofit_manager	physiofit_data_manager	Handling of physiofit input files								Up-to-date	physiofit.readthedocs.io	Metabolomics	physiofit_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/PhysioFit_Data_Manager	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/physiofit_manager	1.0.1	physiofit_data_manager	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pi_db_tools	calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+picard	picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile	Picard SAM/BAM manipulation tools.	picard_samtofastq	picard_samtofastq, picard_replacesamheader, picard_fastqtosam, picard_reordersam		picard_samtofastq	Create a FASTQ file.	Formatting	Sequencing	To update	http://broadinstitute.github.io/picard/	SAM	picard	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard	3.1.1	picard	3.2.0	Formatting	Sequencing	31	31	31	0	31	31	31	0	0	0	0	0	0	0	0	0	0	31	4	31	0	0	31	0	0	0	31	0	0	0	0	0	0	31	31	31	0	386934	399039	11024	11956	366646	589980	32000	57111	56622	62258	2845	3398	810202	1051277	45869	72465	False		
+pick_value	pick_value	Compose a text parameter value using text, integer and float values								To update		Text Manipulation	pick_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	0.2.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1607	1607	41	41	490	490	53	53	127	127	4	4	2224	2224	98	98	False		
+picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	0	0	6	5	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	867	1128	144	165	0	0	0	0	2106	2106	121	121	2973	3234	265	286	False		
+picrust2	picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	2532	2532	382	382	1	1	1	1	1311	1311	83	83	3844	3844	466	466	False		
+pileup_interval	pileup_interval	Pileup-to-Interval condenses pileup format into ranges of bases								To update		SAM	pileup_interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval	1.0.3	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	613	640	48	54	1381	7804	201	1552	756	815	22	30	2750	9259	271	1636	False		
+pileup_parser	pileup_parser	Filter pileup on coverage and SNPs								To update	https://github.com/galaxyproject/tools-devteam/	SAM	pileup_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser	1.0.2	perl				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	3639	3774	414	461	9754	52522	1247	4531	1893	2433	191	318	15286	58729	1852	5310	False		
+pilon	pilon	pilon is a tool for assembly improvement and variant analysis in bacteria	pilon	pilon		pilon	Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.	Sequence assembly, Analysis, Read alignment	Assembly	To update	https://github.com/broadinstitute/pilon/wiki	Variant Analysis	pilon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon	1.20.1	pilon	1.24	Sequence assembly, Analysis	Assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9045	9458	1115	1144	7989	7989	1070	1070	3945	4137	726	741	20979	21584	2911	2955	False		
+pindel	pindel	Pindel detects genome-wide structural variation.								Up-to-date	http://artbio.fr	Variant Analysis	pindel	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel	https://github.com/ARTbio/tools-artbio/tree/main/tools/pindel	0.2.5b9	pindel	0.2.5b9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pipelign	pipelign	Multipe sequence alignment								Up-to-date	https://github.com/asmmhossain/pipelign/	Next Gen Mappers	pipelign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign	0.2	pipelign	0.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1245	1245	231	231	9046	9046	630	630	0	0	0	0	10291	10291	861	861	False		
+pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	238	283	42	45	0	0	0	0	0	0	0	0	238	283	42	45	False		
+piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1408	2068	94	119	0	0	0	0	0	0	0	0	1408	2068	94	119	False		
+pizzly	pizzly	Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples.								To update	https://github.com/pmelsted/pizzly/	Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly	0.37.3.1	pizzly	0.37.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	201	210	23	24	998	998	76	76	0	0	0	0	1199	1208	99	100	False		
+plantseg	plantseg	Tool for cell instance aware segmentation in densely packed 3D volumetric images	plantseg	plantseg		PlantSeg	Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution.PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. Pre-trained models are provided.	Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	To update	https://github.com/bmcv	Imaging	plantseg	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg	1.8.1	plant-seg		Network analysis, Quantification, Microscope image visualisation	Plant biology, Bioimaging, Light microscopy, Machine learning, Electron microscopy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plasflow	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37086	37272	711	734	6346	6346	583	583	3065	3065	61	61	46497	46683	1355	1378	False		
+plasmid_profiler	plasmid_profiler	Explores plasmid content in WGS data								To update			plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler	0.1.6	r				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plasmid_profiler_suite		Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plasmidfinder	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	14652	14652	251	251	0	0	0	0	101	101	18	18	14753	14753	269	269	False		
+plasmidspades	plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plink	plink	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	plink	plink		PLINK	Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	Genetic variation analysis	GWAS study	Up-to-date	https://www.cog-genomics.org/plink	Genome-Wide Association Study	plink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink	1.90b6.21	plink	1.90b6.21	Genetic variation analysis	GWAS study	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	851	851	127	127	249	249	43	43	0	0	0	0	1100	1100	170	170	False		
+plot_from_lda	plot_for_lda_output1	"Draw ROC plot on ""Perform LDA"" output"								To update		Graphics, Statistics	plot_from_lda	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda	https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda	1.0.1	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	65	77	19	25	153	886	38	343	142	155	8	10	360	1118	65	378	False		
+plotheatmap	plotheatmap	This tool can be used to plot heatmap of gene expression data. The genes are chosen based on p-value, FDR, log FC and log CPM from edgeR output.								To update		Computational chemistry	plotheatmap	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap	1.0	bioconductor-preprocesscore	1.64.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.4	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1342	1472	184	197	902	902	156	156	630	630	24	24	2874	3004	364	377	False		
+plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	408	664	91	122	627	627	118	118	605	605	26	26	1640	1896	235	266	False		
+plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	764	879	213	237	304	304	95	95	193	193	26	26	1261	1376	334	358	False		
+pmd_fdr	pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pneumocat	pneumocat	Pneumococcal Capsular Typing of illumina fastq reads								Up-to-date	https://github.com/phe-bioinformatics/PneumoCaT	Variant Analysis	pneumocat	nml	https://github.com/phe-bioinformatics/PneumoCaT	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pneumocat	1.2.1	pneumocat	1.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+points2labelimage	ip_points_to_label	Points to label image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	points2labelimage	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage	0.4	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	33	33	2	2	0	0	0	0	0	0	0	0	33	33	2	2	False		
+points_association_nn	ip_points_association_nn	Association of points in consecutive frames	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	points_association_nn	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn	0.0.3-2	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	4	4	0	0	0	0	0	0	0	0	29	29	4	4	False		
+poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	112	120	16	16	4	562	1	140	320	347	7	8	436	1029	24	164	False		
+polypolish	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	731	731	86	86	0	0	0	0	42	42	4	4	773	773	90	90	False		
+porechop	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads								To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop	https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop		porechop	0.2.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	262015	262852	2627	2711	83623	83623	1918	1918	52558	52558	1037	1037	398196	399033	5582	5666	False		
+poretools	poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	poretools		Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools	0.6.1a1	poretools	0.6.1a1	Nucleic acid sequence analysis	DNA, Sequencing	13	13	13	0	13	13	13	0	0	0	0	0	0	0	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	13	0	19942	20587	1055	1245	33619	40808	2183	2594	9261	9261	365	365	62822	70656	3603	4204	False		
+positions2snv_alignment	positions2snv_alignment	Generate alignment of SNVs from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+positions2snv_invariant_alignment	positions2snv_invariant_alignment	Generate alignment of SNVs and non-variant positions from SNVPhyl variant table.								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Variant Analysis	positions2snv_invariant_alignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/positions2snv_invariant_alignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+presto	presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	11	0	0	0	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	63244	65177	1392	1599	0	0	0	0	63244	65177	1392	1599	False		
+pretext	pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6			3	2	3	0	3	2	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	3463	3463	538	538	1853	1853	256	256	1097	1097	70	70	6413	6413	864	864	False		
+principal_component_analysis	pca1	Principal Component Analysis								To update		Statistics	principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis	1.0.2	rpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	9788	10032	207	244	3072	8054	607	1488	0	0	0	0	12860	18086	814	1732	False		
+prinseq	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10152	10626	253	281	10581	10581	1240	1240	0	0	0	0	20733	21207	1493	1521	False		
+probecoverage	probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+prodigal	prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	Genome annotation	Genomics, Sequence analysis	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1902	1902	167	167	0	0	0	0	0	0	0	0	1902	1902	167	167	False		
+progressivemauve	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update	http://darlinglab.org/mauve/user-guide/progressivemauve.html	Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2064	2173	678	695	2900	2900	1034	1034	0	0	0	0	4964	5073	1712	1729	False		
+projective_transformation	ip_projective_transformation	Projective transformation	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation	0.1.2	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40	86	4	6	0	0	0	0	0	0	0	0	40	86	4	6	False		
+projective_transformation_points	ip_projective_transformation_points	Projective transformation of ROIs defined by pixel (point) coordinates	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	projective_transformation_points	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points	0.1.1	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20858	21444	14	18	0	0	0	0	0	0	0	0	20858	21444	14	18	False		
+prokka	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	1	0	1	1	1	0	464359	476554	7475	7721	313285	331256	11243	12384	131211	141875	4358	4947	908855	949685	23076	25052	False		
+promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+prot-scriber	prot_scriber	Protein annotation of short human readable descriptions								Up-to-date	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.6	prot-scriber	0.1.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	10	10	7	7	0	0	0	0	0	0	0	0	10	10	7	7	False		
+protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	129	155	15	21	0	0	0	0	0	0	0	0	129	155	15	21	False		
+protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	11743	12752	1137	1278	2	2	1	1	0	0	0	0	11745	12754	1138	1279	False		
+protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	465	638	81	100	0	0	0	0	0	0	0	0	465	638	81	100	False		
+proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	3962	3962	501	501	0	0	0	0	0	0	0	0	3962	3962	501	501	False		
+proteinpilot	convert_windows_newlines, proteinpilot, proteinpilot_group_extractor, proteinpilot_tabular, proteinpilot_xml									To update			proteinpilot	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteinpilot	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+proteomiqon_joinquantpepionswithproteins	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	366	366	4	4	0	0	0	0	0	0	0	0	366	366	4	4	False		
+proteomiqon_labeledproteinquantification	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	8	8	0	0	0	0	0	0	0	0	16	16	8	8	False		
+proteomiqon_labelfreeproteinquantification	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	6	6	4	4	0	0	0	0	0	0	0	0	6	6	4	4	False		
+proteomiqon_mzmltomzlite	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	721	721	8	8	0	0	0	0	0	0	0	0	721	721	8	8	False		
+proteomiqon_peptidedb	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	96	96	12	12	0	0	0	0	0	0	0	0	96	96	12	12	False		
+proteomiqon_peptidespectrummatching	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	686	686	5	5	0	0	0	0	0	0	0	0	686	686	5	5	False		
+proteomiqon_proteininference	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	89	89	6	6	0	0	0	0	0	0	0	0	89	89	6	6	False		
+proteomiqon_psmbasedquantification	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	604	604	4	4	0	0	0	0	0	0	0	0	604	604	4	4	False		
+proteomiqon_psmstatistics	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	694	694	6	6	0	0	0	0	0	0	0	0	694	694	6	6	False		
+proteore_venn_diagram	proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	1	1	0	0	0	0	0	0	0	0	15	15	1	1	False		
+protxml_to_xls	protxml_to_xls									To update			protxml_to_xls	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/protxml_to_xls	0.1.0	trans_proteomic_pipeline				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pseudogenome	pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+psiclass	psiclass	PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.	psiclass	psiclass		PsiCLASS	Reference-based transcriptome assembler for single or multiple RNA-seq samples	Transcriptome assembly	Sequence assembly	Up-to-date	https://github.com/splicebox/PsiCLASS	Transcriptomics	psiclass	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass	https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass	1.0.3	psiclass	1.0.3	Transcriptome assembly	Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	24	24	5	5	0	0	0	0	0	0	0	0	24	24	5	5	False		
+psm2sam	PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+psm_eval	psm_eval									To update			psm_eval	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_eval	0.1.0	binaries_for_psm_eval				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+psm_validation	psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	20	20	4	4	0	0	0	0	0	0	0	0	20	20	4	4	False		
+psy-maps	psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.3.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	333	502	62	62	0	0	0	0	0	0	0	0	333	502	62	62	False		
+pureclip	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1319	1507	81	92	0	0	0	0	0	0	0	0	1319	1507	81	92	False		
+purge_dups	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	Genome assembly, Read binning, Scaffolding	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	17782	17782	287	287	853	853	65	65	2224	2224	65	65	20859	20859	417	417	False		
+pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	22742	22742	557	557	2159	2159	716	716	776	776	448	448	25677	25677	1721	1721	False		
+pyega3	pyega3	EGA python client uses the EGA REST API to download authorized datasets and files.								To update	https://github.com/EGA-archive/ega-download-client	Data Source	ega_download_client	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3	5.0.2	pyega3	5.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2716	2716	104	104	134	134	43	43	40	40	1	1	2890	2890	148	148	False		
+pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	12858	13232	986	996	8092	8092	943	943	3238	3238	124	124	24188	24562	2053	2063	False		
+pyprophet	pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5			0	5	6	0	0	5	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	6	6	0	2626	2626	150	150	0	0	0	0	609	609	9	9	3235	3235	159	159	False		
+pyscenic	pyscenic_aucell, pyscenic_binarize, pyscenic_ctx, pyscenic_grn	PySCENIC scripts based on usage at https://pyscenic.readthedocs.io/								To update		Transcriptomics, RNA, Sequence Analysis	suite_pyscenic	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/pyscenic	0.12.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+pysradb	pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.2	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	163	163	35	35	0	0	0	0	0	0	0	0	163	163	35	35	False		
+pyteomics	mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.4	Protein identification	Proteomics, Proteomics experiment	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	92	92	4	4	0	0	0	0	0	0	0	0	92	92	4	4	False		
+pyvo_integration	astronomical_archives	Astronomical archives tools contains tools for querying and fetching resources from astronomical archives into Galaxy								To update		Data Source	astronomicalarchivestool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/archives/pyvo_integration	0.10.0	astropy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	53	53	6	6	0	0	0	0	0	0	0	0	53	53	6	6	False		
+qcxms	qcxms_getres, qcxms_neutral_run, qcxms_production_run	QCxMS is a quantum chemical (QC) based program that enables users to calculate mass spectra (MS) using Born-Oppenheimer Molecular Dynamics (MD).								To update	https://github.com/grimme-lab/QCxMS	Computational chemistry, Molecular Dynamics	QCxMS	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms	5.2.1					0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11246	11246	13	13	0	0	0	0	0	0	0	0	11246	11246	13	13	False		
+qfilt	qfilt	Filter sequencing data								To update	https://github.com/veg/qfilt	Fastq Manipulation	qfilt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qfilt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt	1.0.0+galaxy1	qfilt	0.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on, qiime_core		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2092	2342	209	238	0	0	0	0	2	2	1	1	2094	2344	210	239	False		
+qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core		qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	0	0	0	32	0	0	0	0	0	0	0	0	0	0	31	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	0	31825	34677	3375	3785	1	1	1	1	14	14	4	4	31840	34692	3380	3790	False		
+qiime_extract_viz	qiime_extract_viz	Extract vizualization from QIIME artifacts								To update	http://www.qiime.org	Metagenomics	qiime_extract_viz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz	0.1.0	unzip				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	8	8	0	0	0	0	0	0	0	0	17	17	8	8	False		
+qq_tools	qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1	0	0	0	1	0	0	0	0	0	0	4	4	4	0	684820	684820	3239	3239	90503	90503	3881	3881	29018	29018	826	826	804341	804341	7946	7946	False		
+quality_filter	qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.13.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	98	724	35	62	0	0	0	0	98	724	35	62	False		
+quantp	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	197	241	17	22	0	0	0	0	0	0	0	0	197	241	17	22	False		
+quantwiz_iq	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	32	3	3	0	0	0	0	0	0	0	0	32	32	3	3	False		
+quasitools	aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0			0	12	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13483	13483	434	434	13483	13483	434	434	False		
+quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	67737	69738	7787	7971	51925	56602	9692	10646	32003	34145	3890	4127	151665	160485	21369	22744	False		
+query	query	Execute an SQL statement on a set of tables								To update		Text Manipulation	query	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/query	https://github.com/RECETOX/galaxytools/tree/master/tools/query	0.2	click				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+query_impc	query_impc	Contains a tool to query the IMPC database.								To update	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	Convert Formats, Web Services	query_impc	iuc	https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc	0.9.0	requests				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	2	0	0	0	0	0	0	0	0	3	3	2	2	False		
+query_tabular	filter_tabular, query_tabular, sqlite_to_tabular	Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular	https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular	3.3.1	python				3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	3	2	0	0	0	0	0	0	1	0	0	0	0	0	0	3	3	3	0	130124	135361	1265	1305	11135	11135	922	922	5939	5939	153	153	147198	152435	2340	2380	False		
+quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+qupath_roi_splitter	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type								To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/qupath_roi_splitter	0.3.2	geojson				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	172	172	9	9	0	0	0	0	0	0	0	0	172	172	9	9	False		
+rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3077	4581	395	518	2856	2856	1093	1093	1977	1977	19	19	7910	9414	1507	1630	False		
+racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	27113	27315	839	850	9089	9089	475	475	5452	5452	171	171	41654	41856	1485	1496	False		
+ragtag	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4844	4844	480	480	0	0	0	0	7	7	3	3	4851	4851	483	483	False		
+ramclustr	ramclustr, ramclustr_define_experiment		ramclustr	ramclustr		RAMClustR	A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	To update	https://rdrr.io/cran/RAMClustR/	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr	1.3.0	r-ramclustr	1.3.1	Imputation, Standardisation and normalisation, Clustering, Correlation	Metabolomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	58	58	22	22	29	29	14	14	344	344	4	4	431	431	40	40	False		
+rapidnj	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2		Phylogeny	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	339	339	30	30	1737	1737	256	256	6	6	1	1	2082	2082	287	287	False		
+rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	42	42	9	9	0	0	0	0	0	0	0	0	42	42	9	9	False		
+raven	raven	Raven is a de novo genome assembler for long uncorrected reads.								Up-to-date	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.3	raven-assembler	1.8.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	9477	9477	438	438	0	0	0	0	10585	10585	182	182	20062	20062	620	620	False		
+rawtools	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	166	179	32	33	0	0	0	0	414	414	13	13	580	593	45	46	False		
+raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	10905	10905	966	966	5100	5114	587	587	4955	6094	765	892	20960	22113	2318	2445	False		
+rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	1.0		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	90	90	6	6	0	0	0	0	0	0	0	0	90	90	6	6	False		
+rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	860	1257	88	98	0	0	0	0	0	0	0	0	860	1257	88	98	False		
+rcorrector	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	rcorrector		Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.7	Sequencing error detection	RNA, RNA-Seq	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	655	655	57	57	0	0	0	0	0	0	0	0	655	655	57	57	False		
+rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	49	191	5	46	0	0	0	0	49	191	5	46	False		
+rcx-tk	rcx-tk	Tools to process metadata or alkane files.								To update	https://github.com/RECETOX/rcx-tk	Metabolomics	rcx_tk	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk/	https://github.com/RECETOX/galaxytools/tree/master/tools/rcx-tk	0.1.0+galaxy0	rcx-tk	0.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rdock	rdock	Docking ligands to proteins and nucleic acids								To update	http://rdock.sourceforge.net/	Computational chemistry	rdock	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rdock	1.0	rDock	2013.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3710	3710	80	80	7	7	6	6	0	0	0	0	3717	3717	86	86	False		
+reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+recentrifuge	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.15.0	recentrifuge	1.15.0	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	472	472	92	92	32	32	13	13	6	6	4	4	510	510	109	109	False		
+recetox_aplcms	recetox_aplcms_align_features, recetox_aplcms_compute_clusters, recetox_aplcms_compute_template, recetox_aplcms_correct_time, recetox_aplcms_generate_feature_table, recetox_aplcms_merge_known_table, recetox_aplcms_recover_weaker_signals, recetox_aplcms_remove_noise	Peak detection tool for HRMS profile data.	recetox-aplcms	recetox-aplcms		recetox-aplcms	recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	Up-to-date	https://github.com/RECETOX/recetox-aplcms	Metabolomics	recetox-aplcms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms	0.13.3	r-recetox-aplcms	0.13.3	Chromatographic alignment, Quantification, Peak detection, Feature extraction, Alignment	Metabolomics	0	8	8	0	0	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	862	862	12	12	0	0	0	0	48	48	1	1	910	910	13	13	False		
+recetox_msfinder	recetox_msfinder		recetox-msfinder	recetox-msfinder		recetox-msfinder	This is a modified copy of MS-FINDER with source code modifications to make the tool accessible in Galaxy.MS-FINDER - software for structure elucidation of unknown spectra with hydrogen rearrangement (HR) rulesThe program supports molecular formula prediction, metabolie class prediction, and structure elucidation for EI-MS and MS/MS spectra, and the assembly is licensed under the CC-BY 4.0.	Annotation	Metabolomics	To update	https://github.com/RECETOX/recetox-msfinder	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder	v3.5.2			Annotation	Metabolomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47	47	4	4	0	0	0	0	0	0	0	0	47	47	4	4	False		
+recetox_xmsannotator	recetox_xmsannotator_advanced		recetox-xmsannotator	recetox-xmsannotator		recetox-xMSannotator	Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		Up-to-date	https://github.com/RECETOX/recetox-xMSannotator	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_xmsannotator	0.10.0	r-recetox-xmsannotator	0.10.0	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	93	93	2	2	93	93	2	2	False		
+red	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	859	859	203	203	305	305	142	142	227	227	58	58	1391	1391	403	403	False		
+refseq_masher	refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	428	428	35	35	141	141	42	42	0	0	0	0	569	569	77	77	False		
+regex_find_replace	regex1, regexColumn1	Use python regular expressions to find and replace text								To update		Text Manipulation	regex_find_replace	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace	1.0.3	python				2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	2	2	2	0	78648	78834	1144	1156	18063	18063	870	870	4455	6051	194	289	101166	102948	2208	2315	False		
+regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv				0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	7	7	0	438	542	128	157	0	0	0	0	0	0	0	0	438	542	128	157	False		
+rem_complex	rem_complex	Removes molecular coordination complexes.								To update	https://github.com/RECETOX/galaxytools	Metabolomics	rem_complex	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	18	18	2	2	0	0	0	0	0	0	0	0	18	18	2	2	False		
+remove_beginning	Remove beginning1	Remove lines from the beginning of a file.								To update		Text Manipulation	remove_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	148572	169964	3525	3682	36694	113826	3910	8163	9713	10577	1475	1598	194979	294367	8910	13443	False		
+remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	39	44	6	7	0	0	0	0	0	0	0	0	39	44	6	7	False		
+rename_annotated_feature	rename_annotated_feature	Update column names in an abundance table using a annotation table with spectral matching results								To update	https://github.com/RECETOX/galaxytools/	Metabolomics	rename_annotated_feature	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature	1.0.0	pandas				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+repeat_channels	repeat_channels	Convert single-channel to multi-channel image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	repeat_channels	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/repeat_channels	1.26.4	numpy		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	1	1	0	0	0	0	0	0	0	0	5	5	1	1	False		
+repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.0.9_p2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5998	5998	810	810	7618	7618	803	803	3135	3135	292	292	16751	16751	1905	1905	False		
+repeatexplorer2	repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	95	95	38	38	0	0	0	0	0	0	0	0	95	95	38	38	False		
+repeatmasker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.0.9_p2	Genome annotation	Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5998	5998	810	810	7618	7618	803	803	3135	3135	292	292	16751	16751	1905	1905	False		
+repeatmodeler	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7963	7963	413	413	1485	1485	220	220	8402	8402	168	168	17850	17850	801	801	False		
+repenrich	edger-repenrich, repenrich	Repeat element profiling								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	Transcriptomics	repenrich	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich	2.31.1					0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1725	1790	56	57	1725	1790	56	57	False		
+repenrich2	edger-repenrich2, repenrich2	Repeat element profiling using bowtie2 aligner								To update	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	Transcriptomics	repenrich2	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2	2.31.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+replaceColumn	replace_column_with_key_value_file	A tool to replace all column entries of a file given by values of a key-value file.								To update		Text Manipulation	replace_column_by_key_value_file	bgruening	https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn	https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn	0.2					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	577184	577312	463	492	43900	44233	283	373	2190	2190	112	112	623274	623735	858	977	False		
+replace_chromosome_names	replace_chromosome_names	Replace chromosome names								To update		Text Manipulation	replace_chromosome_names	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names	0.1	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	514	573	69	83	0	0	0	0	0	0	0	0	514	573	69	83	False		
+repmatch_gff3	repmatch_gff3	Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria.								To update		ChIP-seq	repmatch_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repmatch_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3		matplotlib				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	415	721	128	219	0	0	0	0	415	721	128	219	False		
+reshape2	cast, melt	Flexibly restructure and aggregate data using just the two functions melt and dcast								To update	https://cran.r-project.org/web/packages/reshape2/index.html	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2	1.4.2	r-reshape2				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	3543	3619	108	111	536	536	157	157	0	0	0	0	4079	4155	265	268	False		
+resize_coordinate_window	resize_coordinate_window	Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.								To update		Genomic Interval Operations	resize_coordinate_window	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window	https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window	1.0.2	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	75	86	8	9	138	216	30	57	0	0	0	0	213	302	38	66	False		
+rest_tool	pubchem_rest_tool	This tool fetches data from pubchem via the PubChem REST API.								To update	https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html	Data Source	pubchem_rest_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+retip	retip_apply, retip_descriptors, retip_filter_rt, retip_train		retip	retip		Retip	Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.	Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	To update	https://github.com/PaoloBnn/Retip	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	0.5.4			Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+retrieve_bold	retrieve_bold	Search a list of sequences in BOLD (Barcode of Life Data System) from specified taxa list and markers								To update	https://anaconda.org/conda-forge/r-bold	Ecology	retrieve_bold	ecology	https://github.com/wpearman1996/MARES_database_pipeline/tree/master	https://github.com/galaxyecology/tools-ecology/tree/master/tools/retrieve_bold	1.3.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+retrieve_ensembl_bed	retrieve_ensembl_bed	Retrieve cDNA features from Ensembl REST API in BED format								To update	http://rest.ensembl.org/	Data Source	retrieve_ensembl_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+revertR2orientationInBam	revertR2orientationInBam	Revert the mapped orientation of R2 mates in a bam.								To update		SAM	revertr2orientationinbam	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	0.0.2	samtools	1.21			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	40	40	11	11	520	520	31	31	0	0	0	0	560	560	42	42	False		
+revoluzer	revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	Structural variation detection	Molecular evolution, Phylogeny	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2444	2444	52	52	0	0	0	0	0	0	0	0	2444	2444	52	52	False		
+rfove	rfove	Perform segmentation region-based fitting of overlapping ellipses	rfove	rfove		RFOVE	RFOVE (Region-based Fitting of Overlapping Ellipses and its Application to Cells Segmentation) is a MATLAB script for performing image segmentation on cells.	Image analysis	Cell biology, Biomedical science, Imaging	To update	https://sites.google.com/site/costaspanagiotakis/research/cs	Imaging	rfove	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove	2023.11.12			Image analysis	Cell biology, Biomedical science, Imaging	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	7	7	0	0	0	0	0	0	0	0	15	15	7	7	False		
+rgcca	rgcca	multi-block analysis								To update	https://github.com/rgcca-factory/RGCCA	Statistics	rgcca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca	3.0.2	rgccacmd	3.0.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	44	44	6	6	77	77	35	35	0	0	0	0	121	121	41	41	False		
+rgrnastar	rna_star, rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	star	star		STAR	Ultrafast universal RNA-seq data aligner	Sequence alignment	RNA-Seq, Transcriptomics	To update	https://github.com/alexdobin/STAR	Next Gen Mappers, Transcriptomics	rgrnastar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar	2.7.11a	star	2.7.11b	Sequence alignment	RNA-Seq, Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	2	0	0	0	2	0	0	0	0	0	1	2	2	2	0	438078	473957	10142	10900	325474	403925	15284	18791	49662	53138	1359	1449	813214	931020	26785	31140	False		
+riassigner	riassigner, riassigner_from_comment		riassigner	riassigner		RIAssigner	RIAssigner is a python tool for retention index (RI) computation for GC-MS data.	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/RIAssigner	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	0.4.1	riassigner	0.4.1	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	1	2	2	0	1	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	46	46	19	19	15	15	4	4	1	1	1	1	62	62	24	24	False		
+ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	0	661	681	78	78	0	0	0	0	0	0	0	0	661	681	78	78	False		
+ribowaltz	ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0		Computational biology	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	171	171	20	20	0	0	0	0	0	0	0	0	171	171	20	20	False		
+rmap	rmap_wrapper	RMAP for Solexa Short Reads Alignment								To update		Next Gen Mappers	rmap	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rmapq	rmapq_wrapper	RMAPQ for Solexa Short Reads Alignment with Quality Scores								To update		Next Gen Mappers	rmapq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rmassbank	rmassbank	RMassBank is an R package for processing tandem MS files and building of MassBank records.								To update	https://github.com/MassBank/RMassBank	Metabolomics	rmassbank	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	3.0.0	python				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	48	48	1	1	48	48	1	1	False		
+rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	137	173	40	49	0	0	0	0	0	0	0	0	137	173	40	49	False		
+rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	90	196	9	11	0	0	0	0	0	0	0	0	90	196	9	11	False		
+rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	878	1363	29	35	0	0	0	0	0	0	0	0	878	1363	29	35	False		
+rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1024	1077	18	21	0	0	0	0	0	0	0	0	1024	1077	18	21	False		
+rnaformer	infer_rnaformer	RNAformer: RNA secondary structure prediction								To update	https://github.com/automl/RNAformer	RNA	rnaformer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer	1.0.0	rnaformer				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	6	6	0	0	0	0	0	0	0	0	26	26	6	6	False		
+rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	23	33	10	14	0	0	0	0	0	0	0	0	23	33	10	14	False		
+rnaquast	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.3.0	rnaquast	2.3.0	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1522	1522	254	254	372	372	75	75	5	5	1	1	1899	1899	330	330	False		
+rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	65	89	14	18	0	0	0	0	0	0	0	0	65	89	14	18	False		
+rnaz	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	0	1156	43309	93	121	0	0	0	0	0	0	0	0	1156	43309	93	121	False		
+roary	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	Genome assembly	DNA, Genomics, Mapping	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	15196	15685	1459	1501	12188	12188	1768	1768	4881	5539	518	555	32265	33412	3745	3824	False		
+rp2biosensor	rp2biosensor	Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output								To update	https://github.com/brsynth/rp2biosensor	Synthetic Biology	rp2biosensor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor	3.2.1	rp2biosensor				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rp2paths	rp2paths	Enumerate and seperate the different pathways generated by RetroPath2.0								To update	https://github.com/brsynth/rp2paths	Synthetic Biology	rp2paths	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths	1.5.1	rp2paths				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rpbasicdesign	rpbasicdesign	Extracting enzyme IDs from rpSBML files								To update	https://github.com/brsynth/rpbasicdesign	Synthetic Biology	rpbasicdesign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign	1.2.2	rpbasicdesign				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rpfba	rpfba	Perform FBA for the RetroPath2.0 heterologous pathways								To update	https://github.com/brsynth/rptools/releases	Synthetic Biology	rpfba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba	5.12.3	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rptools	rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz	Suite of tools that work on rpSBML format								To update	https://github.com/brsynth/rptools	Synthetic Biology	rptools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools	5.13.1	rptools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rrparser	rrparser	Reaction Rules Parser								To update	https://github.com/brsynth/RRParser	Synthetic Biology	rrparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser	2.5.2	rrparser				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rsat_filter_snps	rsat_filter_snps	Filter SNPs in RSAT Matrix Scan output								To update	https://github.com/TGAC/earlham-galaxytools/	ChIP-seq, Systems Biology	rsat_filter_snps	earlham	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/rsat_filter_snps	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+rsem	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	1	1	0	363	430	158	183	0	0	0	0	67	146	13	39	430	576	171	222	False		
+rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	0	22	22	22	0	0	0	0	0	0	0	0	0	0	22	0	0	0	0	22	0	0	0	22	0	0	0	0	0	0	22	22	22	0	136315	147595	8341	9385	138707	161046	10696	12789	22718	23767	1593	1695	297740	332408	20630	23869	False		
+ruvseq	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	Differential gene expression analysis	Gene expression	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1286	1364	178	193	2220	2220	299	299	0	0	0	0	3506	3584	477	492	False		
+sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3628	4168	165	199	8399	14473	573	1147	2710	3000	151	175	14737	21641	889	1521	False		
+salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	0	2	2	3	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	2	0	0	0	0	0	0	3	3	3	0	73085	77081	2243	2319	90634	122835	3402	4726	13371	15818	513	586	177090	215734	6158	7631	False		
+salmon-kallisto-mtx-to-10x	_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	682	682	172	172	322	322	74	74	3	3	3	3	1007	1007	249	249	False		
+salsa2	salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	463	463	119	119	1038	1038	87	87	410	410	24	24	1911	1911	230	230	False		
+sam2interval	sam2interval	Convert SAM to interval.								To update		SAM	sam2interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval	1.0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1155	1251	57	63	2264	18187	189	1748	525	590	10	17	3944	20028	256	1828	False		
+sam_bitwise_flag_filter	sam_bw_filter	Filter SAM on bitwise flag values								To update		SAM	sam_bitwise_flag_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter	1.0.1	python				1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	96	278	12	26	3554	76029	450	6346	229	345	16	29	3879	76652	478	6401	False		
+sambamba	sambamba_sample_or_filter	filter BAM/SAM on flags, fields, tags, and region, or down-sample, or slice BAM/SAM								To update	http://artbio.fr	SAM	sambamba	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sambamba	https://github.com/ARTbio/tools-artbio/tree/main/tools/sambamba	0.7.1+galaxy1	sambamba	1.0.1			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	684	684	17	17	684	684	17	17	False		
+sambamba	sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort	Sambamba: process your BAM data faster!								Up-to-date	https://github.com/biod/sambamba	SAM	sambamba	bgruening	https://github.com/biod/sambamba	https://github.com/bgruening/galaxytools/tree/master/tools/sambamba	1.0.1	sambamba	1.0.1			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	297	297	51	51	0	0	0	0	0	0	0	0	297	297	51	51	False		
+samblaster	samblaster	samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files	samblaster	samblaster		SAMBLASTER	A tool to mark duplicates and extract discordant and split reads from SAM files.	Split read mapping	DNA, Sequencing, Mapping	Up-to-date	https://github.com/GregoryFaust/samblaster	SAM, Fastq Manipulation, Variant Analysis	samblaster	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster	https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster	0.1.26	samblaster	0.1.26	Split read mapping	DNA, Sequencing, Mapping	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3421	3859	340	382	883	883	109	109	1138	1138	15	15	5442	5880	464	506	False		
+samtools										To update	https://github.com/samtools/samtools	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools	1.20	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	1	6485	6549	720	726	10127	10127	1518	1518	238	238	37	37	16850	16914	2275	2281	False		
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.21			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	52099	55110	4053	4497	73194	108684	6930	9936	14771	15714	1222	1419	140064	179508	12205	15852	False		
+sansa	sansa_annotate	Sansa is a tool for structural variant annotation.								To update	https://github.com/dellytools/sansa	Variant Analysis	sansa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa	0.2.1	sansa	0.2.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	138	138	36	36	0	0	0	0	0	0	0	0	138	138	36	36	False		
+sarscov2formatter	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	174	174	16	16	399	399	29	29	0	0	0	0	573	573	45	45	False		
+sarscov2summary	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	140	140	5	5	253	253	6	6	0	0	0	0	393	393	11	11	False		
+sashimi_plot	sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sbml2sbol	sbml2sbol	Convert SBML to SBOL format								To update	https://github.com/neilswainston/SbmlToSbol	Synthetic Biology	sbml2sbol	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sbml2sbol	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol	0.1.13	sbml2sbol				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sc3	sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	10	10	0	0	0	0	0	0	0	0	13	13	10	10	False		
+scaffold	scaffold, scaffold_export									To update			scaffold	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/scaffold	0.1.0	scaffold				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+scale_image	ip_scale_image	Scale image	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	scale_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image	0.18.3	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	477	520	13	16	0	0	0	0	0	0	0	0	477	520	13	16	False		
+scanpy	anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301			27	27	27	0	27	27	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	14	13	0	45501	45666	4832	4868	7304	7304	1846	1846	3106	3106	457	457	55911	56076	7135	7171	False		
+scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	63789	64034	2543	2547	29962	29962	1185	1185	18028	18028	379	379	111779	112024	4107	4111	False		
+scater	scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5			1	2	6	0	1	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	381	388	99	100	0	0	0	0	297	297	9	9	678	685	108	109	False		
+scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	1345	1371	350	351	0	0	0	0	903	903	29	29	2248	2274	379	380	False		
+scatterplot	scatterplot_rpy	Scatterplot of two numeric columns								To update		Graphics, Statistics	scatterplot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot	1.0.3	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1234	1752	179	261	680	9223	231	1927	0	49	0	18	1914	11024	410	2206	False		
+sccaf	run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out	SCCAF: Single Cell Clustering Assessment Framework.								To update	https://github.com/sccaf/sccaf	Transcriptomics	SCCAF	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sccaf	0.0.9	sccaf	0.0.10			4	3	4	0	4	3	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	110	110	19	19	0	0	0	0	0	0	0	0	110	110	19	19	False		
+sceasy	sceasy_convert	Convert scRNA data object between popular formats								To update		Transcriptomics	sceasy	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/sceasy	0.0.5	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1059	1059	222	222	426	426	71	71	1	1	1	1	1486	1486	294	294	False		
+sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1059	1059	222	222	426	426	71	71	1	1	1	1	1486	1486	294	294	False		
+schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	809	809	78	78	3	3	2	2	105	105	16	16	917	917	96	96	False		
+scikit-bio	scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1503	1955	283	402	0	0	0	0	1504	1956	284	403	False		
+scmap	scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0			0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	97	97	41	41	0	0	0	0	0	0	0	0	97	97	41	41	False		
+scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	901	901	90	90	0	0	0	0	0	0	0	0	901	901	90	90	False		
+scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	284	632	34	38	786	786	61	61	1	1	1	1	1071	1419	96	100	False		
+scpred	scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	25	25	5	5	0	0	0	0	0	0	0	0	25	25	5	5	False		
+scripting	singularity_scriptrunner	suite_scripting								To update	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	Text Manipulation	scripting tools	mbernt	https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/scripting/	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/scripting	0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sdmpredictors	sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+seacr	seacr	SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes.								Up-to-date	https://github.com/FredHutch/SEACR	Epigenetics, ChIP-seq	seacr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seacr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr	1.3	seacr	1.3			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5106	5106	116	116	6419	6419	241	241	0	0	0	0	11525	11525	357	357	False		
+sed	sed_stream_editor	Manipulate your data with the sed command line tool.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/sed	Text Manipulation	sed_wrapper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sed	https://github.com/bgruening/galaxytools/tree/master/tools/sed	0.0.1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	281	2284	10	53	0	0	0	0	0	0	0	0	281	2284	10	53	False		
+segalign	segalign	A Scalable GPU System for Pairwise Whole Genome Alignments based on LASTZ's seed-filter-extend paradigm.								Up-to-date	https://github.com/gsneha26/SegAlign	Next Gen Mappers	segalign	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign	0.1.2.7	segalign-galaxy	0.1.2.7			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	252	252	47	47	0	0	0	0	252	252	47	47	False		
+segemehl	segemehl	segemehl - short read mapping with gaps								To update	http://www.bioinf.uni-leipzig.de/Software/segemehl/	Next Gen Mappers	segemehl	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	0.2.0.4	segemehl	0.3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1095	1306	98	113	0	0	0	0	0	0	0	0	1095	1306	98	113	False		
+segmetrics	ip_segmetrics	Image segmentation and object detection performance measures	segmetrics	segmetrics	segmetrics	SegMetrics	Image segmentation and object detection performance measures	Image analysis		To update	https://github.com/bmcv	Imaging	segmetrics	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/segmetrics	1.4	segmetrics	1.5	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	2	2	0	0	0	0	0	0	0	0	7	7	2	2	False		
+selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	305	463	43	50	0	0	0	0	0	0	0	0	305	463	43	50	False		
+selenzy_wrapper	selenzy_wrapper	Performs enzyme selection from a reaction query.								Up-to-date	https://github.com/brsynth/selenzy-wrapper	Synthetic Biology	selenzy_wrapper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/selenzy_wrapper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper	0.3.0	selenzy_wrapper	0.3.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	931	931	93	93	0	0	0	0	0	0	0	0	931	931	93	93	False		
+seq2hla	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	342	342	40	40	0	0	0	0	0	0	0	0	342	342	40	40	False		
+seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1053	1186	137	195	680	680	206	206	0	0	0	0	1733	1866	343	401	False		
+seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	30300	32553	732	799	21726	31891	619	621	2886	2886	144	144	54912	67330	1495	1564	False		
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	4322	4714	180	205	0	0	0	0	0	0	0	0	4322	4714	180	205	False		
+seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.2.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2196	3529	260	289	2196	3529	260	289	False		
+seqcomplexity	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	70	70	19	19	109	109	47	47	0	0	0	0	179	179	66	66	False		
+seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	0	0	2	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	3364	3364	247	247	0	0	0	0	244	244	33	33	3608	3608	280	280	False		
+seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2424	2424	102	102	0	0	0	0	0	0	0	0	2424	2424	102	102	False		
+seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4182	4182	42	42	0	0	0	0	0	0	0	0	4182	4182	42	42	False		
+seqtk	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	Data handling, Sequence file editing		15	15	15	0	15	15	15	0	0	0	0	0	0	0	0	0	0	14	0	14	0	0	14	0	0	0	15	0	0	0	0	0	0	14	14	14	14	72816	73514	2210	2300	102777	107831	2313	2669	154613	154613	682	682	330206	335958	5205	5651	False		
+seqtk_nml	seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sequence_format_converter	sequence_format_converter	various fasta to tabular conversions								To update	http://artbio.fr	Convert Formats, Fasta Manipulation	sequence_format_converter	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter	https://github.com/ARTbio/tools-artbio/tree/main/tools/sequence_format_converter	2.2.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+seqwish	seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	271	271	2	2	0	0	0	0	0	0	0	0	271	271	2	2	False		
+seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	0	1	1	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	121	121	11	11	32	32	5	5	0	0	0	0	153	153	16	16	False		
+seurat	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.4.0			14	14	14	0	14	14	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	0	0	0	0	0	0	0	0	0	2296	2328	673	676	141	141	39	39	0	0	0	0	2437	2469	712	715	False		
+sgwb	sgwb_astro_tool	SGWB								To update		Astronomy	sgwb_astro_tool	astroteam	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools	https://github.com/esg-epfl-apc/tools-astro/tree/main/tools/sgwb	0.0.1+galaxy0	ipython				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	2	2	0	0	0	0	0	0	0	0	5	5	2	2	False		
+shasta	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.13.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	913	913	308	308	0	0	0	0	568	568	73	73	1481	1481	381	381	False		
+shift-longitudes	shyft_longitudes	Shift longitudes ranging from 0. and 360 degrees to -180. and 180. degrees								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/shift-longitudes/	Climate Analysis	shift_longitudes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/shift-longitudes	0.1.0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	54	64	4	4	0	0	0	0	0	0	0	0	54	64	4	4	False		
+shorah	shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+short_reads_figure_score	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	145	163	25	30	196	3360	23	711	0	0	0	0	341	3523	48	741	False		
+short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	175	220	51	60	350	6657	85	1602	0	0	0	0	525	6877	136	1662	False		
+shovill	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	46125	47376	2273	2356	40577	40577	3971	3971	19960	21130	1085	1199	106662	109083	7329	7526	False		
+show_beginning	Show beginning1	Select lines from the beginning of a file.								To update		Text Manipulation	show_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	27232	36366	2184	2789	16648	84460	4191	18767	2785	3276	373	452	46665	124102	6748	22008	False		
+show_tail	Show tail1	Select lines from the end of a file.								To update		Text Manipulation	show_tail	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail	1.0.0					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	1620	2660	378	589	10551	24579	682	1851	284	398	67	83	12455	27637	1127	2523	False		
+sicer	peakcalling_sicer	Statistical approach for the Identification of ChIP-Enriched Regions								Up-to-date	https://home.gwu.edu/~wpeng/Software.htm	ChIP-seq	sicer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer	1.1	SICER	1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	276	379	30	42	972	9053	146	1008	644	689	5	7	1892	10121	181	1057	False		
+sickle	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	Sequence trimming	Data quality management	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	1	0	18184	18937	555	608	10514	10514	1063	1063	0	0	0	0	28698	29451	1618	1671	False		
+simtext	abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix	A text mining framework for interactive analysis and visualization of similarities among biomedical entities.								To update	https://github.com/dlal-group/simtext	Text Manipulation	simtext	iuc	https://github.com/galaxyproject/tools-iuc/tools/simtext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext	0.0.2	r-argparse	1.0.1			0	2	4	0	0	2	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	220	220	68	68	0	0	0	0	416	416	10	10	636	636	78	78	False		
+sina	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1369	1369	125	125	2398	2398	420	420	0	0	0	0	3767	3767	545	545	False		
+sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								Up-to-date	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.10.1	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	284	284	70	70	165	165	38	38	14	14	2	2	463	463	110	110	False		
+sistr_cmd	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3457	3457	301	301	0	0	0	0	556	556	65	65	4013	4013	366	366	False		
+sixgill	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	312	312	71	71	0	0	0	0	0	0	0	0	312	312	71	71	False		
+sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	0	30	14	31	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	0	82169	116810	2402	2666	18101	18101	2375	2375	17549	17549	321	321	117819	152460	5098	5362	False		
+skyline2isocor	skyline2isocor	Converting skyline output to IsoCor input								Up-to-date	https://github.com/MetaboHUB-MetaToul-FluxoMet/Skyline2IsoCor	Metabolomics	skyline2isocor	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/skyline2isocor	1.0.0	skyline2isocor	1.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+slamdunk	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	346	362	16	16	872	872	67	67	0	0	0	0	1218	1234	83	83	False		
+sleuth	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	141	141	26	26	0	0	0	0	0	0	0	0	141	141	26	26	False		
+slice_image	ip_slice_image	Slice image	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image	0.3-4	scikit-image		Image analysis	Imaging, Bioinformatics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	96	103	4	5	0	0	0	0	4	4	1	1	100	107	5	6	False		
+small_rna_clusters	small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+small_rna_maps	small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+small_rna_signatures	overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	158	158	8	8	0	0	0	0	0	0	0	0	158	158	8	8	False		
+smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smart_domains	smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smina	smina	smina is a fork of Autodock Vina (http://vina.scripps.edu/) that focuses on improving scoring and minimization								To update	https://sourceforge.net/projects/smina/	Computational chemistry	smina	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina	1.0	smina	2017.11.9			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	499	499	16	16	44	44	10	10	0	0	0	0	543	543	26	26	False		
+smithsonian-volcanoes	smithsonian_volcanoes	Retrieve data from Volcanoes of the World (VOTW) Database								To update	https://volcano.si.edu/gvp_votw.cfm	Retrieve Data	smithsonian_volcanoes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/smithsonian-volcanoes	0.1.0	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+smudgeplot	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	To update	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.3.0	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	325	325	61	61	137	137	54	54	843	843	63	63	1305	1305	178	178	False		
+snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1499	1638	331	358	779	779	244	244	467	467	83	83	2745	2884	658	685	False		
+snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1817	1817	14	14	4	4	2	2	136	136	4	4	1957	1957	20	20	False		
+sniffles	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	Up-to-date	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	2.4	sniffles	2.4	Sequence analysis, Structural variation detection	Sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1141	1141	134	134	606	606	156	156	2267	2267	80	80	4014	4014	370	370	False		
+snipit	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	Base position variability plotting	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	905	905	44	44	0	0	0	0	0	0	0	0	905	905	44	44	False		
+snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	2	0	121363	124773	3448	3602	92504	92504	3945	3945	48068	52034	2705	3073	261935	269311	10098	10620	False		
+snp-dists	snp_dists	Compute pairwise SNP distance matrix from a FASTA sequence alignment								Up-to-date	https://github.com/tseemann/snp-dists	Variant Analysis	snp_dists	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-dists	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists	0.8.2	snp-dists	0.8.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6555	6555	807	807	5336	5336	171	171	1143	1143	182	182	13034	13034	1160	1160	False		
+snp-sites	snp_sites	Finds SNP sites from a multi-FASTA alignment file								Up-to-date	https://github.com/sanger-pathogens/snp-sites	Variant Analysis	snp_sites	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites	2.5.1	snp-sites	2.5.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6597	6597	663	663	1467	1467	256	256	1279	1279	114	114	9343	9343	1033	1033	False		
+snpeff	snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names	SnpEff is a genetic variant annotation and effect prediction toolbox								To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff		biopython	1.70			5	5	5	0	5	5	5	0	0	0	0	0	0	0	1	0	0	0	5	5	0	0	5	0	0	0	5	0	0	0	0	0	0	5	5	5	0	103826	108296	7181	7908	115727	178110	15871	22769	11817	13155	2148	2321	231370	299561	25200	32998	False		
+snpeff-covid19	snpeff_sars_cov_2	SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox	snpeff	snpeff		snpEff	Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).	SNP detection	DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs	To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff_sars_cov_2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19				SNP detection	DNA polymorphism, Nucleic acid sites, features and motifs	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	764895	764895	1276	1276	94572	94572	1636	1636	26990	26990	561	561	886457	886457	3473	3473	False		
+snpfreq	hgv_snpFreq	snpFreq significant SNPs in case-control data								To update		Variant Analysis, Statistics	snpfreq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	35	44	10	12	307	649	68	181	227	260	16	23	569	953	94	216	False		
+snpfreqplot	snpfreqplot	A plotting app to visualise the SNPs across a region								To update	https://github.com/BrownfieldPlantLab/SNPFreqPlot	Variant Analysis	snpfreqplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot	1.0	r-base				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	3683	3683	338	338	1401	1401	433	433	1029	1029	95	95	6113	6113	866	866	False		
+snpsift	snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck	snpEff SnpSift tools from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html	Variant Analysis	snpsift	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift		snpsift	5.2			8	8	8	0	8	8	8	0	0	0	0	0	0	0	8	0	0	0	0	8	0	0	8	0	0	0	8	0	0	0	0	0	0	8	8	8	0	5142904	5146618	3602	4283	382391	421190	7013	9678	104030	105024	960	1184	5629325	5672832	11575	15145	False		
+snpsift_dbnsfp	snpSift_dbnsfp	snpEff SnpSift dbnsfp tool from Pablo Cingolani								To update	http://snpeff.sourceforge.net/SnpSift.html#dbNSFP	Variant Analysis	snpsift_dbnsfp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	52	55	23	24	421	421	75	75	0	0	0	0	473	476	98	99	False		
+snpsift_genesets	snpSift_geneSets	Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome								To update	http://snpeff.sourceforge.net/SnpSift.html#geneSets	Variant Analysis	snpsift_genesets	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets		snpsift	5.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	509	554	107	128	474	474	190	190	0	0	0	0	983	1028	297	318	False		
+snv_matrix	snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+snvtocnv	sequenzaindex, snvtocnv	infer copy number variations from a vcf file with SNVs using R sequenza								To update	http://artbio.fr	Variant Analysis	snvtocnv	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv	https://github.com/ARTbio/tools-artbio/tree/main/tools/snvtocnv	3.0.0+galaxy1	sequenza-utils	3.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+socru	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	659	659	42	42	296	296	92	92	0	0	0	0	955	955	134	134	False		
+sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	19865	21034	1047	1126	3141	3141	328	328	3304	3304	189	189	26310	27479	1564	1643	False		
+spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, plasmidspades, biosyntheticspades, metaviralspades, metaplasmidspades, coronaspades, rnaviralspades, rnaspades, metaspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	0	9	9	9	0	0	0	0	0	0	0	0	0	0	1	3	8	0	0	2	0	0	0	3	0	0	0	0	0	0	3	9	3	0	82716	87113	8209	8526	120471	120475	14787	14790	54067	61541	5817	6653	257254	269129	28813	29969	False		
+spades_header_fixer	spades_header_fixer	Fixes Spades Fasta ids								To update	https://github.com/phac-nml/galaxy_tools	Fasta Manipulation	spades_fasta_header_fixer	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spades_header_fixer	1.1.2+galaxy1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spaln	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	0	450	491	91	100	4270	4270	288	288	0	0	0	0	4720	4761	379	388	False		
+spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spatyper	spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spec2vec	spec2vec_similarity, spec2vec_training	Mass spectra similarity scoring using a trained Spec2Vec model.	spec2vec	spec2vec		Spec2Vec	Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	Up-to-date	https://github.com/iomega/spec2vec	Metabolomics	spec2vec	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	0.8.0	spec2vec	0.8.0	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	0	0	0	0	0	0	0	0	1	1	1	1	False		
+spectrast2spectrast_irt	gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spectrast2tsv	gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+split_file_on_column	tp_split_on_column	Split a file on a specific column.								To update		Text Manipulation	split_file_on_column	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	0.6	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5995	6261	408	453	2150	2150	311	311	26	26	2	2	8171	8437	721	766	False		
+split_file_to_collection	split_file_to_collection	Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	Text Manipulation	split_file_to_collection	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	0.5.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	16415	16623	968	984	9133	9133	672	672	4140	4140	148	148	29688	29896	1788	1804	False		
+split_labelmap	ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmap	0.2-3	scikit-image		Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	44	51	2	3	0	0	0	0	0	0	0	0	44	51	2	3	False		
+split_paired_reads	split_paired_reads	Split paired end reads								To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13	0	3	200	384	31	66	200	397	31	69	False		
+splitfasta	rbc_splitfasta	Split a multi-sequence fasta file into files containing single sequences								To update		Text Manipulation	splitfasta	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	0.4.0	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1772	1811	278	294	3012	3012	564	564	0	0	0	0	4784	4823	842	858	False		
+spocc	spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	789	840	130	134	0	0	0	0	0	0	0	0	789	840	130	134	False		
+spolpred	spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+spot_detection_2d	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	galaxy_image_analysis		Galaxy Image Analysis	Galaxy Image Analysis is mainly developed by the Biomedical Computer Vision (BMCV) Group at Heidelberg University. Its dedication is to provide tools for image analysis and image processing for the Galaxy platform.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d	0.1	giatools	0.3.1	Image analysis	Imaging, Bioinformatics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	16	16	4	4	0	0	0	0	0	0	0	0	16	16	4	4	False		
+spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1436	1436	23	23	0	0	0	0	0	0	0	0	1436	1436	23	23	False		
+spyboat	spyboat	Wavelet analysis for 3d-image stacks								To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat	0.1.2	spyboat				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	142	142	5	5	0	0	0	0	0	0	0	0	142	142	5	5	False		
+sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	80	80	1	1	0	0	0	0	80	80	1	1	False		
+sr_bowtie_dataset_annotation	sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+sra-tools	fasterq_dump, fastq_dump, sam_dump	NCBI Sequence Read Archive toolkit utilities	sra-tools	sra-tools		SRA Software Toolkit	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.	Data handling	DNA, Genomics, Sequencing	Up-to-date	https://github.com/ncbi/sra-tools	Data Source, Fastq Manipulation	sra_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools	3.1.1	sra-tools	3.1.1	Data handling	DNA, Genomics, Sequencing	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	2	0	3	0	0	3	0	0	0	3	0	0	0	0	0	0	3	3	3	0	364871	376580	16710	17342	583675	678448	53271	59638	48131	50455	5910	6181	996677	1105483	75891	83161	False		
+srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base				4	0	7	0	4	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	239	239	34	34	44	44	13	13	0	0	0	0	283	283	47	47	False		
+srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41	False		
+srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	297	297	40	40	71	71	1	1	0	0	0	0	368	368	41	41	False		
+sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	214	225	17	18	0	0	0	0	0	0	0	0	214	225	17	18	False		
+stacks	stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	Data handling	Mapping, Population genetics	0	13	13	0	0	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	13	0	6440	11998	465	593	0	0	0	0	4070	4070	76	76	10510	16068	541	669	False		
+stacks2	stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65			0	12	12	0	0	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	8437	8592	626	646	0	0	0	0	18016	18016	270	270	26453	26608	896	916	False		
+star_fusion	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update	https://github.com/STAR-Fusion/STAR-Fusion	Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1312	1383	82	95	2198	3076	234	303	173	173	3	3	3683	4632	319	401	False		
+staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	20778	20891	2030	2045	9520	9520	1424	1424	6753	6753	864	864	37051	37164	4318	4333	False		
+statistics	bg_statistical_hypothesis_testing	Tool for computing statistical tests.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	Statistics	bg_statistical_hypothesis_testing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	0.3	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	169	346	46	61	0	0	0	0	0	0	0	0	169	346	46	61	False		
+stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2					0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	0	328	328	38	38	0	0	0	0	0	0	0	0	328	328	38	38	False		
+straindesign	straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion	Toolbox to optimize biological model								To update	https://github.com/brsynth/straindesign	Systems Biology, Synthetic Biology	straindesign	iuc	https://github.com/brsynth/straindesign	https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign	3.2.2	straindesign	3.2.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+strelka	strelka_germline, strelka_somatic	Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision.								Up-to-date	https://github.com/Illumina/strelka/	Variant Analysis	strelka	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/strelka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka	2.9.10	strelka	2.9.10			2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	669	669	112	112	1261	1261	417	417	0	0	0	0	1930	1930	529	529	False		
+stress_ng	stress_ng	stress test a computer system in various selectable ways								To update		Web Services	stress_ng	bgruening-util	https://github.com/ColinIanKing/stress-ng	https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng	0.12.04	stress-ng				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	62	62	3	3	0	0	0	0	0	0	0	0	62	62	3	3	False		
+stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+stringtie	stringtie, stringtie_merge	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	stringtie	stringtie		StringTie	Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.	Transcriptome assembly, RNA-Seq analysis	Transcriptomics, RNA-seq	Up-to-date	http://ccb.jhu.edu/software/stringtie/	Transcriptomics	stringtie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie	2.2.3	stringtie	2.2.3	Transcriptome assembly, RNA-Seq analysis	Transcriptomics	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	2	0	178677	187728	4972	5347	320780	407379	10825	15171	26375	28921	1032	1167	525832	624028	16829	21685	False		
+structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2858	3001	118	123	0	0	0	0	0	0	0	0	2858	3001	118	123	False		
+structureharvester	structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date	http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/	Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+substitution_rates	subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	121	3901	34	747	105	114	4	4	226	4015	38	751	False		
+substitutions	substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	93	901	13	84	0	0	0	0	93	901	13	84	False		
+subtract	gops_subtract_1	Subtract the intervals of two datasets								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract	1.0.0	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	566512	567199	410	470	49985	184650	1473	7631	20648	20897	155	188	637145	772746	2038	8289	False		
+subtract_query	subtract_query1	Subtract Whole Dataset from another dataset								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract_query	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query	0.1	bx-python	0.13.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1178	1450	124	141	3169	40539	636	3435	799	950	26	38	5146	42939	786	3614	False		
+suite_qiime2__alignment	qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	249	249	32	32	16	16	10	10	102	102	16	16	367	367	58	58	False		
+suite_qiime2__composition	qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	117	117	41	41	84	84	24	24	161	161	13	13	362	362	78	78	False		
+suite_qiime2__cutadapt	qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	217	217	47	47	42	42	20	20	96	96	12	12	355	355	79	79	False		
+suite_qiime2__dada2	qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	721	721	160	160	350	350	91	91	214	214	35	35	1285	1285	286	286	False		
+suite_qiime2__deblur	qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	125	125	30	30	13	13	9	9	83	83	8	8	221	221	47	47	False		
+suite_qiime2__demux	qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	396	396	134	134	121	121	57	57	144	144	39	39	661	661	230	230	False		
+suite_qiime2__diversity	qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_alpha_diversity, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.5.0+q2galaxy.2024.5.0					21	21	22	0	21	21	22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	0	0	964	964	318	318	249	249	118	118	475	475	108	108	1688	1688	544	544	False		
+suite_qiime2__diversity_lib	qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	8	8	8	8	13	13	11	11	1302	1302	19	19	1323	1323	38	38	False		
+suite_qiime2__emperor	qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	58	58	23	23	24	24	11	11	92	92	11	11	174	174	45	45	False		
+suite_qiime2__feature_classifier	qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.5.0+q2galaxy.2024.5.0					10	10	10	0	10	10	10	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	10	0	0	863	863	220	220	237	237	98	98	181	181	41	41	1281	1281	359	359	False		
+suite_qiime2__feature_table	qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.5.0+q2galaxy.2024.5.0					17	17	17	0	17	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	0	0	983	983	287	287	375	375	144	144	907	907	106	106	2265	2265	537	537	False		
+suite_qiime2__fragment_insertion	qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	46	46	13	13	9	9	5	5	0	0	0	0	55	55	18	18	False		
+suite_qiime2__longitudinal	qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.5.0+q2galaxy.2024.5.0					11	11	11	0	11	11	11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	0	37	37	16	16	22	22	7	7	89	89	14	14	148	148	37	37	False		
+suite_qiime2__metadata	qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.5.0+q2galaxy.2024.5.0					3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	615	615	143	143	246	246	75	75	115	115	27	27	976	976	245	245	False		
+suite_qiime2__phylogeny	qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.5.0+q2galaxy.2024.5.0					12	12	12	0	12	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	330	330	83	83	64	64	40	40	195	195	49	49	589	589	172	172	False		
+suite_qiime2__quality_control	qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.5.0+q2galaxy.2024.5.0					6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	0	4	4	4	4	5	5	5	5	1	1	1	1	10	10	10	10	False		
+suite_qiime2__quality_filter	qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.5.0+q2galaxy.2024.5.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	29	29	14	14	16	16	6	6	37	37	2	2	82	82	22	22	False		
+suite_qiime2__rescript	qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+suite_qiime2__sample_classifier	qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.5.0+q2galaxy.2024.5.0					15	15	15	0	15	15	15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	0	0	10	10	3	3	14	14	10	10	5	5	5	5	29	29	18	18	False		
+suite_qiime2__taxa	qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.5.0+q2galaxy.2024.5.0					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	664	664	145	145	113	113	43	43	255	255	50	50	1032	1032	238	238	False		
+suite_qiime2__vsearch	qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.5.0+q2galaxy.2024.5.0					8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	8	0	0	84	84	52	52	25	25	16	16	9	9	5	5	118	118	73	73	False		
+suite_qiime2_core										To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+suite_qiime2_core__tools	qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.5.0+dist.he540b0b0					2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	14941	14941	383	383	25941	25941	255	255	2856	2856	112	112	43738	43738	750	750	False		
+suite_snvphyl		SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+superdsm	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	superdsm	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm	0.2.0	superdsm	0.4.0	Image analysis		0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	26	26	5	5	0	0	0	0	0	0	0	0	26	26	5	5	False		
+swift	swiftlink	Parallel MCMC Linkage Analysis								Up-to-date	https://github.com/ajm/swiftlink	Variant Analysis	swiftlink	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/swiftlink/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift	1.0	swiftlink	1.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+syndiva	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	30	30	2	2	0	0	0	0	0	0	0	0	30	30	2	2	False		
+t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	411	472	68	90	102	7952	13	1240	0	0	0	0	513	8424	81	1330	False		
+t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	927	959	65	78	130	7194	18	1143	0	0	0	0	1057	8153	83	1221	False		
+t_coffee	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3783	9125	211	229	1	1	1	1	0	0	0	0	3784	9126	212	230	False		
+t_test_two_samples	t_test_two_samples	T Test for Two Samples								To update		Statistics	t_test_two_samples	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples	https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	141	215	20	31	520	1166	79	274	1025	1118	11	12	1686	2499	110	317	False		
+table_annovar	table_annovar	Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered								To update		Variant Analysis	table_annovar	devteam	Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar	https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar	0.2	annovar				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16526	64515	2803	7456	0	0	0	0	16526	64515	2803	7456	False		
+table_compute	table_compute	Perform general-purpose table operations								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	Text Manipulation	table_compute	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute	https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute	1.2.4	pandas				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	216072	216115	1811	1814	12326	12326	1558	1558	16136	16136	256	256	244534	244577	3625	3628	False		
+tables_arithmetic_operations	tables_arithmetic_operations	Arithmetic Operations on tables								To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	tables_arithmetic_operations	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations	1.0.0	perl				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2188	2220	33	38	0	0	0	0	0	0	0	0	2188	2220	33	38	False		
+tabular_to_fasta	tab2fasta	Tabular-to-FASTA								To update		Convert Formats	tabular_to_fasta	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta	1.1.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	329032	333057	1489	1702	79033	215770	2441	8587	27876	33727	296	360	435941	582554	4226	10649	False		
+tabular_to_fastq	tabular_to_fastq	Tabular to FASTQ converter								To update	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.2.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	7011	8135	449	482	9473	28494	626	2183	850	1090	80	104	17334	37719	1155	2769	False		
+tag_pileup_frequency	tag_pileup_frequency	Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup	Statistics, SAM, Genomic Interval Operations	tag_pileup_frequency	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tag_pileup_frequency	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency	1.0.2	openjdk				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	158	164	15	16	722	865	40	73	0	0	0	0	880	1029	55	89	False		
+tapscan	tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	19	6	6	0	0	0	0	0	0	0	0	19	19	6	6	False		
+tarfast5	tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	827	838	89	92	114	114	41	41	900	900	29	29	1841	1852	159	162	False		
+tasmanian_mismatch	tasmanian_mismatch	Analysis of positional mismatches								Up-to-date	https://github.com/nebiolabs/tasmanian-mismatch	Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tasmanian_mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	4	61	61	7	7	0	0	0	0	65	65	11	11	False		
+taxonkit	name2taxid, profile2cami	TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit	taxonkit	taxonkit		TaxonKit	TaxonKit is a practical and efficient NCBI taxonomy toolkit.	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	Up-to-date	https://bioinf.shenwei.me/taxonkit/	Metagenomics	taxonkit	iuc	https://github.com/shenwei356/taxonkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit	0.17.0	taxonkit	0.17.0	Formatting, Data retrieval	Taxonomy, Biotechnology, Ecology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_filter_refseq	taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	1	0	1	1	1	0	36069	36922	5257	5431	25255	30822	5066	5826	7949	7949	1584	1584	69273	75693	11907	12841	False		
+taxpasta	taxpasta	standardise taxonomic profiles	taxpasta	taxpasta		taxpasta	TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	Up-to-date	https://taxpasta.readthedocs.io/en/latest/	Sequence Analysis	taxpasta	iuc	https://github.com/taxprofiler/taxpasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta	0.7.0	taxpasta	0.7.0	Standardisation and normalisation, Aggregation, Formatting, Conversion	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	34	34	5	5	0	0	0	0	0	0	0	0	34	34	5	5	False		
+tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6372	6395	372	379	7339	7339	378	378	6966	6966	154	154	20677	20700	904	911	False		
+tb_variant_filter	tb_variant_filter	M. tuberculosis H37Rv VCF filter								Up-to-date	https://github.com/COMBAT-TB/tb_variant_filter	Variant Analysis	tb_variant_filter	iuc	https://github.com/COMBAT-TB/tb_variant_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter	0.4.0	tb_variant_filter	0.4.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22977	22977	461	461	3888	3888	274	274	3611	3611	80	80	30476	30476	815	815	False		
+tbl2gff3	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1941	1941	466	466	0	0	0	0	463	463	112	112	2404	2404	578	578	False		
+tbvcfreport	tbvcfreport	Generate HTML report from SnpEff M.tuberculosis VCF(s)								Up-to-date	https://github.com/COMBAT-TB/tbvcfreport	Variant Analysis	tbvcfreport	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport	1.0.1	tbvcfreport	1.0.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2955	2955	335	335	6090	6090	348	348	2347	2347	72	72	11392	11392	755	755	False		
+te_finder	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.21	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	203	203	20	20	0	0	0	0	0	0	0	0	203	203	20	20	False		
+telescope	telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+tetoolkit	tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1013	1013	74	74	0	0	0	0	70	70	4	4	1083	1083	78	78	False		
+tetyper	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	106	106	16	16	155	155	47	47	0	0	0	0	261	261	63	63	False		
+text_processing	tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq	High performance text processing tools using the GNU coreutils, sed, awk and friends.								To update	https://www.gnu.org/software/	Text Manipulation	text_processing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	9.3	coreutils	8.25			20	20	20	0	20	20	20	0	0	0	0	0	0	0	0	0	0	19	1	19	0	0	19	0	0	0	20	0	0	0	0	0	0	19	19	19	0	3898014	4015573	37698	42095	648268	915282	47636	69828	103365	105214	7778	7953	4649647	5036069	93112	119876	False		
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	547	547	51	51	0	0	0	0	0	0	0	0	547	547	51	51	False		
+tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	15	15	8	8	0	0	0	0	0	0	0	0	15	15	8	8	False		
+tn93	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								Up-to-date	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.14	tn93	1.0.14			4	0	4	0	4	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	4	0	0	1915	1915	42	42	1972	1972	225	225	0	0	0	0	3887	3887	267	267	False		
+tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	445	445	25	25	71	71	32	32	0	0	0	0	516	516	57	57	False		
+tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9.1	tooldistillator	0.9.1	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	65	65	9	9	6	6	5	5	0	0	0	0	71	71	14	14	False		
+tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	158	66524	28	7228	0	0	0	0	158	66525	28	7229	False		
+tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	15496	26623	1076	1664	83063	343017	8372	27829	5388	14057	508	1012	103947	383697	9956	30505	False		
+tophat_fusion_post	tophat_fusion_post	Wrapper for Tophat-Fusion post step								To update		Transcriptomics	tophat_fusion_post	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post	0.1	blast+				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	220	242	41	46	6	814	2	191	100	120	8	12	326	1176	51	249	False		
+topologyeditors	gromacs_modify_topology, gromacs_extract_topology	Set of python scripts and associated tool files that can be used to modify topology files.								To update	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	Molecular Dynamics, Computational chemistry	topologyeditors	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	0	python				2	0	2	0	2	0	2	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	57	57	10	10	20	20	8	8	0	0	0	0	77	77	18	18	False		
+tracegroomer	tracegroomer	TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool.								Up-to-date	https://github.com/cbib/TraceGroomer	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer	0.1.4	tracegroomer	0.1.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	7	1	1	0	0	0	0	0	0	0	0	7	7	1	1	False		
+tracy	tracy_align, tracy_assemble, tracy_basecall, tracy_decompose									To update				iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy	0.6.1	tracy	0.7.8			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	3314	3314	124	124	0	0	0	0	0	0	0	0	3314	3314	124	124	False		
+transdecoder	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	5964	6418	944	970	5450	5450	1066	1066	2610	2796	317	344	14024	14664	2327	2380	False		
+transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	5	5	0	1039	1039	189	189	2672	3349	467	485	358	358	47	47	4069	4746	703	721	False		
+translate_bed	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	649	685	138	142	473	473	105	105	761	761	18	18	1883	1919	261	265	False		
+translate_bed_sequences	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57	69	16	21	0	0	0	0	0	0	0	0	57	69	16	21	False		
+transtermhp	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	250	254	31	31	174	174	45	45	0	0	0	0	424	428	76	76	False		
+tree_relabeler	tree_relabel	Relabels the tips of a newick formatted tree.								To update		Text Manipulation	tree_relabeler	nml	https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler	https://github.com/phac-nml/galaxy_tools/tree/master/tools/tree_relabeler	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	229489	275008	5733	6500	228708	324716	11708	16638	22644	23869	1439	1527	480841	623593	18880	24665	False		
+trimmer	trimmer	Trim leading or trailing characters.								To update		Text Manipulation	trimmer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer	0.0.1					1	1	1	0	1	1	1	0	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	0	1	1	1	1	5304	7438	447	512	15698	108672	658	2946	266	822	53	81	21268	116932	1158	3539	False		
+trimmomatic	trimmomatic	A flexible read trimming tool for Illumina NGS data								Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic	0.39	trimmomatic	0.39			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	1	1	0	1	1	1	0	352353	383014	14547	15408	632385	839058	39323	49850	125340	139097	5268	5975	1110078	1361169	59138	71233	False		
+trinity	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	To update	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.2	Transcriptome assembly	Transcriptomics, Gene transcripts	9	13	13	0	9	13	13	0	0	0	0	0	0	0	0	0	0	1	2	1	0	0	0	0	0	0	11	0	0	1	0	0	0	11	13	12	0	35698	39132	4376	4632	44509	44509	6714	6714	21883	23889	1924	2070	102090	107530	13014	13416	False		
+trinotate	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	Gene functional annotation	Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1968	2080	374	390	1825	1825	527	527	862	1060	161	195	4655	4965	1062	1112	False		
+tripal	analysis_add_analysis, analysis_get_analyses, analysis_load_blast, analysis_load_fasta, analysis_load_gff3, analysis_load_go, analysis_load_interpro, analysis_sync, db_index, db_populate_mviews, entity_publish, expression_add_biomaterial, expression_add_expression, expression_delete_biomaterials, expression_get_biomaterials, expression_sync_biomaterials, feature_delete_orphans, feature_sync, organism_add_organism, organism_get_organisms, organism_sync, phylogeny_sync	Galaxy tools allowing to load data into a remote Tripal server.Tripal is a toolkit for construction of online biological (genetics, genomics, breeding, etc), community database,and is a member of the GMOD family of tools. Tripal provides by default integration with the GMOD Chado database schema and Drupal, a popular Content Management Systems (CMS).https://github.com/galaxy-genome-annotation/python-tripal								To update	https://github.com/galaxy-genome-annotation/python-tripal	Web Services		gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal		python-tripal	3.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	2	2	0	4361	4601	741	807	0	0	0	0	2469	2469	190	190	6830	7070	931	997	False		
+trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5			0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	14681	14681	265	265	0	0	0	0	4488	4488	147	147	19169	19169	412	412	False		
+tsebra	tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.5	tsebra	1.1.2.5	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	17	17	7	7	0	0	0	0	0	0	0	0	17	17	7	7	False		
+tsne	tsne	T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation								To update	https://cran.r-project.org/web/packages/Rtsne/	Text Manipulation	tsne	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne	0.0.2	r-rtsne	0.13			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	255	379	31	37	281	281	64	64	0	0	0	0	536	660	95	101	False		
+twobittofa	ucsc-twobittofa	twoBitToFa is a tool to convert all or part of .2bit file to FASTA	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenpath/help/twoBit.html	Convert Formats	ucsc_twobittofa	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa	469	ucsc-twobittofa	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	413	511	84	118	441	441	123	123	21	21	2	2	875	973	209	243	False		
+tximport	tximport	Wrapper for the Bioconductor package tximport	tximport	tximport		tximport	An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	Up-to-date	http://bioconductor.org/packages/tximport/	Transcriptomics	tximport	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport	1.30.0	bioconductor-tximport	1.30.0	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1802	1802	225	225	6963	6963	904	904	0	0	0	0	8765	8765	1129	1129	False		
+ucsc-cell-browser	ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets								To update	https://cells.ucsc.edu/	Transcriptomics	ucsc_cell_browser	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/main/tools/tertiary-analysis/ucsc-cell-browser	1.0.0+galaxy1	ucsc-cell-browser	1.2.8			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	965	975	178	181	0	0	0	0	0	0	0	0	965	975	178	181	False		
+ucsc_axtchain	ucsc_axtchain	Chain together genome alignments	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_axtchain	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain	469	ucsc-axtchain	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_axttomaf	ucsc_axtomaf	Convert dataset from axt to MAF format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_axttomaf	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf	469	ucsc-axttomaf	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_blat	ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	Up-to-date	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	469	ucsc-blat	469	Sequence alignment	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainnet	ucsc_chainnet	Make alignment nets out of chains	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainnet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet	469	ucsc-chainnet	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainprenet	ucsc_chainprenet	Remove chains that don't have a chance of being netted	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainprenet	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet	469	ucsc-chainprenet	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_chainsort	ucsc_chainsort	Sort chains. By default sorts by score.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_chainsort	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort	469	ucsc-chainsort	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	373	463	134	151	2249	18611	638	4080	0	0	0	0	2622	19074	772	4231	False		
+ucsc_netfilter	ucsc_netfilter	Filter out parts of net	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netfilter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter	469	ucsc-netfilter	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_netsyntenic	ucsc_netsyntenic	Add synteny info to a net dataset	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Sequence Analysis	ucsc_netsyntenic	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netsyntenic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic	469	ucsc-netsyntenic	469		Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+ucsc_nettoaxt	ucsc_nettoaxt	Convert net (and chain) to axt format.	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_nettoaxt	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_nettoaxt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt	469	ucsc-nettoaxt	469		Sequence analysis	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	0	3	5	5	0	55050	68123	1090	1223	9001	9001	906	906	12444	12444	187	187	76495	89568	2183	2316	False		
+unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	74120	77648	3798	3963	64946	90075	5451	7380	19516	20422	2010	2080	158582	188145	11259	13423	False		
+unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4900	5146	257	270	251	251	81	81	1069	1069	29	29	6220	6466	367	380	False		
+uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.6	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2117	2725	341	412	3111	5779	594	1011	806	806	50	50	6034	9310	985	1473	False		
+uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1488	1596	230	266	0	0	0	0	743	743	35	35	2231	2339	265	301	False		
+unzip	unzip	Unzip file								To update	https://github.com/bmcv	Convert Formats	unzip	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip	6.0	unzip				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	6942	7024	1345	1356	1	1	1	1	2461	2461	266	266	9404	9486	1612	1623	False		
+upload_roi_and_measures_to_omero	uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server								To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	1060	1060	5	5	0	0	0	0	0	0	0	0	1060	1060	5	5	False		
+valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	518	677	75	87	234	234	65	65	0	0	0	0	752	911	140	152	False		
+validate_fasta_database	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	112	112	38	38	0	0	0	0	0	0	0	0	112	112	38	38	False		
+vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5936	5936	147	147	523	523	15	15	0	0	0	0	6459	6459	162	162	False		
+vardict	vardict_java	VarDict - calls SNVs and indels for tumour-normal pairs								To update	https://github.com/AstraZeneca-NGS/VarDictJava	Variant Analysis	vardict_java	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict	1.8.3	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	381	381	37	37	0	0	0	0	0	0	0	0	381	381	37	37	False		
+variant_analyzer	mut2read, mut2sscs, read2mut	Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data								To update		Variant Analysis	variant_analyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer	2.0.0	matplotlib				3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	95	95	14	14	516	516	67	67	0	0	0	0	611	611	81	81	False		
+varscan	varscan_copynumber, varscan_mpileup, varscan_somatic	VarScan is a variant caller for high-throughput sequencing data								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/varscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan	2.4.3	varscan	2.4.6			3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	10711	11502	1442	1560	16705	16705	3135	3135	1036	1036	100	100	28452	29243	4677	4795	False		
+varscan_vaf	varscan_vaf	Compute variant allele frequency in vcf files generated by varscan.								To update	http://artbio.fr	Variant Analysis	varscan_vaf	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf	https://github.com/ARTbio/tools-artbio/tree/main/tools/varscan_vaf	0.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+varscan_version_2	varscan	VarScan wrapper								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan_version_2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2	2.4.2	varscan	2.4.6			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	5058	6139	606	699	17232	53268	2965	5686	2298	2656	424	482	24588	62063	3995	6867	False		
+varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	273	273	12	12	0	0	0	0	0	0	0	0	273	273	12	12	False		
+vcf2maf	vcf2maf	vcf2maf: Convert VCF into MAF								To update	https://github.com/mskcc/vcf2maf	Convert Formats	vcf2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf	1.6.21	vcf2maf	1.6.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1097	1097	46	46	0	0	0	0	65	65	5	5	1162	1162	51	51	False		
+vcf2pgsnp	vcf2pgSnp	VCF to pgSnp								To update		Variant Analysis	vcf2pgsnp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	191	221	57	65	1399	2700	209	584	0	0	0	0	1590	2921	266	649	False		
+vcf2snvalignment	vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vcf2tsv	vcf2tsv	Converts VCF files into tab-delimited format								To update	https://github.com/ekg/vcflib	Variant Analysis, Convert Formats	vcf2tsv	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	169090	169679	823	874	16304	42215	1141	2594	2485	2511	169	172	187879	214405	2133	3640	False		
+vcf_annotate	vcf_annotate	Annotate a VCF file (dbSNP, hapmap)								To update		Variant Analysis	vcf_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	1	0	1	263	340	31	54	263	342	31	56	False		
+vcf_extract	vcf_extract	Extract reads from a specified region								To update		Variant Analysis	vcf_extract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	513	569	6	9	513	569	6	9	False		
+vcf_filter	vcf_filter	Filter a VCF file								To update		Variant Analysis	vcf_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	400	455	129	140	0	0	0	0	238	606	19	56	638	1061	148	196	False		
+vcf_intersect	vcf_intersect	Generate the intersection of two VCF files								To update		Variant Analysis	vcf_intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	0	3	0	0	0	0	335	463	19	28	335	482	19	31	False		
+vcfaddinfo	vcfaddinfo	Adds info fields from the second dataset which are not present in the first dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfaddinfo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfaddinfo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	882	888	30	32	6118	8261	36	114	175	184	6	6	7175	9333	72	152	False		
+vcfallelicprimitives	vcfallelicprimitives	Splits alleleic primitives (gaps or mismatches) into multiple VCF lines								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfallelicprimitives	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfallelicprimitives	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	6879	17157	897	1219	7585	14509	1245	1925	1648	1681	225	229	16112	33347	2367	3373	False		
+vcfanno	vcfanno	Annotate VCF files	vcfanno	vcfanno		vcfanno	Fast, flexible annotation of genetic variants.	SNP annotation	Genetic variation, Data submission, annotation and curation	Up-to-date	https://github.com/brentp/vcfanno	Variant Analysis	vcfanno	iuc	https://github.com/galaxyproject/tools-iuc/vcfanno/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno	0.3.5	vcfanno	0.3.5	SNP annotation	Genetic variation, Data submission, annotation and curation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1139	1139	174	174	0	0	0	0	0	0	0	0	1139	1139	174	174	False		
+vcfannotate	vcfannotate	Intersect VCF records with BED annotations								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotate	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2797	2850	157	181	3668	14532	652	1392	494	507	61	63	6959	17889	870	1636	False		
+vcfannotategenotypes	vcfannotategenotypes	Annotate genotypes in a VCF dataset using genotypes from another VCF dataset.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfannotategenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	189	203	62	66	497	1828	155	387	184	197	11	11	870	2228	228	464	False		
+vcfbedintersect	vcfbedintersect	Intersect VCF and BED datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbedintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbedintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3017	4049	185	210	4709	20250	406	1147	507	527	40	42	8233	24826	631	1399	False		
+vcfbreakcreatemulti	vcfbreakcreatemulti	Break multiple alleles into multiple records, or combine overallpoing alleles into a single record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfbreakcreatemulti	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfbreakcreatemulti	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	416	478	35	40	3969	10457	82	309	362	378	8	8	4747	11313	125	357	False		
+vcfcheck	vcfcheck	Verify that the reference allele matches the reference genome								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcheck	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcheck	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	745	767	96	106	803	1895	222	627	241	256	16	17	1789	2918	334	750	False		
+vcfcombine	vcfcombine	Combine multiple VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcombine	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcombine	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	1422	2020	284	505	4951	19530	1021	2669	493	516	60	62	6866	22066	1365	3236	False		
+vcfcommonsamples	vcfcommonsamples	Output records belonging to samples commong between two datasets.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfcommonsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfcommonsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	233	253	37	42	234	1839	79	287	199	214	11	12	666	2306	127	341	False		
+vcfdistance	vcfdistance	Calculate distance to the nearest variant.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfdistance	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	572	585	90	92	2063	2427	139	296	272	290	19	22	2907	3302	248	410	False		
+vcffilter	vcffilter2	Tool for filtering VCF files								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffilter	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	37489	47142	2113	2218	75128	162296	5730	10533	2626	2736	320	331	115243	212174	8163	13082	False		
+vcffixup	vcffixup	Count the allele frequencies across alleles present in each record in the VCF file.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcffixup	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffixup	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	926	957	155	173	2291	5323	313	985	251	265	28	31	3468	6545	496	1189	False		
+vcfflatten	vcfflatten2	Removes multi-allelic sites by picking the most common alternate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfflatten	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfflatten	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	172	183	21	25	351	879	67	201	312	342	15	16	835	1404	103	242	False		
+vcfgeno2haplo	vcfgeno2haplo	Convert genotype-based phased alleles into haplotype alleles								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgeno2haplo	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgeno2haplo	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	778	794	107	112	2414	3721	179	508	209	225	20	21	3401	4740	306	641	False		
+vcfgenotypes	vcfgenotypes	Convert numerical representation of genotypes to allelic.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfgenotypes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfgenotypes	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	502	555	134	143	3428	6338	266	858	220	235	23	24	4150	7128	423	1025	False		
+vcfhethom	vcfhethom	Count the number of heterozygotes and alleles, compute het/hom ratio.								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfhethom	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfhethom	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1964	1991	182	186	1937	3846	188	644	567	601	26	27	4468	6438	396	857	False		
+vcfleftalign	vcfleftalign	Left-align indels and complex variants in VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfleftalign	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfleftalign	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	269	310	38	42	358	1071	89	287	179	213	12	14	806	1594	139	343	False		
+vcfprimers	vcfprimers	Extract flanking sequences for each VCF record								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfprimers	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfprimers	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	590	711	28	33	403	831	75	200	190	214	10	12	1183	1756	113	245	False		
+vcfrandomsample	vcfrandomsample	Randomly sample sites from VCF dataset								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfrandomsample	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfrandomsample	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	161	168	13	15	153	350	27	75	184	192	6	6	498	710	46	96	False		
+vcfselectsamples	vcfselectsamples	Select samples from a VCF file								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfselectsamples	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfselectsamples	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	830	900	69	88	1315	6257	237	959	344	363	20	21	2489	7520	326	1068	False		
+vcfsort	vcfsort	Sort VCF dataset by coordinate								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfsort	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	1868	1904	174	185	18378	24175	422	1279	537	674	70	73	20783	26753	666	1537	False		
+vcftools_annotate	vcftools_annotate	Annotate VCF using custom/user-defined annotations								To update	https://vcftools.github.io/	Variant Analysis	vcftools_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate	0.1	echo				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	155	192	81	90	1853	3943	581	1280	144	156	13	16	2152	4291	675	1386	False		
+vcftools_compare	vcftools_compare	Compare VCF files to get overlap and uniqueness statistics								To update	https://vcftools.github.io/	Variant Analysis	vcftools_compare	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	440	594	127	142	0	0	0	0	0	16	0	12	440	610	127	154	False		
+vcftools_consensus	vcftools_consensus	Apply VCF variants to a fasta file to create consensus sequence								To update	https://vcftools.github.io/	Variant Analysis	vcftools_consensus	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus	0.1.11	samtools	1.21			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vcftools_isec	vcftools_isec	Intersect multiple VCF datasets								To update	https://vcftools.github.io/	Variant Analysis	vcftools_isec	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec	0.1.1	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	379	537	104	118	0	1	0	1	39	496	28	48	418	1034	132	167	False		
+vcftools_merge	vcftools_merge	Merge multiple VCF datasets into a single dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge	0.1.11	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	817	1084	244	273	0	0	0	0	93	448	44	60	910	1532	288	333	False		
+vcftools_slice	vcftools_slice	Subset VCF dataset by genomic regions								To update	https://vcftools.github.io/	Variant Analysis	vcftools_slice	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice	0.1	echo				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	410	423	56	60	6261	8115	133	362	127	157	10	19	6798	8695	199	441	False		
+vcftools_subset	vcftools_subset	Select samples from a VCF dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_subset	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	134	142	46	49	0	0	0	0	120	142	12	19	254	284	58	68	False		
+vcfvcfintersect	vcfvcfintersect	Intersect two VCF datasets								To update	https://github.com/ekg/vcflib	Variant Analysis	vcfvcfintersect	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfvcfintersect	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect		vcflib	1.0.10			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	1	1	1	0	976544	977015	703	748	64155	81830	981	2103	11044	11069	225	229	1051743	1069914	1909	3080	False		
+vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	2157	2287	198	209	3930	5591	446	744	0	0	0	0	6087	7878	644	953	False		
+velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	4	4	22	22	6	6	16	16	1	1	45	45	11	11	False		
+velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	25171	27943	3899	4270	51187	51187	7557	7557	28546	28619	3585	3613	104904	107749	15041	15440	False		
+velvet_optimiser	velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4715	5343	888	965	9575	9576	2117	2117	3271	5524	1050	1397	17561	20443	4055	4479	False		
+venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.2.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	4519	5476	667	730	9858	18420	986	2010	0	0	0	0	14377	23896	1653	2740	False		
+verify_map	verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+verkko	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.2.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	48	48	25	25	0	0	0	0	0	0	0	0	48	48	25	25	False		
+vg	vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.59.0			0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	3	0	478	478	17	17	0	0	0	0	0	0	0	0	478	478	17	17	False		
+vibrant	vibrant	Virus Identification By iteRative ANnoTation	VIBRANT	VIBRANT		VIBRANT	Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences.Virus Identification By iteRative ANnoTation.Discovery Environment Applications List.Created by upendra_35, last modified on Nov 04, 2019.If you find VIBRANT useful please consider citing our preprint on bioRxiv:.Kieft, K., Zhou, Z., and Anantharaman, K. (2019). VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences. BioRxiv 855387.VIBRANT is a tool for automated recovery and annotation of bacterial and archaeal viruses, determination of genome completeness, and characterization of virome function from metagenomic assemblies.The QuickStart tutorial provides an introduction to basic DE functionality and navigation.Please work through the tutorial and use the intercom button on the bottom right of this page if you have any questions	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	Up-to-date	https://github.com/AnantharamanLab/VIBRANT	Metagenomics	vibrant	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/vibrant	1.2.1	vibrant	1.2.1	Sequence trimming, Scaffolding, Genome annotation	Metagenomics, Microbial ecology, Sequence assembly, Molecular interactions, pathways and networks, Endocrinology and metabolism	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vienna_rna	viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	0	3197	8107	344	415	0	0	0	0	0	0	0	0	3197	8107	344	415	False		
+vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1					0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	0	14412	14590	722	732	0	0	0	0	0	0	0	0	14412	14590	722	732	False		
+virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot		virAnnot	"VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy."	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	94	94	16	16	0	0	0	0	0	0	0	0	94	94	16	16	False		
+virheat	virheat	generates a heatmap of allele frequencies from vcf files	virheat	virheat		virHEAT	VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists.  The tool provides a condensed look at variant frequencies after mapping  raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.			Up-to-date	https://github.com/jonas-fuchs/virHEAT	Visualization, Variant Analysis	virheat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat	0.7.1	virheat	0.7.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	2	2	0	0	0	0	0	0	0	0	12	12	2	2	False		
+virhunter	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	virhunter		VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter	1.0.0	numpy		Sequence classification	Virology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	574	574	76	76	0	0	0	0	0	0	0	0	574	574	76	76	False		
+virsorter	virsorter	VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.	virsorter	virsorter		virsorter	Identify DNA and RNA virus sequences.	Taxonomic classification	Metagenomics	Up-to-date	https://github.com/jiarong/VirSorter2/	Metagenomics	virsorter	ufz	https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/virsorter	https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/virsorter	2.2.4	virsorter	2.2.4	Taxonomic classification	Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+visceral_evaluatesegmentation	ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool			evaluatesegmentation-tool					To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral_evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	20	25	1	1	0	0	0	0	0	0	0	0	20	25	1	1	False		
+vmd		vmd is a package for  visualizing and analyzing trajectories from molecular dynamics (MD) simulations								To update	https://www.ks.uiuc.edu/Research/vmd/	Computational chemistry	vmd	chemteam	https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/vmd						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+volcanoplot	volcanoplot	Tool to create a Volcano Plot								To update	https://ggplot2.tidyverse.org/	Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.6	r-ggplot2	2.2.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	34917	36852	3670	3786	54931	54931	5597	5597	7183	7183	905	905	97031	98966	10172	10288	False		
+voronoi_tessellation	voronoi_tessellation	Compute Voronoi tesselation	scikit-image	scikit-image	scikit-image	scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.	Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	To update	https://github.com/bmcv	Imaging	voronoi_tesselation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tesselation	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/voronoi_tessellation	0.22.0	scikit-image		Image analysis, Image annotation, Visualisation, Data handling	Imaging, Software engineering, Literature and language	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	43	43	3	3	0	0	0	0	0	0	0	0	43	43	3	3	False		
+vsearch	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.29.0	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	0	8	8	8	0	0	0	0	0	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	0	0	0	0	0	0	8	8	8	0	9694	10338	559	628	12282	53546	1031	2007	5334	5672	246	277	27310	69556	1836	2912	False		
+vsnp	vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+w4mclassfilter	w4mclassfilter	Filter W4M data by values or metadata								To update	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper	Metabolomics	w4mclassfilter	eschen42	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master/tools/w4mclassfilter	0.98.19	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	2370	2836	9	10	0	0	0	0	1482	1509	4	4	3852	4345	13	14	False		
+w4mconcatenate	W4Mconcatenate	[W4M][Utils] concatenate two Metadata tables								To update	http://workflow4metabolomics.org	Metabolomics	w4mconcatenate	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/w4mconcatenate	1.0.0+galaxy0	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+w4mcorcov	w4mcorcov	OPLS-DA Contrasts of Univariate Results								To update	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper	Metabolomics	w4mcorcov	eschen42	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master/tools/w4mcorcov	0.98.18	r-base				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	238	375	10	10	0	0	0	0	10	10	2	2	248	385	12	12	False		
+w4mjoinpn	w4mjoinpn	Join positive- and negative-mode W4M datasets								To update	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper	Metabolomics	w4mjoinpn	eschen42	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master	https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master/tools/w4mjoinpn	0.98.2	coreutils	8.25			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	150	171	7	7	0	0	0	0	7	7	2	2	157	178	9	9	False		
+wade	wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+waveica	waveica	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.	waveica	waveica		WaveICA	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.	Standardisation and normalisation	Metabolomics	Up-to-date	https://github.com/RECETOX/WaveICA	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	0.2.0	r-recetox-waveica	0.2.0	Standardisation and normalisation	Metabolomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	39	39	6	6	4	4	3	3	0	0	0	0	43	43	9	9	False		
+weather_app	simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+weblogo3	rgweblogo3	Sequence Logo generator for fasta	weblogo	weblogo		WebLogo	Web-based application designed to make generate sequence logos.	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	To update		Graphics	weblogo3	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weblogo3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3	3.5.0	weblogo	3.7.9	Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition	Nucleic acid sites, features and motifs, Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	1	0	2720	2818	206	228	10299	30578	1354	3657	1226	1285	50	59	14245	34681	1610	3944	False		
+weightedaverage	wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	227	2307	17	75	0	0	0	0	227	2307	17	75	False		
+whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	96	96	13	13	0	0	0	0	0	0	0	0	96	96	13	13	False		
+wigtobigwig	ucsc_wigtobigwig	converts bedGraph (wig) files into binary bigwig	UCSC_Genome_Browser_Utilities	UCSC_Genome_Browser_Utilities		UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenPath/help/bigWig.html	Convert Formats	ucsc_wigtobigwig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig	469	ucsc-wigtobigwig	469		Sequence analysis	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1601	1601	106	106	1108	1108	172	172	200	200	15	15	2909	2909	293	293	False		
+windowmasker	windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.16.0			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	537	537	19	19	12	12	7	7	297	297	2	2	846	846	28	28	False		
+windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.13.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11	0	2	171	3961	34	328	0	0	0	0	171	3972	34	330	False		
+winnowmap	winnowmap	A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences.								Up-to-date	https://github.com/marbl/Winnowmap	Next Gen Mappers	winnowmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap	2.03	winnowmap	2.03			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	279	279	46	46	12	12	4	4	0	0	0	0	291	291	50	50	False		
+woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	31	31	1	1	0	0	0	0	0	0	0	0	31	31	1	1	False		
+wsi_extract_top_view	ip_wsi_extract_top_view	WSI Extract Top View								To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view	0.2-2	scikit-image				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	32	38	2	3	0	0	0	0	0	0	0	0	32	38	2	3	False		
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1619	1715	337	376	0	0	0	0	0	0	0	0	1619	1715	337	376	False		
+xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray				5	2	6	0	5	2	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	2	0	5995	5995	275	275	66	66	23	23	295	295	3	3	6356	6356	301	301	False		
+xcms	abims_xcms_fillPeaks, abims_xcms_group, abims_xcms_refine, abims_xcms_retcor, abims_xcms_summary, abims_xcms_xcmsSet, msnbase_readmsdata, xcms_export_samplemetadata, xcms_merge, xcms_plot_chromatogram, xcms_plot_eic, xcms_plot_raw		XCMS	XCMS		xcms	Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data.  The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling.	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Biological imaging, Data visualisation, Metabolomics	Up-to-date	https://github.com/sneumann/xcms	Metabolomics	xcms	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/xcms	4.0.0	bioconductor-xcms	4.0.0	Mass spectrum visualisation, Label-free quantification, Validation, Filtering, Chromatographic alignment, Peak detection, Chromatogram visualisation	Data visualisation, Metabolomics	9	11	12	0	9	11	12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	10	9	0	31909	35790	1357	1384	7099	7099	413	413	5333	5357	330	330	44341	48246	2100	2127	False		
+xmlstarlet	xmlstarlet	Tool to convert a xml file from one metadata standard to another								To update		Convert Formats	xmlstarlet	ecology	https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet	https://github.com/galaxyecology/tools-ecology/tree/master/tools/xmlstarlet	1.6.1	xmlstarlet				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	59	59	17	17	0	0	0	0	0	0	0	0	59	59	17	17	False		
+xpath	xpath	XPath XML querying tool								To update	http://search.cpan.org/dist/XML-XPath/	Text Manipulation	xpath	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/xpath	https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath		perl-xml-xpath	1.47			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	128	235	7	8	0	1	0	1	0	0	0	0	128	236	7	9	False		
+xpore	xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+xtb	xtb_molecular_optimization	Performs semiempirical molecular optimization.								To update	https://github.com/grimme-lab/xtb	Metabolomics	xtb_molecular_optimization	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	https://github.com/RECETOX/galaxytools/tree/master/tools/xtb	6.6.1	xtb				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	143	143	4	4	0	0	0	0	0	0	0	0	143	143	4	4	False		
+xy_plot	XY_Plot_1	Plotting tool for multiple series and graph types								To update		Graphics, Statistics	xy_plot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot	1.0.2	r-base				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4490	6169	768	889	6120	15516	1921	3653	2033	2212	556	590	12643	23897	3245	5132	False		
+yac_clipper	yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+yahs	yahs	Yet Another Hi-C scaffolding tool								To update	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2.2			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	618	618	176	176	336	336	62	62	588	588	25	25	1542	1542	263	263	False		
+zeiss_lmd_converter	ZeissLMDconverter	Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter	2.0.4	shapely				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	1	1	0	0	0	0	0	0	0	0	4	4	1	1	False		
+zerone	zerone	ChIP-seq discretization and quality control								Up-to-date	https://github.com/nanakiksc/zerone	ChIP-seq	zerone	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone	https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone	1.0	zerone	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	83	96	9	12	0	0	0	0	0	0	0	0	83	96	9	12	False		
+zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	26	26	4	4	0	0	0	0	0	0	0	0	26	26	4	4	False		
diff --git a/communities/proteomics/resources/tools_wordcloud.png b/communities/proteomics/resources/tools_wordcloud.png
new file mode 100644
index 00000000..764a31ab
Binary files /dev/null and b/communities/proteomics/resources/tools_wordcloud.png differ
diff --git a/communities/spoc/resources/tools.html b/communities/spoc/resources/tools.html
index 2a0f5c66..cd9ec249 100644
--- a/communities/spoc/resources/tools.html
+++ b/communities/spoc/resources/tools.html
@@ -95,7 +95,6 @@
       <th>Tools available on CoralSNP</th>
       <th>Tools available on CropGalaxy</th>
       <th>Tools available on Dintor</th>
-      <th>Tools available on FreeBioinfo</th>
       <th>Tools available on GASLINI</th>
       <th>Tools available on Galaxy@AuBi</th>
       <th>Tools available on Galaxy@Pasteur</th>
@@ -112,12 +111,27 @@
       <th>Tools available on Oqtans</th>
       <th>Tools available on Palfinder</th>
       <th>Tools available on PepSimili</th>
+      <th>Tools available on PhagePromotor</th>
       <th>Tools available on UseGalaxy.be</th>
       <th>Tools available on UseGalaxy.cz</th>
       <th>Tools available on UseGalaxy.no</th>
       <th>Tools available on Viral Variant Visualizer (VVV)</th>
-      <th>No. of tool users (2022-2023) (usegalaxy.eu)</th>
-      <th>Total tool usage (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.eu)</th>
+      <th>No. of tool users (all time) (usegalaxy.eu)</th>
+      <th>Tool usage (5 years) (usegalaxy.eu)</th>
+      <th>Tool usage (all time) (usegalaxy.eu)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org)</th>
+      <th>No. of tool users (all time) (usegalaxy.org)</th>
+      <th>Tool usage (5 years) (usegalaxy.org)</th>
+      <th>Tool usage (all time) (usegalaxy.org)</th>
+      <th>No. of tool users (5 years) (usegalaxy.org.au)</th>
+      <th>No. of tool users (all time) (usegalaxy.org.au)</th>
+      <th>Tool usage (5 years) (usegalaxy.org.au)</th>
+      <th>Tool usage (all time) (usegalaxy.org.au)</th>
+      <th>No. of tool users (5 years) - all main servers</th>
+      <th>No. of tool users (all time) - all main servers</th>
+      <th>Tool usage (5 years) - all main servers</th>
+      <th>Tool usage (all time) - all main servers</th>
       <th>Deprecated</th>
     </tr>
   </thead>
@@ -183,8 +197,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>625</td>
-      <td>35620</td>
+      <td>43047</td>
+      <td>43139</td>
+      <td>1826</td>
+      <td>1827</td>
+      <td>17240</td>
+      <td>17240</td>
+      <td>878</td>
+      <td>878</td>
+      <td>9309</td>
+      <td>9309</td>
+      <td>298</td>
+      <td>298</td>
+      <td>69596</td>
+      <td>69688</td>
+      <td>3002</td>
+      <td>3003</td>
       <td></td>
     </tr>
     <tr>
@@ -248,8 +276,22 @@
       <td>4</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>71</td>
+      <td>111</td>
+      <td>111</td>
+      <td>8</td>
+      <td>8</td>
+      <td>29</td>
+      <td>29</td>
+      <td>10</td>
+      <td>10</td>
+      <td>21</td>
+      <td>21</td>
+      <td>4</td>
+      <td>4</td>
+      <td>161</td>
+      <td>161</td>
+      <td>22</td>
+      <td>22</td>
       <td></td>
     </tr>
     <tr>
@@ -313,8 +355,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>1</td>
+      <td>21</td>
+      <td>21</td>
+      <td>4</td>
+      <td>4</td>
+      <td>9</td>
+      <td>9</td>
+      <td>5</td>
+      <td>5</td>
+      <td>18</td>
       <td>18</td>
+      <td>1</td>
+      <td>1</td>
+      <td>48</td>
+      <td>48</td>
+      <td>10</td>
+      <td>10</td>
       <td></td>
     </tr>
     <tr>
@@ -380,6 +436,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -409,8 +479,7 @@
       <td>1</td>
       <td>1</td>
       <td>1</td>
-      <td>1</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
@@ -439,12 +508,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>126</td>
-      <td>3934</td>
+      <td>4413</td>
+      <td>4442</td>
+      <td>430</td>
+      <td>431</td>
+      <td>4403</td>
+      <td>4403</td>
+      <td>255</td>
+      <td>255</td>
+      <td>1816</td>
+      <td>1816</td>
+      <td>33</td>
+      <td>33</td>
+      <td>10632</td>
+      <td>10661</td>
+      <td>718</td>
+      <td>719</td>
       <td></td>
     </tr>
     <tr>
@@ -508,8 +592,22 @@
       <td>3</td>
       <td>0</td>
       <td>0</td>
-      <td>20</td>
-      <td>736</td>
+      <td>880</td>
+      <td>880</td>
+      <td>80</td>
+      <td>80</td>
+      <td>221</td>
+      <td>221</td>
+      <td>37</td>
+      <td>37</td>
+      <td>49</td>
+      <td>49</td>
+      <td>3</td>
+      <td>3</td>
+      <td>1150</td>
+      <td>1150</td>
+      <td>120</td>
+      <td>120</td>
       <td></td>
     </tr>
     <tr>
@@ -539,11 +637,11 @@
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>1</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>1</td>
+      <td>0</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -573,8 +671,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>82</td>
-      <td>4569</td>
+      <td>3077</td>
+      <td>4581</td>
+      <td>395</td>
+      <td>518</td>
+      <td>2856</td>
+      <td>2856</td>
+      <td>1093</td>
+      <td>1093</td>
+      <td>1977</td>
+      <td>1977</td>
+      <td>19</td>
+      <td>19</td>
+      <td>7910</td>
+      <td>9414</td>
+      <td>1507</td>
+      <td>1630</td>
       <td></td>
     </tr>
     <tr>
@@ -638,8 +750,22 @@
       <td>6</td>
       <td>6</td>
       <td>0</td>
-      <td>766</td>
-      <td>51978</td>
+      <td>63789</td>
+      <td>64034</td>
+      <td>2543</td>
+      <td>2547</td>
+      <td>29962</td>
+      <td>29962</td>
+      <td>1185</td>
+      <td>1185</td>
+      <td>18028</td>
+      <td>18028</td>
+      <td>379</td>
+      <td>379</td>
+      <td>111779</td>
+      <td>112024</td>
+      <td>4107</td>
+      <td>4111</td>
       <td></td>
     </tr>
     <tr>
@@ -703,8 +829,22 @@
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>77</td>
-      <td>1365</td>
+      <td>1345</td>
+      <td>1371</td>
+      <td>350</td>
+      <td>351</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>903</td>
+      <td>903</td>
+      <td>29</td>
+      <td>29</td>
+      <td>2248</td>
+      <td>2274</td>
+      <td>379</td>
+      <td>380</td>
       <td></td>
     </tr>
     <tr>
@@ -757,7 +897,6 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
       <td>1</td>
       <td>0</td>
       <td>0</td>
@@ -768,8 +907,23 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>90</td>
-      <td>721</td>
+      <td>0</td>
+      <td>1059</td>
+      <td>1059</td>
+      <td>222</td>
+      <td>222</td>
+      <td>426</td>
+      <td>426</td>
+      <td>71</td>
+      <td>71</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1486</td>
+      <td>1486</td>
+      <td>294</td>
+      <td>294</td>
       <td></td>
     </tr>
     <tr>
@@ -833,8 +987,22 @@
       <td>16</td>
       <td>16</td>
       <td>0</td>
-      <td>23</td>
-      <td>779</td>
+      <td>809</td>
+      <td>809</td>
+      <td>78</td>
+      <td>78</td>
+      <td>3</td>
+      <td>3</td>
+      <td>2</td>
+      <td>2</td>
+      <td>105</td>
+      <td>105</td>
+      <td>16</td>
+      <td>16</td>
+      <td>917</td>
+      <td>917</td>
+      <td>96</td>
+      <td>96</td>
       <td></td>
     </tr>
     <tr>
@@ -898,8 +1066,22 @@
       <td>1</td>
       <td>1</td>
       <td>0</td>
-      <td>11</td>
-      <td>628</td>
+      <td>284</td>
+      <td>632</td>
+      <td>34</td>
+      <td>38</td>
+      <td>786</td>
+      <td>786</td>
+      <td>61</td>
+      <td>61</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1</td>
+      <td>1071</td>
+      <td>1419</td>
+      <td>96</td>
+      <td>100</td>
       <td></td>
     </tr>
     <tr>
@@ -929,11 +1111,10 @@
       <td>1</td>
       <td>1</td>
       <td>7</td>
-      <td>1</td>
+      <td>0</td>
       <td>1</td>
       <td>1</td>
       <td>7</td>
-      <td>1</td>
       <td>0</td>
       <td>0</td>
       <td>0</td>
@@ -964,7 +1145,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>121</td>
+      <td>121</td>
+      <td>11</td>
+      <td>11</td>
+      <td>32</td>
+      <td>32</td>
+      <td>5</td>
+      <td>5</td>
+      <td>0</td>
+      <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>153</td>
+      <td>153</td>
+      <td>16</td>
+      <td>16</td>
       <td></td>
     </tr>
     <tr>
@@ -1028,8 +1224,22 @@
       <td>2</td>
       <td>0</td>
       <td>0</td>
-      <td>17</td>
-      <td>91</td>
+      <td>284</td>
+      <td>284</td>
+      <td>70</td>
+      <td>70</td>
+      <td>165</td>
+      <td>165</td>
+      <td>38</td>
+      <td>38</td>
+      <td>14</td>
+      <td>14</td>
+      <td>2</td>
+      <td>2</td>
+      <td>463</td>
+      <td>463</td>
+      <td>110</td>
+      <td>110</td>
       <td></td>
     </tr>
     <tr>
@@ -1093,8 +1303,22 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>0</td>
+      <td>1817</td>
+      <td>1817</td>
+      <td>14</td>
+      <td>14</td>
+      <td>4</td>
+      <td>4</td>
+      <td>2</td>
+      <td>2</td>
+      <td>136</td>
+      <td>136</td>
+      <td>4</td>
+      <td>4</td>
+      <td>1957</td>
+      <td>1957</td>
+      <td>20</td>
+      <td>20</td>
       <td></td>
     </tr>
     <tr>
@@ -1160,6 +1384,20 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
+      <td>0</td>
       <td></td>
     </tr>
     <tr>
@@ -1189,8 +1427,7 @@
       <td>5</td>
       <td>5</td>
       <td>5</td>
-      <td>5</td>
-      <td>5</td>
+      <td>0</td>
       <td>5</td>
       <td>5</td>
       <td>5</td>
@@ -1219,12 +1456,27 @@
       <td>0</td>
       <td>0</td>
       <td>0</td>
+      <td>0</td>
       <td>3</td>
       <td>5</td>
       <td>5</td>
       <td>0</td>
-      <td>379</td>
-      <td>61618</td>
+      <td>55050</td>
+      <td>68123</td>
+      <td>1090</td>
+      <td>1223</td>
+      <td>9001</td>
+      <td>9001</td>
+      <td>906</td>
+      <td>906</td>
+      <td>12444</td>
+      <td>12444</td>
+      <td>187</td>
+      <td>187</td>
+      <td>76495</td>
+      <td>89568</td>
+      <td>2183</td>
+      <td>2316</td>
       <td></td>
     </tr>
     <tr>
@@ -1288,8 +1540,22 @@
       <td>1</td>
       <td>0</td>
       <td>0</td>
-      <td>0</td>
-      <td>2</td>
+      <td>7</td>
+      <td>7</td>
+      <td>4</td>
+      <td>4</td>
+      <td>22</td>
+      <td>22</td>
+      <td>6</td>
+      <td>6</td>
+      <td>16</td>
+      <td>16</td>
+      <td>1</td>
+      <td>1</td>
+      <td>45</td>
+      <td>45</td>
+      <td>11</td>
+      <td>11</td>
       <td></td>
     </tr>
   </tbody>
diff --git a/communities/spoc/resources/tools.tsv b/communities/spoc/resources/tools.tsv
index c72a3466..84542951 100644
--- a/communities/spoc/resources/tools.tsv
+++ b/communities/spoc/resources/tools.tsv
@@ -1,19 +1,19 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	625	35620	False		
-baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	71	False		
-cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18	False		
-cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	126	3934	False		
-episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	736	False		
-raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	1	5	5	5	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	82	4569	False		
-scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	766	51978	False		
-scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	77	1365	False		
-sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	90	721	False		
-schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	23	779	False		
-scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	628	False		
-seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	1	1	1	7	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	False		
-sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								Up-to-date	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.10.1	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	17	91	False		
-snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	3	5	5	0	379	61618	False		
-velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	43047	43139	1826	1827	17240	17240	878	878	9309	9309	298	298	69596	69688	3002	3003	False		
+baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	111	111	8	8	29	29	10	10	21	21	4	4	161	161	22	22	False		
+cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	21	4	4	9	9	5	5	18	18	1	1	48	48	10	10	False		
+cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4413	4442	430	431	4403	4403	255	255	1816	1816	33	33	10632	10661	718	719	False		
+episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	880	880	80	80	221	221	37	37	49	49	3	3	1150	1150	120	120	False		
+raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3077	4581	395	518	2856	2856	1093	1093	1977	1977	19	19	7910	9414	1507	1630	False		
+scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	63789	64034	2543	2547	29962	29962	1185	1185	18028	18028	379	379	111779	112024	4107	4111	False		
+scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	1345	1371	350	351	0	0	0	0	903	903	29	29	2248	2274	379	380	False		
+sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1059	1059	222	222	426	426	71	71	1	1	1	1	1486	1486	294	294	False		
+schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	809	809	78	78	3	3	2	2	105	105	16	16	917	917	96	96	False		
+scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	284	632	34	38	786	786	61	61	1	1	1	1	1071	1419	96	100	False		
+seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	0	1	1	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	121	121	11	11	32	32	5	5	0	0	0	0	153	153	16	16	False		
+sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								Up-to-date	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.10.1	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	284	284	70	70	165	165	38	38	14	14	2	2	463	463	110	110	False		
+snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1817	1817	14	14	4	4	2	2	136	136	4	4	1957	1957	20	20	False		
+spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	0	3	5	5	0	55050	68123	1090	1223	9001	9001	906	906	12444	12444	187	187	76495	89568	2183	2316	False		
+velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	4	4	22	22	6	6	16	16	1	1	45	45	11	11	False		
diff --git a/communities/spoc/resources/tools_filtered_by_ts_categories.tsv b/communities/spoc/resources/tools_filtered_by_ts_categories.tsv
index c72a3466..84542951 100644
--- a/communities/spoc/resources/tools_filtered_by_ts_categories.tsv
+++ b/communities/spoc/resources/tools_filtered_by_ts_categories.tsv
@@ -1,19 +1,19 @@
-Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Reviewed	Deprecated	To keep
-anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	625	35620	False		
-baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	71	False		
-cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	18	False		
-cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	126	3934	False		
-episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	20	736	False		
-raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	1	5	5	5	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	82	4569	False		
-scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	766	51978	False		
-scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	77	1365	False		
-sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	90	721	False		
-schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	23	779	False		
-scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	11	628	False		
-seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	1	1	1	7	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	0	False		
-sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								Up-to-date	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.10.1	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	17	91	False		
-snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
-umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	5	5	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	3	5	5	0	379	61618	False		
-velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2	False		
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on CIRM-CFBP	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CoralSNP	Tools available on CropGalaxy	Tools available on Dintor	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (5 years) (usegalaxy.eu)	No. of tool users (all time) (usegalaxy.eu)	Tool usage (5 years) (usegalaxy.eu)	Tool usage (all time) (usegalaxy.eu)	No. of tool users (5 years) (usegalaxy.org)	No. of tool users (all time) (usegalaxy.org)	Tool usage (5 years) (usegalaxy.org)	Tool usage (all time) (usegalaxy.org)	No. of tool users (5 years) (usegalaxy.org.au)	No. of tool users (all time) (usegalaxy.org.au)	Tool usage (5 years) (usegalaxy.org.au)	Tool usage (all time) (usegalaxy.org.au)	No. of tool users (5 years) - all main servers	No. of tool users (all time) - all main servers	Tool usage (5 years) - all main servers	Tool usage (all time) - all main servers	Reviewed	Deprecated	To keep
+anndata	anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Single Cell, Spatial Omics	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.9	anndata	0.6.22.post1			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	43047	43139	1826	1827	17240	17240	878	878	9309	9309	298	298	69596	69688	3002	3003	False		
+baredsc	baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Single Cell, Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	111	111	8	8	29	29	10	10	21	21	4	4	161	161	22	22	False		
+cite_seq_count	cite_seq_count	Count CMO/HTO	CITE-seq-Count	CITE-seq-Count		CITE-seq-Count	Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment.	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	To update	https://github.com/Hoohm/CITE-seq-Count	Single Cell, Transcriptomics, Proteomics	cite_seq_count	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count	1.4.4	cite-seq-count	1.4.5	RNA-Seq quantification	Transcriptomics, Immunoproteins and antigens	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	21	21	4	4	9	9	5	5	18	18	1	1	48	48	10	10	False		
+cosg	cosg	Marker gene identification for single-cell sequencing data using COSG.								Up-to-date	https://github.com/genecell/COSG	Transcriptomics, Sequence Analysis, Single Cell	cosg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg	1.0.1	cosg	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+dropletutils	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Single Cell, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0		Sequencing, Transcriptomics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	4413	4442	430	431	4403	4403	255	255	1816	1816	33	33	10632	10661	718	719	False		
+episcanpy	episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	episcanpy		epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Single Cell, Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy	0.3.2	episcanpy	0.4.0	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	3	3	3	0	3	3	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	880	880	80	80	221	221	37	37	49	49	3	3	1150	1150	120	120	False		
+raceid	raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory	RaceID3, StemID2, FateID - scRNA analysis								To update	https://github.com/dgrun/RaceID3_StemID2_package/	Single Cell, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid	0.2.3	r-raceid	0.1.3			5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	3077	4581	395	518	2856	2856	1093	1093	1977	1977	19	19	7910	9414	1507	1630	False		
+scanpy	scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Single Cell, Spatial Omics, Transcriptomics	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.10.2	scanpy	1.7.2	Differential gene expression analysis	Gene expression, Cell biology, Genetics	6	6	6	0	6	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	0	63789	64034	2543	2547	29962	29962	1185	1185	18028	18028	379	379	111779	112024	4107	4111	False		
+scater	scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Single Cell, Transcriptomics, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	Read pre-processing, Sequence visualisation	Quality affairs, Molecular genetics	0	5	5	0	0	5	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	5	5	0	1345	1371	350	351	0	0	0	0	903	903	29	29	2248	2274	379	380	False		
+sceasy	sceasy_convert	Converter between difference single-cell formats								Up-to-date	https://github.com/cellgeni/sceasy/	Single Cell, Spatial Omics, Convert Formats	sceasy_convert	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sceasy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy	0.0.7	r-sceasy	0.0.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1059	1059	222	222	426	426	71	71	1	1	1	1	1486	1486	294	294	False		
+schicexplorer	schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization, Single Cell	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7			16	16	16	0	16	16	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	16	16	16	0	809	809	78	78	3	3	2	2	105	105	16	16	917	917	96	96	False		
+scpipe	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, Single Cell	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	284	632	34	38	786	786	61	61	1	1	1	1	1071	1419	96	100	False		
+seurat	seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension	Seurat - R toolkit for single cell genomics								To update	https://satijalab.org/seurat/	Single Cell, Transcriptomics, Sequence Analysis	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	5.0	r-seurat	3.0.2			1	1	7	0	1	1	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	0	121	121	11	11	32	32	5	5	0	0	0	0	153	153	16	16	False		
+sinto	sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								Up-to-date	https://github.com/timoast/sinto	Single Cell, Epigenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.10.1	sinto	0.10.1			2	2	2	0	2	2	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	284	284	70	70	165	165	38	38	14	14	2	2	463	463	110	110	False		
+snapatac2	snapatac2_clustering, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing	SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis								To update	https://kzhang.org/SnapATAC2/	Single Cell, Epigenetics	snapatac2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2	2.6.4					4	4	4	0	4	4	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1817	1817	14	14	4	4	2	2	136	136	4	4	1957	1957	20	20	False		
+spapros	spapros_evaluation, spapros_selection	Select and evaluate probe sets for targeted spatial transcriptomics.								Up-to-date	https://github.com/theislab/spapros	Single Cell, Transcriptomics, Sequence Analysis	spapros	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros	0.1.5	spapros	0.1.5			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False		
+umi_tools	umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	Up-to-date	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics, Single Cell		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.5	umi_tools	1.1.5	Sequencing quality control	Sequence sites, features and motifs, Quality affairs	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	5	0	0	0	0	0	0	3	5	5	0	55050	68123	1090	1223	9001	9001	906	906	12444	12444	187	187	76495	89568	2183	2316	False		
+velocyto	velocyto_cli	Velocyto is a library for the analysis of RNA velocity.								Up-to-date	http://velocyto.org/	Transcriptomics, Single Cell	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto	0.17.17	velocyto.py	0.17.17			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	7	7	4	4	22	22	6	6	16	16	1	1	45	45	11	11	False		
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